tag:theconversation.com,2011:/global/topics/pathogens-5724/articlesPathogens – The Conversation2024-01-15T13:33:10Ztag:theconversation.com,2011:article/2149192024-01-15T13:33:10Z2024-01-15T13:33:10ZWhat if every germ hit you at the exact same time? An immunologist explains<figure><img src="https://images.theconversation.com/files/565348/original/file-20231212-15-ba3kr2.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C2121%2C1412&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Your immune system encounters a legion of potential pathogens every day.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/woman-shielding-eyes-by-large-green-coronavirus-royalty-free-image/1250588799">Klaus Vedfelt/DigitalVision via Getty Images</a></span></figcaption></figure><figure class="align-left ">
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<p><em><a href="https://theconversation.com/us/topics/curious-kids-us-74795">Curious Kids</a> is a series for children of all ages. If you have a question you’d like an expert to answer, send it to <a href="mailto:curiouskidsus@theconversation.com">curiouskidsus@theconversation.com</a>.</em></p>
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<p><strong>What would happen if all the diseases in the world hit us at the exact same time? – Gabriella, age 12, Irving, Texas</strong></p>
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<p>When I was younger, I would watch “Batman” on my black-and-white television after school. Usually, Batman would face either the Joker, the Penguin, the Puzzler, Catwoman or any one of his usual opponents. However, on some occasions, Batman would have to face them all at the same time.</p>
<p>What would happen if, like Batman, the immune system had to face all of its rivals at once?</p>
<p><a href="https://scholar.google.com/citations?user=6JOQvNwAAAAJ&hl=en">I am an immunologist</a> who teaches the fundamentals of immunology to college undergraduates. My research generally focuses on factors that regulate immune responses and prevent autoimmune diseases – conditions where the immune system attacks your own body. As a scientist studying how we build immunity against pathogens such as the virus that causes COVID-19, understanding how the immune system combats multiple threats at the same time is immensely important to me. </p>
<p>There’s no reason why you can’t come down with strep throat at the same time as when you have a cold. In fact, sometimes fighting off one enemy can leave a hole in your defenses that another opportunistic pathogen can take advantage of.</p>
<h2>BAM! Understanding the rivals</h2>
<p>The first point to consider is what your immune system protects you from. The potential bad guys <a href="https://theconversation.com/immune-cells-that-fight-cancer-become-exhausted-within-hours-of-first-encountering-tumors-new-research-210947">include cancer cells</a> and dangerous microorganisms – including bacteria, viruses, fungi and more – that cause infections. The immune system must also be careful <a href="https://theconversation.com/immune-health-is-all-about-balance-an-immunologist-explains-why-both-too-strong-and-too-weak-an-immune-response-can-lead-to-illness-215217">not to damage</a> healthy cells and beneficial microorganisms that live on and inside you. </p>
<p>You interact with <a href="https://kids.frontiersin.org/articles/10.3389/frym.2022.629355">thousands of microorganisms</a> with every breath of air you take. Is the immune system facing off against all of them? Sort of. </p>
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<a href="https://images.theconversation.com/files/565525/original/file-20231213-27-oegbgf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Microscope images of two T regulatory cells wrapped around an antigen-presenting cell" src="https://images.theconversation.com/files/565525/original/file-20231213-27-oegbgf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/565525/original/file-20231213-27-oegbgf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/565525/original/file-20231213-27-oegbgf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/565525/original/file-20231213-27-oegbgf.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/565525/original/file-20231213-27-oegbgf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=754&fit=crop&dpr=1 754w, https://images.theconversation.com/files/565525/original/file-20231213-27-oegbgf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=754&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/565525/original/file-20231213-27-oegbgf.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=754&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<span class="caption">T regulatory cells (red) determine whether an immune response should be mounted.</span>
<span class="attribution"><a class="source" href="https://flic.kr/p/SjQFf7">NIAID/Flickr</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
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<p>It takes a <a href="https://theconversation.com/how-does-fever-help-fight-infections-theres-more-to-it-than-even-some-scientists-realize-210240">tremendous amount of energy</a> to fight a battle once a rival gains a foothold within your blood or tissues, so your immune system works to <a href="https://theconversation.com/how-do-viruses-get-into-cells-their-infection-tactics-determine-whether-they-can-jump-species-or-set-off-a-pandemic-216139">prevent it from getting in the body</a> in the first place. Your skin, <a href="https://theconversation.com/why-do-our-noses-get-snotty-when-we-are-sick-a-school-nurse-explains-the-powers-of-mucus-212949">snot</a>, saliva and <a href="https://theconversation.com/can-you-cry-underwater-205464">tears</a> form a critical <a href="https://www.ncbi.nlm.nih.gov/books/NBK279396/">first line of defense</a>. This is why <a href="https://doi.org/10.1089%2Fsur.2013.134">burn victims</a> who lose too much skin often die from overwhelming infection – their defensive barriers are too compromised and pathogens pour in.</p>
<p>The immune system greatly prefers <a href="https://theconversation.com/a-pediatric-nurse-explains-the-science-of-sneezing-160970">catching a microbe in snot</a> and blowing it out of your nose, or giving you time to wash it off the skin of your hands, over having to wage a cellular war. Gathering an army of <a href="https://theconversation.com/coronavirus-b-cells-and-t-cells-explained-141888">immune cells</a> to fight pathogens takes a lot of energy and makes you feel awful. </p>
<p>For example, the immune system <a href="https://theconversation.com/how-does-fever-help-fight-infections-theres-more-to-it-than-even-some-scientists-realize-210240">increases your body temperature</a> to make it an uncomfortable place for microorganisms to live and grow, but that fever can also make you want to lie down for days.</p>
<h2>BOOM! Where are their weaknesses?</h2>
<p>When Batman faced multiple opponents, he would find a weakness shared by all of the opponents and target it to foil their plans. The immune system uses the exact same strategy.</p>
<p>Certain microbes are considered pathogens largely because they are in the wrong place – such as inside your body instead of on your skin – and causing damage. Pathogens have specific parts on their surfaces called <a href="https://doi.org/10.1038/s41392-021-00687-0">pathogen associated molecular patterns, or PAMPs</a>.</p>
<p>Very importantly, your body doesn’t make PAMPS. This means if your immune system comes across a PAMP, it knows it isn’t supposed to be there and will mount an attack. Because the same PAMP is present on many different pathogens, a strategy to combat one PAMP can defeat many pathogens.</p>
<p>There are molecules in cells all over your body that can recognize PAMPS and destroy anything those PAMPS are on. It’s as though your immune system set up booby traps that can only attack your enemies.</p>
<p>Many of those booby traps are <a href="https://doi.org/10.1038/35100529">toll-like receptors</a>. This family of molecules is located on the surface and inside of many of your cells. Once microbes contact these booby traps, they trigger an alarm that warn other cells of potential danger. In technical terms, this alarm is <a href="https://theconversation.com/what-is-inflammation-two-immunologists-explain-how-the-body-responds-to-everything-from-stings-to-vaccination-and-why-it-sometimes-goes-wrong-193503">called inflammation</a>.</p>
<h2>SPLAT! Raising an army of defenders</h2>
<p>Whereas Batman would need to think of a new strategy to combat the Joker, the Penguin and Catwoman, your immune system devised a plan long ago. </p>
<p>When the virus that causes COVID-19 emerged in 2019, it was something people’s immune systems likely had never seen before. However, some people already had immune cells that could target components of the virus. How is that possible?</p>
<p>The immune system makes many immune cells that are specific to antigens, or unique and recognizable parts of cancers and microorganisms, it hasn’t encountered before. This occurs through a process where pieces of your DNA <a href="https://doi.org/10.1038/nri2941">randomly recombine to form</a> unique immune cell receptors. The DNA in each of these immune cells is different from the DNA in any other cell in your body. Researchers believe that each person can generate <a href="https://www.ncbi.nlm.nih.gov/books/NBK27140/">at least a trillion different combinations</a> of immune receptors, which is <a href="https://doi.org/10.1038/nrmicro2644">more than the number of pathogens</a> an average person would ever face in their lifetime overall.</p>
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<figcaption><span class="caption">Your immune system can churn out billions of unique antibodies.</span></figcaption>
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<p>Although the immune system makes a lot of immune cells, most of them aren’t used because you’re not exposed to the antigen they’re made to recognize. However, when an immune cell recognizes an antigen, it rapidly <a href="https://bio.libretexts.org/Bookshelves/Microbiology/Microbiology_(Boundless)/11%3A_Immunology/11.07%3A_Antibodies/11.7C%3A_Clonal_Selection_of_Antibody-Producing_Cells">makes many copies of itself</a>. Since pathogens can also multiply rapidly, clonal selection allows you to rapidly raise an army to fight them.</p>
<p>Usually this strategy works well with <a href="https://theconversation.com/when-covid-19-or-flu-viruses-kill-they-often-have-an-accomplice-bacterial-infections-187056">one or two coinfections</a>, such as if you have the common cold and an eye infection at the same time. But what if you were infected with a trillion pathogens at the same time? It would take a tremendous amount of energy and time to build an appropriate army against each microorganism all at once. Unfortunately, the immune system likely would be overwhelmed by this challenge, and you would probably die. </p>
<p>Fortunately, your immune system – like Batman – usually figures out the best way to shift a battle against rivals to its favor, pulling out a victory in the final minutes of the episode.</p>
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<p><em>Hello, curious kids! Do you have a question you’d like an expert to answer? Ask an adult to send your question to <a href="mailto:curiouskidsus@theconversation.com">CuriousKidsUS@theconversation.com</a>. Please tell us your name, age and the city where you live.</em></p>
<p><em>And since curiosity has no age limit – adults, let us know what you’re wondering, too. We won’t be able to answer every question, but we will do our best.</em></p><img src="https://counter.theconversation.com/content/214919/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Joseph Larkin III receives funding from the Grayson Jockey Research Foundation, The National Institutes of Health, and industry. </span></em></p>Your immune system is often able to fend off pathogens it’s never seen before. But defending your body against all of them all at once is a tough challenge.Joseph Larkin III, Associate Professor of Microbiology and Cell Science, University of FloridaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2197342023-12-15T11:02:43Z2023-12-15T11:02:43ZDiverse gut microbiomes give better protection against harmful bugs – now we know why<figure><img src="https://images.theconversation.com/files/565752/original/file-20231214-21-8x6yy5.jpg?ixlib=rb-1.1.0&rect=17%2C0%2C5973%2C3988&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/child-hands-hold-decorative-model-intestine-2029232825">Helena Nechaeva/Shutterstock</a></span></figcaption></figure><p>In the last decade, it has become increasingly clear that a gut full of friendly microbes (the microbiome) is vital for our good health. It has also become clear that a healthy microbiome is one with a diverse population of microbes (bacteria, viruses, fungi). What we haven’t known is why a diverse array of friendly bugs is important for keeping the harmful microbes (pathogens) at bay. But now we think we have found the answer.</p>
<p>Our <a href="https://www.science.org/doi/10.1126/science.adj3502">latest study</a>, published in Science, shows that the main reason a diverse microbiome is helpful for resisting pathogens is that the friendly microbes collectively consume the nutrients needed for a pathogen to grow in the gut. </p>
<p>In other words, a diverse microbiome blocks pathogen growth by using its nutrients – a phenomenon we call “nutrient blocking”. Understanding how nutrient blocking works is powerful because it allows us to predict which gut communities will be protective against a given pathogen.</p>
<p>Our research team started by conducting a large screen of 100 common strains of human gut bacteria. We tested the individual ability of these strains to restrict the growth of two bacterial pathogens, <em>Klebsiella pneumoniae</em> and <em>Salmonella enterica</em> serovar Typhimurium. These two species are a problem because many strains are becoming resistant to antibiotics. </p>
<p>Alone, the gut strains could not prevent pathogen growth. However, this was different when several of these species were pooled into larger communities. Higher diversity communities tended to offer more protection against invading pathogens, both in test-tube experiments and when tested in mice.</p>
<p>However, not all higher diversity communities tested restricted pathogen growth. Crucially, certain species must be present for a community to be protective. </p>
<p>We then went on to investigate the reason why. We compared the nutrients that could be consumed by each of the individual species with the nutrients consumed by the pathogens. We realised that certain gut species had a higher nutrient use overlap with the pathogens than other species. </p>
<p>Still, individually, the nutrient use overlap of even these key species with the pathogens was not high enough to block pathogen growth. But when we considered which nutrients the community as a whole can use, we found that the communities with the highest degree of overlap with the pathogens provided the most protection.</p>
<h2>Suggesting treatments</h2>
<p>This finding is important as it provides a route for the design of beneficial, probiotic communities that aim to boost the microbiome’s ability to resist colonisation by disease-causing pathogens. </p>
<p>We tested this idea by taking a set of 50 human gut species and predicting which combinations of species would be protective against a new pathogen: a drug-resistant <em>Escherichia coli</em>. </p>
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<img alt="Scanning electron micrograph of an E coli colony" src="https://images.theconversation.com/files/565992/original/file-20231215-17-4ya1tj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/565992/original/file-20231215-17-4ya1tj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=407&fit=crop&dpr=1 600w, https://images.theconversation.com/files/565992/original/file-20231215-17-4ya1tj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=407&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/565992/original/file-20231215-17-4ya1tj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=407&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/565992/original/file-20231215-17-4ya1tj.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=512&fit=crop&dpr=1 754w, https://images.theconversation.com/files/565992/original/file-20231215-17-4ya1tj.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=512&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/565992/original/file-20231215-17-4ya1tj.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=512&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<span class="caption">Some strains of <em>E coli</em> bacteria (seen here) cause us harm.</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/w/index.php?curid=57721205">CDC/Janice Haney Carr</a></span>
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<p>We selected the communities that were predicted to be poor at blocking the growth of this pathogenic <em>E coli</em> isolate, and communities that were predicted to be good, and tested them against the new pathogen. In all cases, the nutrient blocking principle was able to successfully predict the ability of the community to block the growth of the pathogen.</p>
<p>Antibiotic treatment failure is <a href="https://theconversation.com/antimicrobial-resistance-is-a-silent-killer-that-leads-to-5-million-deaths-a-year-solutions-must-include-the-poor-217693">becoming more common</a> due to the spread of resistant pathogens. Alternative solutions that harness the body’s natural ability to resist disease, such as by tinkering with the microbiome’s composition, are becoming more attractive. </p>
<p>The gut microbiome is integral to our health, but it is very complex and therefore hard to understand. Our study provides a template for how one might rationally design probiotic communities to engineer microbiomes for better health.</p><img src="https://counter.theconversation.com/content/219734/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Frances Spragge received PhD funding from UKRI (BBSRC). </span></em></p><p class="fine-print"><em><span>Erik Bakkeren receives funding from the Swiss National Science Foundation. </span></em></p>Gut bacteria consume the nutrients that harmful pathogens need to survive, thereby keeping them in check, a new study finds.Frances Spragge, DPhil in Microbiology, University of OxfordErik Bakkeren, Postdoctoral Research Fellow, Department of Biology, University of OxfordLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2134042023-09-28T15:52:22Z2023-09-28T15:52:22ZI’m a microbiologist and here’s what (and where) I never eat<figure><img src="https://images.theconversation.com/files/550869/original/file-20230928-17-d1ixap.jpg?ixlib=rb-1.1.0&rect=20%2C0%2C6689%2C4476&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/chafing-dish-food-1020163570">Alex Andrei/Shutterstock</a></span></figcaption></figure><p>Every year, around <a href="https://www.ukri.org/news/food-safety-network-to-tackle-9-billion-food-poisoning-challenge/#:%7E:text=Food%20poisoning%20key%20facts%3A,foodborne%20illness%20in%20the%20UK">2.4 million people</a> in the UK get food poisoning – mostly from viral or bacterial contamination. Most people recover <a href="https://www.nhsinform.scot/illnesses-and-conditions/infections-and-poisoning/food-poisoning/">within a few days without treatment</a>, but <a href="https://bmjopengastro.bmj.com/content/7/1/e000377">not all are that lucky</a>.</p>
<p>As a microbiologist, I’m probably more acutely aware of the risk of food-borne infections than most. Here are some of the things I look out for.</p>
<h2>Eating outdoors</h2>
<p>I rarely eat alfresco – whether picnics or barbecues – as the risk of food poisoning goes up when food is taken outdoors. </p>
<p>Keeping your hands clean when handling food is key to not getting sick, but how often do you find hot running water and soap in a park or on a beach? You can use alcohol hand gels (they’re better than nothing), but they don’t kill all germs. </p>
<p>Also, food tends to attract an array of flying and crawling critters, such as flies, wasps and ants, all of which can transfer germs, including <em>E coli</em>, <em>Salmonella</em> and <em>Listeria</em>, to your food. </p>
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Read more:
<a href="https://theconversation.com/a-fruit-fly-has-landed-in-your-wine-is-it-ok-to-drink-211847">A fruit fly has landed in your wine – is it OK to drink?</a>
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<p>Keeping perishable food cold and covered is essential as germs can double in numbers if food is allowed to warm up to 30°C for more than a few hours. For barbecues, meat needs to be thoroughly cooked, and a meat thermometer is a good investment to avoid food poisoning. Do not eat meat if its internal temperature is <a href="https://www.betterhealth.vic.gov.au/health/healthyliving/food-safety-outdoors">less than 70°C</a>. </p>
<h2>Buffets</h2>
<p>Knowing what food-related conditions bacteria prefer to grow in, I am very mindful of the microbiological safety of hot and cold buffet displays. </p>
<p>Indoors, food can be exposed to contamination from insects, dust and above all, people. Food poisoning is, therefore, an inevitable risk when dining at a <a href="https://www.fda.gov/food/buy-store-serve-safe-food/serving-safe-buffets">buffet</a>. </p>
<p>Contamination comes from buffet visitors touching food, and germs can be sprayed on to buffets from people sneezing or coughing close to the food. Even indoors, one must consider contamination by insects, such as flies or wasps, settling on the uncovered food. Also, germs may be deposited from the air, which is rich in bacteria, fungi and viruses. </p>
<p>I always look at the clock when I’m at a buffet as there is a <a href="https://www.cdc.gov/foodsafety/serving-food-safely.html">two-hour catering rule</a>: perishable food will become unsafe to eat within two hours if not kept covered and refrigerated. The problem is buffets tend to be laid out before you arrive, so it is difficult to tell if the platters of cooked meat, seafood, salads, desserts and appetisingly arranged fruit and vegetables will have been sitting for more than two hours when you come to eat them. </p>
<p>For hot buffets, such as those served at breakfast in hotels, I always avoid lukewarm food, as bacteria that cause food poisoning can grow quickly when food is <a href="https://www.fda.gov/food/buy-store-serve-safe-food/serving-safe-buffets">kept at less than 60°C</a>. Hot food should be served hot, that is at a temperature of at least 60°C. If there is any uncertainty about the safety of the food on offer, I reluctantly breakfast on freshly toasted bread and individually packaged marmalade. </p>
<h2>Oysters</h2>
<p>There are some foods I never eat, and raw shellfish, such as oysters, is one of them. This is because oysters are filter feeders and can concentrate germs, such as <em>Vibrio</em> and norovirus, in their tissue. </p>
<p>A <em>Vibrio</em>-contaminated oyster does not look, smell, or taste different, but can still make you very ill. The US Centers for Disease Control and Prevention estimates that about 80,000 people get <em>Vibrio</em> infections from raw oysters, and in the US alone 100 people <a href="https://www.cdc.gov/foodsafety/communication/oysters-and-vibriosis.html">die from vibriosis</a> each year.</p>
<p>It is also possible to pick up food poisoning from eating any raw shellfish (clams, mussels, whelks, cockles). I only eat shellfish that are well-cooked because heat effectively kills harmful germs. </p>
<h2>Bagged salads</h2>
<p>I never eat bagged salads, largely because one of my research areas is fresh salad safety. It has been found that bagged lettuce can contain food poisoning germs such as <em>E coli</em>, <em>Salmonella</em> and <em>Listeria</em>. </p>
<p>My research group <a href="https://journals.asm.org/doi/10.1128/aem.02416-16">has found</a> that these pathogens grow more than a thousand times better when given juices from salad leaves, even if the salad bag is refrigerated. Worryingly, the same germs use the salad juices to become more virulent, and so better at causing an infection.</p>
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Read more:
<a href="https://theconversation.com/the-sniff-test-is-not-reliable-for-food-safety-heres-why-211808">The sniff test is not reliable for food safety – here's why</a>
</strong>
</em>
</p>
<hr>
<p>For those salad lovers alarmed by this information, most bagged salads are safe if stored refrigerated, washed well before use (even ready-to-eat salad should be washed) and eaten as soon as possible after buying it. </p>
<figure class="align-center ">
<img alt="An open bag of lettuce." src="https://images.theconversation.com/files/550872/original/file-20230928-15-irzk45.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/550872/original/file-20230928-15-irzk45.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/550872/original/file-20230928-15-irzk45.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/550872/original/file-20230928-15-irzk45.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/550872/original/file-20230928-15-irzk45.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/550872/original/file-20230928-15-irzk45.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/550872/original/file-20230928-15-irzk45.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">If there are salad ‘juices’, throw it out.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/open-bag-salad-lettuce-carrots-white-528025258">Noel V. Baebler/Shutterstock</a></span>
</figcaption>
</figure>
<h2>Cooking practices</h2>
<p>In terms of cooking practices, I have a list of dos and don’ts. </p>
<p>For perishable foods, I regularly check use-by dates, but if it is before the expiry date and the food package looks swollen, or when opened the food looks or smells different than expected, I throw it in the bin as it could be contaminated.</p>
<p>I never use the same chopping boards for raw and cooked foods, and washing my hands before and after handling food is instinctual. </p>
<p>One of my “never do” practices is reheating cooked rice. This is because uncooked rice can contain spores of <em>Bacillus cereus</em>, a food-poisoning germ. </p>
<p>Although the <em>Bacillus</em> cells are killed by cooking, the spores survive. If the rice is left to cool and sit at room temperature, <a href="https://www.nhs.uk/common-health-questions/food-and-diet/can-reheating-rice-cause-food-poisoning/#:%7E:text=Yes%2C%20you%20can%20get%20food,been%20stored%20before%20it%E2%80%99s%20reheated">the spores grow into bacteria</a>, which will increase in numbers quickly as rice is a good <em>Bacillus</em> culture medium when at room temperature. </p>
<p>The rice-cultured <em>Bacillus</em> can produce toxins that, within a few hours of ingestion, can cause vomiting and diarrhoea lasting up to 24 hours.</p>
<h2>Dining out</h2>
<p>I find that having a high level of food safety awareness causes me to be first in line for buffets, to be cautious about eating from breakfast bars, and to watch the clock for how often perishable food is replaced. I never collect “doggy bags” of food leftovers (they have usually exceeded the two-hour time limit), even if they really are intended for a pet. </p>
<p>The benefits of being a microbiologist are that we know how to avoid food poisoning and, in return, people have confidence our cooking is very safe to eat.</p><img src="https://counter.theconversation.com/content/213404/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Primrose Freestone has previously received funding from the BBSRC for her salad research work..</span></em></p>You’ll never look at bagged lettuce the same way again.Primrose Freestone, Senior Lecturer in Clinical Microbiology, University of LeicesterLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2085382023-09-21T21:27:36Z2023-09-21T21:27:36ZLyme disease: The pathogen’s cunning strategies for persistent infection offer clues for vaccine development<figure><img src="https://images.theconversation.com/files/547386/original/file-20230911-25-n5os9t.JPG?ixlib=rb-1.1.0&rect=65%2C23%2C1709%2C1158&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The black-legged tick is the vector that spreads Lyme disease. Its bite can infect humans with the Borrelia burgdorferi bacterium.</span> <span class="attribution"><span class="source">(Jim Gathany/CDC)</span></span></figcaption></figure><iframe style="width: 100%; height: 100px; border: none; position: relative; z-index: 1;" allowtransparency="" allow="clipboard-read; clipboard-write" src="https://narrations.ad-auris.com/widget/the-conversation-canada/lyme-disease-the-pathogens-cunning-strategies-for-persistent-infection-offer-clues-for-vaccine-development" width="100%" height="400"></iframe>
<p>Lyme disease is the leading <a href="https://www.who.int/news-room/fact-sheets/detail/vector-borne-diseases">vector-borne disease</a> — meaning diseases that are transmitted to humans from another organism like a tick or mosquito — in <a href="https://doi.org/10.1186/s12889-019-7069-6">North America and Europe</a>. </p>
<p><a href="https://doi.org/10.3201/eid2702.202731">New human cases are estimated</a> at over <a href="http://dx.doi.org/10.15585/mmwr.ss6622a1">400,000 in the United States each year</a>. Canada has experienced a drastic increase in human cases, <a href="https://www.canada.ca/en/public-health/services/diseases/lyme-disease/surveillance-lyme-disease.html#a5">from 266 cases in 2011 to 3,147 in 2021</a>, as the habitat of its vector, a tick, expands north. </p>
<p>The initial symptoms of human Lyme disease can be vague, such as fever, headache, fatigue and often rash. It is a potentially serious condition that can affect multiple systems in the body — including the heart, nervous system and joints — and can become a chronic illness.</p>
<p>Lyme disease is caused by a unique, spiral-shaped (spirochete) bacterium called <a href="https://doi.org/10.1099/00207713-34-4-496"><em>Borrelia burgdorferi</em></a>. <em>B. burgdorferi</em> cannot survive in the environment on its own. For <a href="https://doi.org/10.21775/cimb.042.473">survival and transmission</a>, it requires susceptible hosts (usually small mammals or birds) and a <a href="https://doi.org/10.1056/NEJM198303313081301">specific vector</a>: the black-legged tick, also called the deer tick.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/535388/original/file-20230703-257464-m0lz6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/535388/original/file-20230703-257464-m0lz6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=420&fit=crop&dpr=1 600w, https://images.theconversation.com/files/535388/original/file-20230703-257464-m0lz6y.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=420&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/535388/original/file-20230703-257464-m0lz6y.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=420&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/535388/original/file-20230703-257464-m0lz6y.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=528&fit=crop&dpr=1 754w, https://images.theconversation.com/files/535388/original/file-20230703-257464-m0lz6y.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=528&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/535388/original/file-20230703-257464-m0lz6y.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=528&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Lyme disease infectious cycle: Adult ticks lay egg sacs that can hatch thousands of tick larvae. Larvae are not born with Borrelia burgdorferi but can acquire the bacterium when they feed on an infected host. After feeding, larvae molt to nymphs which must feed once to molt to adults. Female adult ticks also feed once before laying the egg sac. Nymphs and adult ticks can transmit B. burgdorferi to susceptible hosts while feeding.</span>
<span class="attribution"><span class="source">(BioRender)</span></span>
</figcaption>
</figure>
<h2>Evading the immune system</h2>
<p><em>B. burgdorferi</em> must survive extremely diverse conditions over the course of its transmission and infection cycle: from host to tick vector, and then into new hosts. </p>
<p>This bacterium senses and responds to its surroundings, most notably by <a href="https://doi.org/10.1128/iai.70.7.3382-3388.2002">modifying its appearance</a> by changing the <a href="https://doi.org/10.1073/pnas.92.7.2909" title="). _B. burgdorferi_ has over [50 surface-exposed proteins](https://doi.org/10.1128/jb.00658-16 "">proteins on its outer surface</a> to <a href="https://doi.org/10.1111/j.1574-695X.2012.00980.x">help it survive</a> in either <a href="https://doi.org/10.1038/s41467-023-35897-3">the tick</a> or the host.</p>
<p>When a tick infected by <em>B. burgdorferi</em> bites and feeds on a vertebrate host, it provides a signal for the bacteria to switch its proteins to those required to infect the host, and to begin migrating through the tick and into the bite site. This process takes between <a href="https://doi.org/10.4269/ajtmh.1995.53.397">36 and 72 hours</a>. </p>
<p>However, many of these proteins are recognized by the host as foreign, and the host’s immune system works to try to clear the infection. This includes a strong, antibody response targeted against <em>B. burgdorferi</em>. </p>
<p>Despite these immune responses, <em>B. burgdorferi</em> is able to cause long-term infections. In natural host reservoirs — the animals that the bacterium usually finds itself in via tick bites, such as small rodents — these infections do not cause diseases like those seen in humans and other <a href="https://doi.org/10.1016/j.idc.2007.12.013">non-natural reservoirs</a>. </p>
<p>In fact, the bacteria itself does not produce any products that would be <a href="https://doi.org/10.1016/j.cll.2015.07.004">toxic to its hosts</a>, either natural or non-natural. Yet chronic infection in humans can lead to <a href="https://doi.org/10.1038/nrdp.2016.90">Lyme neuroborreliosis, carditis and Lyme arthritis</a>.</p>
<figure class="align-center ">
<img alt="Bacteria that look like bright green and yellow squiggles against a dark green background" src="https://images.theconversation.com/files/548570/original/file-20230915-23-4ysjok.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/548570/original/file-20230915-23-4ysjok.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=612&fit=crop&dpr=1 600w, https://images.theconversation.com/files/548570/original/file-20230915-23-4ysjok.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=612&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/548570/original/file-20230915-23-4ysjok.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=612&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/548570/original/file-20230915-23-4ysjok.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=770&fit=crop&dpr=1 754w, https://images.theconversation.com/files/548570/original/file-20230915-23-4ysjok.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=770&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/548570/original/file-20230915-23-4ysjok.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=770&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Microscopic image of Lyme disease bacteria Borrelia burgdorferi. In this photo, immunofluorescent antibodies have been used to change the colour of spirochetes that express different outer surface proteins.</span>
<span class="attribution"><span class="source">(NIAID)</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>How then, are these bacteria able to cause such a devastating disease in humans and other animals, but not in their natural host reservoirs?</p>
<p>While there is still much to learn about <em>B. burgdorferi</em>, we know of several factors that play a role in the <a href="https://doi.org/10.1038/nrdp.2016.90">range of disease it causes</a>. These include:</p>
<ul>
<li>its genetic make-up, </li>
<li>its ability to access various tissues (such as the joints, heart and nervous system) due to its <a href="https://doi.org/10.1128/iai.01228-12">ability to move around (motility)</a>, and </li>
<li>the immune response of the host. </li>
</ul>
<p>Apart from motility, <em>B. burgdorferi</em> also protects itself from the strong <em>B. burgdorferi</em>-specific targeted antibody response of its host’s immune system by changing the appearance of the main outer surface protein expressed during persistent infection in a process called <a href="https://doi.org/10.1128/iai.66.8.3698-3704.1998">antigenic variation</a>.</p>
<h2>How Lyme disease is perpetuated</h2>
<p>In addition to antigenic variation, <em>B. burgdorferi</em> bacteria can also change their DNA by <a href="https://doi.org/10.1073/pnas.0402745101">exchanging genetic information, a process also known as gene transfer</a>. This process allows these bacteria to further alter their <a href="https://doi.org/10.1128/mbio.00153-10">appearance</a> <a href="https://doi.org/10.1534/genetics.111.130773">during infection</a> to avoid the host immune system.</p>
<p>This process works so well that these <em>B. burgdorferi</em> bacteria appear different enough to allow <a href="https://doi.org/10.7326/0003-4819-127-2-199707150-00006">re-infection</a> or even <a href="https://doi.org/10.1128/iai.01817-14">co-infection</a> (where multiple strains of B. burgdorferi infect a single host at the same time) of a vertebrate host, like a mouse or a human, despite the presence of specific antibodies to fight the bacterium.</p>
<p>In fact, in nature, the majority of host reservoirs and the ticks that carry the bacterium are infected with <a href="https://doi.org/10.1128/AEM.02296-15">multiple strains of <em>B. burgdorferi</em></a>. The ability of <em>B. burgdorferi</em> to reinfect and co-infect both ticks and hosts increases the spread of the bacteria in the environment as well as the chances that humans will encounter Lyme disease.</p>
<h2>Human cases of Lyme disease are increasing</h2>
<p>As a vector-borne pathogen, <em>B. burgdorferi</em> only infects individuals that are bitten by an infected tick. It is not transmitted from <a href="https://doi.org/10.1093/cid/ciz872">person to person</a>.</p>
<p>Environments that support black-legged/deer ticks are at risk of harbouring <em>B. burgdorferi</em>. In North America, these species of ticks are widely distributed throughout the eastern and midwestern United States. Recent <a href="https://doi.org/10.1093/jme/tjy104">geographic expansion</a> to the north is increasing the prevalence of Lyme disease <a href="https://doi.org/10.1503/cmaj.080148">in Canada</a>. </p>
<p>The increase of human Lyme disease cases highlights the failure of existing preventive strategies — such as minimizing exposure to tick habitats, performing diligent tick checks, and wearing suitable clothing when performing activities in known tick habitats — and emphasizes the need for an effective <a href="https://doi.org/10.21775/cimb.042.191">human vaccine</a>.</p>
<h2>A One Health approach</h2>
<p>At <a href="https://www.vido.org/">Vaccine and Infectious Disease Organization</a> at the University of Saskatchewan, we are taking a <a href="https://ipac-canada.org/one-health">One Health</a> approach by recognizing that human health is closely related to the health of animals and the shared environment. We are investigating the role of <em>B. burgdorferi</em>, ticks, and susceptible animals on the spread and survival of the Lyme disease bacterium. </p>
<p>It is important to mimic the natural infectious cycle as much as possible when identifying potential vaccine and drug targets. This is because the way host animals are infected (for example, artificial needle infection or natural tick bite) can produce drastic differences in the resulting infection. </p>
<p>Additionally, despite the prevalence of this disease, there are still many aspects of the infectious cycle that remain unknown due to the uniqueness of <em>B. burgdorferi</em> and a lack of knowledge about the tick vector. </p>
<p>For example, we recently learned that a <em>B. burgdorferi</em> protein is responsible for regulating the components necessary for the bacterium to infect vertebrates, including humans. The absence of this protein, among other things, leads to the <a href="https://doi.org/10.1038/s41467-023-35897-3">death of <em>B. burgdorferi</em> in ticks</a>, making it an exciting target for research investigation. </p>
<p>By learning more about the molecular mechanisms that change or reduce the severity of the disease caused by this bacterium, we can identify new targets for the prevention of human Lyme disease.</p><img src="https://counter.theconversation.com/content/208538/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jenny Wachter does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>The bacterium that causes Lyme disease is a master of disguise, changing its appearance to evade the immune system as it moves from the ticks that carry it to humans or animals.Jenny Wachter, Research scientist/Adjunct professor, University of SaskatchewanLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2102402023-09-11T12:34:57Z2023-09-11T12:34:57ZHow does fever help fight infections? There’s more to it than even some scientists realize<figure><img src="https://images.theconversation.com/files/547038/original/file-20230907-17-4s7zuu.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C2121%2C1412&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Being feverish is unpleasant, but it can help your body overcome invading pathogens.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/mother-measuring-the-temperature-of-her-ill-royalty-free-image/1458502274">Narisara Nami/Moment via Getty Images</a></span></figcaption></figure><p>When you’re <a href="https://doi.org/10.1038%2Fnri3843">sick with a fever</a>, your doctor will likely tell you it’s a sign that your immune system is defending you against an infection. Fever typically results from immune cells at infected sites sending chemical signals to the brain to raise the set point of your body’s thermostat. So, you <a href="https://youtu.be/jRvxnpfCDSo">feel chills</a> when the fever starts and feel hot when the fever breaks.</p>
<p>However, if you were to ask your doctor exactly how fever protects you, don’t expect a completely satisfactory answer.</p>
<p>Despite scientific consensus that fever is beneficial in fighting infections, exactly how is contentious. We are a <a href="https://scholar.google.com/citations?user=2o9r-L8AAAAJ&hl=en">veterinary pathologist</a> and an <a href="https://scholar.google.com/citations?user=RI7ng_YAAAAJ&hl=en">emergency physician</a> interested in <a href="https://isemph.org/what-is-evolutionary-medicine">applying evolutionary principles</a> to medical problems. The evolution of fever is a classic conundrum because fever’s effects seem so harmful. Besides making you feel uncomfortable, you may also worry you’ll dangerously overheat. It is also metabolically costly to generate that much heat. </p>
<p>In our research and review, we propose that since fever occurs throughout much of the animal kingdom, this costly response <a href="https://doi.org/10.1093/emph/eoaa044">must have benefits</a> or it never would have evolved or been retained across species over time. We highlight several important but rarely considered points that help explain how the heat of fever helps your body fight infections.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/jRvxnpfCDSo?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Fever is a physiological response that has persisted for hundreds of millions of years across species.</span></figcaption>
</figure>
<h2>How fever fights infection</h2>
<p>Infections are <a href="https://doi.org/10.1186%2Fs12915-017-0433-z">caused by pathogens</a>. Pathogens can be microbes such as certain species of bacteria, fungi or protozoans. If microbes or viruses have infected your cells and are using them to replicate, your own cells can also be considered pathogens and are treated that way by your immune system.</p>
<p>The main explanation for how fever helps control infections is that <a href="https://theconversation.com/normal-human-body-temperature-is-a-range-around-98-6-f-a-physiologist-explains-why-139270">higher temperatures</a> put heat-induced stress on pathogens, killing them or at least inhibiting their growth. But why would the somewhat higher body temperatures of fever – an increase of about 1.8 to 5.4 degrees Fahrenheit (<a href="https://doi.org/10.1038/nri3843">1 to 4 degrees Celsius</a>) – which can’t even kill your own healthy cells, harm such a wide variety of pathogens?</p>
<p>Immunologists have noted that slight heat <a href="https://doi.org/10.1038/nri3843">makes immune cells work better</a>. The implication is that fever is needed to enhance their defensive function. However, from an evolutionary perspective, it seems strange to require the massive energy cost of generating a fever just to get more activity from immune cells, especially since there are already plentiful and faster molecular signals available to activate them.</p>
<p>In addition to heat, <a href="https://doi.org/10.1186%2Far2632">slightly low oxygen levels</a> and <a href="https://doi.org/10.1155%2F2018%2F1218297">slight acidity</a> <a href="https://doi.org/10.1371/journal.ppat.1000282">also boost</a> immune cell function. Since these stressful conditions also occur at infected sites, it makes sense that immune cells evolved to have their maximum functionality match their stressful working conditions. In fact, since anything in a state of growth is inherently vulnerable to stress – and pathogens are typically growing – researchers, including one of us, have proposed that a function of immune cells is to actively <a href="https://doi.org/10.1098%2Frspb.2016.0266">make local conditions stressful</a> to preferentially harm the growing pathogens.</p>
<h2>Heating up pathogens locally</h2>
<p><a href="https://openstax.org/books/microbiology/pages/17-5-inflammation-and-fever">Inflammation</a> is a local defensive response to infection. It <a href="https://theconversation.com/what-is-inflammation-two-immunologists-explain-how-the-body-responds-to-everything-from-stings-to-vaccination-and-why-it-sometimes-goes-wrong-193503">typically involves</a> heat, pain, redness and swelling in the areas where the immune system is most active. While some scientists are aware that infected sites generate heat, many believe that the feeling of warmth from inflammation is only from dilated blood vessels bringing in warmer blood from core body tissues.</p>
<p>However, researchers have found that inflamed tissues, even in core body tissues, are up to 1.8 to 3.6 F (<a href="https://doi.org/10.1016/j.jacc.2005.11.050">1 to 2 C</a>) warmer than adjacent normal tissues, so warmth is not just a byproduct of more blood flow. Much of that extra heat is coming from the immune cells themselves. When they generate reactive oxygen species to kill pathogens in a process known as the respiratory burst, <a href="https://doi.org/10.1093/infdis/150.3.366">substantial heat</a> is also produced. To date, however, the temperatures involved have not been measured.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/547047/original/file-20230907-19-nezfs6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Over-the-shoulder view of someone holding a thermometer reading 38.5 degrees Celsius." src="https://images.theconversation.com/files/547047/original/file-20230907-19-nezfs6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/547047/original/file-20230907-19-nezfs6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=401&fit=crop&dpr=1 600w, https://images.theconversation.com/files/547047/original/file-20230907-19-nezfs6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=401&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/547047/original/file-20230907-19-nezfs6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=401&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/547047/original/file-20230907-19-nezfs6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/547047/original/file-20230907-19-nezfs6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/547047/original/file-20230907-19-nezfs6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Even an increase of a few degrees can affect how well your body kills pathogens.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/from-above-sick-lady-looking-at-thermometer-while-royalty-free-image/1393759427">Israel Sebastian/Moment via Getty Images</a></span>
</figcaption>
</figure>
<p>While cells can tolerate a wide range of temperatures, all cells experience a sharp decline in their ability to grow and survive at higher temperatures. For mammalian cells, and presumably the pathogens that infect them, even a single degree or two above temperatures around 113 F (45 C) is <a href="https://doi.org/10.1016/S1040-8428(01)00179-2">almost always deadly</a>. So the heat of fever adds to already warmer local temperatures.</p>
<p>There is evidence that pathogens are exposed to temperatures that are much higher than the body temperature routinely measured with a thermometer in the emergency department. A 2018 study finding that local temperatures can be <a href="https://doi.org/10.1371/journal.pbio.2003992">as high as 122 F (50 C) in mitochondria</a> – the powerhouse of the cell – came as a <a href="https://doi.org/10.1371/journal.pbio.2005113">surprise to researchers</a>. The heat mitochondria generate is put to good use in warming the body and <a href="https://doi.org/10.1016/j.bbi.2020.11.031">for fever</a>. Likewise, we suggest that the local heat the respiratory burst produces at the surface of immune cells helps kill pathogens.</p>
<h2>Heat and other stressors</h2>
<p>Immune cells target pathogens with a <a href="https://doi.org/10.1155/2017/9671604">variety of stressors</a> meant to kill or inhibit them. These include reactive oxygen species, toxic peptides, digestive enzymes, high acidity and nutrient deprivation. Most chemical reactions are sped up by increased temperatures, so it isn’t surprising that heat enhances these defenses.</p>
<p>Researchers have shown heat to be <a href="https://pubmed.ncbi.nlm.nih.gov/34477/">synergistic with low oxygen and acidity</a> in killing pathogens. Notably, neither febrile temperatures nor iron restriction on their own were able to inhibit the growth of the infectious bacteria <a href="https://doi.org/10.1126/science.760197"><em>Pasteurella multocida</em></a>, but they could when combined. The stress of heat doesn’t act alone when controlling infections.</p>
<p>The standard view that the heat of fever kills pathogens and enhances immune responses is correct but incomplete. Fever’s ability to control infections comes from the few extra, but critical, degrees it adds to enhance existing locally generated heat to harm vulnerable growing pathogens. And fever also always acts with other defenses, never alone. </p>
<p>At <a href="https://doi.org/10.1038%2Fnri3843">over 600 million years old</a>, fever is an ancient feature of life on this planet that deserves respect. In fact, you owe it to infection-fighting heat that you are still here – alive – to read this. Something to think about the next time you’re sick.</p><img src="https://counter.theconversation.com/content/210240/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>The authors do not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.</span></em></p>The heat and chills that come with fever are not only uncomfortable but also metabolically costly. Increased body temperature, however, can make all the difference when you’re sick.Edmund K. LeGrand, Adjunct Professor of Biomedical and Diagnostic Sciences, University of TennesseeJoe Alcock, Professor of Emergency Medicine, University of New MexicoLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2097952023-07-27T20:11:18Z2023-07-27T20:11:18ZAncient pathogens released from melting ice could wreak havoc on the world, new analysis reveals<figure><img src="https://images.theconversation.com/files/539710/original/file-20230727-23-jtkhdm.jpeg?ixlib=rb-1.1.0&rect=0%2C66%2C4025%2C2565&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>Science fiction is rife with fanciful tales of deadly organisms emerging from the ice and wreaking havoc on unsuspecting human victims. </p>
<p>From <a href="https://www.imdb.com/title/tt0084787/">shape-shifting aliens</a> in Antarctica, to super-parasites emerging from a <a href="https://www.imdb.com/title/tt1235448/">thawing woolly mammoth</a> in Siberia, to exposed <a href="https://www.nytimes.com/2021/05/20/books/review/jim-shepard-phase-six.html">permafrost in Greenland</a> causing a viral pandemic – the concept is marvellous plot fodder.</p>
<p>But just how far-fetched is it? Could pathogens that were once common on Earth – but frozen for millennia in glaciers, ice caps and <a href="https://climate.mit.edu/explainers/permafrost">permafrost</a> – emerge from the melting ice to lay waste to modern ecosystems? The potential is, in fact, quite real. </p>
<h2>Dangers lying in wait</h2>
<p>In 2003, <a href="https://ami-journals.onlinelibrary.wiley.com/doi/abs/10.1046/j.1462-2920.2003.00422.x">bacteria were revived</a> from samples taken from the bottom of an ice core drilled into an <a href="https://byrd.osu.edu/research/groups/ice-core-paleoclimatology/projects/china/guliya">ice cap</a> on the <a href="https://goo.gl/maps/zjN3NVk8TAb6GrxZ9">Qinghai-Tibetan plateau</a>. The ice at that depth was more than 750,000 years old. </p>
<p>In 2014, a giant “zombie” <em>Pithovirus sibericum</em> virus was <a href="https://www.pnas.org/doi/abs/10.1073/pnas.1320670111">revived from</a> 30,000-year-old Siberian permafrost.</p>
<p>And in 2016, an outbreak of <a href="https://www.betterhealth.vic.gov.au/health/conditionsandtreatments/anthrax">anthrax</a> (a disease caused by the bacterium <em>Bacillus anthracis</em>) <a href="https://goo.gl/maps/fjV8u2mRbbC7UoAs5">in western Siberia</a> was attributed to the rapid <a href="https://link.springer.com/article/10.1007/s10393-021-01549-5">thawing of <em>B. anthracis</em> spores</a> in permafrost. It killed thousands of reindeer and affected dozens of people.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/537599/original/file-20230716-126451-ymm8xc.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/537599/original/file-20230716-126451-ymm8xc.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=395&fit=crop&dpr=1 600w, https://images.theconversation.com/files/537599/original/file-20230716-126451-ymm8xc.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=395&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/537599/original/file-20230716-126451-ymm8xc.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=395&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/537599/original/file-20230716-126451-ymm8xc.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=496&fit=crop&dpr=1 754w, https://images.theconversation.com/files/537599/original/file-20230716-126451-ymm8xc.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=496&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/537599/original/file-20230716-126451-ymm8xc.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=496&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption"><em>Bacillus anthracis</em> is a soil bacterium that causes anthrax.</span>
<span class="attribution"><span class="source">William A. Clark/USCDCP</span></span>
</figcaption>
</figure>
<p>More recently, scientists found <a href="https://royalsocietypublishing.org/doi/10.1098/rspb.2022.1073">remarkable genetic compatibility</a> between viruses isolated from lake sediments in the high Arctic and potential living hosts.</p>
<p>Earth’s climate is warming at a <a href="https://theconversation.com/it-can-be-done-it-must-be-done-ipcc-delivers-definitive-report-on-climate-change-and-where-to-now-201763">spectacular rate</a>, and up to four times faster <a href="https://www.nature.com/articles/s43247-022-00498-3">in colder regions</a> such as the Arctic. Estimates suggest we can expect <a href="https://ami-journals.onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2012.02876.x">four sextillion</a> (4,000,000,000,000,000,000,000) microorganisms to be released from ice melt each year. This is about the same as the estimated number of stars <a href="https://www.esa.int/Science_Exploration/Space_Science/Herschel/How_many_stars_are_there_in_the_Universe">in the universe</a>.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/for-110-years-climate-change-has-been-in-the-news-are-we-finally-ready-to-listen-188646">For 110 years, climate change has been in the news. Are we finally ready to listen?</a>
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<hr>
<p>However, despite the unfathomably large number of microorganisms being released from melting ice (including pathogens that can potentially infect modern species), no one has been able to estimate the risk this poses to modern ecosystems.</p>
<p>In <a href="http://doi.org/10.1371/journal.pcbi.1011268">a new study</a> published today in the journal PLOS Computational Biology, we calculated the ecological risks posed by the release of unpredictable ancient viruses.</p>
<p>Our simulations show that 1% of simulated releases of just one dormant pathogen could cause major environmental damage and the widespread loss of host organisms around the world.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/537499/original/file-20230714-15-iyqll0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/537499/original/file-20230714-15-iyqll0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/537499/original/file-20230714-15-iyqll0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/537499/original/file-20230714-15-iyqll0.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/537499/original/file-20230714-15-iyqll0.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/537499/original/file-20230714-15-iyqll0.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/537499/original/file-20230714-15-iyqll0.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/537499/original/file-20230714-15-iyqll0.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Melt water carving a glacier in the Himalayas of India.</span>
<span class="attribution"><span class="source">Sharada Prasad</span></span>
</figcaption>
</figure>
<h2>Digital worlds</h2>
<p>We used a software called <a href="https://alife.org/encyclopedia/digital-evolution/avida/">Avida</a> to run experiments that simulated the release of one type of ancient pathogen into modern biological communities. </p>
<p>We then measured the impacts of this invading pathogen on the diversity of modern host bacteria in thousands of simulations, and compared these to simulations where no invasion occurred.</p>
<p>The invading pathogens often survived and evolved in the simulated modern world. About 3% of the time the pathogen became dominant in the new environment, in which case they were very likely to cause losses to modern host diversity. </p>
<p>In the worst- (but still entirely plausible) case scenario, the invasion reduced the size of its host community by 30% when compared to controls.</p>
<p>The risk from this small fraction of pathogens might seem small, but keep in mind these are the results of releasing just one particular pathogen in simulated environments. With the sheer number of ancient microbes being released in the real world, such outbreaks represent a substantial danger.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/melting-ice-leaves-polar-ecosystems-out-in-the-sun-19807">Melting ice leaves polar ecosystems out in the sun</a>
</strong>
</em>
</p>
<hr>
<h2>Extinction and disease</h2>
<p>Our findings suggest this unpredictable threat which has so far been confined to science fiction could become a powerful driver of ecological change. </p>
<p>While we didn’t model the potential risk to humans, the fact that “time-travelling” pathogens could become established and severely degrade a host community is already worrisome.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/537596/original/file-20230716-122897-5fkiun.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/537596/original/file-20230716-122897-5fkiun.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/537596/original/file-20230716-122897-5fkiun.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/537596/original/file-20230716-122897-5fkiun.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/537596/original/file-20230716-122897-5fkiun.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/537596/original/file-20230716-122897-5fkiun.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/537596/original/file-20230716-122897-5fkiun.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Drilling ice cores in Greenland.</span>
<span class="attribution"><span class="source">Helle Astrid Kjær</span></span>
</figcaption>
</figure>
<p>We highlight yet another source of potential species extinction in the modern era – one which even our <a href="https://theconversation.com/children-born-today-will-see-literally-thousands-of-animals-disappear-in-their-lifetime-as-global-food-webs-collapse-196286">worst-case extinction models</a> do not include. As a society, we need to understand the potential risks so we can prepare for them.</p>
<p>Notable viruses such as <a href="https://www.sciencedirect.com/science/article/pii/S0092867421009910">SARS-CoV-2</a>, <a href="https://www.science.org/doi/full/10.1126/science.1259657">Ebola</a> and <a href="https://perspectivesinmedicine.cshlp.org/content/1/1/a006841">HIV</a> were likely transmitted to humans via contact with other animal hosts. So it is <a href="https://www.huffpost.com/entry/ice-caps-melt-prehistoric_b_9805334">plausible</a> that a once ice-bound virus could enter the human population via a <a href="https://theconversation.com/how-do-viruses-mutate-and-jump-species-and-why-are-spillovers-becoming-more-common-134656">zoonotic pathway</a>.</p>
<p>While the likelihood of a pathogen emerging from melting ice and causing catastrophic extinctions is low, our results show this is no longer a fantasy for which we shouldn’t prepare.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/539709/original/file-20230727-25-ftjegw.gif?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/539709/original/file-20230727-25-ftjegw.gif?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/539709/original/file-20230727-25-ftjegw.gif?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=300&fit=crop&dpr=1 600w, https://images.theconversation.com/files/539709/original/file-20230727-25-ftjegw.gif?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=300&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/539709/original/file-20230727-25-ftjegw.gif?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=300&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/539709/original/file-20230727-25-ftjegw.gif?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=377&fit=crop&dpr=1 754w, https://images.theconversation.com/files/539709/original/file-20230727-25-ftjegw.gif?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=377&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/539709/original/file-20230727-25-ftjegw.gif?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=377&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">They may only be microscopic – and far from the giant flesh-eating bugs you’ll see in sci-fi films – but the risks posed by pathogens shouldn’t be underestimated.</span>
<span class="attribution"><a class="source" href="https://cloud.blender.org/p/gallery/629f23f908e12d4ff15241d3">Giovanni Strona, 2023 (based on previous work by Oksana Dobrovolska)</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure><img src="https://counter.theconversation.com/content/209795/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Corey J. A. Bradshaw receives funding from the Australian Research Council.</span></em></p><p class="fine-print"><em><span>Giovanni Strona does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Researchers simulated thousands of scenarios of an ancient pathogen being released into modern ecosystems. In the worst cases, up to one-third of host species were destroyed.Corey J. A. Bradshaw, Matthew Flinders Professor of Global Ecology and Models Theme Leader for the ARC Centre of Excellence for Australian Biodiversity and Heritage, Flinders UniversityGiovanni Strona, Doctoral program supervisor, University of HelsinkiLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2042842023-05-11T05:28:46Z2023-05-11T05:28:46ZAfrican scientists are working to pool data that decodes diseases – a giant step<figure><img src="https://images.theconversation.com/files/525336/original/file-20230510-19-rgkrh3.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">African scientists need a central repository where the genomic data they capture can be uploaded and shared.</span> <span class="attribution"><span class="source">iStock/Getty Images Plus</span></span></figcaption></figure><p>Infectious disease outbreaks in African countries are, unfortunately, all too common. <a href="https://theconversation.com/ebola-what-are-the-symptoms-how-does-it-spread-and-where-did-it-come-from-191518">Ebola</a> in the Democratic Republic of the Congo or Uganda; Marburg virus in <a href="https://theconversation.com/the-first-human-case-of-marburg-virus-in-west-africa-is-no-surprise-heres-why-166694">Guinea</a> or <a href="https://theconversation.com/what-is-marburg-virus-and-should-we-be-worried-200082">Equatorial Guinea</a>; cholera in <a href="https://theconversation.com/why-cholera-continues-to-threaten-many-african-countries-197799">Malawi</a>; malaria and tuberculosis are among them. </p>
<p>These diseases do not respect <a href="https://theconversation.com/how-africas-porous-borders-make-it-difficult-to-contain-ebola-118719">human-made or porous borders</a>. So it’s essential that scientists in Africa are able to generate and share critical data on the pathogens in time to inform public-health decisions.</p>
<p>Genomic sequencing technologies are powerful tools in this kind of work. They enable scientists to decode the genetic material of diseases and create biological “fingerprints” to investigate and track the pathogens that cause those diseases. This information aids in developing diagnostics, treatments and vaccines. It also helps public health authorities to guide and prepare their public health systems for effective outbreak detection and response.</p>
<p>Tackling infectious diseases across countries and continents requires many complex, overlapping and broad interventions. One of those is a common repository where countries, public health authorities and their scientists can share information about diseases and the pathogens that cause them. They can then collaborate around the shared data. These <a href="https://www.insdc.org/">kinds of platforms</a> exist in many high-income countries. But the African region lags behind.</p>
<p>This is set to change. In a <a href="https://www.nature.com/articles/s41591-023-02266-y">new publication</a> in Nature Medicine we outline the work that’s being done to create such a repository for the African continent. </p>
<h2>Human and economic costs</h2>
<p>Africa accounts for <a href="https://www.sciencedirect.com/science/article/pii/S0092867420312381#cebib0010">most of the estimated 10 million deaths</a> caused globally every year by infectious diseases. </p>
<p>Those diseases also stomp the brakes on the continent’s development ambitions: according to a World Health Organisation (WHO) report they account for an <a href="https://www.afro.who.int/publications/heavy-burden-productivity-cost-illness-africa">annual estimated productivity loss</a> of US$800 billion. </p>
<p>These figures highlight the urgency of improving the scientific response to infectious diseases. </p>
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<em>
<strong>
Read more:
<a href="https://theconversation.com/investing-in-health-systems-is-the-only-way-to-stop-the-next-ebola-outbreak-124957">Investing in health systems is the only way to stop the next Ebola outbreak</a>
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</p>
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<p>There are some green shoots. The COVID pandemic showed what African institutions are capable of. The Africa Centres for Disease Control (Africa CDC), through the <a href="https://ipg.africacdc.org/initiatives/africa-pathogen-genomics-initiative-africa-pgi">Africa Pathogen Genomics Initiative</a>, oversaw the <a href="https://africacdc.org/news-item/africa-cdc-ramps-up-training-on-sars-cov-2-genomics-and-bioinformatics/">training</a> of hundreds of laboratory staff.</p>
<p>DNA sequencing machines and essential laboratory consumables – like reagents, the chemical cocktails that make testing possible – have been <a href="https://www.sciencedirect.com/science/article/pii/S1473309920309397">put in place</a>. Today, public health laboratories in many African countries, with varying levels of capacity, can generate their own genomic sequences of pathogens. </p>
<p>So, the data is not the problem. The questions are: what is going to happen to and with it? How and where is it going to be secured, and by whom? Will it be, as has been the <a href="https://theconversation.com/global-health-still-mimics-colonial-ways-heres-how-to-break-the-pattern-121951">custom up to now</a>, “exported” and the intellectual property moved offshore?</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/how-biobanks-can-help-improve-the-integrity-of-scientific-research-100035">How biobanks can help improve the integrity of scientific research</a>
</strong>
</em>
</p>
<hr>
<p>Global data sharing platforms have played a significant role in sharing of data. However, <a href="https://www.science.org/content/article/invented-persona-behind-key-pandemic-database">transparency and governance issues</a> are currently being raised by the global community.</p>
<p>Since 2020, the Africa CDC in collaboration with the <a href="https://aslm.org/">African Society for Laboratory Medicine</a>, the <a href="https://www.uwc.ac.za/study/all-areas-of-study/institutes/south-african-national-bioinformatics-institute/overview">South African National Bioinformatics Institute</a> and several public health institutions across Africa are working to develop a continental platform for pathogen genomic data management and sharing. The technology innovation and development involves <a href="https://hominum.global/">industry</a> and other <a href="http://nzconline.co.za">partners</a>.</p>
<p>The development of such a platform is not merely a technical exercise, though. An ecosystem must be created for its adoption. So it is being built in parallel with a consultation led by the Africa CDC with its member states, to refine data sharing agreements between countries and support national data governance frameworks.</p>
<p>The platform rests on six pillars.</p>
<h2>Collaboration and consistency</h2>
<p>The first pillar is adoption and change management. Regional organisations – those that drove training and infrastructure investment during the COVID-19 pandemic – must drive the development of the necessary policies, processes and system changes across the continent.</p>
<p>Second, the platform must offer a good user experience that will allow for seamless, cost-effective data collection and the timely sharing and use of data across Africa.</p>
<p>Third, we need data services and products to facilitate the sharing of data and information with decision-makers who are not scientists or geneticists. </p>
<p>Fourth, standardised and consistent data management processes, practices, tools and controls for how data is processed, stored, shared and deployed are needed across countries and contexts. </p>
<p>Core infrastructure is the fifth pillar: the technical side of the platform must be composed of application and infrastructure components that can be rapidly reconfigured for contexts and diseases. </p>
<p>And, finally, good programme management and sustainable resources will be key.</p>
<h2>A global imperative</h2>
<p>As we argue in <a href="https://www.nature.com/articles/s41591-023-02266-y">our journal article</a>, data management and analytics to support data-driven decision making in public health is a global imperative. It requires continuous engagement with international disease surveillance stakeholders and technology platform developers.</p>
<p>The human and resource costs of unchecked diseases in Africa have been pointed out. If there is going to be a collective response to Africa’s burden of diseases – and it is a massive task – a shared pathogen genomics data platform would be a crucial step in underpinning those efforts.</p>
<p>An African owned and African led data sharing platform will be critical for timely sharing of locally produced data to inform rapid response to outbreaks. It will also be a critical step towards an equitable mechanism to maximise the value and utility of pathogen genetic data for national, regional and global health security.</p><img src="https://counter.theconversation.com/content/204284/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Alan Christoffels receives funding from the South African Medical Research Council, The South African National Research Foundation and the Bill & Melinda Gates Foundation. The partners in this repository development project are the Public Health Alliance for Genomic Epidemiology, the Overture.bio team at the Ontario institute for Cancer Research in Canada, the Centre for High Performance Computing at the CSIR, South Africa, and Hominum Global.</span></em></p><p class="fine-print"><em><span>Sofonias Kifle Tessema does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Time and information is of the essence when tackling infectious diseases across countries and continents.Alan Christoffels, Director South African National Bioinformatics Institute, University of the Western CapeSofonias Kifle Tessema, Program Lead for Pathogen Genomics at the Africa CDCLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2034582023-04-26T12:29:00Z2023-04-26T12:29:00ZLeprosy-causing bacteria found in armadillo specimens highlight value of museum collections for tracking pathogens<figure><img src="https://images.theconversation.com/files/522875/original/file-20230425-26-v4ci28.jpg?ixlib=rb-1.1.0&rect=0%2C54%2C2804%2C1958&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Museum specimens are like time capsules from where and when the organisms and their pathogens lived.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/learning-by-touch-a-youngster-above-touches-the-tail-of-a-news-photo/162008261">Ed Maker/The Denver Post via Getty Images</a></span></figcaption></figure><p><em>The <a href="https://theconversation.com/us/topics/research-brief-83231">Research Brief</a> is a short take about interesting academic work.</em> </p>
<h2>The big idea</h2>
<p>Years-old tissue samples from <a href="https://doi.org/10.3201/eid2903.221636">armadillos in museum collections</a> may harbor <em>Mycobacterium leprae</em>, the <a href="https://www.cdc.gov/leprosy/">bacteria that causes Hansen’s disease</a>, also called leprosy, according to recent research my colleagues <a href="https://scholar.google.com/citations?user=-zU5O_AAAAAJ&hl=en&oi=ao">and I</a> conducted.</p>
<p><a href="https://www.niaid.nih.gov/diseases-conditions/leprosy-hansens-disease">Leprosy can cause nerve damage</a> that, without early effective treatment, can lead to paralysis and blindness in the most severe cases. Approximately <a href="https://apps.who.int/neglected_diseases/ntddata/leprosy/leprosy.html">140,000 new patients were diagnosed</a> worldwide in 2021, mostly concentrated in India, Brazil and Indonesia. Since 2010, evidence has accumulated that the nine-banded armadillo, <em>Dasypus novemcinctus</em>, is <a href="https://doi.org/10.1056/NEJMoa1010536">transmitting leprosy to people in North America</a> and potentially <a href="https://doi.org/10.1371/journal.pntd.0008276">elsewhere</a>.</p>
<p>To investigate this connection, we turned to 10 natural history museums in the U.S. <a href="https://doi.org/10.1073/pnas.1522680112">These institutions offer more</a> than just public exhibitions. They also host thousands of biological samples, collected over many years. Examining these historical specimens could help researchers identify pathogen prevalence and diversity across time and space.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/519981/original/file-20230408-4224-et8tzb.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Diagram illustrating number of museums, locations where armadillos were collected and prevalence of pathogen in samples tested." src="https://images.theconversation.com/files/519981/original/file-20230408-4224-et8tzb.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/519981/original/file-20230408-4224-et8tzb.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=296&fit=crop&dpr=1 600w, https://images.theconversation.com/files/519981/original/file-20230408-4224-et8tzb.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=296&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/519981/original/file-20230408-4224-et8tzb.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=296&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/519981/original/file-20230408-4224-et8tzb.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=373&fit=crop&dpr=1 754w, https://images.theconversation.com/files/519981/original/file-20230408-4224-et8tzb.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=373&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/519981/original/file-20230408-4224-et8tzb.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=373&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Molecular diagnostic techniques identified the leprosy-causing <em>Mycobacterium leprae</em> bacteria in archived tissue samples from 14.8% of nine-banded armadillos tested.</span>
<span class="attribution"><span class="source">Daniel Romero-Alvarez</span></span>
</figcaption>
</figure>
<p>In our study, we used online repositories such as <a href="http://vertnet.org/">VertNet</a> to identify armadillo specimens held by museums. We then physically examined tissue samples from 159 individual animals from 10 armadillo species. Specimens were collected between 1974 and 2017 from eight countries in the Americas.</p>
<p>Using molecular diagnostic techniques, we identified <em>M. leprae</em> bacteria in muscle, spleen and liver tissues in 18 out of 122 nine-banded armadillos – a prevalence of 14.8%. All positive samples were collected between 1996 and 2014. Our research allowed us to peek into the immediate past to see that <em>M. leprae</em> was circulating in armadillos in previously unknown locations.</p>
<h2>Why it matters</h2>
<p>How leprosy is transmitted is still under debate. The bacteria can apparently spread in aerosols and droplets <a href="https://doi.org/10.47276/lr.86.2.142">released by the coughs or sneezes</a> of infected patients. But because some people become sick without being exposed to an infected person or traveling to an area where leprosy is present, researchers think there must be <a href="https://doi.org/10.1371/journal.pntd.0008276">another way it spreads</a>.</p>
<p>In the last decade, molecular examinations of nonhuman samples, water and soils have suggested that wildlife and the environment are potential <a href="https://doi.org/10.1371/journal.pntd.0008276">sources of leprosy</a>. Our analysis revealed that the <em>M. leprae</em> strain identified in the positive museum samples is very similar to one that has been circulating in North American armadillos since the 1990s, when transmission of leprosy through wildlife <a href="https://doi.org/10.1067/mjd.2000.106368">was still only suggested</a>. </p>
<h2>What other research is being done</h2>
<p>In animals, researchers have used museum specimens to study <a href="https://doi.org/10.3201/eid2707.204864">snake fungal disease</a> and the <a href="https://doi.org/10.1007/s10530-017-1390-8">chytrid fungus that affects frogs</a>.</p>
<p>Scientists less often examine museum archives for <a href="https://doi.org/10.1371/journal.ppat.1009583">pathogens that affect humans</a>. Researchers have, however, identified <em>Tripanosoma cruzi</em>, the agent that causes <a href="https://doi.org/10.3201/eid1602.090998">Chagas disease, in wood rats</a> in natural history museum collections, as well as <a href="https://doi.org/10.1641/0006-3568(2002)052%5B0989:TEAEHO%5D2.0.CO;2">hantaviruses in deer mouse</a> specimens.</p>
<p>Since approximately 70% of emerging human infectious diseases <a href="https://doi.org/10.1098/rstb.2001.0888">originate in wildlife</a>, examining museum specimens will likely help identify where and when particular pathogens have existed. Ultimately, understanding more about which pathogens are emerging, and where – as we did with leprosy and armadillos – can help scientists anticipate potential outbreaks and maybe even head them off. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/522705/original/file-20230424-24-ozr82v.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="a rack of centrifuge tubes and a vial of sample" src="https://images.theconversation.com/files/522705/original/file-20230424-24-ozr82v.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/522705/original/file-20230424-24-ozr82v.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/522705/original/file-20230424-24-ozr82v.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/522705/original/file-20230424-24-ozr82v.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/522705/original/file-20230424-24-ozr82v.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/522705/original/file-20230424-24-ozr82v.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/522705/original/file-20230424-24-ozr82v.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Molecular techniques extracted and amplified DNA from the historical samples housed in museum collections.</span>
<span class="attribution"><span class="source">Daniel Romero-Alvarez</span></span>
</figcaption>
</figure>
<h2>What still isn’t known</h2>
<p>Scientists discovered in 2008 that another pathogen, <a href="https://doi.org/10.1073/pnas.1421504112"><em>Mycobacterium lepromatosis</em>, can also cause leprosy</a>. Researchers have yet to untangle the role of this second bacteria in the worldwide incidence of the disease.</p>
<p>All our 159 armadillo samples were negative for <em>M. lepromatosis</em>. But this bacteria has infected humans in <a href="https://doi.org/10.3389/fmicb.2021.698588">Mexico, Colombia, Canada and elsewhere</a>, along with <a href="https://doi.org/10.1126/science.aah3783">red squirrels in the British Isles</a>.</p>
<p>My colleagues and I <a href="https://www.romerostories.com/post/lepra-en-armadillos-parte-i-museos-y-tejidos">hope our discovery</a> prompts further research on the role of nonhuman sources of leprosy transmission across the Americas. <a href="https://doi.org/10.3201/eid2903.221636">Our work</a> is another case study demonstrating that natural history collections can <a href="https://theconversation.com/museums-preserve-clues-that-can-help-scientists-predict-and-analyze-future-pandemics-141175">play an important role</a> in human infectious disease research.</p><img src="https://counter.theconversation.com/content/203458/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Daniel Romero-Alvarez does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Museum archives hold biological specimens that have been collected over years or even decades. Modern molecular analysis of these collections can reveal information about pathogens and their spread.Daniel Romero-Alvarez, Ph.D. Candidate in Ecology of Infectious Diseases, University of KansasLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2015692023-04-18T20:01:07Z2023-04-18T20:01:07ZDiseases gave us the rise of Christianity, the end of the Aztecs and public sanitation. How might future plagues change human history?<figure><img src="https://images.theconversation.com/files/517613/original/file-20230327-27-ualse4.jpg?ixlib=rb-1.1.0&rect=0%2C6%2C4439%2C3183&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Elena Mozhvilo/Unsplash</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span></figcaption></figure><p>“Every once in a while a book lands on your desk that changes the way you perceive the world you live in, a book that fundamentally challenges your understanding of human history.” So began the blurb that came with this book. Aha! I thought. The usual advertising hyperbole, a gross exaggeration. </p>
<p>Yet <a href="https://www.penguin.com.au/books/pathogenesis-9781911709053">Pathogenesis</a> <em>did</em> challenge much of my understanding of world history. Who knew that if it wasn’t for an Ebola-like pandemic in the 2nd century CE, Christianity would never have become a world religion? Or that if it weren’t for retroviruses, women would be laying eggs rather than having live births? (According to the book’s author, a retrovirus inserted DNA into our ancestor’s genome that caused the placenta to develop.)</p>
<hr>
<p><em>Book review: Pathogenesis: How germs made history – by Jonathan Kennedy (Torva)</em></p>
<hr>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/517614/original/file-20230327-20-1geds5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/517614/original/file-20230327-20-1geds5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/517614/original/file-20230327-20-1geds5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=923&fit=crop&dpr=1 600w, https://images.theconversation.com/files/517614/original/file-20230327-20-1geds5.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=923&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/517614/original/file-20230327-20-1geds5.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=923&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/517614/original/file-20230327-20-1geds5.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=1160&fit=crop&dpr=1 754w, https://images.theconversation.com/files/517614/original/file-20230327-20-1geds5.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=1160&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/517614/original/file-20230327-20-1geds5.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=1160&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
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<p>However, this is not another book of Amazing Facts: it is a work of scholarship, with nearly 700 references and notes. At the same time, it is very readable, and even amusing at times. </p>
<p>Many books have been written about the impact of disease on civilisation. I have even written my own modest <a href="https://medium.com/@adrian.esterman/infectious-diseases-and-their-impact-on-civilisation-4eb8ac72cc5b">essay</a> on the topic. However,
Pathogenesis delves deeply into the social history of the world. </p>
<p>Jonathan Kennedy has a PhD in sociology from the University of Cambridge, and his sociological bent comes through strongly. In eight chapters, and some 350 pages, Kennedy takes us on a whirlwind tour of social history, describing how infectious diseases have shaped humanity at every stage. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/viruses-are-both-the-villains-and-heroes-of-life-as-we-know-it-169131">Viruses are both the villains and heroes of life as we know it</a>
</strong>
</em>
</p>
<hr>
<h2>‘It’s a bacterial world’</h2>
<p>Kennedy starts by describing the three great branches of living organisms, <a href="https://theconversation.com/from-peaceful-coexistence-to-potential-peril-the-bacteria-that-live-in-and-on-us-104110">bacteria</a>, <a href="https://microbiologysociety.org/why-microbiology-matters/what-is-microbiology/archaea.html">archaea</a>, and <a href="https://www.britannica.com/science/eukaryote">eukaryotes</a> – it is the latter that contains all complex life forms, including humans. However, fewer than 0.001% of all species are eukaryotes. </p>
<p>Bacteria, on the other hand, are the dominant life form on this planet. As Kennedy puts it, “it’s a bacterial world, and we’re just squatting here”. </p>
<p>Our own species, <em><a href="https://theconversation.com/rethinking-homo-sapiens-the-story-of-our-origins-gets-dizzyingly-complicated-99760">Homo sapiens</a></em>, arose some 315,000 years ago, living for the most part in Africa. At the same time, human species such as Neanderthals and <a href="https://theconversation.com/dna-from-elusive-human-relatives-the-denisovans-has-left-a-curious-mark-on-modern-people-in-new-guinea-196113">Denisovans</a> spread out into Europe. However, about 50,000 years ago, <em>Homo sapiens</em> burst out of Africa and spread across the world, while all other human species simply vanished. There are many <a href="https://www.scientificamerican.com/article/how-homo-sapiens-became-the-ultimate-invasive-species/">theories</a> as to why and how this occurred – for example, perhaps <em>Homo sapiens</em> were just smarter. </p>
<p>However, Kennedy proposes his own theory. Because <em>Homo sapiens</em> lived primarily in Africa, they were exposed to many pathogens, and eventually acquired genetic changes that gave them some protection. The exodus out of Africa exposed other species to these pathogens, causing their demise. </p>
<p>He describes the <a href="https://theconversation.com/who-were-the-mysterious-neolithic-people-that-enabled-the-rise-of-ancient-egypt-heres-what-weve-learned-on-our-digs-121070">Neolithic</a> revolution, which took place about 12,000 years ago and which saw the change from hunter-gatherers to farmers. Because of their nomadic existence in small groups, hunter-gatherers tended to be relatively healthy, with an average lifespan of 72 - better than the average lifespan in some countries today! </p>
<p>It has always been assumed that this revolution was a good thing, bringing better nutrition and more leisure time. However, in Kennedy’s view, the Neolithic revolution led to the emergence of despotism, inequality, poverty and backbreaking work. He describes how settlement and the farming of domestic animals led to the emergence of zoonotic diseases – that is, <a href="https://theconversation.com/preventing-future-pandemics-starts-with-recognizing-links-between-human-and-animal-health-167617">diseases spread by animals</a>. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/517617/original/file-20230327-24-pz4erz.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/517617/original/file-20230327-24-pz4erz.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/517617/original/file-20230327-24-pz4erz.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/517617/original/file-20230327-24-pz4erz.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/517617/original/file-20230327-24-pz4erz.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/517617/original/file-20230327-24-pz4erz.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/517617/original/file-20230327-24-pz4erz.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/517617/original/file-20230327-24-pz4erz.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Settlement and the farming of domestic animals led to the emergence of diseases spread by animals.</span>
<span class="attribution"><span class="source">kallerna/Wikimedia Commons</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
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<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/disease-evolution-our-long-history-of-fighting-viruses-54569">Disease evolution: our long history of fighting viruses</a>
</strong>
</em>
</p>
<hr>
<h2>Plagues and social upheavals</h2>
<p>In a chapter on ancient plagues, Kennedy quotes from Monty Python’s <a href="https://theconversation.com/life-of-brian-at-40-an-assertion-of-individual-freedom-that-still-resonates-114743">The Life of Brian</a>: </p>
<blockquote>
<p>All right, but apart from the sanitation, the medicine, education, wine, public order, irrigation, roads, a fresh water system, and public health, what have the Romans ever done for us?</p>
</blockquote>
<p>He points out that Roman cities were, in fact, “filthy, stinking and disease-ridden”, and goes on to describe the great plagues <a href="https://theconversation.com/how-3-prior-pandemics-triggered-massive-societal-shifts-146467">that weakened the Roman Empire</a>. The first was the Antonine Plague, possibly caused by smallpox. This was followed some 70 years later by the Plague of Cyprian from AD 249-262, which led to the splitting of the Roman Empire and the rise of Christianity. </p>
<p>Kennedy completes this chapter with a description of the Plague of Justinian, caused by bubonic plague. The massive deaths caused by this epidemic led to the demise of the Roman Empire, and the Muslim conquest of the Middle East. </p>
<p>In the period 1346–53, the <a href="https://theconversation.com/did-the-black-death-give-birth-to-modern-plagues-3820">Black Death</a> tore through North Africa and Europe, killing an <a href="https://en.wikipedia.org/wiki/Black_Death">estimated</a> 75 million to 200 million people. Kennedy describes the devastation and huge social upheavals that resulted from this pandemic. Until then, the Roman Catholic Church dominated society. But:</p>
<blockquote>
<p>During the Black Death and subsequent plague outbreaks, people looked to the Church for comfort. All too often they didn’t find it. </p>
</blockquote>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/517616/original/file-20230327-22-23ih7j.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/517616/original/file-20230327-22-23ih7j.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/517616/original/file-20230327-22-23ih7j.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=486&fit=crop&dpr=1 600w, https://images.theconversation.com/files/517616/original/file-20230327-22-23ih7j.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=486&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/517616/original/file-20230327-22-23ih7j.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=486&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/517616/original/file-20230327-22-23ih7j.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=611&fit=crop&dpr=1 754w, https://images.theconversation.com/files/517616/original/file-20230327-22-23ih7j.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=611&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/517616/original/file-20230327-22-23ih7j.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=611&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The Black Death killed an estimated 75–200 million people in Europe and North Africa. Hugo Simberg Black Death.</span>
<span class="attribution"><span class="source">Wikimedia Commons</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>This led to the rise of Protestantism, aided by the invention of the printing press - a shortage of labour encouraged the development of such labour-saving devices. Over the next 200 years, waves of plague repeatedly hit Europe. A quarantine system was developed in Venice, and <em>cordon sanitaires</em> established, to prevent movement of people between cities - ring any bells? </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/did-the-black-death-give-birth-to-modern-plagues-3820">Did the Black Death give birth to modern plagues?</a>
</strong>
</em>
</p>
<hr>
<h2>Pathogens as New World killers</h2>
<p>In the period from 1500 onwards, white colonialists nearly wiped out indigenous people by infecting them. Kennedy starts with the early 16th century, when Spanish conquistador Hernán Cortés led an expedition to Mexico. His arrival <a href="https://theconversation.com/how-smallpox-devastated-the-aztecs-and-helped-spain-conquer-an-american-civilization-500-years-ago-111579">introduced smallpox</a>, which resulted in the total destruction of the Aztec Empire within just two years. However, this was just the start. </p>
<p>In the early 1530s, Mexico was hit by an epidemic of <a href="https://theconversation.com/measles-new-efforts-needed-to-stop-an-old-disease-13706">measles</a> that killed 80% of its population, making it the deadliest epidemic in recorded history. Over the following decades, across the whole of the Americas, the introduction of infectious diseases from Europe resulted in a 90% fall in the population. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/517624/original/file-20230327-15-s0x2ks.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/517624/original/file-20230327-15-s0x2ks.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/517624/original/file-20230327-15-s0x2ks.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=441&fit=crop&dpr=1 600w, https://images.theconversation.com/files/517624/original/file-20230327-15-s0x2ks.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=441&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/517624/original/file-20230327-15-s0x2ks.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=441&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/517624/original/file-20230327-15-s0x2ks.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=554&fit=crop&dpr=1 754w, https://images.theconversation.com/files/517624/original/file-20230327-15-s0x2ks.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=554&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/517624/original/file-20230327-15-s0x2ks.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=554&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Hernán Cortés brought smallpox to Mexico, resulting in the total destruction of the Aztec Empire within two years, as illustrated in this 16th-century drawing of Aztec smallpox victims.</span>
<span class="attribution"><span class="source">Wikimedia Commons</span></span>
</figcaption>
</figure>
<p>However, during this period, it wasn’t just the New World that was profoundly affected by pathogens. On the west coast of Africa, explorers and would-be colonialists died in droves from <a href="https://theconversation.com/worlds-first-mass-malaria-vaccine-rollout-could-prevent-thousands-of-children-dying-169457">malaria</a> and <a href="https://theconversation.com/zika-dengue-yellow-fever-what-are-flaviviruses-53969">yellow fever</a>. </p>
<p>Interestingly, Kennedy starts his chapter on revolutionary plagues with the murder of <a href="https://theconversation.com/george-floyd-deserved-a-better-life-a-new-book-charts-his-trajectory-from-poverty-to-the-us-prison-industrial-complex-and-the-impact-of-his-death-182947">George Floyd</a> and the <a href="https://theconversation.com/the-black-lives-matter-movement-has-provoked-a-cultural-reckoning-about-how-black-stories-are-told-149544">Black Lives Matter</a> movement, before delving deep into the history of slavery. He describes slavery in Greek and Roman times, and the booming trade in slaves in the medieval Mediterranean. </p>
<p>The association between black Africans and <a href="https://theconversation.com/slavery-is-not-a-crime-in-almost-half-the-countries-of-the-world-new-research-115596">slavery</a> only began in the 15th century. In fact, only 3% of the 12.5 million humans trafficked across the Atlantic ended up in the United States. The most common destinations of the slave ships were the European colonies in the Caribbean, where African slave labour was first used more than a century before their shipment to North America. </p>
<p>Meanwhile, in the Caribbean, slave labour from tropical West Africa toiled on sugar plantations owned by the English, Spanish, French and Dutch. Yellow fever carried by mosquitoes wiped out many of the Europeans, including military garrisons, leading to slave revolts.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/friday-essay-a-slave-state-how-blackbirding-in-colonial-australia-created-a-legacy-of-racism-187782">Friday essay: a slave state - how blackbirding in colonial Australia created a legacy of racism</a>
</strong>
</em>
</p>
<hr>
<h2>Diseases ‘thrived’ in Dickensian habitats</h2>
<p>When Kennedy switches his focus to Britain, and the industrial revolution, he describes it as the change from a Thomas Hardy novel to one by <a href="https://theconversation.com/great-expectations-by-charles-dickens-class-prejudices-the-convict-stain-and-a-corpse-bride-159816">Charles Dickens</a>. The crowded and unsanitary conditions in working-class urban districts created new habitats, in which pathogens thrived. </p>
<p>Kennedy again evokes Monty Python to invoke the scenery of those days, reminding readers of the famous four Yorkshiremen sketch. The scene made me think of a different quote from the same sketch:</p>
<blockquote>
<p>You were lucky to have a house! We used to live in one room, all hundred and twenty-six of us, no furniture. Half the floor was missing; we were all huddled together in one corner for fear of falling!</p>
</blockquote>
<p>Every Epidemiology 101 course covers the story of <a href="https://www.newscientist.com/people/john-snow/">John Snow</a> (no – not the “Winter is coming” one!). <a href="https://www.cdc.gov/csels/dsepd/ss1978/lesson1/section2.html">Two decades</a> before the development of the microscope, Snow examined cholera outbreaks to discover the cause of disease and how to prevent it. </p>
<figure class="align-left zoomable">
<a href="https://images.theconversation.com/files/517625/original/file-20230327-14-jix57.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/517625/original/file-20230327-14-jix57.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/517625/original/file-20230327-14-jix57.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=619&fit=crop&dpr=1 600w, https://images.theconversation.com/files/517625/original/file-20230327-14-jix57.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=619&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/517625/original/file-20230327-14-jix57.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=619&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/517625/original/file-20230327-14-jix57.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=778&fit=crop&dpr=1 754w, https://images.theconversation.com/files/517625/original/file-20230327-14-jix57.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=778&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/517625/original/file-20230327-14-jix57.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=778&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">John Snow proved in 1854 that cholera is a waterborne disease: a London pub is named for him.</span>
<span class="attribution"><a class="source" href="https://www.geograph.org.uk/profile/6699">ceridwen/Wikimedia Commons</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>During the third UK cholera outbreak in 1854, Snow famously removed London’s Broad Street water pump, to demonstrate that cholera was a waterborne disease. For those interested, there is a <a href="https://londonspubswherehistoryreallyhappened.wordpress.com/2019/03/05/john-snow/">John Snow</a> pub in London. Kennedy, of course, includes this story in his book.</p>
<p>Kennedy points out that 3.5 billion people – half of the world’s population – have no access to proper toilets, while a billion don’t have clean drinking water and 1.5 million people, mainly children, die every year from waterborne diarrhoeal diseases. </p>
<p>We still have massive <a href="https://theconversation.com/explainer-why-cholera-remains-a-public-health-threat-74444">cholera outbreaks</a>, especially in areas where normal life has been disrupted by war or natural disasters. <a href="https://theconversation.com/tuberculosis-kills-as-many-people-each-year-as-covid-19-its-time-we-found-a-better-vaccine-151590">Tuberculosis</a> still kills 1.2 million people a year, despite the availability of antibiotics. Malaria kills another 600,000. </p>
<p>Finally in this section, he briefly covers <a href="https://theconversation.com/covid-hospitalisations-and-deaths-are-rising-faster-than-cases-but-that-doesnt-mean-more-severe-disease-187163">COVID</a>. He points out that not everyone in the world benefited from the medical advances that came about because of COVID, and the self-interested actions of high-income countries have deprived the poorer countries. As he puts it, “pathogens thrive on inequality and injustice”. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/fleas-to-flu-to-coronavirus-how-death-ships-spread-disease-through-the-ages-137061">Fleas to flu to coronavirus: how 'death ships' spread disease through the ages</a>
</strong>
</em>
</p>
<hr>
<h2>Future plagues</h2>
<p>Kennedy concludes by looking at future plagues. He points out humanity’s precarious position: we live on a planet dominated by bacteria and viruses. He believes our best chance of surviving the threat posed by pathogens will come from working collaboratively and reducing inequality both within and between countries. </p>
<p>Based on its title, I assumed this book would be about the role of pathogens in shaping civilisation. Instead, I found a social history of the world, with the odd foray into diseases and their influence on society. Nonetheless, I thoroughly enjoyed the book, and can highly recommend it to those with an interest in history, sociology and epidemiology.</p><img src="https://counter.theconversation.com/content/201569/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Adrian Esterman does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>This whirlwind tour of social history describes how infectious diseases have shaped humanity at every stage. It suggests reducing inequality will give us our best chance of surviving future plagues.Adrian Esterman, Professor of Biostatistics and Epidemiology, University of South AustraliaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1995932023-02-16T19:05:16Z2023-02-16T19:05:16ZBefore The Last of Us, I was part of an international team to chart the threat of killer fungi. This is what we found<figure><img src="https://images.theconversation.com/files/510490/original/file-20230216-26-fl8d1b.jpg?ixlib=rb-1.1.0&rect=2%2C0%2C1579%2C1055&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://pressroom.warnermedia.com/us/image/tlu106120221lh0106">Liane Hentscher/HBO</a></span></figcaption></figure><p>Fungal infections have received a frenzy of attention thanks to the popularity of HBO’s <a href="https://www.hbo.com/the-last-of-us">The Last of Us</a>. The show depicts a fungal pandemic caused by the real-life zombie-ant fungus, <em><a href="https://www.nationalgeographic.com/animals/article/cordyceps-zombie-fungus-takes-over-ants">Ophiocordyceps unilateralis</a></em>. It imagines the outcome of society’s collapse and a brutal approach to maintaining public health.</p>
<p><div data-react-class="Tweet" data-react-props="{"tweetId":"1625837601482502145"}"></div></p>
<p>But in (real-life) laboratories, hospitals and public health units around the world, researchers have been warning about the rise of potentially deadly fungal infections for years. </p>
<p>With few drugs to treat major fungal infections, and no vaccines on the horizon, the potential harm caused by fungal infections have raised alarms at the highest levels of public health. </p>
<p>I was part of a large international team of researchers commissioned by the <a href="https://www.who.int/publications/i/item/9789240060241">World Health Organization</a> (WHO) to understand which fungal pathogens we most needed to research and which posed the greatest public health threat. This is what its report found. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/the-last-of-us-fungal-infections-really-can-kill-and-theyre-getting-more-dangerous-198184">The Last of Us: fungal infections really can kill – and they’re getting more dangerous</a>
</strong>
</em>
</p>
<hr>
<h2>Fungi back in the spotlight</h2>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/uLtkt8BonwM?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">The Last of Us reminds us how deadly some fungi can be.</span></figcaption>
</figure>
<p>Before The Last of Us, many people thought “fungus” meant mushrooms or something mouldy in the compost heap. If they thought of fungi in relation to health, they thought of <a href="https://www.cdc.gov/healthywater/hygiene/disease/athletes_foot.html">athlete’s foot</a> or <a href="https://theconversation.com/explainer-why-do-we-get-fungal-nail-infections-and-how-can-we-treat-them-75212">toenail infections</a> – familiar, but not frightening. </p>
<p>However, fungi do cause serious infections, especially in people with other health conditions. People living with cancer, HIV, or diabetes are especially at risk of these infections, but they can also strike those who have had major surgery, ended up in an intensive care unit, or who have experienced another serious infection. This is because their immune system is weakened or distracted, opening up a space for “opportunistic infections”.</p>
<p>We’ve seen this in India where black mould infections (<a href="https://theconversation.com/what-is-mucormycosis-the-fungal-infection-affecting-covid-patients-in-india-160707">mucormycosis</a>) complicated cases of COVID, resulting in <a href="https://www.bbc.com/news/world-asia-india-57897682">thousands of deaths</a>.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/what-is-mucormycosis-the-fungal-infection-affecting-covid-patients-in-india-160707">What is mucormycosis, the fungal infection affecting COVID patients in India?</a>
</strong>
</em>
</p>
<hr>
<h2>A threat and becoming more so</h2>
<p>Well before The Last of Us, health authorities had been starting to take notice of serious fungal infections.</p>
<p>In 2019 the US Centers for Disease Control <a href="https://www.cdc.gov/drugresistance/biggest-threats.html">designated</a> the deadly yeast <em><a href="https://theconversation.com/explainer-what-is-candida-auris-and-who-is-at-risk-115293">Candida auris</a></em> – which appeared out of nowhere <a href="https://onlinelibrary.wiley.com/doi/full/10.1111/j.1348-0421.2008.00083.x">in 2009</a> – as an “<a href="https://www.nytimes.com/2019/04/06/health/drug-resistant-candida-auris.html">urgent threat</a>” because of its resistance to many (and sometimes all) known antifungal drugs.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/510271/original/file-20230215-1870-uc209n.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Candida auras" src="https://images.theconversation.com/files/510271/original/file-20230215-1870-uc209n.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/510271/original/file-20230215-1870-uc209n.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/510271/original/file-20230215-1870-uc209n.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/510271/original/file-20230215-1870-uc209n.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/510271/original/file-20230215-1870-uc209n.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/510271/original/file-20230215-1870-uc209n.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/510271/original/file-20230215-1870-uc209n.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption"><em>Candida auris</em> is an ‘urgent threat’ as it’s resistant to most antifungal drugs.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-illustration/candida-auris-fungi-emerging-multidrug-resistant-1164101620">Kateryna Kon/Shutterstock</a></span>
</figcaption>
</figure>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/explainer-what-is-candida-auris-and-who-is-at-risk-115293">Explainer: what is Candida auris and who is at risk?</a>
</strong>
</em>
</p>
<hr>
<p>A drug-resistant strain of <em>Aspergillus fumigatus</em>, which arose from <a href="https://www.theatlantic.com/science/archive/2018/11/when-tulips-kill/574489/">overuse of antifungal chemicals</a> in agriculture, made the “watch” list.</p>
<p>New and increasingly drug-resistant pathogens like these are one challenge to public health. Another is the increasing number of people at risk of these infections. </p>
<p>Rich countries are delivering ever-more sophisticated health care, resulting in more people vulnerable to serious fungal infections. Chemotherapy, organ transplants, major surgery, extra healthy years lived with diabetes all give opportunities for fungi to take hold. </p>
<p>Although the risk factors in lower income settings are different, the numbers tell the same story – rates of serious fungal infections <a href="https://www.nbcnews.com/health/health-news/fungal-infections-more-common-as-ranges-expand-rcna58258">globally</a> <a href="https://www.sciencedirect.com/science/article/pii/S0740257019300425?via%3Dihub">are rising</a>.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/why-the-cdc-warns-antibiotic-resistant-fungal-infections-are-an-urgent-health-threat-127095">Why the CDC warns antibiotic-resistant fungal infections are an urgent health threat</a>
</strong>
</em>
</p>
<hr>
<h2>Then we worked with the WHO</h2>
<p>I was part of a large team of international researchers commissioned by the WHO to analyse the past ten years of research on fungal pathogens.</p>
<p>We conducted a worldwide survey of fungal disease experts to understand which pathogens were most in need of research and which posed the greatest public health threat. The WHO <a href="https://www.who.int/publications/i/item/9789240060241">published the results</a> in a report released last year.</p>
<p>They highlighted four critical priority pathogens: </p>
<ul>
<li><p><em>Candida auris</em>, which is resistant to most antifungals and is a problem for vulnerable patients in hospitals</p></li>
<li><p><em>Aspergillus fumigatus</em>, which mainly affects the lungs. Infections can be deadly, even more so when drug-resistant strains are involved </p></li>
<li><p><em>Candida albicans</em>, which can cause invasive infections, typically in vulnerable patients</p></li>
<li><p><em>Cryptococcus neoformans</em>, which can infect the brain, especially in immunocompromised people. This is especially the case in people with HIV, where it’s a leading killer.</p></li>
</ul>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/510272/original/file-20230215-3916-slyox6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Aspergillus fumigatus" src="https://images.theconversation.com/files/510272/original/file-20230215-3916-slyox6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/510272/original/file-20230215-3916-slyox6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=338&fit=crop&dpr=1 600w, https://images.theconversation.com/files/510272/original/file-20230215-3916-slyox6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=338&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/510272/original/file-20230215-3916-slyox6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=338&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/510272/original/file-20230215-3916-slyox6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=425&fit=crop&dpr=1 754w, https://images.theconversation.com/files/510272/original/file-20230215-3916-slyox6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=425&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/510272/original/file-20230215-3916-slyox6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=425&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption"><em>Aspergillus fumigatus</em> mainly affects the lungs.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-illustration/fungi-aspergillus-black-mold-that-produce-2128528781">Kateryna Kon/Shutterstock</a></span>
</figcaption>
</figure>
<p>The WHO report calls for enhanced surveillance, a focus on research and development, and improvements in public health interventions, such as improved prophylaxis (preventive treatments) or infection prevention strategies.</p>
<p>Viewers of The Last of Us will understand why these are so important. We need surveillance so we know where threats are coming from before they arrive, otherwise we cannot prepare.</p>
<p>We need more research and development to develop vaccines and new treatments.</p>
<p>So far, we have failed to develop any <a href="https://www.nature.com/articles/s41541-021-00294-8">anti-fungal vaccines</a> and there is no chance we could produce and distribute one as we did for COVID.</p>
<p>Although some new anti-fungals have become available, the range is still too small, and some strains of fungi are resistant to all available drugs.</p>
<p>Developing vaccines and drugs is hard because fungal cells are similar to human ones. So basic laboratory research is vital to identify ways we can kill fungal cells without harming our own.</p>
<p>Without giving any spoilers, it’s safe to say the public health interventions in The Last of Us are pretty extreme. So research on how to contain and control fungal pathogens is also vital to avoid such draconian and ineffective measures.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/curious-kids-are-zombies-real-79347">Curious Kids: Are zombies real?</a>
</strong>
</em>
</p>
<hr>
<h2>Are fungal pandemics possible?</h2>
<p>The fungal frog plague, <a href="https://theconversation.com/deadly-frog-fungus-has-wiped-out-90-species-and-threatens-hundreds-more-113846">chytrid disease</a>, has killed countless amphibians. Researchers say it has caused the <a href="https://www.science.org/doi/10.1126/science.aav0379">greatest loss of biodiversity</a> from a single disease ever recorded. </p>
<p>Is a fungal zombie apocalypse possible? Not for humans. The fungus in The Last of Us evolved over millennia to infect a specific ant species and influence its behaviour. There is no realistic prospect of this organism crossing over into humans and controlling us. </p>
<p>However, we do face very real threats from fungi if we don’t work hard to understand them better – threats to our health, to biodiversity, even food security. By taking action now, we can prevent a potential public health crisis.</p><img src="https://counter.theconversation.com/content/199593/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Justin Beardsley receives funding from the NHMRC and has received honoraria from Gilead for hosting education meetings. He was part of a WHO-commissioned study group, but any views expressed here are his alone and do not represent the official views of the WHO. </span></em></p>Dangerous fungal infections are on the rise globally. But we have few drugs that work and no prospect of anti-fungal vaccines any time soon.Justin Beardsley, Associate Professor in Infectious Diseases, Sydney Institute for Infectious Diseases Westmead Clinical School, University of SydneyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1985372023-02-08T14:28:15Z2023-02-08T14:28:15ZHow do I improve my immunity? Expert shares tips on what to do - and what to avoid<figure><img src="https://images.theconversation.com/files/507107/original/file-20230130-7241-9z07f6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Exercising regularly, and spending time outdoors can improve your health. </span> <span class="attribution"><span class="source">Shutterstock</span></span></figcaption></figure><p>The human immune system is arguably the most complex system in the human body. But scientists have made a lot of progress in understanding how it functions.</p>
<p>That’s important for understanding illnesses and how to manage them. For instance, it’s important to understand that an immune response takes several days to fully develop. This knowledge would hopefully prevent people from getting impatient and seeking inappropriate care. </p>
<p>The immune system is made up of an intricate network of cells, tissues and molecules. These control the delicate balance between eliminating cancerous or infected cells, and not harming the body in the process. </p>
<p>A poorly functioning immune system can cause a variety of health problems. </p>
<p>It could lead to a person getting recurrent infections. Depending on the nature of the immune deficiency, the infections can range from viral (such as colds, flu, shingles and fever blisters) to bacterial (such as tuberculosis) or fungal (such as thrush). </p>
<p>Immune system dysfunction can also present as excessive inflammation or even auto-immunity. In this case the body starts seeing its own tissues as foreign and attacks them. Some examples of these conditions are rheumatoid arthritis, lupus and psoriasis.</p>
<p>The factors that affect our immune system range from things we can’t change, such as our genetic make-up and exposure to past pathogens, to things we may be able to control or modify.</p>
<p>I am an immunologist, and in this article I unpack the changes you can make today to help your immune system function better. They include diet, managing stress levels, and limiting exposure to environmental factors, such as germs, pollution and toxins. </p>
<p>Optimal immune function plays an important role in maintaining health. Given the immense complexity of the immune system, simplistic solutions are not effective. It’s important to understand some of the things you should – and shouldn’t – do. </p>
<h2>What not to do</h2>
<p>Many products claim to “boost” the immune system. But given the complex interplay between the cells in our bodies, it’s not really possible to “boost” just one part of the immune system. </p>
<p>And even if it was possible, “boosting” one aspect of your immune system can set off bad reactions by upsetting the delicate balance that makes up our bodies. For instance, “boosting” the immune system’s ability to fight infection could also “boost” other aspects, such as inflammation, that could harm normal tissue. </p>
<p>It is true that the immune system relies on vitamins and minerals to perform its tasks. But there is no solid evidence that taking vitamins and mineral supplements will improve its functioning. </p>
<p>The exception is when a person has a known deficiency, such as vitamin D deficiency. Most people with vitamin D deficiency do not have any symptoms or only have vague, non-specific symptoms, such as tiredness or lower back ache. People living with osteoporosis, diabetes, kidney disease, obesity, or depression, or those with limited sun exposure, especially the elderly, are at increased risk of having a deficiency. It’s important to address the problem because it can increase the risk of fractures, as well as infection from various pathogens, especially those affecting the lungs, such as flu and SARS-CoV-2. </p>
<p>If you think you’ve got a nutrient deficiency you should consult a healthcare practitioner for an accurate diagnosis. They can set out an evidence-based management strategy for you. </p>
<p>The reason for seeking professional help is that dosing up on supplements can be bad for you. </p>
<p>Firstly, some vitamins, such as vitamin A, D, E and K, are fat-soluble and are stored in the body. It is therefore possible to have levels that are too high, which can cause its own problems. For instance, too-high levels of vitamin D can cause kidney stones, constipation and high blood pressure. Too much vitamin A or iron can cause damage to the liver and other organs. </p>
<p>Secondly, nutrients should not be seen as independent components. Rather they should be seen as parts of a whole. Many supplements can interact negatively with other supplements and even with medication. For instance, vitamin K can reduce the ability of the blood thinner warfarin to prevent blood clots.</p>
<p>Combining different supplements can also lead to excessive or inadequate amounts of certain nutrients, with potentially detrimental effects. For example, prolonged zinc supplementation can cause copper deficiency, which has been linked to anaemia and impaired brain function. </p>
<h2>What to do</h2>
<p>The best way to ensure that your immune system gets what it needs is through a healthy and balanced lifestyle. </p>
<p>Diet is critical. Eat food that is unprocessed, preservative-free, and rich in a variety of vitamins, minerals and antioxidants. Your diet should include green and yellow vegetables, fruit and berries, whole grains, seeds and nuts. </p>
<p>And it’s not just the individual components of food that are important. The interplay between them matters too. This is something that cannot be reproduced in a tablet. </p>
<p>Lifestyle factors are also key. Stress is a normal and essential part of life, but it must be switched off to protect the body. Finding effective ways to control stress, such as breathing exercises, yoga and meditation, is important. </p>
<p>Activities that have been shown to improve health include getting enough rest, exercising regularly, spending time outdoors, and staying connected socially. Smoking and excessive alcohol use are clearly harmful. </p>
<p>Finally, we often forget to be kind to ourselves. When you are ill, take time to recover. When you are going through an especially stressful time, make an extra effort to de-stress. </p>
<p>Most importantly, don’t regard these as emergency measures. Make them part of your lifestyle. As tempting as it may be, it is not possible to “supplement” yourself out of a bad lifestyle.</p><img src="https://counter.theconversation.com/content/198537/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Theresa Rossouw does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>As tempting as it is, it is not possible to “supplement” oneself out of a bad lifestyle.Theresa Rossouw, Professor, University of PretoriaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1925672022-12-14T13:14:47Z2022-12-14T13:14:47ZNasal vaccines promise to stop the COVID-19 virus before it gets to the lungs – an immunologist explains how they work<figure><img src="https://images.theconversation.com/files/493959/original/file-20221107-19718-xu583n.jpg?ixlib=rb-1.1.0&rect=0%2C11%2C7360%2C4891&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Nasal vaccines for COVID-19 are still in early development.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/little-cute-blonde-boy-getting-vaccinated-covid-19-royalty-free-image/1282728128?phrase=COVID-19%20nasal%20vaccine&adppopup=true">Paul Biris/Moment via Getty Images</a></span></figcaption></figure><p><em>The Pfizer-BioNTech and Moderna mRNA vaccines have played a large role in preventing deaths and severe infections from COVID-19. But researchers are still in the process of developing alternative approaches to vaccines to improve their effectiveness, including how they’re administered. Immunologist and microbiologist <a href="https://www.researchgate.net/profile/Michael-Russell-10">Michael W. Russell</a> of the University at Buffalo explains how nasal vaccines work, and where they are in the development pipeline.</em></p>
<h2>How does the immune system fight pathogens?</h2>
<p>The immune system has two distinct components: mucosal and circulatory.</p>
<p>The <a href="http://dx.doi.org/10.1016/B978-0-12-415847-4.00001-X">mucosal immune system</a> provides protection at the mucosal surfaces of the body. These include the mouth, eyes, middle ear, the mammary and other glands, and the gastrointestinal, respiratory and urogenital tracts. Antibodies and a variety of other anti-microbial proteins in the <a href="https://theconversation.com/slime-is-all-around-and-inside-you-new-research-on-its-origins-offers-insight-into-genetic-evolution-189278">sticky secretions</a> that cover these surfaces, as well as immune cells located in the lining of these surfaces, directly attack invading pathogens.</p>
<p>The <a href="https://doi.org/10.1186/1741-7007-8-84">circulatory part of the immune system</a> generates antibodies and immune cells that are delivered through the bloodstream to the internal tissues and organs. These circulating antibodies do not usually reach the mucosal surfaces in large enough amounts to be effective. Thus mucosal and circulatory compartments of the immune system are largely <a href="http://dx.doi.org/10.3389/fimmu.2022.957107">separate and independent</a>.</p>
<h2>What are the key players in mucosal immunity?</h2>
<p>The immune components people may be most familiar with are proteins known as <a href="https://www.ncbi.nlm.nih.gov/books/NBK513460/">antibodies, or immunoglobulins</a>. The immune system generates antibodies in response to invading agents that the body identifies as “non-self,” such as viruses and bacteria.</p>
<p>Antibodies bind to specific antigens: the part or product of a pathogen that induces an immune response. Binding to antigens allows antibodies to either inactivate them, as they do with toxins and viruses, or kill bacteria with the help of additional immune proteins or cells.</p>
<p>The mucosal immune system generates a specialized form of antibody called <a href="http://dx.doi.org/10.1038/mi.2011.39">secretory IgA, or SIgA</a>. Because SIgA is located in mucosal secretions, such as saliva, tears, nasal and intestinal secretions, and breast milk, it is resistant to digestive enzymes that readily destroy other forms of antibodies. It is also superior to most other immunoglobulins at neutralizing viruses and toxins, and at preventing bacteria from attaching to and invading the cells lining the surfaces of organs.</p>
<p>There are also many <a href="http://dx.doi.org/10.1002/9780470015902.a0000942.pub2">other key players</a> in the mucosal immune system, including different types of anti-microbial proteins that kill pathogens, as well as immune cells that generate antibody responses.</p>
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<figcaption><span class="caption">Mucus is one of the central secretions of the mucosal immune system.</span></figcaption>
</figure>
<h2>How does the COVID-19 virus enter the body?</h2>
<p>Almost all infectious diseases in people and other animals are <a href="https://www.ncbi.nlm.nih.gov/books/NBK209710/">acquired through mucosal surfaces</a>, such as by eating or drinking, breathing or sexual contact. Major exceptions include infections from wounds, or pathogens delivered by insect or tick bites.</p>
<p>The virus that causes COVID-19, SARS-CoV-2, enters the body via droplets or aerosols that get into your <a href="http://dx.doi.org/10.1038/s41385-020-00359-2">nose, mouth or eyes</a>. It can cause severe disease if it descends deep into the lungs and causes an <a href="https://theconversation.com/long-covid-19-and-other-chronic-respiratory-conditions-after-viral-infections-may-stem-from-an-overactive-immune-response-in-the-lungs-186970">overactive, inflammatory immune response</a>.</p>
<p>This means that the virus’s first contact with the immune system is probably through the surfaces of the nose, mouth and throat. This is supported by the presence of SIgA antibodies against SARS-CoV-2 <a href="http://dx.doi.org/10.3389/fimmu.2020.611337">in the secretions of infected people</a>, including their saliva, nasal fluid and tears. These locations, especially the tonsils, have specialized areas that specifically trigger mucosal immune responses.</p>
<p><a href="http://dx.doi.org/10.3390/pathogens11040397">Some research suggests</a> that if these SIgA antibody responses form as a result of vaccination or prior infection, or occur quickly enough in response to a new infection, they could prevent serious disease by confining the virus to the upper respiratory tract until it is eliminated.</p>
<h2>How do nasal vaccines work?</h2>
<p>Vaccines can be <a href="http://dx.doi.org/10.1016/B978-0-12-415847-4.00055-0">given through mucosal routes</a> via the mouth or nose. This induces an immune response through areas that stimulate the mucosal immune system, leading mucosal secretions to produce SIgA antibodies.</p>
<p>There are <a href="http://dx.doi.org/10.1016/B978-0-12-811924-2.00001-8">several existing mucosal vaccines</a>, most of them taken by mouth. Currently only one, the flu vaccine, is delivered nasally.</p>
<p>In the case of nasal vaccines, the viral antigens intended to stimulate the immune system would be taken up by immune cells within the lining of the nose or tonsils. While the exact mechanisms by which nasal vaccines work in people have not been thoroughly studied, researchers believe they <a href="http://dx.doi.org/10.1007/BF00915547">work analogously to oral mucosal vaccines</a>. Antigens in the vaccine induce B cells in mucosal sites to mature into plasma cells that secrete a form of IgA. That IgA is then transported into mucosal secretions throughout the body, where it becomes SIgA.</p>
<p>If the SIgA antibodies in the nose, mouth or throat target SARS-CoV-2, they could neutralize the virus before it can drop down into the lungs and establish an infection.</p>
<figure>
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<figcaption><span class="caption">Nasal vaccines could provide a more approachable alternative to injections for patients leery of needles.</span></figcaption>
</figure>
<h2>What advantage do mucosal vaccines have against COVID-19?</h2>
<p>I believe that arguably the best way to protect an individual against COVID-19 is to block the virus at its point of entry, or at least to confine it to the upper respiratory tract, where it might inflict relatively little damage.</p>
<p>Breaking chains of viral transmission is crucial to controlling epidemics. Researchers know that <a href="http://dx.doi.org/10.1093/cid/ciab691">COVID-19 spreads</a> during normal breathing and speech, and is exacerbated by sneezing, coughing, shouting, singing and other forms of exertion. Because these emissions mostly originate from saliva and nasal secretions, where the predominant form of antibody present is SIgA, it stands to reason that secretions with a sufficiently high level of SIgA antibodies against the virus could neutralize and thereby diminish its transmissibility.</p>
<p><a href="http://dx.doi.org/10.3389/fimmu.2022.957107">Existing vaccines</a>, however, do not induce SIgA antibody responses. Injected vaccines primarily induce circulating IgG antibodies, which are effective in preventing serious disease in the lungs. Nasal vaccines specifically induce SIgA antibodies in nasal and salivary secretions, where the virus is initially acquired, and can more effectively prevent transmission.</p>
<p>Nasal vaccines may be a useful supplement to injected vaccines in hot spots of infection. Since they don’t require needles, they might also help overcome vaccine hesitancy due to <a href="https://theconversation.com/over-half-of-adults-unvaccinated-for-covid-19-fear-needles-heres-whats-proven-to-help-161636">fear of injections</a>.</p>
<h2>How close are researchers to creating a nasal COVID-19 vaccine?</h2>
<p>There have been <a href="https://doi.org/10.1038/d41586-022-02824-3">over 100 oral or nasal COVID-19 vaccines in development</a> around the world.</p>
<p>Most of these have been or are currently being tested in animal models. <a href="http://dx.doi.org/10.1126/scitranslmed.abn6868">Many</a> <a href="http://dx.doi.org/10.1126/science.abo2523">have reported</a> successfully inducing protective antibodies in the blood and secretions, and have prevented infection in these animals. However, few have been successfully tested in people. Many <a href="https://www.pharmalive.com/altimmune-to-halt-trials-for-intranasal-covid-19-vaccine">have been abandoned</a> without fully reporting study details.</p>
<p>According to the <a href="https://www.who.int/publications/m/item/draft-landscape-of-covid-19-candidate-vaccines">World Health Organization</a>, 14 nasal COVID-19 vaccines are in clinical trials as of late 2022. Reports from <a href="https://doi.org/10.1038/d41586-022-02851-0">China and India</a> indicate that nasal or inhaled vaccines have been approved in these countries. But little information is publicly available about the results of the studies supporting approval of these vaccines.</p><img src="https://counter.theconversation.com/content/192567/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Michael W. Russell receives consultation fees from Therapyx, Inc., and has received previous research grants (now inactive) from the National Institutes of Health; he is also named on current grants to Therapyx, Inc. Therapyx has no interests in products for COVID-19.</span></em></p>An effective nasal vaccine could stop the virus that causes COVID-19 right at its point of entry. But devising one that works has been a challenge for researchers.Michael W. Russell, Professor Emeritus of Microbiology and Immunology, University at BuffaloLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1879052022-08-19T12:42:26Z2022-08-19T12:42:26ZWhat is listeria? A microbiologist explains the bacterium behind recent deadly food poisoning outbreaks<figure><img src="https://images.theconversation.com/files/479719/original/file-20220817-21-a18luh.jpg?ixlib=rb-1.1.0&rect=132%2C0%2C3875%2C2951&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Investigators in Florida traced a listeria outbreak to ice cream.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/ice-cream-jar-with-4-flavors-strawberry-vanilla-royalty-free-image/1279372828?adppopup=true">Graiki/Moment via Getty Images</a></span></figcaption></figure><p>Bacteria do, and will, end up in food. Everyone eats – intentionally or unintentionally – <a href="https://doi.org/10.7717/peerj.659">millions to billions</a> of live microbes every day. </p>
<p>Most are completely harmless, but some can cause serious illnesses in humans. Because of these potential pathogens, there is a long <a href="https://www.mayoclinic.org/healthy-lifestyle/pregnancy-week-by-week/in-depth/pregnancy-nutrition/art-20043844">list of foods to avoid</a>, including uncooked eggs, raw fish and unwashed fruits and vegetables, particularly for pregnant women. The foods themselves are not bad, but the same cannot be said for certain bacterial passengers, such as <em>Listeria monocytogenes</em>, or listeria for short. </p>
<p>This particular pathogen has found ways to indiscriminately get into our foods. While deli and dairy foods like cold cuts, cheese, milk and eggs are frequently culprits for causing listeriosis – the general name for listeria-caused infections – fresh vegetables and fruits have also been implicated.</p>
<p>The variety of foods responsible for <a href="https://www.cdc.gov/listeria/outbreaks/index.html">U.S. listeria outbreaks in the past decade</a> shows just how easily these bacteria get around. Listeria has turned up in <a href="https://www.cdc.gov/listeria/outbreaks/eggs-12-19/index.html">hard-boiled eggs</a>, <a href="https://www.cdc.gov/listeria/outbreaks/enoki-mushrooms-03-20/index.html">enoki mushrooms</a>, <a href="https://www.cdc.gov/listeria/outbreaks/precooked-chicken-07-21/index.html">cooked chicken</a> and, <a href="https://www.cdc.gov/listeria/outbreaks/packaged-salad-12-21-b/index.html">in 2021, packaged salad</a> – <a href="https://www.cdc.gov/listeria/outbreaks/packaged-salad-mix-12-21/index.html">twice</a>.</p>
<p>Even the frozen aisle is not spared from listeria contamination. Contaminated ice cream in Florida was behind this year’s listeria outbreak, with 25 reported cases spanning 11 states since January 2021, according to <a href="https://www.cdc.gov/listeria/outbreaks/monocytogenes-06-22/details.html">an early August 2022 report</a> from the Centers for Disease Control and Prevention. Those who fell ill ranged in age from less than 1 to 92 years old, and 24 of the cases have involved hospitalizations.</p>
<p>How can such a tiny organism bypass extensive disinfection efforts and wreak such havoc? <a href="https://scholar.google.com/citations?user=G_tH2rUAAAAJ&hl=en">As a microbiologist</a> who has been working with listeria and trying to solve these mysteries, I’d like to share some insider secrets about this unique little pathogen and its strategies of survival inside and outside our bodies.</p>
<h2>Farm to table</h2>
<p>To prevent consumer exposure to listeria, the food industries follow <a href="https://www.fda.gov/files/food/published/Draft-Guidance-for-Industry--Control-of-Listeria-monocytogenes-in-Ready-To-Eat-Foods-%28PDF%29.pdf">stringent disinfection and surveillance guidelines</a> from the Food and Drug Administration and the U.S. Department of Agriculture. Any detection of listeria triggers a recall of potentially contaminated food products. </p>
<p>Since 2017, there have been <a href="https://www.fsis.usda.gov/recalls">over 270 listeria-related food recalls</a>. These are incredibly costly and can sometimes lead to fears in consumers <a href="https://www.npr.org/sections/thetwo-way/2018/01/29/581531318/panera-bread-recalls-cream-cheese-across-u-s-over-listeria-fears">as well as nationwide disruptions in food services</a>. However, the recalls represent one of the few tools that the food industry has to protect consumers from foodborne infections. </p>
<p>Not all listeria strains are created equal. <a href="https://doi.org/10.1016/j.ijmm.2010.05.002">Genetic variations</a> in listeria make a big difference in whether the pathogen ends up being involved in multistate outbreaks or simply hitching a ride harmlessly through our digestive tract. Essentially, based on the <a href="https://doi.org/10.1093/jaoac/85.2.524">different methods used</a>, listeria can be subtyped into different lineages, with some associated with outbreaks more frequently than others.</p>
<p>Researchers are investigating ways to tell these listeria strains apart, distinguishing the less harmful ones from those that are particularly dangerous, or hypervirulent. Being able to accurately identify them can help policymakers assess risks and make economically feasible decisions to improve food safety.</p>
<figure class="align-center ">
<img alt="Illustration of red-orange rod-shaped Listeria bacteria." src="https://images.theconversation.com/files/477025/original/file-20220801-70681-jygdr6.jpg?ixlib=rb-1.1.0&rect=0%2C0%2C6000%2C3979&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/477025/original/file-20220801-70681-jygdr6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/477025/original/file-20220801-70681-jygdr6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/477025/original/file-20220801-70681-jygdr6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/477025/original/file-20220801-70681-jygdr6.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/477025/original/file-20220801-70681-jygdr6.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/477025/original/file-20220801-70681-jygdr6.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Listeria is an intracellular pathogen. Inside the body, it can grow inside a cell and spread to neighboring cells.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/illustration/listeria-monocytogenes-illustration-royalty-free-illustration/685023881">Kateryna Kon/Science Photo Library via Getty Images</a></span>
</figcaption>
</figure>
<h2>Listeria is tough</h2>
<p>Listeria can live in any place where food is grown, packaged, stored, transported, prepared or served. Our research team has even found listeria in <a href="https://doi.org/10.3390/pathogens7030060">organic lettuce harvested from a backyard garden</a>. </p>
<p>Listeria can survive and grow in temperatures as cold as <a href="https://ask.usda.gov/s/article/Can-Listeria-grow-at-refrigerator-temperatures">24 degrees Fahrenheit</a> (-4.4 Celsius) because it has <a href="https://doi.org/10.1080/10408390701856272">adapted to cold temperatures</a> and developed <a href="https://doi.org/10.4315/0362-028X-69.6.1473">tricks for overcoming cold stress</a>. Considering the average refrigerator maintains a temperature range of 35 F to 38 F (1.7 C to 3.3 C), even when the food is stored properly at refrigeration temperatures, a harmless few listeria can grow to dangerous levels of contamination over time.</p>
<p>Listeria is also extremely versatile in adapting to and surviving all kinds of disinfection processes. When it grows on surfaces, listeria protects itself with <a href="https://doi.org/10.3390%2Fpathogens6030041">a biofilm structure</a>, a kind of coating that forms a physical and chemical barrier and prevents disinfectants from reaching the bacteria within.</p>
<p>Surviving the harsh conditions outside our body is only the first part of the story. Before even beginning to cause infections, listeria needs to get to the intestines without getting caught and destroyed by the body’s defenses.</p>
<p>Traveling and surviving passage through a <a href="https://doi.org/10.3389%2Ffcimb.2014.00009">human digestive tract is not easy</a> for bacteria. Saliva enzymes can degrade bacterial cell walls. So can stomach acids and bile salts. Antibodies in our digestive tract can recognize and target bacteria for degradation. Moreover, <a href="https://doi.org/10.1084%2Fjem.20170495">resident gut microbes</a> are strong competitors for the limited amount of space and nutrients in our intestines.</p>
<p>After digestion, the body’s intestinal movement sends traffic one way – out of the body. In order to stick around and cause infections, bacteria have to attach themselves and hang on against the bowel movement while competing for nutrients. Successful pathogens can establish these survival and attachment tasks while undermining our immune defenses. </p>
<p>Listeria that manage to stick around in our intestines can trigger an immune response. In healthy people, that might manifest as <a href="https://www.cdc.gov/listeria/symptoms.html">minor diarrhea or vomiting that goes away without medical attention</a>. </p>
<p>However, those with compromised immune systems or immune systems temporarily weakened as a result of medication or <a href="https://doi.org/10.3389/fimmu.2020.575197">pregnancy</a> can be more susceptible to severe infections. In the absence of an effective immune system, listeria can invade other tissues and organs by creating an efficient niche for growth.</p>
<h2>Listeria in stealth mode</h2>
<p>Listeria is what we microbiologists call an intracellular pathogen. In an infected individual, listeria can grow inside a cell and <a href="https://doi.org/10.1083%2Fjcb.146.6.1333">spread to neighboring cells</a>. Hiding inside our cells this way, listeria avoids detection by antibodies or other immune defenses that are designed to detect and destroy threats that exist outside of our cells.</p>
<p>Once in stealth mode, listeria can move into and infect different organs. Wherever it goes, inflammation follows as the body’s immune system tries to go after the bacteria. The inflammation eventually results in collateral damage in nearby tissues. </p>
<p>In fact, deaths from listeria infections are often associated with the more invasive forms of the disease in which the microbes have breached the intestinal barriers and moved to other body parts. <a href="https://www.cdc.gov/listeria/symptoms.html">Life-threatening illnesses</a> that can result from listeria include meningitis – inflammation around the brain and spinal cord that can occur when these microbes infect the brain – or <a href="https://doi.org/10.1016/j.ijantimicag.2017.12.032">endocarditis</a>, infection of the heart’s inner lining. And in pregnant individuals, if the pathogen reaches the placenta, it can spread to the fetus and cause stillbirth or miscarriage.</p>
<p>As such, invasive listeria cases often have an alarmingly high <a href="https://www.fda.gov/animal-veterinary/animal-health-literacy/get-facts-about-listeria#">hospitalization rate of more than 90% and a fatality rate that can reach 30%</a>. </p>
<p>The scary statistics argue for a proactive and effective infection control to protect vulnerable populations, such as elderly or pregnant individuals, from listeria exposure. </p>
<h2>Think, cook and eat</h2>
<p>If you have risk factors and want to take extra precautions, maybe turn that unpasteurized cider into a hot, mulled cider to kill the bacteria with boiling and simmering. Eat soft cheeses on foods that get cooked, such as pizzas or grilled sandwiches, instead of eating them cold, straight from the refrigerator. Essentially, use heat to bring out the delicious flavors and eliminate potential listeria contamination in your food. </p>
<p>Ultimately, it’s nearly impossible to live in a completely sterile environment, eating food devoid of all living microorganisms. So enjoy your favorites, but <a href="https://www.fsis.usda.gov/food-safety">stay up to date with ongoing recalls</a> and follow the expiration guidelines, especially for ready-to-eat food.</p><img src="https://counter.theconversation.com/content/187905/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Yvonne Sun does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Listeria causes serious illness and food recalls nearly every year.Yvonne Sun, Assistant Professor of Microbiology, University of DaytonLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1844232022-08-16T12:29:28Z2022-08-16T12:29:28ZFrom watering via ice cubes to spritzing with hydrogen peroxide – 4 misguided plant health trends on social media<figure><img src="https://images.theconversation.com/files/470313/original/file-20220622-25-3avjqj.jpg?ixlib=rb-1.1.0&rect=0%2C11%2C7377%2C4885&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The internet has become a new player in plant care advice.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/two-female-friends-watching-online-gardening-royalty-free-image/1295397619">Kanawa_Studio/iStock via Getty Images Plus</a></span></figcaption></figure><p>The internet is full of advice on just about everything, including plant care.</p>
<p>As the <a href="https://plant.lab.uconn.edu/">director of a plant diagnostic laboratory</a> and expert on plant medicine, I help people manage their plants’ health. Here are four trends I’ve seen online recently that have stood out as being especially misleading or potentially damaging to plants. </p>
<h2>Watering orchids and other plants with ice cubes</h2>
<p>Multiple sites claim ice cubes can be used to give orchids a “just right” amount of water. The fact is tropical plants hate cold temperatures. Leaving <a href="http://www.ladybug.uconn.edu/FactSheets/house-plants---growing-.php">ice near an orchid’s roots may damage them</a>.</p>
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<iframe width="440" height="260" src="https://www.youtube.com/embed/_AA2Kt72DQg?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Orchids on ice?</span></figcaption>
</figure>
<p>Nearly all houseplants, including orchids, will prefer lukewarm or room temperature water, about 70 degrees Fahrenheit (21 degrees Celsius). Use fact sheets from educational institutions and reputable organizations to determine the correct amount of water and watering schedule for the types of plants you’re growing, and then set a reminder on your phone. </p>
<p>Use a potting medium that drains well and quickly. For orchids, <a href="https://www.aos.org/orchids/orchid-care/what-is-the-best-potting-media.aspx">a mix of bark chips and sphagnum moss is much better</a> than 100% soil or coco coir. </p>
<h2>‘No Mow May’</h2>
<p>Many campaigns have sprung up recently promoting “<a href="https://beecityusa.org/no-mow-may/">No Mow May</a>.” The idea is to delay regular mowing for the month of May to provide more feeding sites for pollinators, which are trying to shore up calories after their winter hibernation.</p>
<iframe src="https://www.tiktok.com/embed/v2/7093152050682514734" height="800" width="100%">
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<p>Unfortunately, this practice usually does not benefit pollinators and could damage your lawn’s health. Here’s why:</p>
<p>Mowing more than 30% of a grass leaf at once is never a good idea. Grasses depend on their blades to photosynthesize and meet their energy needs. When more than 30% is lost at once, the plants may not have enough remaining leaf surface area to photosynthesize properly.</p>
<p>Overgrown lawns have overgrown root systems, which require more energy. Failure to provide it leads to <a href="https://hgic.clemson.edu/mowing-height-matters/">increased susceptibility to disease</a>, poor water management and potential collapse. Such damage is pretty much unavoidable after a monthlong “no mow” period. </p>
<p>Few lawns actually contain enough flowers to be beneficial to pollinators, anyway. For many people, the “perfect lawn” is an unwavering green carpet. But that uniformity is useless to bees and other pollinators that require <a href="https://www.epa.gov/pollinator-protection/what-you-can-do-protect-honey-bees-and-other-pollinators">pollen and nectar that other plants can provide</a>. </p>
<p>It’s great to <a href="https://www.epa.gov/pollinator-protection/what-you-can-do-protect-honey-bees-and-other-pollinators">prioritize pollinator health</a>, but the “no mow” trend is best implemented in prairie, field and wetland environments, where there is a lot of plant diversity and flowering plants. </p>
<p>If you’re looking to support pollinator health in your own yard, <a href="https://www.nwf.org/NativePlantFinder">plant native wildflowers</a> that pollinators will actually want to visit. Most require less water and management compared to grass lawns. Replace your entire lawn or even a small strip. Any amount of lawn replaced is beneficial – and will save you water and money. </p>
<p>Make sure not to mow the wildflowers until they’ve finished flowering. A wildflower patch usually only needs to be cut once or twice a year. Mowing after the last frost in early spring will spread the previous year’s seeds and <a href="https://extension.psu.edu/planting-pollinator-friendly-gardens">provide a home for insects to spend the winter</a>. </p>
<h2>Using hydrogen peroxide to ‘cure’ plant diseases</h2>
<p><div data-react-class="Tweet" data-react-props="{"tweetId":"917613551988097024"}"></div></p>
<p>Hydrogen peroxide <a href="https://pubchem.ncbi.nlm.nih.gov/compound/Hydrogen-peroxide">does sterilize surfaces and can reduce bacteria and some fungi</a>. But the rapid reaction that gives hydrogen peroxide its sterilizing properties occurs almost immediately after coming in contact with other compounds. This does not permit hydrogen peroxide to move throughout a plant.</p>
<p>So most pathogens – the organisms that cause disease – will not be affected if they are in a plant’s tissues rather than on its exterior. Applying hydrogen peroxide excessively or improperly may even <a href="https://pubchem.ncbi.nlm.nih.gov/compound/Hydrogen-peroxide">make plant health issues worse</a> by drying surfaces and killing beneficial microbes. </p>
<p>While there is certainly a time and place for sterilizing surfaces in plant care – like with your pruners and propagation tools – the best defense against plant diseases is proper care. </p>
<p>Water your plants only when necessary and provide proper light and nutrition. Research what your plant likes best from educational institutions or other reputable sources. Routine pruning to increase airflow, proper plant spacing, avoiding single-crop planting and crop rotation are just some examples of chemical-free techniques to <a href="https://ipm.cahnr.uconn.edu/">reduce plant stress and decrease disease susceptibility</a>.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/470069/original/file-20220621-15-io6uku.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A woman holds up her cell phone to photograph the roots of a plant." src="https://images.theconversation.com/files/470069/original/file-20220621-15-io6uku.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/470069/original/file-20220621-15-io6uku.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/470069/original/file-20220621-15-io6uku.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/470069/original/file-20220621-15-io6uku.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/470069/original/file-20220621-15-io6uku.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/470069/original/file-20220621-15-io6uku.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/470069/original/file-20220621-15-io6uku.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Virtual diagnosis?</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/woman-holding-and-taking-photo-of-potato-crop-royalty-free-image/1322163523">Sanja Radin/E+ via Getty Images</a></span>
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</figure>
<h2>Diagnosing diseases using phone apps</h2>
<p>Many apps exist that use photographs submitted by the user to identify plant diseases and offer solutions. </p>
<p>The truth is, to diagnose most plant diseases, a scientist needs to culture plant tissue to correctly identify pathogens. Only after an accurate diagnosis <a href="https://apsjournals.apsnet.org/journal/pdis">can they recommend management solutions</a>. I have a pretty strong opinion here, since disease identification is what I do every day. Plant symptoms that accompany one disease may be practically identical to those of another. </p>
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<a href="https://images.theconversation.com/files/472617/original/file-20220705-4524-eyxbyp.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Photos of four different plants with curled leaves labeled herbicide exposure, virus, insect feeding and fungal infection." src="https://images.theconversation.com/files/472617/original/file-20220705-4524-eyxbyp.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/472617/original/file-20220705-4524-eyxbyp.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=397&fit=crop&dpr=1 600w, https://images.theconversation.com/files/472617/original/file-20220705-4524-eyxbyp.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=397&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/472617/original/file-20220705-4524-eyxbyp.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=397&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/472617/original/file-20220705-4524-eyxbyp.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=499&fit=crop&dpr=1 754w, https://images.theconversation.com/files/472617/original/file-20220705-4524-eyxbyp.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=499&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/472617/original/file-20220705-4524-eyxbyp.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=499&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The same symptom can be caused by very different problems.</span>
<span class="attribution"><span class="source">Bugwood.org</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
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<p>For example, herbicide exposure, viruses, insect feeding and fungal infections can all cause twisted and deformed leaves. To properly diagnose an issue, the plant’s own history, location, site history, time of year and other factors need to be considered before I can take a guess as to what may be contributing to symptoms. </p>
<p>Don’t rely on an app to guess at what disease your plant may have – and don’t act on bogus recommendations. Instead, reach out to your local university diagnostic lab or extension office for support. </p>
<p>Not sure where to go? Start with the <a href="https://www.npdn.org/lab_directory">National Plant Diagnostic Network’s lab directory</a>. Many, including mine, offer free consultations and recommendations. If you end up submitting a sample to a diagnostic lab, most are affordable – my lab’s fee is US$20 – and will be worthwhile, especially when you consider the cost of replacing the plant with something that could eventually have the same issue.</p><img src="https://counter.theconversation.com/content/184423/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Nick Goltz (UConn Plant Diagnostic Laboratory) receives funding from the USDA-NIFA and the state of Connecticut. </span></em></p>Plant care advice abounds on TikTok, Twitter, Instagram and YouTube – but not all of it is good. A plant expert debunks four common recommendations.Nick Goltz, Assistant Extension Educator and Director, UConn Plant Diagnostic Laboratory, University of ConnecticutLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1816472022-05-10T14:57:51Z2022-05-10T14:57:51ZBanning wild meat is not the solution to reducing future disease outbreaks<figure><img src="https://images.theconversation.com/files/460263/original/file-20220428-4038-33jm5u.jpg?ixlib=rb-1.1.0&rect=18%2C27%2C5988%2C3980&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/tomohon-indonesia-02-19-2020-grilled-1689513163">Happy Auer/Shutterstock</a></span></figcaption></figure><p>There have been widespread calls for a global ban on the sale and consumption of wild meat. Following the spread of COVID in early 2020 (which is thought to have originated in bats), over 200 conservation organisations signed an <a href="https://lioncoalition.org/2020/04/04/open-letter-to-world-health-organisation/">open letter</a> to the World Health Organization, urging a permanent ban on all live wildlife markets and the use of wild animal products in traditional medicine. </p>
<hr>
<iframe id="noa-web-audio-player" style="border: none" src="https://embed-player.newsoveraudio.com/v4?key=x84olp&id=https://theconversation.com/banning-wild-meat-is-not-the-solution-to-reducing-future-disease-outbreaks-181647&bgColor=F5F5F5&color=D8352A&playColor=D8352A" width="100%" height="110px"></iframe>
<p><em>You can listen to more articles from The Conversation, narrated by Noa, <a href="https://theconversation.com/uk/topics/audio-narrated-99682">here</a>.</em></p>
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<p>The risk of disease spillover has been used by conservationists to legitimise arguments about the perceived need to <a href="https://www.nationalgeographic.co.uk/environment-and-conservation/2020/05/to-prevent-pandemics-stop-disrespecting-nature">separate humans from “wild” nature</a>. Since the pandemic began, bans on wild animal consumption and trade have been introduced in several countries. Before COVID, bird flu and <a href="https://www.sciencedirect.com/science/article/pii/S027795361730758X">Ebola virus</a> outbreaks also triggered bans on wildlife trade and consumption in northern Vietnam and west Africa, respectively.</p>
<p>By restricting contact between humans and wild animals, such bans should in theory minimise the risk of future disease outbreaks. Yet these restrictions neglect their potential impact on rural and Indigenous groups, who often depend on wild produce, particularly meat, fish and insects, as sources of dietary protein, fat and micronutrients. </p>
<p>Our <a href="https://www.jstor.org/stable/j.ctt19b9jsg">previous work</a> has documented the importance of “wild foods” worldwide. And we continue to find evidence that wild meat plays a critical role in enhancing the diets of Indigenous groups, such as Khasi communities in <a href="https://www.nesfas.in/research/">Meghalaya</a>, northeast India. (To be clear, we’re not in any way promoting the consumption of endangered animals, which is strictly prohibited around the world.)</p>
<figure class="align-center ">
<img alt="Khasi women carrying baskets." src="https://images.theconversation.com/files/460295/original/file-20220428-20-m86ogi.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/460295/original/file-20220428-20-m86ogi.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/460295/original/file-20220428-20-m86ogi.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/460295/original/file-20220428-20-m86ogi.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/460295/original/file-20220428-20-m86ogi.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/460295/original/file-20220428-20-m86ogi.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/460295/original/file-20220428-20-m86ogi.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Wild meat is an important source of nutrition for the Khasi people of north-eastern India.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/meghalaya-india-february-8-2016-two-742386562">gregorioa/Shutterstock</a></span>
</figcaption>
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<h2>Understanding spillover events</h2>
<p>For our <a href="https://www.thelancet.com/journals/lanplh/article/PIIS2542-5196(22)00064-X/fulltext">latest review</a>, we extracted evidence on “spillover events” (the transmission of a pathogen from an animal to a human) linked to wild meat consumption and related practices (such as hunting and butchering), from available scientific papers published between 1940 and 2021. We found such evidence to be limited and often of poor quality. </p>
<p>Of course, there are <a href="https://wedocs.unep.org/bitstream/handle/20.500.11822/32060/zoonoses.pdf?sequence=1&isAllowed=y">risks to eating wild meat</a>, but we need to better understand the specific consumption behaviour and practices that give rise to disease so that we can devise more targeted approaches to mitigate future outbreaks.</p>
<p>There is a risk that castigating wild meat harvesting practices in low-income settings fails to recognise the risks of zoonotic diseases (diseases that can be transmitted from animals to humans) associated with western food production and consumption practices. </p>
<p>We found that the highest number of spillover events reported in the scientific papers were from the US, and these were primarily linked to recreational hunting. While there are probably spatial biases in reporting (in some places, diseases may go undiagnosed or be under-reported), elsewhere, <a href="https://www.nature.com/articles/nature06536/">research</a> has suggested that only 3% of emerging infectious diseases from 1940 to 2004 were attributable to wild meat, compared with 17% from conventional agriculture and the food industry. And 31% was linked to changes in land use, including deforestation and habitat fragmentation.</p>
<p>We highlighted specific mechanisms that appeared to heighten spillover risk from wild meat harvesting and consumption, such as involvement in hunting or wild meat preparation, including skinning and butchering. Cooking methods also mattered, with the consumption of raw or undercooked meat often mentioned in reports.</p>
<h2>Towards more targeted policy responses</h2>
<p>Our research suggests the need for more nuanced approaches to protect an increasingly globalised and interconnected world from the potential risks of zoonotic spillover while not stigmatising the consumption practices of communities that rely on wild resources.</p>
<p>Knowing which animals harbour disease, knowing who is most exposed to high-risk animal species, understanding seasonal changes in exposure, and disseminating an understanding of safe and unsafe hunting and cooking practices could be more effective than total bans, and may result in better adoption of protective behaviour. </p>
<p>Simply banning wild meat consumption stigmatises consumers and risks pushing consumption practices underground, where they become harder to understand and regulate. </p>
<p>With the rate of emergence of new diseases accelerating, there is a need for more <a href="https://www.euro.who.int/en/health-topics/health-policy/one-health">inclusive approaches</a>, which balance the vulnerabilities of diverse, local communities and their continued need for wild food sources, with the need to reduce the risk of future spillover associated with eating wild meat.</p><img src="https://counter.theconversation.com/content/181647/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>The authors do not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Following the global spread of COVID, there have been widespread calls for blanket bans on the consumption and trade of wild animals. But such bans may have unintended consequences.Charlotte Milbank, PhD Candidate in Geography and Epidemiology, University of CambridgeBhaskar Vira, Professor of Political Economy at the Department of Geography and Fellow of Fitzwilliam College., University of CambridgeLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1807752022-05-04T12:33:48Z2022-05-04T12:33:48ZWastewater monitoring took off during the COVID-19 pandemic – and here’s how it could help head off future outbreaks<figure><img src="https://images.theconversation.com/files/460684/original/file-20220502-23-iuraw7.jpg?ixlib=rb-1.1.0&rect=0%2C416%2C5067%2C3284&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Sampling wastewater can be time-intensive.</span> <span class="attribution"><span class="source">John Eisele/Colorado State University</span></span></figcaption></figure><p><em>A community’s sewage holds clues about its COVID-19 burden. Over the course of the pandemic, wastewater surveillance has become an increasingly popular way to try to understand local infection trends.</em></p>
<p><em>Microbiologists <a href="https://scholar.google.com/citations?user=NXca5vEAAAAJ&hl=en&oi=ao">Susan De Long</a> and <a href="https://scholar.google.com/citations?user=Flb9Tp8AAAAJ&hl=en&inst=6416714965532506866">Carol Wilusz</a> met and became wastewater aficionados in April 2020 when a grassroots group of wastewater treatment plant operators asked them to develop and deploy a test to detect SARS-CoV-2 in samples from the sewers of Colorado. De Long is an environmental engineer who studies useful bacteria. Wilusz’s expertise is in RNA biology. Here they describe how wastewater surveillance works and what it could do in a post-pandemic future.</em></p>
<h2>How is wastewater monitored for SARS-CoV-2?</h2>
<p>Wastewater surveillance takes advantage of the fact that many human pathogens and products of human drug metabolism end up in urine, feces or both. The SARS-CoV-2 virus that causes COVID-19 shows up in surprisingly <a href="https://doi.org/10.1186/s12879-021-06443-7">large quantities in feces of infected people</a>, even though this is not a major route of disease transmission.</p>
<p>To figure out whether any pathogens are present, we first need to collect a representative sample of wastewater, either directly from the sewer or at the point where what engineers call “influent” enters a treatment plant. We can also use solids that have settled out of the wastewater.</p>
<p>Technicians then need to remove large particles of fecal matter and concentrate any microbes or viruses. The next step is extracting their nucleic acids – the DNA or RNA that holds the pathogens’ genetic information.</p>
<p>The sequences contained in the DNA or RNA act as unique bar codes for the pathogens present. For instance, if we detect genes that are unique to SARS-CoV-2, we know that the coronavirus is in our sample. We use PCR-based approaches, similar to those <a href="https://theconversation.com/whats-the-difference-between-a-pcr-and-antigen-covid-19-test-a-molecular-biologist-explains-170917">used in clinical diagnostic tests</a>, to detect and quantify SARS-CoV-2 sequences.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="masked lab worker with glassware and lab equipment" src="https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">A lab technician prepares to process wastewater samples for SARS-CoV-2 detection at Colorado State University.</span>
<span class="attribution"><span class="source">John Eisele/Colorado State University</span></span>
</figcaption>
</figure>
<p>Characterizing the nucleic acid sequence in more detail can provide information about viral strains – for instance, <a href="https://doi.org/10.1016/j.scitotenv.2022.153171">it can identify variants</a> like omicron BA.2. </p>
<p>Currently, the vast majority of wastewater surveillance efforts are focused on SARS-CoV-2, but the same techniques work with other pathogens, including <a href="https://doi.org/10.3390/v11090775">poliovirus</a>, <a href="https://doi.org/10.1101/2022.02.15.22271027">influenza</a> and <a href="https://doi.org/10.1111/j.1365-2672.2012.05231.x">noroviruses</a>. </p>
<p>Before the pandemic, one application was <a href="https://theconversation.com/sewage-surveillance-is-the-next-frontier-in-the-fight-against-polio-105012">monitoring for rare poliovirus outbreaks</a> in areas where polio vaccination is ongoing. Wastewater can also be monitored for signs of various drugs to give insights into the <a href="https://doi.org/10.1016/j.scitotenv.2020.138376">level and type of drug use in a population</a>.</p>
<h2>Where does the data go?</h2>
<p>During the pandemic, the U.S. Centers for Disease Control and Prevention developed the <a href="https://www.cdc.gov/healthywater/surveillance/wastewater-surveillance/wastewater-surveillance.html">National Wastewater Surveillance System</a> specifically to track SARS-CoV-2 across the country. <a href="https://covid.cdc.gov/covid-data-tracker/#wastewater-surveillance">Over 800 sites report data</a> to this NWSS system, but not all states and counties are currently represented.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Map of U.S. with dots for sites that report to NWSS" src="https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=375&fit=crop&dpr=1 600w, https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=375&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=375&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=471&fit=crop&dpr=1 754w, https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=471&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=471&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">More than 800 sites that cover populations of various sizes report COVID-19 wastewater numbers to the CDC.</span>
<span class="attribution"><a class="source" href="https://covid.cdc.gov/covid-data-tracker/?ACSTrackingID=USCDC_2145-DM80954&ACSTrackingLabel=4.29.2022%20-%20COVID-19%20Data%20Tracker%20Weekly%20Review&deliveryName=USCDC_2145-DM80954#wastewater-surveillance">CDC COVID Data Tracker</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Many state agencies, like the <a href="https://cdphe.maps.arcgis.com/apps/dashboards/d79cf93c3938470ca4bcc4823328946b">Colorado Department of Public Health and Environment</a>, and cities, like <a href="https://covid19.tempe.gov/pages/indicators#Wastewater%20Dash">Tempe, Arizona</a>, have their own dashboards for reporting data. Some companies performing wastewater analysis report data <a href="https://biobot.io/data/">on their own dashboards</a>, too.</p>
<p>In our opinion, the NWSS represents an exciting first step in monitoring population health through wastewater. Similar systems are being established in other countries, <a href="https://www.health.nsw.gov.au/Infectious/covid-19/Pages/sewage-surveillance.aspx">including Australia</a> and <a href="https://www.esr.cri.nz/our-expertise/covid-19-response/wastewater-testing-results/">New Zealand</a>.</p>
<h2>What does wastewater data really show?</h2>
<p>SARS-CoV-2 levels in wastewater from large populations are an excellent indicator of the infection level in a community. The system automatically monitors everyone who lives in the sewershed, so it’s anonymous, unbiased and equitable. Importantly, it is also impossible to track the infection back to a particular person, household or neighborhood without taking additional samples.</p>
<p>Wastewater surveillance doesn’t rely on the availability of clinical tests or people reporting their test results. It also picks up asymptomatic and pre-symptomatic cases of COVID-19; this is critical because people who are <a href="https://doi.org/10.1038/s41591-020-0869-5">infected but don’t feel sick can still spread COVID-19</a>.</p>
<p>In our opinion, wastewater testing is increasingly important as more COVID-19 tests are done at home. And because vaccination has also led to <a href="https://academic.oup.com/cid/article/74/7/1275/6345339">more mild and asymptomatic cases of COVID-19</a>, people may be infected without getting tested at all. These factors mean that clinical case data are less informative than earlier in the pandemic, while wastewater data remains a consistent indicator of community infection level. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="COVID-19 rapid tests for home use on a pharmacy shelf" src="https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Wastewater surveillance doesn’t rely on people reporting a positive home test or even being aware of their infections.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/take-home-covid-19-testing-kit-is-displayed-on-the-shelf-of-news-photo/1360415081">Spencer Platt/Getty Images News</a></span>
</figcaption>
</figure>
<p>So far, you can’t accurately predict the number of infected individuals in a community based on the level of virus in its wastewater. The stage of someone’s infection, how their body responds to the virus, the viral variant, how far a person was from where the wastewater sample was taken, even the weather can all <a href="https://doi.org/10.1016/j.jhazmat.2021.127456">affect the amounts of SARS-CoV-2 measured in sewage</a>. </p>
<p>But scientists can infer relative changes in infection rates. Watching viral levels go up and down in sewage provides a glimpse of whether cases are rising or falling in the community as a whole.</p>
<p>Because SARS-CoV-2 can be detected in wastewater days or even weeks before outbreaks occur, wastewater monitoring can provide an early warning that public health measures may be warranted. And trends in the signal are important – <a href="https://twitter.com/drericding/status/1468627450049540099?lang=en">if you know levels are rising</a>, it may be a good time to reinstitute a mask mandate or recommend working from home. At present, public health officials use wastewater monitoring data <a href="http://dx.doi.org/10.15585/mmwr.mm7030e2">along with other information</a> like test positivity rates and the number of clinical cases and hospitalizations in the community to make these kinds of decisions.</p>
<p>Data from sequencing can also help detect new variants and monitor their levels, allowing health responses to take into account the characteristics of the variant present.</p>
<p>In smaller populations, such as in college dormitories and nursing homes, wastewater monitoring can detect a small number of infected people. That can sound the alarm that targeted clinical testing is in order to identify infected people for isolation. Early detection, targeted testing and quarantining are <a href="https://doi.org/10.1126/science.abc5798">effective at preventing outbreaks</a>. Rather than using clinical testing for routine monitoring, administrators can reserve disruptive clinical tests for times when SARS-CoV-2 is detected in the wastewater.</p>
<h2>What will monitoring look like in the future?</h2>
<p>Widespread and routine use of wastewater monitoring would give public health officials access to information about the levels of a range of potential infections in U.S. communities. This data could guide decisions about where to provide additional resources to communities, like holding testing or vaccination clinics in places where infection is on the rise. It could also help determine when interventions like masking or school closures are necessary.</p>
<p>In the best case, wastewater monitoring might catch a new virus when it first arrives in a new area; an early shutdown in the very localized area could potentially prevent a future pandemic. Interestingly, researchers have detected SARS-CoV-2 in <a href="https://www.reuters.com/article/health-coronavirus-italy-sewage/italy-sewage-study-suggests-covid-19-was-there-in-december-2019-idINL1N2DV2XE">archived wastewater samples collected before</a> anyone had been diagnosed with COVID-19. If wastewater monitoring had been part of the established public health infrastructure back in late 2019, it could have provided an earlier warning that SARS-CoV-2 was becoming a global threat.</p>
<p>For now, though, establishing and operating a national wastewater surveillance system, particularly one that includes building-level monitoring at key locations, is still too costly and labor-intensive.</p>
<p>Ongoing research and development efforts are trying to simplify and automate wastewater sampling. On the analysis side, adaptation of PCR and sequencing technologies to detect other pathogens, including novel ones, will be vital to take full advantage of such a system. Ultimately, wastewater surveillance could help support a future in which pandemics are far less deadly and have less social and economic impact.</p>
<p>[<em>Research into coronavirus and other news from science</em> <a href="https://memberservices.theconversation.com/newsletters/?nl=science&source=inline-science-corona-research">Subscribe to The Conversation’s new science newsletter</a>.]</p><img src="https://counter.theconversation.com/content/180775/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Susan De Long receives funding from Colorado Department of Public Health and Environment, the Anschutz Foundation, the National Science Foundation, and the Department of Energy.</span></em></p><p class="fine-print"><em><span>Carol Wilusz receives funding from Colorado Department of Public Health & Environment and the Anschutz Foundation. </span></em></p>Over 800 sites across the US report coronavirus data from sewage to the CDC. Here’s how this kind of surveillance system works and what it can and can’t tell you.Susan De Long, Associate Professor of Civil and Environmental Engineering, Colorado State UniversityCarol Wilusz, Professor of Microbiology, Immunology and Pathology, Colorado State UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1818242022-04-26T18:39:43Z2022-04-26T18:39:43ZDisease-causing parasites can hitch a ride on plastics and potentially spread through the sea, new research suggests<figure><img src="https://images.theconversation.com/files/459606/original/file-20220425-25-tfbr1v.png?ixlib=rb-1.1.0&rect=0%2C0%2C2310%2C1296&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The sticky biofilms that form on microplastics can harbor disease-causing pathogens and help them spread.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/sea-water-contaminated-by-micro-plastic-royalty-free-image/1036767280">Tunatura/iStock via Getty Images Plus</a></span></figcaption></figure><p>Typically when people hear about plastic pollution, they might envision seabirds with bellies full of trash or sea turtles with plastic straws in their noses. However, plastic pollution poses another threat that’s invisible to the eye and has important consequences for both human and animal health.</p>
<p><a href="https://doi.org/10.1016/j.marenvres.2016.05.012">Microplastics</a>, tiny plastic particles present in many cosmetics, can form when larger materials, such as clothing or fishing nets, break down in water. Microplastics are now widespread in the ocean and have been found in fish and shellfish, including <a href="https://doi.org/10.1016/j.envpol.2014.06.010">those that</a> <a href="https://doi.org/10.1016/j.marpolbul.2018.05.047">people eat</a>.</p>
<p>As <a href="https://scholar.google.com/citations?user=v15DbVcAAAAJ&hl=en">researchers</a> <a href="https://shapirolab.vetmed.ucdavis.edu/people/emma-zhang">studying</a> how waterborne pathogens spread, we wanted to better understand what happens when microplastics and disease-causing pathogens end up in the same body of water. In our recent study published in the journal <a href="https://doi.org/10.1038/s41598-022-10485-5">Scientific Reports</a>, we found that pathogens from land can hitch a ride to the beach on microscopic pieces of plastic, providing a new way for germs to concentrate along coastlines and travel to the deep sea.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/459605/original/file-20220425-2721-yy4mz1.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Aerial shot of boat floating through plastic pollution on water" src="https://images.theconversation.com/files/459605/original/file-20220425-2721-yy4mz1.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/459605/original/file-20220425-2721-yy4mz1.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/459605/original/file-20220425-2721-yy4mz1.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/459605/original/file-20220425-2721-yy4mz1.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/459605/original/file-20220425-2721-yy4mz1.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/459605/original/file-20220425-2721-yy4mz1.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/459605/original/file-20220425-2721-yy4mz1.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Microplastic pollution has negative consequences for human, animal and environmental health.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/plastic-pollution-in-the-ocean-man-cleaning-plastic-royalty-free-image/1301941387">Yunaidi Joepoet/Moment via Getty Images</a></span>
</figcaption>
</figure>
<h2>Investigating how plastics and pathogens interact</h2>
<p>We focused on three parasites that are <a href="https://www.who.int/publications/i/item/9789241563826">common contaminants</a> in marine water and seafoods: the single-celled protozoans <em>Toxoplasma gondii</em> (<em>Toxo</em>), <em>Cryptosporidium</em> (<em>Crypto</em>) and <em>Giardia</em>. These parasites end up in waterways when feces from infected animals, and sometimes people, contaminate the environment.</p>
<p><a href="https://doi.org/10.1146/annurev.publhealth.18.1.135"><em>Crypto</em> and <em>Giardia</em></a> cause gastrointestinal disease that can be deadly in young children and immunocompromised individuals. <a href="https://doi.org/10.1128/cmr.05013-11"><em>Toxo</em></a> can cause lifelong infections in people, and can prove fatal for those with weak immune systems. Infection in <a href="https://www.waterpathogens.org/book/toxoplasma-gondii">pregnant women</a> can also cause miscarriage or blindness and neurological disease in the baby. <em>Toxo</em> also infects a wide range of marine wildlife and kills endangered species, including <a href="https://doi.org/10.7589/0090-3558-39.3.495">southern</a> <a href="https://doi.org/10.1017/s0031182015001377">sea otters</a>, <a href="https://doi.org/10.1016/j.vetpar.2012.11.001">Hector’s dolphins</a> and <a href="https://doi.org/10.3354/dao03047">Hawaiian monk seals</a>.</p>
<p>To test whether these parasites can stick onto plastic surfaces, we first placed microplastic beads and fibers in beakers of seawater in our lab for two weeks. This step was important to induce the formation of a <a href="https://www.livescience.com/57295-biofilms.html">biofilm</a> – a sticky layer of bacteria and gellike substances that coats plastics when they enter fresh or marine waters. Researchers also call this sticky layer an <a href="https://doi.org/10.1126/sciadv.abd1211">eco-corona</a>. We then added the parasites to the test bottles and counted how many became stuck on the microplastics or remained freely floating in the seawater over a seven-day period.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/pHLP5CZMnL4?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Biofilms are vast communities of microbes that can form on almost any surface, including your teeth.</span></figcaption>
</figure>
<p>We found that significant numbers of parasites were clinging to the microplastic, and these numbers were increasing over time. So many parasites were binding to the sticky biofilms that, gram for gram, plastic had two to three times more parasites than did seawater.</p>
<p>Surprisingly, we found that microfibers (commonly from clothes and fishing nets) harbored a greater number of parasites than did microbeads (commonly found in cosmetics). This result is important, because microfibers are the most common type of microplastic found in <a href="https://doi.org/10.1016/j.marpolbul.2013.12.035">marine waters</a>, on <a href="https://doi.org/10.1016/j.scitotenv.2017.09.100">coastal beaches</a> and even in <a href="https://doi.org/10.1016/j.marpolbul.2018.12.039">seafood</a>.</p>
<h2>Plastics could change ocean disease transmission</h2>
<p>Unlike <a href="https://doi.org/10.1016/j.marenvres.2016.07.004">other pathogens</a> that are commonly found in seawater, the pathogens we focused on are derived from terrestrial animal and human hosts. Their presence in marine environments is entirely due to <a href="https://doi.org/10.1016/j.pt.2004.08.008">fecal waste</a> <a href="https://dx.doi.org/10.1016%2Fj.fawpar.2019.e00049">contamination</a> that ends up in the sea. Our study shows that microplastics could also serve as transport systems for these parasites.</p>
<p>These pathogens <a href="https://doi.org/10.1016/j.pt.2004.08.008">cannot replicate in the sea</a>. Hitching a ride on plastics into marine environments, however, could fundamentally alter how these pathogens move around in marine waters. We believe that microplastics that float along the surface could potentially <a href="https://www.nationalgeographic.com/science/article/microplastics-in-virtually-every-crevice-on-earth">travel long distances</a>, spreading pathogens far from their original sources on land and bringing them to regions they would not otherwise be able to reach.</p>
<p>On the other hand, plastics that sink will concentrate pathogens on the sea bottom, where filter-feeding animals like clams, mussels, oysters, abalone and other shellfish live. A sticky biofilm layer can camouflage synthetic plastics in seawater, and animals that typically eat dead organic material may <a href="https://doi.org/10.1126/sciadv.abd1211">unintentionally ingest them</a>. Future experiments will test whether live oysters placed in tanks with and without plastics end up ingesting more pathogens.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/459555/original/file-20220425-14-c1bmzs.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Diagram illustrating how pathogens can associate with biofilms on microplastics and spread through the sea." src="https://images.theconversation.com/files/459555/original/file-20220425-14-c1bmzs.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/459555/original/file-20220425-14-c1bmzs.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=344&fit=crop&dpr=1 600w, https://images.theconversation.com/files/459555/original/file-20220425-14-c1bmzs.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=344&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/459555/original/file-20220425-14-c1bmzs.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=344&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/459555/original/file-20220425-14-c1bmzs.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=432&fit=crop&dpr=1 754w, https://images.theconversation.com/files/459555/original/file-20220425-14-c1bmzs.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=432&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/459555/original/file-20220425-14-c1bmzs.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=432&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The biofilms that form on microplastics can help pathogens spread through the sea.</span>
<span class="attribution"><span class="source">Emma Zhang</span>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span>
</figcaption>
</figure>
<h2>A One Health problem</h2>
<p><a href="https://www.cdc.gov/onehealth/basics/index.html">One Health</a> is an approach to research, policy and veterinary and human medicine that emphasizes the close connection of animal, human and environmental health. While it may seem that plastic pollution affects only animals in the ocean, it can ultimately have consequences on human health.</p>
<p>Our project was conducted by a multidisciplinary team of experts, ranging from microplastics researchers and parasitologists to shellfish biologists and epidemiologists. This study highlights the importance of collaboration across human, animal and environmental disciplines to address a challenging problem affecting our shared marine environment.</p>
<p>Our hope is that better understanding how microplastics can move disease-causing pathogens in new ways will encourage others to think twice before reaching for that plastic straw or polyester T-shirt.</p>
<p>[<em>Get fascinating health and science news in your inbox.</em> <a href="https://memberservices.theconversation.com/newsletters/?nl=science&source=inline-science-fascinating">Sign up for The Conversation’s weekly science newsletter</a>.]</p><img src="https://counter.theconversation.com/content/181824/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Karen Shapiro receives funding from the Ocean Protection Council and California Sea Grant program
(Grant #19-0592).</span></em></p><p class="fine-print"><em><span>Emma Zhang received student funding from STAR (Students Training in Advanced Research) Program at UC Davis School fo Veterinary Medicine.</span></em></p>Normally land-bound pathogens that cause deadly diseases for both humans and animals can cling to microplastics and end up in your seafood.Karen Shapiro, Associate Professor of Pathology, Microbiology and Immunology, University of California, DavisEmma Zhang, Veterinary researcher, University of California, DavisLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1795902022-03-25T11:28:12Z2022-03-25T11:28:12ZThe dangers of eating raw meat<figure><img src="https://images.theconversation.com/files/453023/original/file-20220318-13-f1w6ml.jpg?ixlib=rb-1.1.0&rect=11%2C11%2C7337%2C4891&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><a class="source" href="https://www.shutterstock.com/image-photo/handsome-man-biting-raw-meat-on-566969275">RossHelen/Shutterstock</a></span></figcaption></figure><p>Rising energy and gas prices might make you think twice about firing up your stove for a roast or stew. Why cook that meat? After all, your menu could include trendy beef carpaccio, flavoursome wild boar’s liver, coppa or pancetta. If you learned to like raw meat, you might become a paleo-keto-carnivorous pilgrim, with visions of developing a <a href="https://www.dailymail.co.uk/femail/article-10620271/Fitness-coach-reveals-eats-raw-meat-including-brains-testicles-day.html">ripped torso</a>. </p>
<p>Humans are omnivores: we can digest raw meat and thrive. The Inuit, among others living in frozen latitudes, <a href="https://www.nationalgeographic.org/photo/blubber-inuitgirl-743-60352/">eat raw meat</a> from seals, caribou, elk or whale. Uncooked cuts from <a href="https://www.atlasobscura.com/foods/basashi-horse-meat">horses</a>, <a href="https://www.tasteatlas.com/torisashi">chickens</a> and goats are presented as small delicacies on tables from Europe to Japan. While some <a href="https://www.news.com.au/lifestyle/food/eat/bodybuilder-brian-johnson-swears-by-gross-raw-meat-diet/news-story/5e0c53e1c83a7931db08537f95d02754#:%7E:text=Bodybuilder%20Brian%20Johnson%20swears%20by%20a%20diet%20of%20raw%20liver,meals%20with%20thousands%20of%20followers.&text=A%20man%20who%20swears%20by,and%20bone%20marrow%20every%20day.">bodybuilders promote raw meat</a> and offal diets (carefully selected). </p>
<p>Raw meat has also been used as medicine. In the late 19th century, French doctors suggested it as a <a href="https://www.scientificamerican.com/article/meat-pills-fight-tuberculosis/">treatment for tuberculosis</a>. It seemed successful, sometimes. But the researchers described two problems. First, obtaining clean raw meat was difficult. Second, their patients disliked their daily dose of half a pound of raw meat. Treatments were adjusted to using the meat juice instead. This “zomotherapy” was more popular and, they said, less likely to cause tapeworm infections. </p>
<p>Raw liver therapy for pernicious anaemia <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2376267/">was investigated by George Minot and William Murphy</a>. They received the Nobel prize in 1934 for this pioneering work that paved the way to isolating vitamin B12. B12 is stored in a herbivore’s liver and damaged by cooking. These early studies all showed that raw meat came with some dangers from infection and infestation. </p>
<figure class="align-center ">
<img alt="Inuit elders eating muktuk (raw whale skin and blubber)." src="https://images.theconversation.com/files/454219/original/file-20220324-15-1vqbj48.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/454219/original/file-20220324-15-1vqbj48.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=410&fit=crop&dpr=1 600w, https://images.theconversation.com/files/454219/original/file-20220324-15-1vqbj48.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=410&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/454219/original/file-20220324-15-1vqbj48.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=410&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/454219/original/file-20220324-15-1vqbj48.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=515&fit=crop&dpr=1 754w, https://images.theconversation.com/files/454219/original/file-20220324-15-1vqbj48.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=515&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/454219/original/file-20220324-15-1vqbj48.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=515&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Inuit elders eating muktuk (raw whale skin and blubber).</span>
<span class="attribution"><a class="source" href="https://commons.wikimedia.org/w/index.php?curid=787741">Ansgar Walk/Wikimedia Commons</a>, <a class="license" href="http://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a></span>
</figcaption>
</figure>
<h2>Microbial hazards</h2>
<p>The animals we eat share this planet with us. We are all surrounded by an amazing diversity of uncountable microbes, some of which may be shared at mealtimes. A tempting piece of raw meat, therefore, requires elaborate checking. Has it any prions, viruses, bacteria, fungi or parasites? </p>
<p>Although many of these critters are harmless, some are quite lethal unless treated. Some, such as prion-linked brain diseases, <a href="https://pubmed.ncbi.nlm.nih.gov/24956437/">cannot be treated</a>. And some will treat us as <em>their</em> food. If that steak is venison from your recent hunt, its pathogens will be different compared to a farm-reared steer. </p>
<p>The bacteria <em>Escherichia coli</em>, for example, were thought harmless when described in 1885. Up to 50% of healthy cattle may carry <em>E. coli 0157</em>. These are resistant to our stomach acid; their Shiga toxins can cause <a href="https://www.nhsinform.scot/illnesses-and-conditions/infections-and-poisoning/escherichia-coli-e-coli-o157">kidney failure, shock and death</a>.</p>
<p>Listeria is named after Joseph Lister, the father of surgical sterilisation. It is a skilled soil organism that can multiply on a steak in your fridge, then infect your bloodstream and brain, or cross a placenta resulting in miscarriage and foetal death.</p>
<p>Beef can be contaminated with <em>Toxoplasmosis gondii</em>, a protozoal parasite from cats that happily survives in cattle and humans. <a href="https://theconversation.com/toxoplasma-cat-poo-parasite-infects-billions-so-why-is-it-so-hard-to-study-120688">Toxoplasmosis</a> tends to find its way into the brain, retina, heart muscle or cross the placenta, where it can damage the foetal brain. Some of these effects may take years to become evident; you would probably not notice anything after that raw lunch.</p>
<p>Although there are no proven advantages to eating raw meat, there are great microbial hazards. (Feeding your pets raw meat has <a href="https://theconversation.com/should-you-feed-your-pet-raw-meat-the-real-risks-of-a-traditional-dog-diet-90271">similar risks</a>.) Not only is there a risk of being infected with <em>Campylobacters</em> and <em>Salmonellas</em>, but also parasites such as roundworms and tapeworms.</p>
<p>The passion – in some quarters – for returning to a habit of consuming raw meat should be checked against the facts of “<a href="https://theconversation.com/one-health-a-crucial-approach-to-preventing-and-preparing-for-future-pandemics-173637">one health</a>” – that is, taking into consideration the combined health of people, animals and our environments. We are not alone. Many, many microbes, usually checked by safe food management and cooking, would just love us to take up a wolverine lifestyle.</p><img src="https://counter.theconversation.com/content/179590/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Colin Michie does not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Some ‘influencers’ are pushing a raw-meat diet. Here’s why you should avoid it.Colin Michie, Deputy Lead, School of Medicine, University of Central LancashireLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1708562021-12-01T13:35:43Z2021-12-01T13:35:43ZCharting changes in a pathogen’s genome yields clues about its past and hints about its future<figure><img src="https://images.theconversation.com/files/434799/original/file-20211130-14-gx51zb.jpg?ixlib=rb-1.1.0&rect=50%2C100%2C6176%2C4134&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A virus's genes hold a record of where it's traveled, and when.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/global-pandemic-infographic-royalty-free-image/1270842570">imaginima/E+ via Getty Images</a></span></figcaption></figure><p>More than <a href="https://ourworldindata.org/covid-cases?country=%7EOWID_WRL">250 million people worldwide</a> have tested positive for SARS-CoV-2, usually after a diagnostic nose swab. Those swabs aren’t trash once they’ve delivered their positive result, though. For <a href="https://scholar.google.com/citations?user=L7pQoysAAAAJ&hl=en&oi=ao">scientists</a> <a href="https://scholar.google.com/citations?user=aDRW1JMAAAAJ&hl=en&oi=ao">like</a> <a href="https://scholar.google.com/citations?user=9hWmfYoAAAAJ&hl=en&oi=ao">us</a> they carry additional valuable information about the coronavirus. Leftover material from swabs can help us uncover hidden aspects of the COVID-19 pandemic.</p>
<p>Using what are called phylodynamic methods that can track a pathogen’s travels via changes in its genes, researchers are able to pinpoint factors like <a href="https://doi.org/10.1073/pnas.2012008118">where and when outbreaks start</a>, the <a href="https://doi.org/10.1038/s43856-021-00031-1">number of undetected infections</a> and <a href="https://doi.org/10.1038/s41467-020-19346-z">common routes of transmission</a>. Phylodynamics can also aid in understanding and tracking the spread of new pathogen variants, such as the recently detected <a href="https://twitter.com/trvrb/status/1464353224417325066">omicron variant of SARS-CoV-2</a>.</p>
<h2>What’s in a swab?</h2>
<p>Pathogens, just like people, each have a genome. This is RNA or DNA that contains an organism’s genetic code – its instructions for life and the information necessary for reproduction. </p>
<p>It’s now relatively <a href="https://www.nature.com/articles/d42859-020-00103-7">fast</a> and <a href="https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data">cheap</a> to sequence a pathogen’s genome. In Switzerland, <a href="https://bsse.ethz.ch/cevo/research/sars-cov-2/swiss-sars-cov-2-sequencing-consortium.html">a consortium of government and academic scientists</a> that we’re a part of as already extracted viral genome sequences from <a href="https://cov-spectrum.ethz.ch/explore/Switzerland/AllSamples/AllTimes">almost 80,000 SARS-CoV-2 positive swab tests</a>.</p>
<p>By lining up genetic sequences obtained from different patients, scientists can see which positions in the sequence differ. These differences represent mutations, small errors incorporated into the genome when the pathogen copies itself. We can use these mutational differences as clues to reconstruct chains of transmission and learn about epidemic dynamics along the way. </p>
<h2>Phylodynamics: Piecing together genetic clues</h2>
<p><a href="https://doi.org/10.1126/science.1090727">Phylodynamic methods</a> provide a way to describe how mutational differences relate to epidemic dynamics. These approaches allow researchers to get from the raw data about where mutations have occurred in the viral or bacterial genome to understanding all the implications. It might sound complicated, but it’s actually pretty easy to give an intuitive idea of how it works. </p>
<p>Mutations in the pathogen genome get passed from person to person in a transmission chain. Many pathogens acquire lots of <a href="https://doi.org/10.1016/S0169-5347(03)00216-7">mutations over the course of an epidemic</a>. Scientists can summarize these mutational similarities and differences using what’s essentially a family tree for the pathogen. Biologists call it <a href="https://docs.nextstrain.org/en/latest/learn/interpret/how-to-read-a-tree.html">a phylogenetic tree</a>. Each branching point represents a transmission event, when the pathogen moved from one person to another.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/434467/original/file-20211129-19-1niweey.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="diagram of sample to sequence to tree" src="https://images.theconversation.com/files/434467/original/file-20211129-19-1niweey.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/434467/original/file-20211129-19-1niweey.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=225&fit=crop&dpr=1 600w, https://images.theconversation.com/files/434467/original/file-20211129-19-1niweey.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=225&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/434467/original/file-20211129-19-1niweey.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=225&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/434467/original/file-20211129-19-1niweey.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=283&fit=crop&dpr=1 754w, https://images.theconversation.com/files/434467/original/file-20211129-19-1niweey.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=283&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/434467/original/file-20211129-19-1niweey.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=283&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">A phylogenetic tree is an approximation of the past transmission chain, based on variations in the pathogen’s genetic sequence.</span>
<span class="attribution"><span class="source">Guinat, Windels, Nadeau</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>The branch lengths are proportional to the number of differences between sequenced samples. Short branches mean little time between branching points – fast transmission from person to person. Studying the length of branches on this tree can tell us about pathogen spread in the past – maybe even before we knew an epidemic was on the horizon.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/434470/original/file-20211129-15-rzms02.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="diagram of hypothetical virus outbreak's phylogenetic tree" src="https://images.theconversation.com/files/434470/original/file-20211129-15-rzms02.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/434470/original/file-20211129-15-rzms02.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=254&fit=crop&dpr=1 600w, https://images.theconversation.com/files/434470/original/file-20211129-15-rzms02.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=254&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/434470/original/file-20211129-15-rzms02.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=254&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/434470/original/file-20211129-15-rzms02.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=319&fit=crop&dpr=1 754w, https://images.theconversation.com/files/434470/original/file-20211129-15-rzms02.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=319&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/434470/original/file-20211129-15-rzms02.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=319&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Pathogen genome sequences can be used to construct phylogenetic trees and estimate hidden epidemic dynamics. Shorter branches stand for quicker transmission.</span>
<span class="attribution"><span class="source">Guinat, Windels, Nadeau</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Mathematical models of disease dynamics</h2>
<p>Models in general are simplifications of reality. They try to describe core real-life processes with mathematical equations. In phylodynamics, these equations describe the relationship between epidemic processes and the phylogenetic tree. </p>
<p>Take, for example, tuberculosis. It’s the <a href="https://www.who.int/publications/i/item/9789240037021">deadliest bacterial infection in the world</a>, and it is getting even more threatening because of the widespread evolution of antibiotic resistance. If you catch an antibiotic-resistant version of the tuberculosis bacterium, <a href="https://doi.org/10.1186/s40249-016-0214-x">treatment can take years</a>.</p>
<p>To predict the future burden of resistant tuberculosis, we want to estimate how fast it spreads.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/434837/original/file-20211130-14-kaj3am.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="diagram of epidemiological processes in transmission of TB" src="https://images.theconversation.com/files/434837/original/file-20211130-14-kaj3am.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/434837/original/file-20211130-14-kaj3am.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=432&fit=crop&dpr=1 600w, https://images.theconversation.com/files/434837/original/file-20211130-14-kaj3am.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=432&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/434837/original/file-20211130-14-kaj3am.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=432&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/434837/original/file-20211130-14-kaj3am.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=543&fit=crop&dpr=1 754w, https://images.theconversation.com/files/434837/original/file-20211130-14-kaj3am.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=543&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/434837/original/file-20211130-14-kaj3am.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=543&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Epidemiologists work to track infections as the pathogen moves through a population.</span>
<span class="attribution"><span class="source">Guinat, Windels, Nadeau</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>To do this, we need a model that captures two important processes. First, there’s the course of infection, and second, there’s the development of antibiotic resistance. In real life, infected people can infect others, get treatment and, in the end, either be cured or, in the worst case, die from the infection. On top of this, the pathogen can develop resistance.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/434480/original/file-20211129-27-e5whvt.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="diagram of information fed into mathematical model" src="https://images.theconversation.com/files/434480/original/file-20211129-27-e5whvt.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/434480/original/file-20211129-27-e5whvt.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=282&fit=crop&dpr=1 600w, https://images.theconversation.com/files/434480/original/file-20211129-27-e5whvt.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=282&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/434480/original/file-20211129-27-e5whvt.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=282&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/434480/original/file-20211129-27-e5whvt.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=354&fit=crop&dpr=1 754w, https://images.theconversation.com/files/434480/original/file-20211129-27-e5whvt.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=354&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/434480/original/file-20211129-27-e5whvt.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=354&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Phylodynamic models capture real-life epidemiological processes into mathematical equations and parameters.</span>
<span class="attribution"><span class="source">Guinat, Windels, Nadeau</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>We can translate these epidemiological processes into a mathematical model with two groups of patients – one group infected with normal tuberculosis and one with antibiotic-resistant tuberculosis. The important processes – transmission, recovery and death – can happen at different rates for each group. Finally, patients whose infection develops antibiotic resistance move from the first group to the second.</p>
<p>This model does ignore some aspects of tuberculosis outbreaks, such as asymptomatic infections or relapses after treatment. Even so, when applied to a set of tuberculosis genomes, this model helps us <a href="https://doi.org/10.1016/j.epidem.2021.100471">estimate how fast resistant tuberculosis spreads</a>. </p>
<h2>Capturing hidden aspects of epidemics</h2>
<p>Uniquely, phylodynamic approaches can help researchers answer questions in situations where diagnosed cases do not give the full picture. For example, what about the number of undetected cases or the source of a new epidemic? </p>
<p>A good example of this type of genome-based investigation is our recent work on <a href="https://ec.europa.eu/food/animals/animal-diseases/diseases-and-control-measures/avian-influenza_en#hpai-epidemic-20162017">highly pathogenic avian influenza (HPAI)</a> H5N8 in Europe. This epidemic spread to poultry farms and wild birds across <a href="https://doi.org/10.1111/tbed.12861">30 European countries</a> in 2016. In the end, <a href="https://www.bbc.com/news/world-europe-54825971">tens of millions of birds</a> were culled, devastating the poultry industry.</p>
<p>But were poultry farms or wild birds the real driver of spread? Obviously we cannot ask the birds themselves. Instead, phylodynamic modeling based on H5N8 genomes sampled from poultry farms and wild birds helped us get an answer. It turns out that in some countries the pathogen mainly spread from farm to farm, while in others it spread from wild birds to farms. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/433527/original/file-20211123-21-lof9wy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="ducks outside" src="https://images.theconversation.com/files/433527/original/file-20211123-21-lof9wy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/433527/original/file-20211123-21-lof9wy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=381&fit=crop&dpr=1 600w, https://images.theconversation.com/files/433527/original/file-20211123-21-lof9wy.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=381&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/433527/original/file-20211123-21-lof9wy.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=381&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/433527/original/file-20211123-21-lof9wy.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=479&fit=crop&dpr=1 754w, https://images.theconversation.com/files/433527/original/file-20211123-21-lof9wy.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=479&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/433527/original/file-20211123-21-lof9wy.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=479&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Phylodynamic models can estimate the number of avian influenza virus transmissions between wild birds and poultry.</span>
<span class="attribution"><span class="source">C. LeGall</span>, <a class="license" href="http://creativecommons.org/licenses/by-nc-nd/4.0/">CC BY-NC-ND</a></span>
</figcaption>
</figure>
<p>In the case of HPAI H5N8, <a href="https://doi.org/10.1101/2021.10.22.465255">we helped animal health authorities focus control efforts</a>. In some countries this meant limiting transmission between poultry farms while in others limiting contact between domestic and wild birds.</p>
<p>More recently, phylodynamic analyses helped evaluate the impact of control strategies for SARS-CoV-2, including the <a href="https://doi.org/10.1073/pnas.2012008118">first border closures</a> and <a href="https://doi.org/10.1038/s41467-020-20235-8">strict early lockdowns</a>. A big advantage of phylodynamic modeling is that it can account for undetected cases. The models can even describe early stages of the outbreak in the absence of samples from that time period. </p>
<p>Phylodynamic models are under intensive development, continuously expanding the field to new applications and larger datasets. However, there are still challenges in extending genome sequencing efforts to undersampled species and regions and upholding <a href="https://doi.org/10.1038/d41586-021-00331-5">rapid public data sharing</a>. Ultimately, these data and models will help everyone gain new insights on epidemics and how to control them.</p>
<p>[<em>The Conversation’s science, health and technology editors pick their favorite stories.</em> <a href="https://theconversation.com/us/newsletters/science-editors-picks-71/?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=science-favorite">Weekly on Wednesdays</a>.]</p><img src="https://counter.theconversation.com/content/170856/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Claire Guinat receives funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 842621.</span></em></p><p class="fine-print"><em><span>Sarah Nadeau receives funding from the Swiss National Science Foundation and ETH Zurich. </span></em></p><p class="fine-print"><em><span>Etthel Windels does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>After a nose swab tests positive for a virus or bacteria, scientists can use the sample’s genetic sequence to figure out where and when the pathogen emerged and how fast it’s changing.Claire Guinat, Postdoctoral Fellow in Computational Evolution, Swiss Federal Institute of Technology ZurichEtthel Windels, Postdoctoral Fellow in Computational Evolution, Swiss Federal Institute of Technology ZurichSarah Nadeau, PhD Student in Computational Evolution, Swiss Federal Institute of Technology ZurichLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1631972021-07-14T12:24:12Z2021-07-14T12:24:12ZWe work with dangerous pathogens in a downtown Boston biocontainment lab – here’s why you can feel safe about our research<figure><img src="https://images.theconversation.com/files/410851/original/file-20210712-70807-1iay608.JPG?ixlib=rb-1.1.0&rect=600%2C0%2C4959%2C3275&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Security precautions, thoughtful facilities design, careful training and safe lab practices help keep pathogens isolated.</span> <span class="attribution"><span class="source">Boston University Photography</span></span></figcaption></figure><p><em><a href="http://www.bumc.bu.edu/microbiology/people/faculty/ronald-b-corley-phd/">Microbiologist Ronald Corley</a> has gone to work every day throughout the pandemic as director of the <a href="https://www.bu.edu/neidl/">National Emerging Infectious Diseases Laboratories</a>. Within this secure lab facility in Boston, scientists study pathogens as diverse as tuberculosis, Ebola virus, yellow fever virus and Zika virus. Many investigators there quickly turned their attention in 2020 to SARS-CoV-2, the virus that causes COVID-19.</em></p>
<p><em>Here Corley answers some of the most frequently asked questions about this kind of biosecure lab and the work researchers do inside it.</em></p>
<h2>What is the purpose of a biocontainment facility?</h2>
<p><a href="https://doi.org/10.1016/j.cell.2020.08.021">A newly emerging or reemerging human pathogen</a> is detected somewhere around the globe <a href="http://infectiousdiseases.edc.org/">every 12 to 18 months</a>.</p>
<p>Infectious diseases don’t respect borders. Because of the global economy and unprecedented mobility, everyone on the planet is vulnerable to potentially devastating infectious diseases that may have originated halfway across the world. In this age of high-speed travel, we are as little as 36 hours away from any outbreak.</p>
<p>As with SARS-CoV-2, scientists may know little about emerging pathogens or the diseases they cause. Studying these germs – whether bacteria, viruses or other microorganisms – in the safe environment of a biocontainment laboratory is the best protection humankind has against these diseases. In the lab, researchers can safely test new diagnostics, therapeutics and vaccines. The more scientists learn about these new diseases, the better prepared we are for the ones that will come after.</p>
<p>This is where labs like the NEIDL, and our stringent safety measures, are important. I feel safer from infection working in the NEIDL than I do in my apartment building. We know what we’re working with in the lab and how to keep ourselves and others safe. But outside, I don’t know who I might pass who could have a transmissible pathogen, including the coronavirus.</p>
<p>This is not to say that there is no risk working within the laboratory – there is. But we minimize it through a series of safety measures – including building systems, laboratory design, personal protective equipment, training and safety protocols – that have been tried and tested in laboratories across the world.</p>
<h2>How do you try to minimize risk?</h2>
<p><a href="http://www.bu.edu/researchsupport/compliance/ibc/#biosafety-manual-tab">Our biosafety manual</a> sets the standards for all work with biological material in the NEIDL. Requirements increase in complexity from Biosafety Level 2 (BSL-2) on to BSL-3 and BSL-4.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=329&fit=crop&dpr=1 600w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=329&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=329&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=413&fit=crop&dpr=1 754w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=413&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=413&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Biosafety levels are defined by how much risk is involved in working with particular pathogens.</span>
<span class="attribution"><span class="source">The Conversation</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>In the U.S., the Centers for Disease Control and Prevention determines each pathogen’s biocontainment level, based on what’s known about how it infects its host, the severity of the disease it causes, how easily transmissible the pathogen may be and the nature of the work itself – does it potentially create aerosols, for example.</p>
<p>The biosafety levels require <a href="https://www.cdc.gov/cpr/infographics/biosafety.htm">different types of engineering controls</a> – such as the building materials the space uses, directional air flow to ensure pathogens can’t get out, HEPA filtration so that only sterile air is discharged from the lab space and so on.</p>
<p>The administrative controls required vary by biosafety level, as well – safety protocols, requirements for personnel training, limiting access and so forth.</p>
<p>Each level requires different types of personal protective equipment: gloves and lab coats in a BSL-2 laboratory, protective lab wear and N95 or PAPR respirators in BSL-3 or a fully encapsulating suit in a BSL-4 laboratory.</p>
<p>“Safety First” is not just a bumper-sticker phrase at the NEIDL. Everyone from public safety officers to support staff to researchers has fully bought into the culture of safety. It informs the way we’re trained and drilled, the way pathogens are transported to the facility, and policies that govern our employees. We know the risks of the work, train on protective measures, and ensure every member of our staff follows our protocols.</p>
<h2>What does containment look like with these safety strategies in place?</h2>
<p>Everyone undergoes annual background checks, medical clearances and training. Only cleared staff can enter the building alone. </p>
<p>There are limited ways into the space, one for pedestrians, and one for vehicles, like delivery trucks. Entry requires access via biometric or card access or both, and screening by security. Access controls limit staff members to entering spaces where they have permission to work, based on their training, clearances and biosafety protocols. A network of security systems and closed-circuit cameras monitors the facility.</p>
<p>Entering laboratories requires that workers don the appropriate PPE for the area. Within the labs, we know what pathogen we are working with and how it is being used and are confident staff are following the safety measures required to keep them safe. This ensures the safety of others in the building as well as the surrounding community.</p>
<p>Importantly, the biosafety practices ensure that each pathogen we’re studying is restricted to the appropriate spaces. Researchers work at biosafety cabinets that sterile-filter the air before releasing it back into the lab.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Scientist in full PPE works under the hood of a biosafety cabinet" src="https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/410845/original/file-20210712-27-1o9ypjl.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Working with pathogens only within a specially ventilated biosafety cabinet provides another layer of security.</span>
<span class="attribution"><span class="source">Boston University Photography</span></span>
</figcaption>
</figure>
<h2>What kinds of regulation and oversight are there?</h2>
<p>Biocontainment laboratories do not function in a vacuum. The building and laboratory designs, and the PPE and operating procedures that protect staff, meet the guidelines set by the CDC and by the 574-page book “<a href="https://www.cdc.gov/labs/pdf/SF__19_308133-A_BMBL6_00-BOOK-WEB-final-3.pdf">Biosafety in Microbiological and Biomedical Laboratories</a>” from the CDC and National Institutes of Health.</p>
<p>To carry out a project, the lead scientist begins with an application to the Institutional Biosafety Committee. Experts in biosafety and science review the application, as do laypersons who provide a community perspective. These deliberations are open and transparent thanks to public participation on the committee. Its <a href="https://www.bu.edu/researchsupport/compliance/ibc/about-the-ibc/ibc-meeting-minutes/">minutes are posted online</a>. Safety professionals also inspect the laboratory facilities before work gets underway. </p>
<p>In the city of Boston, projects that involve any BSL-3 or BSL-4 work require review and approval from the Boston Public Health Commission, one of the only local public health departments with this type of oversight. Work with certain types of pathogens called “<a href="https://www.selectagents.gov/sat/list.htm">select agents</a>” that pose a severe threat is further regulated by the <a href="https://www.cdc.gov/cpr/dsat/fsap.htm">Division of Select Agents and Toxins</a> within the CDC.</p>
<p>Here at the NEIDL, both city and federal officials inspect the laboratories, interviewing personnel and reviewing records, including maintenance records. They also inspect pathogen inventories. Inspections can be announced or unannounced. </p>
<h2>What would happen if something went wrong?</h2>
<p>An important aspect of safety is making sure everyone knows what to do in an emergency. Three trainings per year involve first responders from the city as well as from Boston University. These are done as either live drills or tabletop exercises with experts walking through what an emergency would look like. Afterward we review how we did and develop plans for improvement.</p>
<p>Community members are also part of the exercises, and this keeps our neighbors involved and hopefully provides assurance of our ability to handle accidents, keeping ourselves and the community safe.</p>
<p>At Boston University, we post all laboratory incidents, including those at the NEIDL, on a quarterly basis to ensure that we remain transparent in our activities. Depending on what went wrong, we may also report to the BPHC and the CDC. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="exterior of a building" src="https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=502&fit=crop&dpr=1 754w, https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=502&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/410846/original/file-20210712-27-14f8fjq.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=502&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">The safety of a facility like the NEIDL benefits from the expertise and resources available in a densely populated area.</span>
<span class="attribution"><span class="source">Boston University Photography</span></span>
</figcaption>
</figure>
<h2>Why place these high-security labs in urban environments with lots of neighbors instead of the middle of nowhere?</h2>
<p>Scientific research is a communal activity, and advances happen in places where diverse expertise is concentrated. It’s no different for research on emerging pathogens. Research on pathogens relies on faculty with expertise in not only the pathogens themselves but chemistry, engineering, stem cell biology, structural biology, immunology and more.</p>
<p>Biocontainment research also requires facilities engineers, safety professionals and security personnel. You can find personnel with diverse experience and expertise in metropolitan areas that are already home to biomedical research.</p>
<p>The original permitting process of the NEIDL mandated a <a href="https://www.bu.edu/neidl/files/2013/01/SFEIR-Volume-III.pdf">comprehensive risk assessment</a> to determine any potential danger for the community. After two years and independent review by two scientific panels, we ended up with the most extensive analysis of risk for any BSL-3 or BSL-4 facility in the U.S. It considered hundreds of possible scenarios that might result in exposure of a worker to a pathogen, or the release of a biological agent. The report concluded that it’s as safe, or even safer, to have such a facility in an urban environment than in a rural or suburban environment.</p>
<p>“Near misses” have occurred at these kinds of labs within the U.S. and Europe. A near miss might, for example, involve glove tears and a potential exposure to a pathogen during laboratory work, but these have never resulted in any community infections. At the NEIDL, we intend to maintain this track record.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="three men in full PPE gather around lab equipment" src="https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/410849/original/file-20210712-25-gcc2ln.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Scientists put their intellectual curiosity to work on problems that challenge public health.</span>
<span class="attribution"><span class="source">Boston University Photography</span></span>
</figcaption>
</figure>
<h2>What are the risks of not doing this research?</h2>
<p>Science builds on what’s been learned before, accelerating our ability to respond to new outbreaks. The data we generate speeds progress on other pathogens as well, and informs how we develop and test potential therapeutics and vaccines. The risk of not doing this work is to leave ourselves more vulnerable to emerging pathogens as they arise.</p>
<p>Professionals working on emerging infectious diseases are interested in solving problems that benefit the public’s health. We take pride in our work and are serious about our responsibility to perform our work safely and securely. We recognize that this research is often viewed skeptically and thus strive to keep the trust of the public by ensuring transparency around the work we do.</p>
<p>[<em>The Conversation’s science, health and technology editors pick their favorite stories.</em> <a href="https://theconversation.com/us/newsletters/science-editors-picks-71/?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=science-favorite">Weekly on Wednesdays</a>.]</p><img src="https://counter.theconversation.com/content/163197/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Ronald Corley receives funding from the National Institutes of Health, and the Massachusetts Consortium on Pathogen Readiness. </span></em></p>The microbiologist who directs the National Emerging Infectious Diseases Laboratories at Boston University explains all the biosafety precautions in place that help him feel safer in the lab than out.Ronald Corley, Director of the National Emerging Infectious Diseases Laboratories and Chair of Microbiology, Boston UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1624932021-06-21T12:21:04Z2021-06-21T12:21:04ZWhy gain-of-function research matters<figure><img src="https://images.theconversation.com/files/407279/original/file-20210618-12-jbsi1e.jpg?ixlib=rb-1.1.0&rect=54%2C9%2C5948%2C3956&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">In February 2021, a World Health Organization team investigating the origins of COVID-19 visited the Wuhan Institute of Virology in Wuhan, China.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/peter-daszak-thea-fischer-and-other-members-of-the-world-news-photo/1230937740">Hector Retamal/AFP via Getty Images</a></span></figcaption></figure><p><em>Due to unanswered questions into the origins of the coronavirus pandemic, both the <a href="https://www.whitehouse.gov/briefing-room/statements-releases/2021/05/26/statement-by-president-joe-biden-on-the-investigation-into-the-origins-of-covid-19/">U.S. government</a> and <a href="https://science.sciencemag.org/content/372/6543/694.1">scientists</a> have called for a deeper examination into the validity of claims that a virus could have escaped from a lab in Wuhan, China.</em></p>
<p><em>Much of the discussion surrounds “gain-of-function” research. So The Conversation asked <a href="https://scholar.google.com/citations?user=CcisQ1kAAAAJ&hl=en">David Gillum</a> and <a href="https://scholar.google.com/citations?user=YkYvOhoAAAAJ&hl=en">Rebecca Moritz</a>, who work closely with virologists on a day-to-day basis to ensure the safety and security of the research, and <a href="https://scholar.google.com/citations?user=GwJ0SvMAAAAJ&hl=en">Sam Weiss Evans</a> and <a href="https://scholar.google.com/citations?user=JtIC7noAAAAJ&hl=en">Megan Palmer</a>, who are science and technology policy experts, to explain what this term means and why this kind of research is important.</em></p>
<h2>What does gain of function mean?</h2>
<p>Any organism can acquire a new ability or property, or “gain” a “function.” This can happen through natural selection or a researcher’s experiments. In research, many different types of experiments generate functions, and some pose certain safety and security concerns. </p>
<p>Scientists use a variety of techniques to modify organisms depending on the properties of the organism itself and the end goal. Some of these methods involve directly making changes at the level of genetic code. Others may involve placing organisms in environments that select for functions linked to genetic changes. </p>
<p>Gain of function can occur in an organism in either nature or the laboratory. Some lab examples include creating more <a href="https://www.pnas.org/content/98/20/11444.short">salt- and drought-resistant plants</a> or modifying disease vectors to produce mosquitoes that are <a href="https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008103">resistant to transmitting dengue fever</a>. Gain of function can also be useful for environmental reasons, such as modifying <em>E. coli</em> so that it can <a href="https://www.washingtonpost.com/food/2021/06/15/plastic-bottles-vanilla-ecoli/">convert plastic waste into a valuable commodity</a>.</p>
<p>In the current debate around SARS-CoV-2, the virus that causes COVID-19, gain of function has a much narrower meaning related to a virus becoming easier to move between humans, or becoming more lethal in humans. It is important to remember, though, that the term “gain of function” by itself covers much more than this type of research.</p>
<h2>Why would researchers do gain-of-function work on potentially dangerous pathogens?</h2>
<p>Gain-of-function experiments may help researchers test scientific theories, develop new technologies and find treatments for infectious diseases. For example, in 2003, when the <a href="https://www.cdc.gov/about/history/sars/timeline.htm">original SARS-CoV outbreak</a> occurred, researchers developed a method to study the virus in the laboratory. One of the experiments was to <a href="https://pubmed.ncbi.nlm.nih.gov/17222058/">grow the virus in mice</a> so they could study it. This work led to a model for researching the virus and testing potential vaccines and treatments.</p>
<p>Gain-of-function research that focuses on potential pandemic pathogens has been supported on the premise that it will help researchers better understand the evolving pathogenic landscape, be better prepared for a pandemic response and develop treatments and countermeasures. </p>
<p>But critics argue that this research to anticipate potential pandemic pathogens does not lead to substantial benefit and is not worth the potential risks. And they say getting out ahead of such threats can be achieved through other means – biological research and otherwise. For instance, the current pandemic has provided numerous lessons on the social and behavioral dynamics of disease prevention measures, which could lead to robust new research programs on the cultural aspects of pandemic preparedness. Understanding when the risks of gain-of-function research outweigh the potential benefits and alternatives, therefore, continues to be subject to debate.</p>
<h2>What are some examples of gain-of-function research, and how risky is it?</h2>
<p>Some potential outcomes of gain-of-function research may include the creation of organisms that are more transmissible or more virulent than the original organism. Other examples include engineering organisms that can evade current detection methods and available treatments, or grow in another part of an organism, such as the ability to cross the blood-brain barrier. </p>
<p>There is no such thing as zero risk in conducting experiments. So the question is whether certain gain-of-function research can be performed at an acceptable level of safety and security by utilizing <a href="https://www.frontiersin.org/articles/10.3389/fbioe.2020.613253/full">risk-mitigation measures</a>. These strategies for reducing risk include the use of biocontainment facilities, exposure control plans, strict operating procedures and training, incident response planning and much more. These efforts involve dedication and meticulous attention to detail at multiple levels of an institution. </p>
<p>Lab incidents will still occur. A robust biosafety and biosecurity system, along with appropriate institutional response, helps to ensure that these incidents are inconsequential. <a href="https://science.sciencemag.org/content/367/6482/1057">The challenge</a> is to make sure that any research conducted – gain-of-function or otherwise – doesn’t pose unreasonable risks to researchers, the public and the environment. </p>
<p>Determining whether specific experiments with potential pathogens should be conducted remains a difficult and contentious topic.</p>
<h2>How do experts determine which gain-of-function research poses too much risk?</h2>
<p>There are multiple ways to answer this question. The first is if the research is intended to develop a biological weapon. The <a href="https://www.un.org/disarmament/biological-weapons/">United Nations Biological Weapons Convention</a>, which went into effect in 1975, forbids state parties from developing, producing, stockpiling, or otherwise acquiring or sharing biological agents, toxins and equipment that have no justification for peaceful or defensive purposes. There should be no research, then, whether gain-of-function or otherwise, that seeks to purposefully develop a biological weapon.</p>
<p>Another way to answer the question is by focusing on the content of the research, rather than its intent. Through experience, researchers and governments have developed lists of both experiments and organisms that need additional oversight because of their potential safety and security risks. One example of this arose when flu researchers placed a self-imposed pause on gain-of-function research involving the transmissibility of highly pathogenic avian influenza H5N1 viruses in 2012. The U.S. government subsequently <a href="https://journals.asm.org/doi/full/10.1128/mBio.00379-12">imposed a moratorium</a> on the work in 2014. Both moratoriums were lifted by the end of 2017 following a lengthy debate and study of the risks and the development of additional oversight and reporting requirements.</p>
<p>In the past decade, the United States has developed oversight for research that could be directly misused for <a href="https://osp.od.nih.gov/biotechnology/dual-use-research-of-concern/">nefarious purposes</a>. This includes policies on
“<a href="https://osp.od.nih.gov/biotechnology/dual-use-research-of-concern/">dual-use research of concern</a>” (DURC) and policies on “<a href="https://osp.od.nih.gov/biotechnology/gain-of-function-research/">pathogens of pandemic potential</a>” enhanced to gain transmissibility or virulence. </p>
<p>[<em>Over 100,000 readers rely on The Conversation’s newsletter to understand the world.</em> <a href="https://theconversation.com/us/newsletters/the-daily-3?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=100Ksignup">Sign up today</a>.]</p>
<p>The main point is that our understanding is constantly evolving. Just before the COVID-19 pandemic began, <a href="https://osp.od.nih.gov/wp-content/uploads/NSABB_January_2020_Meeting_Minutes.pdf">the U.S. government had started to review and update its policies</a>. It is an open question what lessons will be learned from this pandemic, and how that will reshape our understanding of the value of gain-of-function research. One thing that is likely to happen, though, is that we will rethink the assumptions we have been making about the relationships between biological research, security and society. This may be an opportunity to <a href="https://science.sciencemag.org/content/368/6487/138.full">review and enhance</a> systems of biosecurity and biosafety governance.</p><img src="https://counter.theconversation.com/content/162493/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>David Gillum is the past president of the American Biological Safety Association (ABSA) International. He is a past-judge and member of the safety and security committee for the International Genetically Engineered Machine Competition.</span></em></p><p class="fine-print"><em><span>Megan J. Palmer receives funding from the Open Philanthropy Project and the Nuclear Threat Initiative. She is on the Council of the Engineering Biology Research Consortium, co-chairs a World Economic Forum Global Future Council on Synthetic Biology, is an Advisor to the International Genetically Engineered Machine Competition, is a member of a World Health Organization Working Group on the Responsible Use of Life Sciences, and is a member of the Board of Directors of Revive and Restore.</span></em></p><p class="fine-print"><em><span>Sam Weiss Evans receives funding from the Schmidt Futures Foundation. He is a member of the Engineering Biology Research Consortium’s Security Working Group, and an Advisor to the international Genetically Engineered Machines Competition. </span></em></p><p class="fine-print"><em><span>Rebecca Moritz does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>The research community is taking a closer look at the lab-leak hypothesis for the origin of COVID-19, prompting discussion about the risks and benefits of engineering viruses.David Gillum, Senior Director of Environmental Health and Safety and Chief Safety Officer, Arizona State UniversityRebecca Moritz, Biosafety Director and Responsible Official, Colorado State UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1617212021-06-10T12:36:13Z2021-06-10T12:36:13ZWorking with dangerous viruses sounds like trouble – but here’s what scientists learn from studying pathogens in secure labs<figure><img src="https://images.theconversation.com/files/405550/original/file-20210610-23-dvc6ay.jpg?ixlib=rb-1.1.0&rect=105%2C0%2C6285%2C3592&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Microbes are everywhere – and they aren't all friendly.
</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/bacterium-closeup-royalty-free-image/1203775802">spawns/E+ via Getty Images</a></span></figcaption></figure><p>There are about <a href="https://www.nature.com/articles/nrmicro2644">1,400 known human pathogens</a> – viruses, bacteria, fungi, protozoa and helminths that can cause a person’s injury or death. But in a world with <a href="https://doi.org/10.1073/pnas.1521291113">a trillion individual species of microorganisms</a>, where scientists have counted only <a href="https://aeon.co/ideas/there-are-more-microbial-species-on-earth-than-stars-in-the-sky">one one-thousandth of one percent</a>, how likely is it researchers have <a href="https://doi.org/10.1038/nmicrobiol.2016.48">discovered and characterized</a> everything that might threaten people?</p>
<p>Not very likely at all. And there’s a lot to be gained from knowing these microscopic enemies better. </p>
<p>So even though in day-to-day life it makes sense to avoid these dangerous microorganisms, scientists <a href="https://scholar.google.com/citations?view_op=list_works&hl=en&user=ZvAUt2kAAAAJ">like me</a> are motivated to study them up close and personal to learn how they work. Of course, we want to do it in as safe a way as possible.</p>
<p>I’ve worked in biocontainment laboratories and have published scientific articles on both bacteria and viruses, including influenza <a href="https://doi.org/10.3389/fgene.2020.612571">and the SARS-CoV-2 coronavirus</a>. Here at Oklahoma State University, 10 research groups are currently studying pathogens in biosecure labs. They’re identifying genetic variations of viruses and bacteria, studying how they operate within cells of their hosts. Some are untangling how the host immune system responds to these invaders and is affected by so-called comorbidities of obesity, diabetes or advanced age. Others are investigating how to detect and eliminate pathogens.</p>
<p>This kind of research, to understand how pathogens cause harm, is crucial to human and veterinary medicine, as well as the health of mammals, birds, fish, plants, insects and other species around the globe.</p>
<h2>Forewarned is forearmed</h2>
<p>Think about all scientists have learned in the past century about how to prevent diseases based on understanding which microorganism is responsible, where it is in the environment and how it overcomes humans’ natural defenses.</p>
<p>Understanding what these organisms do, how they do it, and how they spread helps researchers develop measures to detect, mitigate and control their expansion. The goal is to be able to cure or prevent the disease they cause. The more dangerous the pathogen, the more urgently scientists need to understand it.</p>
<p>This is where lab research comes in. </p>
<p>Scientists have basic questions about how a pathogen conducts itself. What machinery does it use to enter a host cell and replicate? What genes does it activate, to make which proteins? This kind of information can be used to pinpoint strategies to eliminate the pathogen or lead to disease treatments or vaccines.</p>
<p>As the library of what is known about pathogens grows, there’s more chance researchers can apply some of that knowledge when faced with an emerging pathogen.</p>
<p>People might encounter new pathogens as they move into different parts of the world, or alter ecosystems. Sometimes a pathogen adapts to a new vector – meaning it can be carried by a different organism – allowing it to spread into new areas and infect new populations. <a href="https://doi.org/10.1098/rstb.2001.0888">Roughly 70% of emerging infectious diseases</a> around the world are transmitted through animals to people; these are called zoonotic diseases. It is critical to understand how these pathways work in order to have even a modest ability to predict what could happen.</p>
<p>While there are patterns in nature that can provide clues, the tremendous diversity of the microbial world and the rate at which these organisms evolve new strategies for their own defense and survival makes it imperative to study and understand each one as it’s discovered.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/405532/original/file-20210610-14622-yakcdd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="seated researcher in PPE seen from behind in lab" src="https://images.theconversation.com/files/405532/original/file-20210610-14622-yakcdd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/405532/original/file-20210610-14622-yakcdd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/405532/original/file-20210610-14622-yakcdd.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/405532/original/file-20210610-14622-yakcdd.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/405532/original/file-20210610-14622-yakcdd.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/405532/original/file-20210610-14622-yakcdd.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/405532/original/file-20210610-14622-yakcdd.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">A scientist wearing personal protective gear works with coronavirus within a biosafety cabinet.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/scientists-wearing-ppe-carry-out-tests-in-a-bio-safety-news-photo/1266591090?adppopup=true">Pallava Bagla/Corbis News via Getty Images</a></span>
</figcaption>
</figure>
<h2>Can this research be done safely?</h2>
<p>There is no such thing as zero risk in any endeavor, but over many years, researchers have developed safe laboratory methods for working with dangerous pathogens.</p>
<p>Each study must document in advance what is to be done, how, where and by whom. These descriptions are reviewed by independent committees to make sure the plans outline the safest way to do the work. There’s independent follow-up by trained professionals within the institution and, in some cases, by the U.S. Centers for Disease Control and Prevention, the U.S. Department of Agriculture, or both, to ensure researchers are following the approved procedures and regulations.</p>
<p>Those who work with dangerous pathogens <a href="https://doi.org/10.3389/fbioe.2020.00650">adhere to two</a> <a href="https://www.who.int/influenza/pip/BiosecurityandBiosafety_EN_20Mar2018.pdf">sets of principles</a>. There’s biosafety, which refers to containment. It includes all the engineering controls that keep the scientists and their surroundings safe: enclosed, ventilated workspaces called biosafety cabinets, directional airflows and anterooms to control air movement inside the lab. Special high-efficiency particulate air filters (HEPA) clean the air moving in and out of the laboratory.</p>
<p>We stick to good laboratory work practices, and everyone suits up in personal protective equipment including gowns, masks and gloves. Sometimes we use special respirators to filter the air we breathe while in the lab. Additionally we often inactivate the pathogen we’re studying – essentially taking it apart so it is not functional – and work on the pieces one or a few at a time.</p>
<p>Then there’s biosecurity, meaning the measures designed to prevent loss, theft, release or misuse of a pathogen. They include access controls, inventory controls and certified methods for decontaminating and disposing of waste. Part of these security measures is keeping the details close.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=329&fit=crop&dpr=1 600w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=329&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=329&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=413&fit=crop&dpr=1 754w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=413&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/341976/original/file-20200615-65961-1md20md.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=413&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Biosafety levels are defined by how much risk is involved in working with particular pathogens.</span>
<span class="attribution"><span class="source">The Conversation</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>The research community recognizes <a href="https://www.who.int/csr/resources/publications/biosafety/Biosafety7.pdf">four levels of biosafety practices</a>. Biosafety level-1 (BSL-1) and BSL-2 are applied to general laboratory spaces where there is low to no risk. They would not work with microorganisms that pose a serious threat to people or animals.</p>
<p>BSL-3 refers to laboratories where there is high individual risk but low community risk, meaning there is a pathogen that can cause serious human disease but treatments are available. This is the kind of work my colleagues and I, and many medical and veterinary schools, will do.</p>
<p>BSL-4 refers to work with pathogens that pose a high risk of significant disease in people, animals or both that is transmitted among individuals and for which an effective treatment may not be available. BSL-4 laboratories are relatively rare, by one estimate <a href="https://en.wikipedia.org/wiki/Biosafety_level">only about 50 exist in the world</a>.</p>
<p>At each level the increased risk requires increasingly stringent precautions to keep workers safe and prevent any accidental or malicious misuse.</p>
<p>[<em><a href="https://theconversation.com/us/newsletters/science-editors-picks-71/?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=science-corona-important">The Conversation’s most important coronavirus headlines, weekly in a science newsletter</a></em>]</p>
<h2>What’s at risk if science ignores these microbes?</h2>
<p>In recent years, the world has seen <a href="https://doi.org/10.1111/1556-4029.14034">outbreaks of severe disease</a> caused by several types of pathogens. Even for the pathogens scientists do know about, much remains unknown. It is reasonable to expect there are more threats out there yet to be discovered.</p>
<p>It is critical for scientists to study new disease pathogens in the lab as they’re discovered and to understand how they move from host to host and are affected by conditions; what variations develop over time; and what effective control measures can be developed. In addition to more well-known viruses such as rabies, West Nile virus and Ebola, there are <a href="https://doi.org/10.1016/j.tmaid.2019.101471">several critically important pathogens</a> circulating in the world today that pose a serious threat. <a href="https://doi.org/10.1016/j.onehlt.2017.12.002">Hantaviruses</a>, <a href="https://doi.org/10.1038/nrmicro2460">dengue</a>, <a href="http://dx.doi.org/10.2471/BLT.16.171082">Zika virus</a> and the <a href="https://doi.org/10.1080/01652176.2019.1580827">Nipah virus</a> are all under investigation in various labs, where researchers are working to understand more about how they’re transmitted, develop rapid diagnostics and produce vaccines and therapeutics.</p>
<p>Microorganisms are the most abundant form of life on the planet and extremely important to human health and the health of plants and animals. In general, people have adapted to their presence, and vice versa. For those microbes with the capacity to do real harm, it makes sense to study as many as scientists can now, before the next pandemic hits.</p>
<p><em>This article has been updated to clarify the kinds of pathogens studied in BSL-3 laboratories.</em></p><img src="https://counter.theconversation.com/content/161721/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jerry Malayer does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Scientists get up close and personal with deadly pathogens to give doctors the tools they need to treat people sickened by germs. The key is keeping the researchers – and everyone around them – safe.Jerry Malayer, Associate Dean for Research and Graduate Education and Professor of Physiological Sciences in the College of Veterinary Medicine, Oklahoma State UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1614002021-05-26T12:10:27Z2021-05-26T12:10:27ZThink like a virus to understand why the pandemic isn’t over yet – and what the US needs to do to help other countries<figure><img src="https://images.theconversation.com/files/402700/original/file-20210525-23-1w8zh3.jpg?ixlib=rb-1.1.0&rect=36%2C0%2C2662%2C1768&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">To stop the spread of COVID-19 across the globe, it's important to understand the evolutionary imperative that viruses have to spread their genetic material.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/business-man-holding-global-bomb-royalty-free-image/97542406?adppopup=true">Dazeley/Getty Images</a></span></figcaption></figure><p>Kill every human on the planet.</p>
<p>This is the first assignment I give students in my public health classes, filled with do-gooders passionate about saving the world. Their homework is to <a href="https://www.ndemiccreations.com/en/22-plague-inc">play a game called Plague</a>, in which they pretend to be pathogens bent on infecting everyone on the globe before humans can develop a cure or a vaccine.</p>
<p>Why this assignment? Because as a <a href="https://deohs.washington.edu/faculty/karen-levy">professor of infectious disease epidemiology</a>, I aim to teach students to think like pathogens so they can learn how to control them.</p>
<p>With COVID-19, thinking like a pathogen leads to an inevitable conclusion: Getting the vaccine out to everyone in the world as quickly as possible is not just an ethical imperative, but also a selfish one. </p>
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<iframe width="440" height="260" src="https://www.youtube.com/embed/WOVJ9XgYvac?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Viruses use their hosts to replicate their genetic material.</span></figcaption>
</figure>
<h2>Passing on genetic material a key goal</h2>
<p>While many <a href="https://www.theguardian.com/commentisfree/2021/mar/17/rich-countries-hoarding-vaccines-us-eu-africa">wealthy countries</a> soon will offer vaccines to their entire populations, people in <a href="https://www.vox.com/2021/4/28/22405279/covid-19-vaccine-india-covax">poorer countries</a> might have to wait years for their shots. About half of U.S. residents are now at least <a href="https://covid.cdc.gov/covid-data-tracker/#vaccinations">partially vaccinated</a>. Many other countries have yet to reach 1% <a href="https://www.nytimes.com/interactive/2021/world/covid-vaccinations-tracker.html">vaccination coverage</a>. </p>
<p>In the interim, SARS-CoV-2 will take advantage of this opening.</p>
<p>In reality, pathogens don’t actually want to kill all of their human hosts, because they would eventually have nowhere to live. Their goal is to pass on their genetic material to the next generation. They will do what they can to answer their evolutionary call. </p>
<h2>A virus to-do list</h2>
<p>Of course, viruses and bacteria don’t have brains so they don’t “think,” per se. But like all life forms, these particular living creatures are trying to <a href="https://theconversation.com/how-worried-should-you-be-about-coronavirus-variants-a-virologist-explains-his-concerns-158360">maximize their chances of reproducing</a> and having their offspring survive and reproduce.</p>
<p>As a single virus particle, you have two key items on the to-do list. First, you need a place to propagate. You need to reproduce yourself in large numbers, to increase the chances that one of your kids will do the right thing and provide you with some grandchildren. As a virus you are very good at this bit. No need to visit Tinder and find the perfect match, as you reproduce asexually. Instead you use the <a href="https://theconversation.com/coronavirus-variants-viral-mutation-and-covid-19-vaccines-the-science-you-need-to-understand-153771">cellular machinery of your host</a> – the human you infect – to reproduce yourself. </p>
<p>Second, you need a way to get from your current host to the next host that you will infect, otherwise known as transmission. For that you need both a portal of exit – the way to get out of your current host – and a portal of entry – the way to get into your next host. <a href="https://doi.org/10.1016/B978-0-12-811257-1.00005-X">You need a susceptible host.</a> And you need a way to travel to your next host. </p>
<p>Susceptible hosts? That was easy for SARS-CoV-2 when it first came on the scene. Because it was a novel pathogen, the entire global population was susceptible. No humans had full immunity to this particular virus from previous exposure, because it didn’t exist in human populations before 2019. Now, with each person who gets exposed or vaccinated, the number of susceptible hosts dwindles.</p>
<p>For a <a href="https://www.cdc.gov/csels/dsepd/ss1978/lesson1/section10.html">portal of exit</a>, SARS-CoV-2 has a few options – mostly exhalation through breathing, but also through pooping and expelling other bodily fluids. For a portal of entry it has inhalation – the new host breathes it in – and to a lesser extent ingestion – the new host consumes it orally. </p>
<p>This means that transmission of this virus is relatively easy, involving an activity that people of all ages do all day: breathing. Other viruses require more specific activities or conditions, such as sexual intercourse or needle-sharing for HIV, or being bitten by a particular species of mosquito for Zika.</p>
<figure class="align-center ">
<img alt="A woman inserting a swab into her mouth." src="https://images.theconversation.com/files/402704/original/file-20210525-15-1nv9ilr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/402704/original/file-20210525-15-1nv9ilr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=381&fit=crop&dpr=1 600w, https://images.theconversation.com/files/402704/original/file-20210525-15-1nv9ilr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=381&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/402704/original/file-20210525-15-1nv9ilr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=381&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/402704/original/file-20210525-15-1nv9ilr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=479&fit=crop&dpr=1 754w, https://images.theconversation.com/files/402704/original/file-20210525-15-1nv9ilr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=479&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/402704/original/file-20210525-15-1nv9ilr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=479&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">A woman at a testing site for asymptomatic COVID-19 in Portsmouth, England, on Feb. 22, 2021.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/woman-takes-the-lateral-flow-test-on-february-22-2021-in-news-photo/1303479211?adppopup=true">Finnbarr Webster/Getty Images</a></span>
</figcaption>
</figure>
<h2>SARS-CoV-2 is one smart virus</h2>
<p>SARS-CoV-2 has had a lot of things playing in its favor, aside from having a global population naïve to it. Several other characteristics make it particularly successful.</p>
<p>First, while it does kill, it can also cause mild or <a href="https://doi.org/10.1001/jamanetworkopen.2020.35057">asymptomatic infections</a> in others. When pathogens kill most of their hosts, they are not so successful in spreading, because humans change their behavior in response to the perceived threat of the disease. </p>
<p><a href="https://www.who.int/news-room/fact-sheets/detail/ebola-virus-disease">Ebola </a>is a perfect example. College students would have been more likely to cancel their spring break plans to Florida in 2020 if they had expected that it might cause them to bleed out of their eyeballs, as happens in some people infected with the Ebola virus.</p>
<p>SARS-CoV-2 also has a long incubation period – the time between its infection of a new host and the start of the host’s symptoms. Yet it can be transmitted during the time before symptoms occur, which allows it to spread unnoticed.</p>
<figure class="align-center ">
<img alt="Grieving women hugging one another." src="https://images.theconversation.com/files/402717/original/file-20210525-17-be12p4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/402717/original/file-20210525-17-be12p4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=415&fit=crop&dpr=1 600w, https://images.theconversation.com/files/402717/original/file-20210525-17-be12p4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=415&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/402717/original/file-20210525-17-be12p4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=415&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/402717/original/file-20210525-17-be12p4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=522&fit=crop&dpr=1 754w, https://images.theconversation.com/files/402717/original/file-20210525-17-be12p4.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=522&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/402717/original/file-20210525-17-be12p4.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=522&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Family members of a COVID-19 victim mourn as they wait outside Maulana Azad Medical College mortuary to collect the body on May 24, 2021, in New Delhi, India.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/family-members-of-a-covid-victim-mourn-as-they-wait-outside-news-photo/1233097413?adppopup=true">Sanjeev Verma/Hindustan Times via Getty Images</a></span>
</figcaption>
</figure>
<h2>More transmission, more new variants</h2>
<p>If you’re thinking like the SARS-CoV-2 pathogen now, you’re furiously searching for a way around current vaccine formulations. The more cases you cause, the more chances you have for new variants that can break through the vaccines. You don’t care whether these cases occur in Montana or Mumbai. This is why no human is safe from the pandemic until transmission is controlled everywhere.</p>
<p>Thinking like a pathogen requires thinking over an evolutionary time scale, which for a virus is very short, sometimes the course of a single human infection. SARS-CoV-2 and other viruses have astonishing powers to adapt to changing conditions. </p>
<p>One of their survival strategies is the built-in mistakes in their reproduction machinery that cause mutations. Occasionally, a mutation occurs that improves the ability of a virus to survive and spread.</p>
<p>This leads to new <a href="https://www.cdc.gov/coronavirus/2019-ncov/variants/variant.html">variants</a>, like those we have seen emerge recently. So far, available vaccines <a href="https://www.axios.com/pfizer-biontech-astrazeneca-covid-variants-effective-28bc0355-e361-4b32-9c6c-328185a36036.html">appear effective</a> against the variants. But new variants may reduce vaccine effectiveness, or lead to a need for booster shots. The increased transmissibility of the new variants has already likely made chances of reaching <a href="https://www.nature.com/articles/d41586-021-00728-2">herd immunity</a> through vaccination out of reach.</p>
<p>We watch in horror as the <a href="https://www.reuters.com/world/india/india-posts-lowest-rise-daily-covid-19-cases-since-april-14-2021-05-25/">virus ravages India</a>, and to some it may seem like a distant threat. But every new case offers another opportunity for a new variant to emerge and spread worldwide.</p>
<figure class="align-center ">
<img alt="A woman receiving a vaccine in Ecuador." src="https://images.theconversation.com/files/402740/original/file-20210525-15-1bvbqiy.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/402740/original/file-20210525-15-1bvbqiy.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=449&fit=crop&dpr=1 600w, https://images.theconversation.com/files/402740/original/file-20210525-15-1bvbqiy.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=449&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/402740/original/file-20210525-15-1bvbqiy.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=449&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/402740/original/file-20210525-15-1bvbqiy.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=564&fit=crop&dpr=1 754w, https://images.theconversation.com/files/402740/original/file-20210525-15-1bvbqiy.jpeg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=564&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/402740/original/file-20210525-15-1bvbqiy.jpeg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=564&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Grace Macias, a fieldworker who works on the author’s projects, gets vaccinated in Quito, Ecuador, on May 23, 2021.</span>
<span class="attribution"><span class="source">Grace Macias</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>To outsmart the virus, we need shots in arms everywhere</h2>
<p>That is why global access to vaccines is not only a moral imperative but also the only way to outsmart the virus. The U.S. can do a lot right now to ensure global access to vaccines even as we step up vaccination here.</p>
<p>The U.S. has already made <a href="https://www.npr.org/sections/goatsandsoda/2021/05/19/998228372/what-is-this-covax-program-that-the-u-s-is-pouring-millions-of-vaccines-into">substantial commitments</a> to <a href="https://www.who.int/initiatives/act-accelerator/covax">COVAX</a>, a global collaboration to accelerate the development and manufacture of COVID-19 vaccines and guarantee equitable distribution.</p>
<p>The U.S. could channel additional funds now and pressure other countries to do the same. Funding <a href="https://www.vox.com/22291086/biden-covax-united-states-covid-19-vaccinations-world-g7">commitments to COVAX may be hollow</a> without a concurrent plan to quickly distribute the vaccine stockpile the U.S. has amassed as we raced to buy up the first available doses.</p>
<p>In addition to vaccination, the U.S. and other well-resourced countries can help increase the <a href="https://ourworldindata.org/coronavirus-testing">availability of testing</a> in all countries. These countries can also provide technical and logistics assistance to improve vaccine rollout efforts and work to coordinate and improve global <a href="https://www.nature.com/articles/d41586-021-00065-4">genomic surveillance</a> so new variants are quickly identified. </p>
<p>[<em>Get facts about coronavirus and the latest research.</em> <a href="https://theconversation.com/us/newsletters/the-daily-3?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=coronavirus-facts">Sign up for The Conversation’s newsletter.</a>]</p>
<p>If this all seems expensive, think of the crushing economic costs of going back into lockdown. This is no time to be cheap.</p>
<p>To avoid jeopardizing the effectiveness of the millions of shots going into arms in rich countries, we must get shots into the arms of people in all countries.</p><img src="https://counter.theconversation.com/content/161400/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Karen Levy receives funding from the National Institutes of Health and the Bill & Melinda Gates Foundation. </span></em></p>Viruses want to pass on their genetic material. Recognizing this about SARS-CoV-2 provides insight into how the world is still vulnerable to COVID-19.Karen Levy, Associate Professor of Environmental & Occupational Health Sciences, University of WashingtonLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1586322021-04-21T13:20:20Z2021-04-21T13:20:20ZResearchers unlock the secrets of fungal viruses: why it matters<figure><img src="https://images.theconversation.com/files/395660/original/file-20210419-23-gnlcsr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Fungal viruses have been important in reducing the impact of fungal diseases on chestnuts in Europe.</span> <span class="attribution"><span class="source"> Aygul Bulte/Shutterstock</span></span></figcaption></figure><p>In the past year the world has been overwhelmed with rapidly emerging, important and fascinating information regarding SARS CoV-2, the virus that causes COVID-19. The pace of learning has been astounding, not just for the general public but for virus experts.</p>
<p>There are millions of viruses out there, including many that don’t directly infect animals or humans. Some are better understood than others. Among the least studied are viruses that infect fungi. But it’s becoming increasingly important to address this gap: fungal viruses can cause <a href="https://www.jstor.org/stable/3760453?seq=1">tremendous damage</a>, for instance by hitting agricultural outputs. Researchers estimate that such viruses destroy <a href="https://pubmed.ncbi.nlm.nih.gov/31345409/">up to 30% of crop products</a>. This has huge implications for food security.</p>
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Read more:
<a href="https://theconversation.com/why-maize-is-causing-trade-tensions-between-kenya-and-its-neighbours-156797">Why maize is causing trade tensions between Kenya and its neighbours</a>
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<p>In the past few decades the technology needed to sequence and study fungal viruses has improved in leaps and bounds. This, coupled with a rising understanding among scientists that fungal viruses have very real and frequently negative consequences, hopefully means we’re at the dawn of a new era when it comes to understanding fungal viruses. </p>
<p>Until recently there were only a few types of viruses easily detected in fungi. But this has begun to change. In a <a href="https://doi.org/10.1038/s41598-021-86343-7">recent paper</a> with colleagues we used the latest RNA sequencing technology to identify a whole host of single stranded RNA viruses in the notorious plant pathogenic genus <em>Armillaria</em>. We also confirmed previous studies which had showed that species in this genus did not contain double stranded RNA viruses. Knowing this is important because the first step in managing any disease is identifying and understanding the causal agent.</p>
<p>This illustrates how technology is allowing researchers to better understand fungal viruses, and come up with ways to manage them. </p>
<h2>Varied viruses</h2>
<p>The first fungal viruses were discovered in the 1940s in <em><a href="https://www.mushroomexpert.com/agaricus_bisporus.html">Agaricus bisporus</a></em>, the most common commercially cultivated mushroom. This viral infection causes a malady known as “<a href="https://pubmed.ncbi.nlm.nih.gov/20822315/">La France disease</a>” and results in malformed fruiting bodies (mushrooms) and yield loss. </p>
<p>Certain fungal viruses, when properly understood and harnessed, can become helpful and useful. Some, for instance, make the fungi they infect less aggressive, a phenomenon called hypovirulence. One example is the hypovirus CHV1, which reduces virulence in the tree pathogen <em>Cryphonectria parasitica</em>, one of the most devastating of all plant-killing fungi. It decimated natural populations of the American chestnut tree, beginning in the early 1900s. CHV1 was first discovered in Europe in the 1960s after people noticed that European chestnut trees affected by <em>C. parasitica</em> had begun to recover. They did not suffer the same devastation that befell the American species.</p>
<p>Hypovirulent viruses have been of great interest to researchers because of their potential as biocontrol agents of fungi that cause serious plant diseases. But to work out which fungal viruses are uniformly harmful and which might be harnessed for biocontrol, scientists first have to study the viruses’ genetic makeup.</p>
<p>New DNA sequencing technologies have heightened the ease with which fungal viruses can be studied. This has led to a <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0219207">huge increase</a> in the number of fungal viruses that are being characterised. Researchers have recently used <a href="https://www.mdpi.com/2076-2607/8/11/1680">the latest technology</a> to focus on the earlier-diverging lineages of the fungal kingdom. They found that just over 20% of the microorganisms they studied contained RNA viruses. These viruses also included novel lineages not previously recorded. </p>
<p>All of this deepens our understanding of how these viruses emerge and function – which makes combating them potentially easier in future.</p>
<p>Scientists are also starting to better understand how fungal viruses move between species. Some recently discovered fungal viruses are most closely related to viruses that were thought to infect plants only. It is <a href="https://doi.org/10.1073/pnas.1714916114">speculated</a> that these viruses may have been acquired from plants in a manner similar to the way bat viruses have in some cases adapted to become human pathogens. It is also possible that fungal viruses might infect plants, although little is as yet known regarding this possibility.</p>
<h2>Much more to learn</h2>
<p>As fungal viruses are increasingly studied, the great breadth of their diversity is becoming clear. And their role in the biology of fungi will likewise become more evident. </p>
<p>I have been studying fungal viruses for decades. My PhD, completed nearly 30 years ago, focused on fungal viruses, specifically those of the common brewer’s yeast, <em>Saccharomyces cerevisiae</em>, which is used in brewing and baking. I am convinced that many new opportunities, especially associated with the biological control of plant and human diseases caused by fungi, will emerge from the study of fungal viruses.</p><img src="https://counter.theconversation.com/content/158632/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Brenda Wingfield receives research funding from the National Research Foundation and benefits indirectly from research grants from a number of industries with a focus on tree/plant health . </span></em></p>Technology is allowing scientists to better understand fungal viruses, with the aim of managing them more effectively.Brenda Wingfield, Previous Vice President of the Academy of Science of South Africa and DSI-NRF SARChI chair in Fungal Genomics, Professor in Genetics, University of Pretoria, University of PretoriaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1582862021-04-21T12:29:03Z2021-04-21T12:29:03ZEnvironmental DNA – how a tool used to detect endangered wildlife ended up helping fight the COVID-19 pandemic<figure><img src="https://images.theconversation.com/files/396160/original/file-20210420-23-1rz2nzg.JPG?ixlib=rb-1.1.0&rect=0%2C0%2C6709%2C4466&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Looking for bits of DNA at the University of Florida.</span> <span class="attribution"><span class="source">David Duffy</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p>Imagine discovering an animal species you thought had gone extinct was still living – without laying eyes on it. Such was the case with the Brazilian frog species <em>Megaelosia bocainensis</em>, whose complete disappearance in 1968 led scientists to believe it had become extinct. But through a novel genetic detection technique, <a href="https://doi.org/10.1111/mec.15594">it was rediscovered in 2020</a>. </p>
<p>Such discoveries are now possible thanks to a new approach that recovers and reads the trace amounts of DNA released into the environment by animals. It’s called environmental DNA, or eDNA – and it takes advantage of the fact that <a href="https://doi.org/10.1093/biosci/biab027">every animal sheds DNA into its environment</a> via skin, hair, scales, feces or bodily fluids as it moves through the world.</p>
<p><a href="https://scholar.google.com/citations?hl=en&user=3cQ6umoAAAAJ">As</a> <a href="https://scholar.google.com/citations?hl=en&user=LtNEh9gAAAAJ">wildlife</a> <a href="https://scholar.google.com/citations?hl=en&user=YJAXPpYAAAAJ">biologists</a> at the University of Florida’s <a href="https://www.whitney.ufl.edu/conservation--sea-turtle-hospital/">Whitney Laboratory for Marine Bioscience & Sea Turtle Hospital</a>, we <a href="https://doi.org/10.1038/s42003-021-01656-7">use eDNA to track a virus</a> responsible for a <a href="https://doi.org/10.1038/s42003-021-01656-7">sea turtle pandemic called fibropapillomatosis</a>, which <a href="https://theconversation.com/could-human-cancer-treatments-be-the-key-to-saving-sea-turtles-from-a-disfiguring-tumor-disease-98140">causes debilitating tumors</a>. We also use eDNA to detect sea turtles in the wild. </p>
<p>But in 2020, human health researchers began repurposing eDNA techniques to track the COVID-19 pandemic. This is a prime example of how research in one area – wildlife conservation – can be adapted to another area – human disease mitigation. Going forward, we believe eDNA will prove to be an essential tool for monitoring both human and animal health. </p>
<h2>From soil microbes to sea turtles</h2>
<p>Scientists in the 1980s began <a href="https://doi.org/10.1098/rstb.2013.0383">hunting for microbe DNA in soil samples</a>. Over the next 20 years, the technique was adapted for use with air and water samples, and scientists started using eDNA to <a href="https://doi.org/10.1371/journal.pone.0041781">detect larger animals</a> <a href="https://doi.org/10.1086/685882">and plants</a>. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A flowchart of how snow/ice, freshwater, soil, sand or seawater samples can be collected and analyzed for their DNA." src="https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=420&fit=crop&dpr=1 600w, https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=420&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=420&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=528&fit=crop&dpr=1 754w, https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=528&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/394859/original/file-20210413-21-g6e1rl.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=528&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Scientists now can detect DNA traces from many different environments.</span>
<span class="attribution"><span class="source">Liam Whitmore, University of Limerick</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>While the science behind eDNA techniques is complex, the actual process of collecting and testing a sample is relatively simple. Samples are filtered through very fine paper, which traps loose cells and strands of DNA. The techniques to read what DNA is present are the same as those used for tissue or blood samples, usually <a href="https://www.theguardian.com/science/2013/nov/28/meaning-technology-pcr-history-science">quantitative polymerase chain reaction</a> or <a href="https://www.theguardian.com/australia-news/2020/aug/18/what-is-genomic-sequencing-and-how-is-it-being-used-against-covid-19-in-australia">whole genome sequencing</a>. Scientists can either read all of the DNA present from every organism – or target just the DNA from species of interest. </p>
<p>Scientists now routinely use eDNA to <a href="https://doi.org/10.1371/journal.pone.0221120">detect endangered wildlife and invasive species</a>. The ability to tell whether an animal is present without ever needing to lay eyes or a lens on it is an incredible leap forward, decreasing the time, resources and human effort needed to monitor and protect vulnerable species. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A sea turtle on its back in an exam room. One of its flippers is severely deformed." src="https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/394860/original/file-20210413-21-1e4veem.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=566&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Routine imaging of a juvenile green sea turtle patient afflicted with virus-triggered fibropapillomatosis at the Florida Whitney Sea Turtle Hospital.</span>
<span class="attribution"><span class="source">Devon Rollinson-Ramia</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>However, to truly protect endangered species, it’s not just the animals that need to be monitored, but the pathogens that threaten their survival. Environmental DNA is able to monitor the parasites, fungi and <a href="https://doi.org/10.3390/v11060526">viruses that can cause disease in wildlife</a>.</p>
<h2>Tracking COVID-19</h2>
<p>While scientists originally <a href="https://doi.org/10.1128/AEM.01561-10">applied eDNA to human pathogen detection</a> over a decade ago, it wasn’t until the beginning of the current COVID-19 human pandemic that the repurposing of eDNA took off on a large scale, allowing the technology to make staggering advancements in very short order.</p>
<p>Coronavirus genomes consist not of DNA, but rather its cousin molecule, RNA. So researchers have rapidly optimized a variation of eDNA – eRNA – to detect coronavirus RNA in air and human wastewater. </p>
<p>For example, at the University of Florida Health Shands Hospital, researchers collected air samples from the hospital room of two COVID-19 patients. Using eRNA, they <a href="https://doi.org/10.1016/j.ijid.2020.09.025">successfully isolated and sequenced the virus</a>. Confirming air as a key route of transmission directly influenced public health guidelines.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="A gloved hand holds a sealed plastic bottle of murky-looking water." src="https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/395305/original/file-20210415-17-zjc5tl.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Collecting sewage samples to test for SARS-CoV-2 at Utah State University in September 2020.</span>
<span class="attribution"><span class="source">AP Photo/Rick Bowmer</span></span>
</figcaption>
</figure>
<p>When scientists apply eRNA to <a href="https://doi.org/10.1016/j.scitotenv.2020.138764">archived wastewater samples</a>, the <a href="https://doi.org/10.1101/2020.07.10.20150573">true dates of SARS-CoV-2 appearance can be detected</a>. <a href="https://doi.org/10.1016/j.watres.2020.115942">SARS-CoV-2 concentration in wastewater in Valencia, Spain</a>, peaked on March 9, 2020, but the number of clinical cases didn’t peak until the start of April 2020 because of the lag time between infection and severe clinical symptoms. </p>
<p>This sort of predictive monitoring has profound implications for health care systems, allowing time to prepare – not just for COVID-19, but for any future disease outbreaks that threaten human populations.</p>
<p>[<em>Understand new developments in science, health and technology, each week.</em> <a href="https://theconversation.com/us/newsletters/science-editors-picks-71/?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=science-understand">Subscribe to The Conversation’s science newsletter</a>.]</p>
<h2>Intersection of diseases</h2>
<p>It’s vital that human and animal diseases are studied together. <a href="https://www.rte.ie/brainstorm/2020/0702/1150996-pandemics-coronavirus-animals-birds-humans/">Sixty percent of emerging human pathogens come from animals</a> – with many of these (42%) originating in wildlife populations, including Ebola, Zika, West Nile and Marburg viruses. Alternatively, <a href="https://science.thewire.in/environment/reverse-zoonosis-when-humans-pass-diseases-on-to-animals/">people can also transmit pathogens to animals</a>.</p>
<p>SARS-CoV-2 has already infected <a href="https://apnews.com/article/animals-san-diego-health-coronavirus-pandemic-gorillas-ef6607498782226f58608d7ebfc60d1b">apes at a zoo in San Diego</a>, <a href="https://www.nationalgeographic.com/animals/article/tiger-coronavirus-covid19-positive-test-bronx-zoo">large cats at a zoo in New York</a> and <a href="https://www.theguardian.com/environment/2021/feb/18/mink-farms-a-continuing-covid-risk-to-humans-and-wildlife-warn-eu-experts">minks at farms in Europe</a> - the latter of which <a href="https://www.who.int/csr/don/03-december-2020-mink-associated-sars-cov2-denmark/en/">gave rise to new variants that could prove a new threat to people</a>.</p>
<p>Medics, veterinarians and scientists call this convergence of human, animal and environmental well-being <a href="https://www.cdc.gov/onehealth/index.html">OneHealth</a> or EcoHealth. Studying and treating human and wildlife disease together <a href="https://www.zoobiquity.com/">recognizes their commonalities</a> and often yields breakthroughs. </p>
<p>With eDNA, all pathogens can be monitored in an environment regardless of where they come from. An integrated eDNA monitoring program could cost-effectively provide advanced warning of human, livestock and wildlife diseases.</p><img src="https://counter.theconversation.com/content/158286/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Jessica Alice Farrell receives funding from the National Save The Sea Turtle Foundation, The Sea Turtle Conservancy, Florida Sea Turtle Grants Program, the Save Our Seas Foundation and the Gumbo Limbo Nature Center Inc d/b/a Friends of Gumbo Limbo (a 501c3 non-profit organization). She is affiliated with the University of Florida Whitney Laboratory for Marine Bioscience & Sea Turtle Hospital. </span></em></p><p class="fine-print"><em><span>David Duffy receives funding from the National Save The Sea Turtle Foundation, The Sea Turtle Conservancy, Florida Sea Turtle Grants Program, the Save Our Seas Foundation, the Welsh Government Sêr Cymru II and the European Union’s Horizon 2020 program. He is affiliated with the University of Florida and Wildlife Rehabilitation Ireland. </span></em></p><p class="fine-print"><em><span>Liam Whitmore is funded by a Irish Research Council Government of Ireland Postgraduate Scholarship, under project number GOIPG/2020/1056, and he is an editor at The Turtle Room (tTR) World Turtle News Blog (<a href="https://theturtleroom.org">https://theturtleroom.org</a>).</span></em></p>Technology that can identify stray bits of genetic material in the environment can help scientists monitor human and animal health.Jessica Alice Farrell, PhD Candidate in Biology, University of FloridaDavid Duffy, Assistant Professor of Wildlife Disease Genomics, University of FloridaLiam Whitmore, PhD Candidate, Department of Biological Sciences, University of LimerickLicensed as Creative Commons – attribution, no derivatives.