tag:theconversation.com,2011:/us/topics/disease-surveillance-29674/articlesDisease surveillance – The Conversation2023-09-17T12:07:36Ztag:theconversation.com,2011:article/2129552023-09-17T12:07:36Z2023-09-17T12:07:36ZWhat Canadians need to know about West Nile virus, a mosquito-borne infection that can be life-threatening<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/what-canadians-need-to-know-about-west-nile-virus-a-mosquito-borne-infection-that-can-be-life-threatening" width="100%" height="400"></iframe>
<p>During the late summer of 1999, New York City recorded an <a href="https://doi.org/10.2105%2Fajph.92.8.1218">unusual number of cases of encephalitis</a> (inflammation of the brain). At the same time, the <a href="https://www.nationalgeographic.com/science/article/west-nile-virus-the-stranger-that-came-to-stay">Bronx Zoo</a> reported a massive death of birds and mammals. </p>
<p>The human encephalitis cases might have been attributed to a flare-up of an endemic arbovirus (<a href="https://ndc.services.cdc.gov/case-definitions/arboviral-diseases-neuroinvasive-and-non-neuroinvasive-2015/">a virus transmitted by a tick or mosquito bite</a>) such as <a href="https://www.cdc.gov/sle/index.html">St. Louis encephalitis</a>, but the concurrent bird and mammal deaths suggested the human illnesses warranted further investigation. </p>
<p>Scientists eventually identified these as the first confirmed cases of West Nile virus (WNV) in North America.</p>
<h2>West Nile virus in North America</h2>
<p>WNV was first reported in a woman with a fever in Uganda in 1937. An <a href="https://doi.org/10.2214/ajr.184.3.01840957">outbreak in Israel in 1957</a> established WNV as a cause of <a href="https://doi.org/10.3201/eid0704.017416">severe meningoencephalitis</a> (inflammation of the spinal cord and brain) in elderly patients. </p>
<p>Several clusters or medium-range outbreaks were reported from Asia, Europe and Africa in the 20th century. Finally, the virus managed to cross the Atlantic and landed in North America in 1999.</p>
<figure class="align-center ">
<img alt="Round blue particles nestled in a red matrix" src="https://images.theconversation.com/files/548213/original/file-20230914-19-x6rm98.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/548213/original/file-20230914-19-x6rm98.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=454&fit=crop&dpr=1 600w, https://images.theconversation.com/files/548213/original/file-20230914-19-x6rm98.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=454&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/548213/original/file-20230914-19-x6rm98.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=454&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/548213/original/file-20230914-19-x6rm98.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=570&fit=crop&dpr=1 754w, https://images.theconversation.com/files/548213/original/file-20230914-19-x6rm98.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=570&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/548213/original/file-20230914-19-x6rm98.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=570&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">Microscopic view of West Nile virus particles in a cell.</span>
<span class="attribution"><span class="source">(NIAID)</span>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
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<p>In 1999, the <a href="https://www.cdc.gov/westnile/statsmaps/historic-data.html">case number</a> was limited to 62 in New York City, and there was concern about a huge surge in 2000. Fortunately, the case number in 2000 was 21, which is exceedingly low, but it had spread to New Jersey and Connecticut. The case number remained in a similar low range (only 66 cases) in 2001. </p>
<p>However, the virus hit hard the following year. In 2002, the case number rose to over 4,000 in the United States. The same year, <a href="https://www.canada.ca/en/public-health/services/diseases/west-nile-virus/surveillance-west-nile-virus.html">Canada experienced its first cases</a> in Ontario.</p>
<p>The U.S. has reported a <a href="https://www.cdc.gov/westnile/statsmaps/historic-data.html">cumulative total</a> of 56,569 cases and 2,773 deaths, while <a href="https://www.canada.ca/en/public-health/services/diseases/west-nile-virus/surveillance-west-nile-virus.html#a1">Canada has reported 6,683 cases</a> and about 150 deaths (I’m told by the Centre for Food-borne, Environmental & Zoonotic Infectious Diseases, Public Health Agency of Canada), with the highest number of cases observed in the U.S. in 2003 and in Canada in 2007.</p>
<p>This virus spread across the entire continent very quickly, and covered most of North America by 2005. However, it took almost 10 years for the virus to <a href="https://doi.org/10.1089/vbz.2010.0062">show up in British Columbia</a>. In Canada, most of the cases were found in the Prairie region (Alberta, Saskatchewan and Manitoba). <a href="https://www.cdc.gov/westnile/statsmaps/historic-data.html">In the U.S.</a>, Midwestern states have been most affected.</p>
<p>West Nile virus is an RNA virus, a close cousin of <a href="https://www.who.int/news-room/fact-sheets/detail/dengue-and-severe-dengue">Dengue</a>, <a href="http://www.bccdc.ca/health-info/diseases-conditions/yellow-fever">Yellow fever</a>, St. Louis encephalitis and <a href="http://www.bccdc.ca/health-info/diseases-conditions/zika-virus">Zika virus</a>, to name a few. It belongs to the family Flaviviridae. </p>
<h2>Symptoms and transmission</h2>
<p><a href="https://www.cdc.gov/westnile/symptoms/index.html">Approximately 80 per cent of people</a> exposed to WNV are asymptomatic. <a href="https://doi.org/10.14745/ccdr.v40i10a01">The incubation period</a> in humans is about a week; however, this ranges from two to 15 days after the virus enters the body.</p>
<p>Among symptomatic individuals, all of them experience fever, and many also experience headaches, body aches, a mild rash and swollen lymph glands to varying degrees. </p>
<p>Although most cases go unnoticed, the virus still has deadly potential. <a href="https://nccid.ca/debrief/west-nile-virus/">A small number of people</a> (around one per cent) experience severe symptoms, including encephalitis. However, over the years, the <a href="https://doi.org/10.1038/ncpneuro0176">number of neurological cases has been increasing</a>.</p>
<p>This virus is mostly <a href="https://www.who.int/news-room/fact-sheets/detail/west-nile-virus">transmitted via mosquito bites</a>; however, very rarely it could transmit via blood transfusion, organ or tissue transplants, from mother to unborn babies and through exposure to infected animals. </p>
<p>A number of birds, predominantly corvids such as crows, jays and magpies, act as reservoirs as well as <a href="https://www.biologyonline.com/dictionary/amplifier-host">amplifying hosts</a>. When an uninfected mosquito feeds on an infected bird and then bites a healthy human, the human becomes infected. </p>
<p>Humans are considered dead-end hosts, meaning that even if a mosquito feeds on an infected individual, that mosquito cannot transmit the virus to another individual <a href="https://www.who.int/news-room/questions-and-answers/item/dengue-and-severe-dengue">as can happen with the dengue virus</a>.</p>
<p>Once people are severely infected with West Nile virus, they <a href="https://www.cdc.gov/westnile/symptoms/index.html">acquire longer immunity</a>. Older people are usually at high risk for severe infection due to underlying health conditions. People with diabetes and uncontrolled hypertension <a href="https://www.canada.ca/en/public-health/services/diseases/west-nile-virus/risks-west-nile-virus.html">have a greater risk</a> of developing severe neurological disease from the West Nile virus. </p>
<h2>Diagnosis</h2>
<p>Patients who become ill with a fever and severe headache within a few days of a mosquito bite should visit their family physician or any health-care facility.</p>
<p>Because WNV is closely related to other pathogens, diagnosis is often challenging.
Patient signs and symptoms, history of mosquito bites and laboratory tests are all important when assessing patients for possible infection with West Nile virus.</p>
<p>The most common <a href="https://www.publichealthontario.ca/en/Laboratory-Services/Test-Information-Index/West-Nile-Virus-Serology">laboratory test</a> is to detect antibodies against WNV in the blood. However, WNV antibodies cross-react with dengue, Zika or other flaviviruses, so if this test is positive, an additional test is required to confirm the diagnosis. </p>
<p>This additional test is called the Plaque Reduction Neutralization Test or PRNT for short. It requires a live virus, so it must be done in a containment level 3 (CL3) laboratory. </p>
<p>The laboratory can also diagnose viral RNA using molecular tests, but interestingly, the virus often disappears from the blood when people exhibit symptoms. For encephalitic patients, cerebrospinal fluid can be used to detect the virus using molecular methods such as a polymerase chain reaction (PCR) test.</p>
<h2>Preventive measures</h2>
<p>There is no human vaccine for the West Nile virus. The most important preventive measure to avoid West Nile virus infection is to avoid mosquito bites. This seems simple but is often very challenging. </p>
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<img alt="Close-up view of a mosquito held with tweezers" src="https://images.theconversation.com/files/548224/original/file-20230914-17-vsdb54.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/548224/original/file-20230914-17-vsdb54.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/548224/original/file-20230914-17-vsdb54.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/548224/original/file-20230914-17-vsdb54.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/548224/original/file-20230914-17-vsdb54.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/548224/original/file-20230914-17-vsdb54.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/548224/original/file-20230914-17-vsdb54.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">
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<span class="caption">A Culex tarsalis mosquito, a species that can transmit West Nile virus to humans, and is found across Canada.</span>
<span class="attribution"><span class="source">(AP Photo/Rick Bowmer)</span></span>
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<p>People should use common sense during outdoor and indoor activities. Mosquito bites can be prevented by using bug spray, wearing protective clothing and avoiding areas that may have mosquitoes during the times when the species is most active, typically dusk and dawn. </p>
<p>A few species of mosquitoes can transmit WNV to humans. Among these, two of the most common species — the Culex pipiens and Culex tarsalis — are found across Canada, and their habitat is <a href="https://ncceh.ca/resources/evidence-reviews/impacts-canadas-changing-climate-west-nile-virus-vectors">predicted to expand with climate change</a>. Mosquitoes not only transmit WNV, but also transmit <a href="https://www.canada.ca/en/public-health/services/laboratory-biosafety-biosecurity/pathogen-safety-data-sheets-risk-assessment/california-serogroup-pathogen-safety-data-sheet.html">California serogroup viruses</a>, which cause encephalitis, as well as <a href="https://www.canada.ca/en/public-health/services/laboratory-biosafety-biosecurity/pathogen-safety-data-sheets-risk-assessment/eastern-equine-encephalitis.html">eastern equine encephalitis</a> viruses. </p>
<p>There is also no specific treatment for West Nile virus; medical management is supportive. Patients with severe symptoms often require pain control for headaches and medication and rehydration to treat nausea and vomiting. </p>
<p><a href="https://www.canada.ca/en/public-health/services/diseases/west-nile-virus/surveillance-west-nile-virus/west-nile-virus-weekly-surveillance-monitoring.html">So far in 2023</a>, only a <a href="https://www.cbc.ca/news/canada/hamilton/hamilton-west-nile-virus-2023-1.6957260">few human cases</a> have been identified in Ontario. However, a few mosquito pools in Manitoba and Ontario also tested positive, and also a few WNV-positive birds were found in Saskatchewan, Manitoba, Ontario and Québec.</p>
<p>No matter how many cases we are seeing, everyone is advised to take precautions against mosquito bites to avoid these life-threatening diseases.</p><img src="https://counter.theconversation.com/content/212955/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Muhammad Morshed 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>West Nile virus arrived in North America in 1999 and spread across the continent by 2005. Here’s what you need to know about this mosquito-borne pathogen.Muhammad Morshed, Clinical Professor, Department of Pathology and Laboratory Medicine, University of British ColumbiaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/2011622023-03-08T00:54:10Z2023-03-08T00:54:10ZFirst the floods, then the diseases – why NZ should brace for outbreaks of spillover infections from animals<figure><img src="https://images.theconversation.com/files/513839/original/file-20230306-2723-ijhs9p.jpg?ixlib=rb-1.1.0&rect=0%2C226%2C7955%2C4109&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">
</span> <span class="attribution"><span class="source">Phil Yeo/Getty Images</span></span></figcaption></figure><p>When Cyclone Gabrielle hit New Zealand in February, it left a trail of destruction across the North Island. At least 11 people died, and more than <a href="https://www.stuff.co.nz/national/politics/131249421/more-than-10000-people-displaced-in-wake-of-cyclone--where-will-we-house-them">10,000 were displaced</a>. Bridges were washed out (<a href="https://www.nzherald.co.nz/nz/cyclone-gabrielle-bailey-bridges-could-be-two-to-three-months-away-for-hawkes-bay/SDWPA5BKBJADVKDKPG2VCSEARU/">35 in the Hastings district alone</a>), roads closed and <a href="https://theconversation.com/cyclone-gabrielle-broke-vital-communication-links-when-people-needed-them-most-what-happened-and-how-do-we-fix-it-200711">communications cut</a>. </p>
<p>With potable water and wastewater systems damaged and land covered in silt, there is another consequence that may yet appear – diseases, or more specifically, <a href="https://www.who.int/news-room/fact-sheets/detail/zoonoses">zoonoses</a> that spread between animals and people. </p>
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<p>Floods and their aftermath are a time of higher risk for disease spread. While we do not have much data specific to New Zealand, due partly to the difficulty of diagnosing and reporting diseases during times of crisis, we can use information from overseas to <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3609207/">predict which diseases may flare up after floods</a>.</p>
<h2>First, the tummy bugs</h2>
<p>The first group of diseases for which we expect to see a rise in case numbers soon after floods is gastroenteritis caused by water-borne pathogens. GPs in Auckland are reporting an <a href="https://www.stuff.co.nz/national/politics/local-democracy-reporting/300812782/rise-in-cases-of-bacterial-disease-leptospirosis-could-be-linked-to-flooding">increase in cases</a> since the Auckland anniversary weekend floods. </p>
<p>Many pathogens survive in the gastrointestinal tract of animals and are released in their feces. Rain and floods facilitate their transmission by providing an environment through which they sometimes enter the food chain or water supply. </p>
<p>In 2016, Hawke’s Bay experienced a <a href="https://www.sciencedirect.com/science/article/abs/pii/S016344532030445X">campylobacteriosis outbreak</a> transmitted through the urban water supply that affected more than 6,000 people. The outbreak occurred just after heavy rain, which likely caused water contaminated with sheep feces to enter a bore. </p>
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Read more:
<a href="https://theconversation.com/floods-create-health-risks-what-to-look-out-for-and-how-to-avoid-them-181718">Floods create health risks: what to look out for and how to avoid them</a>
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<p>Salmonellosis cases are also likely to rise during summer floods, aided by <a href="https://www.ehinz.ac.nz/assets/Factsheets/Released_2022/Gastrointestinal-diseases-climate-change_2022.pdf">higher temperatures</a>. The risk is particularly high as cases in dairy cattle have been <a href="https://nzva.org.nz/news/s-bovismorbificans/">steadily increasing</a> during the past eight years. </p>
<p>Local branches of Te Whatu Ora Health New Zealand in affected areas have been proactive in communicating these risks and <a href="https://www.northlanddhb.org.nz/news-and-publications/public-health-warnings/15-feb-2023-public-health-advisory/">prevention measures</a>, including the importance of wearing protective gear during the cleanup.</p>
<h2>Then, leptospirosis</h2>
<p>About a week to a month after floods, rodent-born disease outbreaks can start to appear. </p>
<p>Floods disturb the habitat of rodents, including rats, and they can be attracted to food waste around people’s homes. This was regularly observed after floods in <a href="https://www.abc.net.au/news/2022-04-04/qld-pest-controllers-report-spike-in-rats-snakes-after-floods/100958648">Queensland last year</a> and in <a href="https://www.stuff.co.nz/national/131278164/rats-swarm-redstickered-west-auckland-neighbourhood-after-floods">Auckland earlier this year</a>. </p>
<p>In New Zealand, our main concern is the bacterial disease leptospirosis. Brown rats carry one of the variants, livestock several others, and, once the bacteria are shed in the animals’ urine, they can <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0227055">survive in water and soil for several days</a>. This ability to survive in flood water means the risk of infection is increased for all variants, including those traditionally associated with ruminants and pigs. </p>
<p>Auckland has reported an <a href="https://www.nzherald.co.nz/nz/auckland-floods-rise-in-cases-of-bacterial-disease-leptospirosis-could-be-linked-to-flooding/XMMHXNLRCBE5VMOKJPISYCONK4/">increase in leptospirosis cases in February</a>, likely linked with the floods at the end of January. Hawke’s Bay was already a <a href="https://www.mdpi.com/2076-0817/9/10/841">known leptospirosis hotspot</a> that could worsen. </p>
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<img alt="Public health advice on how to prevent catching leptospirosis from infected animals." src="https://images.theconversation.com/files/513832/original/file-20230306-2225-zztl6s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/513832/original/file-20230306-2225-zztl6s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=600&fit=crop&dpr=1 600w, https://images.theconversation.com/files/513832/original/file-20230306-2225-zztl6s.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=600&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/513832/original/file-20230306-2225-zztl6s.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=600&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/513832/original/file-20230306-2225-zztl6s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=754&fit=crop&dpr=1 754w, https://images.theconversation.com/files/513832/original/file-20230306-2225-zztl6s.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=754&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/513832/original/file-20230306-2225-zztl6s.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">
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<span class="caption">Public health advice on how to prevent catching leptospirosis from infected animals.</span>
<span class="attribution"><span class="source">Te Whatu Ora ‐ Te Matau a Māui Hawke’s Bay</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
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<p>The clinical signs of leptospirosis can vary a lot and it is important people seek medical attention when they feel unwell as it can be treated with antibiotics. People can get infected through contact with urine or a contaminated environment, via the mouth or nose or uncovered skin cuts. </p>
<p><a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2016.21.17.30211">Leptospirosis outbreaks in dogs</a> can also happen. While they are rarely a source of infection for people in New Zealand, dogs can act as sentinels. The New Zealand Veterinary Association (<a href="https://nzva.org.nz/">NZVA</a>) provides <a href="https://nzva.org.nz/flood/companion-animals/">advice to owners of companion animals</a>.</p>
<h2>Finally, the mosquitoes</h2>
<p>New Zealand is likely (at least for now) safe from the final group of diseases emerging after floods: vector-borne diseases. </p>
<p>We don’t have the disease-carrying insects or viruses known to cause outbreaks, but our Fijian neighbours and many other countries often report <a href="https://www.spc.int/updates/news/2023/02/mosquito-borne-diseases-become-climate-reality-in-warming-pacific">dengue outbreaks</a> after floods. </p>
<p>Climate change is making it easier for both the insect carriers and viruses to establish in New Zealand, so we should not <a href="https://www.ehinz.ac.nz/indicators/border-health/mosquito-borne-disease-in-new-zealand">ignore this as a potential future threat</a>.</p>
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Read more:
<a href="https://theconversation.com/how-to-mozzie-proof-your-property-after-a-flood-and-cut-your-risk-of-mosquito-borne-disease-178299">How to mozzie-proof your property after a flood and cut your risk of mosquito-borne disease</a>
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<h2>How to protect ourselves</h2>
<p>Vaccination, early detection and treatment of livestock, which act as a reservoir for many of the pathogens above, are effective ways of protecting humans. </p>
<p>Cattle can be vaccinated against three variants of bacteria causing leptospirosis and four types of <em>Salmonella</em>. But vaccination does not cover all the strains and is more difficult in the current situation when fencing has been destroyed and some communities can only access veterinary medicine by helicopter. </p>
<p>The use of personal protective equipment and good hand hygiene for any outdoor activity that involves contact with animals or flood water and soil is the best way to prevent diseases. Rodent control, including rapid disposal of food waste, is also more important than ever.</p>
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Read more:
<a href="https://theconversation.com/58-of-human-infectious-diseases-can-be-worsened-by-climate-change-we-scoured-77-000-studies-to-map-the-pathways-188256">58% of human infectious diseases can be worsened by climate change – we scoured 77,000 studies to map the pathways</a>
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<p>It is important people seek medical care rapidly, both for themselves and their animals when they are unwell. This is how they can access appropriate treatment, but also how surveillance can happen, so New Zealand starts learning its own lessons on health risks associated with floods. </p>
<p>Our cities, population structures, farming systems and wildlife species are different from overseas, so having local data is crucial. This will help during the next heavy rain and floods – and there is no doubt there will be many more.</p>
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<p><em>We would like to acknowledge the contribution by Masood Sujau.</em></p><img src="https://counter.theconversation.com/content/201162/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Emilie Vallee receives funding from The Wellcome Trust for the project CliZod - Digital Technology Development Award in Climate Sensitive Infectious Disease Modelling number 226044/Z/22/Z. She works at the Tāwharau Ora School of Veterinary Science at Massey University. </span></em></p><p class="fine-print"><em><span>Barry Borman, Deborah Read, and Masako Wada 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>Floods are often followed by waves of diseases because pathogens shed by animals can survive in flood waters for days, raising the risk of infection for humans.Emilie Vallee, Senior Lecturer in Veterinary Epidemiology, Massey UniversityBarry Borman, Professor, Massey UniversityDeborah Read, Associate professor, Massey UniversityMasako Wada, Research Officer in Veterinary Epidemiology, Massey UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1889892022-08-21T20:03:12Z2022-08-21T20:03:12ZThe latest polio cases have put the world on alert. Here’s what this means for Australia and people travelling overseas<figure><img src="https://images.theconversation.com/files/479994/original/file-20220818-459-q63sig.jpg?ixlib=rb-1.1.0&rect=1%2C1%2C997%2C664&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/covid-19-measles-ebola-vaccinated-doctor-2120184491">Shutterstock</a></span></figcaption></figure><p>Until recently, polio had only been detected in a handful of countries, thanks to global eradication efforts.</p>
<p>But this year’s polio alerts in the United States, United Kingdom and Israel are a reminder that as long as poliovirus is found anywhere, it is a potential problem everywhere. </p>
<p>That could include Australia.</p>
<p>Here’s what the latest polio cases mean for Australia – including under-vaccinated communities and people travelling internationally.</p>
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<h2>The US case</h2>
<p>In July this year, a young man in Rockland County, New York, developed paralysis and was diagnosed with polio, the <a href="https://www.statnews.com/2022/07/21/n-y-state-detects-polio-case-first-in-the-u-s-since-2013/">first US case since 2013</a>.</p>
<p>He had never been vaccinated against polio, which is not uncommon among <a href="https://forward.com/news/512089/polio-rockland-county-new-york-vaccine-orthodox-jew/">Orthodox Jewish people</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8549591/">in some countries</a>. Rockland County has the highest percentage of Orthodox Jewish people in the US. Currently, only <a href="https://health.ny.gov/diseases/communicable/polio/county_vaccination_rates.htm">about 60%</a> of children in the county are vaccinated against polio, compared with <a href="https://www.cdc.gov/nchs/fastats/immunize.htm">more than 90%</a> nationally.</p>
<p>As of August 12, poliovirus was <a href="https://www1.nyc.gov/site/doh/about/press/pr2022/nysdoh-and-nycdohm-wastewater-monitoring-finds-polio-urge-to-get-vaccinated.page">still being detected</a> in sewage in New York City and other counties in New York State, indicating the virus is still circulating in the community.</p>
<p>The reason there have been no further cases of paralysis reflects the fact that only around <a href="https://www.who.int/news-room/fact-sheets/detail/poliomyelitis">one in 200 people</a> infected by the virus develops paralysis. </p>
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Read more:
<a href="https://theconversation.com/polio-in-new-york-an-infectious-disease-doctor-explains-this-exceedingly-rare-occurrence-187518">Polio in New York – an infectious disease doctor explains this exceedingly rare occurrence</a>
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<h2>A child in Israel</h2>
<p>One <a href="https://twitter.com/propublica/status/1558140096028737539">indirect link</a> to the New York man may be in Jerusalem where, in March 2022, poliovirus <a href="https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON366">was found</a> in sewage and <a href="https://www.nature.com/articles/s41564-022-01201-0">one case</a> of paralysis occurred in an unvaccinated child.</p>
<p>Vaccination rates among Ultra-Orthodox Jewish people in Israel have been historically low, including <a href="https://apnews.com/article/coronavirus-pandemic-health-middle-east-religion-israel-557e9d18f3f78f4fc141eeddaaefb8eb">low uptake</a> of COVID vaccines.</p>
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<h2>UK ramps up vaccination</h2>
<p>In June this year, the UK government <a href="https://www.gov.uk/government/news/poliovirus-detected-in-sewage-from-north-and-east-london">reported</a> wastewater surveillance in north and east London between February and May had identified poliovirus on consecutive occasions. </p>
<p>This indicated a provisional “silent” outbreak and prompted health officials to instigate catch-up vaccination campaigns. No cases of paralysis have been reported.</p>
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<p>This is reminiscent of an earlier “silent” outbreak of polio in 2013-2014 when, after decades without a case, Israel <a href="https://www.pnas.org/doi/10.1073/pnas.1808798115">detected</a> poliovirus in wastewater samples in many areas, mainly in southern regions.</p>
<p>Stool surveys indicated the outbreak was restricted mainly to children under the age of ten in the Bedouin population of <a href="https://pubmed.ncbi.nlm.nih.gov/27334457/">southern Israel</a>. The virus originated in Pakistan and arrived in Israel via Cairo and then, probably, through Bedouin communities in Egypt and Israel.</p>
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Read more:
<a href="https://theconversation.com/polio-vaccine-boosters-offered-to-london-children-an-expert-explains-whats-going-on-188564">Polio vaccine boosters offered to London children – an expert explains what's going on</a>
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<h2>Hang on, hasn’t polio been eradicated?</h2>
<p>It’s tempting to think polio has been eradicated. </p>
<p>The last case of locally acquired polio in Australia <a href="https://www1.health.gov.au/internet/main/publishing.nsf/Content/cda-pubs-cdi-2002-cdi2602-cdi2602l.htm">was in 1972</a>. Australia was declared polio-free on October 29, 2000, along with the other 36 countries in the Western Pacific Region of the World Health Organization. The last case reported in Australia <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660702/">was in 2007</a>, when a student contracted the infection in Pakistan.</p>
<p>The <a href="https://polioeradication.org">Global Polio Eradication Initiative</a>, launched in 1988, successfully eliminated wild poliovirus from all but two countries – Pakistan and Afghanistan – where in recent years there have been very few cases. </p>
<p>In <a href="https://polioeradication.org/where-we-work/afghanistan/">Afghanistan</a>, there were four cases last year and one so far this year. In <a href="https://polioeradication.org/where-we-work/pakistan/">Pakistan</a>, there was one case in 2021 and 14 so far this year.</p>
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Read more:
<a href="https://theconversation.com/polio-were-developing-a-safer-vaccine-that-uses-no-genetic-material-from-the-virus-185721">Polio: we're developing a safer vaccine that uses no genetic material from the virus</a>
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<p>The recent cases and wastewater detected polioviruses in the UK, US and Israel are not the wild variety. Instead, they are derived from the oral polio vaccine.</p>
<p>When a child receives a dose of the oral vaccine, they excrete the virus in the stool for several weeks. In very rare cases, the vaccine-derived virus mutates to a form that causes paralysis. This form is called a circulating vaccine-derived poliovirus (cVDPV). This occurs only in populations where polio vaccine coverage is low.</p>
<p>Just recently, cVDPV was reported in the Democratic Republic of the Congo, Mozambique and Yemen, as well as in wastewater in five other countries.</p>
<p>Australia, like all high-income countries, does not use the oral polio vaccine. Instead, children receive <a href="https://immunisationhandbook.health.gov.au/contents/vaccine-preventable-diseases/poliomyelitis">injectable inactivated polio vaccine</a>, which prevents paralysis but does not prevent transmission of the virus. </p>
<p>This is why so-called silent outbreaks can occur in countries that use the injectable vaccine. This is when the virus spreads from child to child but does not cause paralysis.</p>
<h2>What are the implications for Australia?</h2>
<p>Given Australia’s open international borders, there is no reason why someone who has recently received the oral polio vaccine wouldn’t enter the country and excrete the virus.</p>
<p>In Australia, at the age of five, <a href="https://www.health.gov.au/node/38782/childhood-immunisation-coverage/current-coverage-data-tables-for-all-children#five-year-olds">about 95% of children</a> are fully vaccinated against polio. </p>
<p>However, there are places with lower vaccine coverage, such as <a href="https://www.theguardian.com/australia-news/2021/aug/14/when-covid-came-to-the-anti-vax-capital-of-australia">Byron Shire</a> in northern New South Wales, with lower rates of childhood vaccination, including against polio.</p>
<p>This vaccine-hesitant community is vulnerable to the introduction of polio and has had cases of diphtheria, whooping cough, measles and tetanus in recent years.</p>
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<p>Unlike some other Orthodox Jewish communities overseas, there is no evidence this community in Australia is more vaccine hesitant than other Australians.</p>
<h2>How do we look out for cases?</h2>
<p>For years, wastewater monitoring has been routinely implemented in many countries. This acts as an early warning system to identify and rapidly mitigate the spread of many pathogens, <a href="https://theconversation.com/sewage-surveillance-is-the-next-frontier-in-the-fight-against-polio-105012">including poliovirus</a>, hepatitis viruses and, recently, SARS-CoV-2 (the virus that causes COVID).</p>
<p>At wastewater treatment facilities, sewage from an entire region is combined. This allows scientists to <a href="https://www.nature.com/articles/s41564-022-01201-0">detect pathogens</a> at the population level and before anyone presents with symptoms.</p>
<p>In December 2017, Victoria’s environmental testing program <a href="https://www.health.vic.gov.au/media-releases/health-surveillance-system-detects-poliovirus">detected</a> a rare type of poliovirus in pre-treated sewage from the Western Treatment Plant in Melbourne. </p>
<p>No cases of paralytic polio were detected but all Victorians up to the age of 19 were offered three doses of vaccine, free of charge, as part of catch-up arrangements.</p>
<p>Australia’s poliovirus infection outbreak response plan <a href="https://www.health.gov.au/sites/default/files/documents/2022/05/poliovirus-infection-outbreak-response-plan-for-australia.pdf">focuses on</a> clinical surveillance (where health workers report suspected cases to health authorities) and laboratory investigations of people who present with acute paralysis. </p>
<p>While the plan refers to examples of wastewater surveillance overseas, it does not propose a specific strategy in Australia. </p>
<p>Other than Victoria, it is not clear where wastewater polio surveillance is being conducted in Australia.</p>
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Read more:
<a href="https://theconversation.com/sewage-surveillance-is-the-next-frontier-in-the-fight-against-polio-105012">Sewage surveillance is the next frontier in the fight against polio</a>
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<h2>What happens next?</h2>
<p>Australia is just as vulnerable to importations of poliovirus – both wild and vaccine-derived – as any other country.</p>
<p>Australia should ensure routine wastewater surveillance for poliovirus is conducted, at least in metropolitan areas.</p>
<p>Community-based vaccination campaigns should be sensitively conducted in vaccine-hesitant communities, such as in Byron Shire, to achieve high coverage.</p>
<p>Education should also be provided through GPs to parents planning to travel to Jerusalem, New York City and Rockland County. They should ensure all travelling family members are fully vaccinated against polio. Visitors to Israel may be able to access a dose of oral polio vaccine in that country for their children (which will prevent them being infected) but this is not available in the US.</p>
<p>Poliovirus enters the body through the mouth, usually from hands contaminated with the stool of an infected person. So parents should also pay special attention to their children’s hand hygiene, particularly if travelling overseas to any of the locations mentioned.</p><img src="https://counter.theconversation.com/content/188989/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Michael Toole receives funding from the National Health and Medical Research council.</span></em></p>Polio cases in the US, UK and Israel remind us that this could also happen in Australia. Here’s what we should watch out for.Michael Toole, Associate Principal Research Fellow, Burnet InstituteLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1872992022-08-19T11:08:55Z2022-08-19T11:08:55ZHow African countries coordinated the response to COVID-19: lessons for public health<figure><img src="https://images.theconversation.com/files/476881/original/file-20220801-20-uy3dte.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">shutterstock</span> </figcaption></figure><p>The COVID-19 pandemic spread much <a href="https://www.sciencedirect.com/science/article/pii/S0140673621006322?casa_token=2DMHndymqfgAAAAA:THwxBLkqWzWe-5ixTLHyWQwSHYaCvoeReCFZulLgFt58cgeKocWlff6_c8hYTuFvdkZNioDZ">slower on the African continent than in the rest of the world</a>, contrary to predictions. </p>
<p>As of 20 July 2022, <a href="https://covid19.who.int">a total of 562,672,324 COVID-19 confirmed cases and 6,367,793 deaths</a> had been recorded globally. Only 1.63% (9,176,657) of the global cases and 2.73% (173,888) of global deaths recorded were from the African continent – which has around <a href="https://www.worldometers.info/geography/7-continents/">17%</a> of the world’s population.</p>
<p>Multiple <a href="https://theconversation.com/the-impact-of-covid-19-has-been-lower-in-africa-we-explore-the-reasons-164955">reasons</a> for the slower spread have been put forward. One was that the continent’s population is <a href="https://www.un.org/ohrlls/news/young-people%E2%80%99s-potential-key-africa%E2%80%99s-sustainable-development#:%7E:text=Africa%20has%20the%20youngest%20population,to%20realise%20their%20best%20potential.">relatively young</a> and younger people were at <a href="https://www.science.org/doi/10.1126/science.abd6165">lower risk</a> of severe illness in the event of SARS-CoV-2 infection. The <a href="https://archive.hshsl.umaryland.edu/bitstream/handle/10713/13734/Doshi_2020.09.17.pdf?sequence=1&isAllowed=y">possible contribution of pre-existing immunity from other viral infections</a> was also put forward. And it was suggested that the slower spread might not be the real picture: there could be underestimation of the true magnitude of the pandemic, resulting from weak surveillance systems. </p>
<p>There is another aspect to consider, though. It is possible that what countries did to slow the spread of SARS-CoV-2 infections actually worked to some extent. Diverse sectors and disciplines <a href="https://apps.who.int/iris/bitstream/handle/10665/331716/9789240003699-eng.pdf">collaborated</a> towards the shared goal of mitigating the pandemic effects. </p>
<p>In our recent <a href="https://bmchealthservres.biomedcentral.com/articles/10.1186/s12913-022-08035-w">study</a> we traced policies retrospectively and related them to patterns of the disease. We set out to understand how the 47 countries forming the World Health Organisation (WHO) African region coordinated the response to COVID-19 – and what we could learn from their strategies. By coordination we mean management to ensure unity of effort.</p>
<p>Our analysis showed that decentralisation strategies and innovation played key roles in coordination. Financing was a challenge to coordination.</p>
<h2>Three levels of coordination</h2>
<p>All 47 countries in the WHO African region instituted three distinct layered coordination mechanisms: strategic, operational and tactical. </p>
<p>Most (41) countries implemented strategic coordination. This means that the highest authority in government or a designated authority oversaw the overall response. One example is the strong leadership by the president of Seychelles, who is also the minister of health. Another is the National Disaster Risk Management Council led by the deputy prime minister’s office in <a href="https://www.dovepress.com/covid-19-in-ethiopia-assessment-of-how-the-ethiopian-government-has-ex-peer-reviewed-fulltext-article-RMHP">Ethiopia</a>. </p>
<p>The second layer was operational coordination. This refers to the provision of <a href="https://apps.who.int/iris/bitstream/handle/10665/258604/9789241512299-eng.pdf">day-to-day technical and operational support to the in-country response team</a>. It was implemented by 28 countries and led by experts in public health emergency operations centres. An example is the Public Health Emergency Operations that provided the operational level leadership in <a href="https://documents1.worldbank.org/curated/en/197511589210291563/pdf/Cote-dIvoire-COVID-19-Strategic-Preparedness-and-Response-Project.pdf">Côte d'Ivoire</a> under the general director of health. </p>
<p>The third layer was tactical coordination. This is decentralised coordination at local levels (such as districts, states or counties), and was implemented by 14 countries. For instance, existing district surveillance teams were immediately called into play to respond to the virus in their jurisdictions in <a href="https://thinkwell.global/wp-content/uploads/2020/09/Uganda-COVID-19-Case-Study-_18-Sept-20201.pdf">Uganda</a>.</p>
<p>The coordination mechanisms and levels of preparedness may not have been strong enough in the first wave of infections. Every country was trying to do a lot within a short period. Many countries were piloting to see what worked and what did not. </p>
<p>Nonetheless, the combined three coordination mechanisms may have been a key to slowing the spread of the initial wave of the pandemic and the length of the subsequent waves. Our study findings showed that the length of the second wave was shortened by an average of 69.73 days among countries that combined all three coordination mechanisms in tandem compared to those that only combined the strategic and tactical. </p>
<p>Governments applied what they learnt on the go. For instance, <a href="https://nef.org/learning-from-the-best-evaluating-covid-19-responses-and-what-africa-can-learn/">Senegal</a> made use of treatment regimens that <a href="https://www.enca.com/news/senegal-says-hydroxychloroquine-virus-treatment-promising">seemed promising</a> and collaborated with private partners to use a diagnostic test for COVID-19 that could be done at home.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/474841/original/file-20220719-14-w4gj90.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/474841/original/file-20220719-14-w4gj90.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=635&fit=crop&dpr=1 600w, https://images.theconversation.com/files/474841/original/file-20220719-14-w4gj90.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=635&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/474841/original/file-20220719-14-w4gj90.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=635&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/474841/original/file-20220719-14-w4gj90.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=798&fit=crop&dpr=1 754w, https://images.theconversation.com/files/474841/original/file-20220719-14-w4gj90.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=798&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/474841/original/file-20220719-14-w4gj90.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=798&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
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<p>Figure 1: The layered coordination mechanisms in Africa (source, <a href="https://bmchealthservres.biomedcentral.com/articles/10.1186/s12913-022-08035-w">Ngoy. et al</a>.)</p>
<h2>Implications</h2>
<p>Our analysis points to several lessons about preparing for and responding to health emergencies.</p>
<p><strong>Engage different players.</strong> Countries have to empower players like government officials, technocrats, expert advisers, development partners, UN agencies and private companies. Governments also need to invest in the technical expertise that can coordinate the multiple elements of a pandemic. These elements include logistics, fund raising, management, healthcare data collection and analysis. </p>
<p><strong>Organise emergency financing.</strong> Setting aside an emergency funding pot will reduce reliance on development partners. Over-reliance on partners slowed down the coordination of the response in most countries. A transparent institutional framework that is accountable for the funds is useful too.</p>
<p><strong>Invest in a decentralised emergency response.</strong> Countries that decentralised their emergency response to the subnational levels (or districts or the grassroots) were able to slow community transmission.</p>
<p>For instance, using <a href="https://gh.bmj.com/content/bmjgh/6/2/e004393.full.pdf">provincial incident management teams in South Africa</a> or existing district surveillance teams and <a href="https://thinkwell.global/wp-content/uploads/2020/09/Uganda-COVID-19-Case-Study-_18-Sept-20201.pdf">district task forces in Uganda</a> left the central government to focus on strategy development and resource mobilisation. </p>
<p>Botswana <a href="https://reliefweb.int/report/botswana/botswanas-communities-stand-strong-against-covid-19-usaids-assistance">built upon existing community health platforms</a> that had been strengthened over many years through PEPFAR investments to combat the HIV epidemic. This helped in contact tracing and helped health workers to manage COVID-19 cases as there were few cases in hospitals.</p>
<p>For all these decentralised strategies to work, countries must have a strong political commitment to provide the required health resources and facilities. They also need a well-coordinated information flow from the centre to the periphery. Information is essential for enhancing the accountability of response actions and tackling misinformation. Besides, it allows communities to be part of the solution.</p>
<p><strong>Keep building on projects and innovations.</strong> Building on existing structures used during <a href="https://www.theigc.org/blog/responding-to-covid-19-in-fragile-states-the-case-of-sierra-leone/">previous emergencies, such as the Ebola outbreak in Sierra Leone</a>, made it easier to activate the response. </p>
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Read more:
<a href="https://theconversation.com/ebola-in-the-drc-expert-sets-out-critical-lessons-learnt-in-liberia-108707">Ebola in the DRC: expert sets out critical lessons learnt in Liberia</a>
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<p>Countries should also develop and use new and adapted technologies. For example, Rwanda used <a href="https://pubmed.ncbi.nlm.nih.gov/33665145/">drones to share public information</a>. In Ghana, <a href="https://innov.afro.who.int/uploads/media-corner/who_afro_covid_19_african_innovation_compendium_20201203075453.pdf">robots were used for screening and inpatient care</a>. Liberia used a communication platform called mHero to connect the ministry of health and health workers. Niger used an app called Alerte COVID-19. Today’s tech-for-health innovations tailored to the pandemic response can be adapted for broader use in future.</p>
<p>Organised and well-directed coordination mechanisms provide a structured pandemic management plan or outline of purposeful actions. Having a collaborative approach involving different stakeholders is essential for future emergencies.</p><img src="https://counter.theconversation.com/content/187299/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Boniface Oyugi works for/consults to the World Health Organisation Regional Office for Africa. </span></em></p>Combining several layers of response to COVID-19 was effective. Decentralisation, innovation and building on existing systems were key.Boniface Oyugi, Health Policy and Health Economics researcher and a Honorary Researcher at the Centre for Health Services Studies, University of KentLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1888372022-08-18T14:11:42Z2022-08-18T14:11:42ZMosquito species from Asia poses growing risk to Africa’s anti-malaria efforts<figure><img src="https://images.theconversation.com/files/479721/original/file-20220817-13-x71gvq.jpeg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The Anopheles stephensi is usually found in South-East Asia. </span> <span class="attribution"><span class="source">Jim Gathany </span></span></figcaption></figure><iframe id="noa-web-audio-player" style="border: none" src="https://embed-player.newsoveraudio.com/v4?key=x84olp&id=https://theconversation.com/mosquito-species-from-asia-poses-growing-risk-to-africas-anti-malaria-efforts-188837&bgColor=F5F5F5&color=D8352A&playColor=D8352A" width="100%" height="110px"></iframe>
<p>The spread of the mosquito species <em>Anopheles stephensi</em> across Africa poses a significant problem to a continent already heavily burdened by malaria. Most – <a href="https://www.who.int/teams/global-malaria-programme/reports/world-malaria-report-2021">90%</a> – of the world’s malaria deaths are on the continent. </p>
<p>Researchers from Djibouti reported the presence of <em>An. stephensi</em> in the Horn of Africa in 2012. Until then it had not been found in Africa although it was known to be widespread in Southeast Asia and parts of the Arabian Peninsula. By <a href="https://ccp.jhu.edu/2022/06/13/malaria-africa-anopheles/">2017</a> it had spread through the Horn of Africa, reaching Ethiopia, Somalia and Sudan. </p>
<p>The spread of <em>An. stephensi</em> is particularly concerning because the mosquito has a number of characteristics that make it <a href="https://www.pnas.org/doi/10.1073/pnas.2006781117?cookieSet=1">difficult to control</a>. This species can thrive in urban areas and likes being near humans. They lay their eggs in any available water source – such as water containers, abandoned tyres and flowerpots – and their eggs can survive being dry for a long period of time. In addition, <em>An. stephensi</em> feeds on its vertebrate host both indoors and outdoors. This reduces the impact of commonly used vector control methods such as insecticide-treated nets and indoor residual spraying.</p>
<p>The invasion of this urban mosquito into Africa threatens the malaria elimination aspirations of the continent, particularly as <a href="https://data.worldbank.org/indicator/SP.URB.TOTL.IN.ZS?locations=ZG">42.5%</a> of Africa’s population now live in urban areas. </p>
<p>As a result, national malaria control programmes have increased surveillance efforts in urban areas to enable early detection and control. Countries have also run awareness campaigns to encourage communities to reduce potential breeding sites. </p>
<p>The species has not yet been detected in southern Africa. Nevertheless the South African national malaria control programme, with the support of the National Institute for Communicable Diseases, is increasing surveillance activities in areas where this species may occur. </p>
<h2>Invasive species</h2>
<p>Many <a href="https://esajournals.onlinelibrary.wiley.com/doi/pdf/10.1890/070151">epidemics and pandemics</a> have been driven by pathogens, hosts and vectors invading new areas. These include the Black Death in 14th century Europe, caused by the invasion of rats carrying fleas infected with the plague. </p>
<p>The Asian tiger mosquito (<em>Aedes albopictus</em>) and the yellow fever mosquito (<em>Aedes aegypti</em>) both carry dangerous diseases such as dengue, yellow fever and Zika. The spread of these mosquito species into North America and Europe during the 1970s and 1980s was associated with large increases in these diseases.</p>
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<a href="https://theconversation.com/invasive-mosquito-species-could-bring-more-malaria-to-africas-urban-areas-147530">Invasive mosquito species could bring more malaria to Africa's urban areas</a>
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<p>While <em>Aedes</em> mosquitoes transmit viral diseases, <em>Anopheles</em> mosquitoes transmit malaria. Of the 500 <em>Anopheles</em> species, only 30-40 can spread malaria. Common species that transmit malaria in Africa are <em>Anopheles gambiae</em>, <em>An. arabiensis</em> and <em>An. funestus</em>.</p>
<p><em>Anopheles gambiae</em> is one of the most effective malaria vectors in the world. It invaded South America in the <a href="https://www.nature.com/articles/143890e0">1930s</a>. This species rapidly established itself in Brazil, causing a malaria epidemic with an estimated fatality rate of 13%. <em>Anopheles gambiae</em> was eventually eliminated from Brazil in the 1940s after a highly co-ordinated and resource-intensive effort.</p>
<p><em>Anopheles stephensi</em> is a malaria vector native to South Asia. It transmits both <em>Plasmodium falciparum</em> and <em>P. vivax.</em> It rapidly adapts to changes in the environment and is found in both rural and urban areas. This is different from African malaria vectors, which are typically found in rural areas. </p>
<p>Controlling this invasive mosquito is very challenging. It is difficult to find, particularly in urban areas, and is resistant to a number of insecticides. Although there are no specific programmes to eliminate this species from Africa, the affected countries are <a href="https://www.who.int/publications/i/item/WHO-HTM-GMP-2019.09/">implementing</a> a range of control measures.</p>
<h2>Urgent action</h2>
<p>The presence of <em>An. stephensi</em> in Africa is a call to action to all interested in controlling and eliminating malaria. </p>
<p>It is imperative that entomological surveillance (the search for and biological investigation of insects, including malaria vectors) is strengthened across the continent. New information about the species must be shared promptly to ensure malaria control programmes use the correct methods to prevent it from spreading further into the continent.</p>
<p>And an integrated approach to vector control is urgently required. Vector control measures, adapted to local conditions, are key to preventing the spread of <em>An. stephensi</em>. National malaria control programmes cannot rely solely on insecticides to control this mosquito. They must invest in novel vector control methods that target outdoor-biting mosquitoes.</p>
<p>Governments must also invest in educating communities on the appropriate methods for storing water as well as eliminating potential breeding sources. South America has implemented strong policies to reduce breeding areas for <em>Aedes</em> mosquitoes. Similar approaches in Africa would reduce the presence of <em>An. stephensi</em>, as well as of <em>Aedes</em> mosquitoes, which carry many dreaded diseases including dengue, yellow fever, chikungunya and Zika.</p>
<p>Crucially, a healthy population without circulating parasites is key to a malaria-free future. Integrating clinical care, vector control and community awareness of the disease is the best way to ensure a malaria-free future for the continent.</p><img src="https://counter.theconversation.com/content/188837/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Shüné Oliver receives funding from the National Research Foundation and the Female Academic Leadership Fellowship. </span></em></p><p class="fine-print"><em><span>Jaishree Raman receives funding from the Gates Foundation, the Global Fund, South African Medical Research, Research Trust, National Research Foundation and National Institute for Communicable Diseases</span></em></p>The spread of this urban malaria vector species threatens the gains made against malaria and the achievement of malaria elimination.Shüné Oliver, Medical scientist, National Institute for Communicable DiseasesJaishree Raman, Principal Medical Scientist and Head of Laboratory for Antimalarial Resistance Monitoring and Malaria Operational Research, National Institute for Communicable DiseasesLicensed 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>
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<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>
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<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>
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<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>
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</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/1816182022-04-24T09:05:19Z2022-04-24T09:05:19ZFresh signs of mosquito insecticide resistance in South Africa<figure><img src="https://images.theconversation.com/files/459335/original/file-20220422-22-ogj1sg.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A man sprays the walls of a house with insecticide against mosquitoes. </span> <span class="attribution"><span class="source">Cristina Aldehuela/AFP via Getty Images</span></span></figcaption></figure><p>Most South Africans aren’t worried about malaria even though the disease is endemic in the country. Four of the country’s nine provinces carry malaria risk while 10% of the population is at risk of <a href="https://www.health.gov.za/malaria/">contracting malaria</a>.</p>
<p>The lack of concern can be attributed to the fact that the country has a relatively low burden of the disease. In <a href="http://www.xinhuanet.com/english/africa/2021-04/23/c_139901749.htm">2020</a>, South Africa had 8,126 cases and 38 deaths. This is low when compared to the estimated <a href="https://malariajournal.biomedcentral.com/articles/10.1186/s12936-022-04090-0#:%7E:text=According%20to%20the%202020%20NMCP,2019%2C%20to%20812%2C239%20in%202020">10,007,802 cases and 23,766 deaths</a> in Mozambique during the same period. </p>
<p>The low number of cases means that South Africa is a candidate for malaria elimination. To reach this goal the country would need to record no new infections for three years. This goal has recently been achieved by China and El Salvador in 2021, and Argentina and Algeria in 2019. </p>
<p>The region in South Africa <a href="https://www.nicd.ac.za/wp-content/uploads/2019/10/MALARIA-ELIMINATION-STRATEGIC-PLAN-FOR-SOUTH-AFRICA-2019-2023-MALARIA-ELIMINATION-STRATEGIC-PLAN-2019-2023.pdf">most likely</a> to achieve this status is KwaZulu-Natal where the incidence rate is very low. But there are threats to achieving the goal.</p>
<p>In <a href="https://sajs.co.za/article/view/11755">a recent paper</a> we set out our findings on malaria in northern Kwa-Zulu Natal. We found that certain species of malaria-carrying mosquitoes showed resistance to insecticides. Though the resistance levels are low, they nevertheless point to a potentially worrying trend. </p>
<p>This is not the first time that insecticide resistance has been reported in the province. Monitoring resistance is important because it gives an early warning sign of coming danger. The <a href="https://www.nature.com/articles/nature15535">loss of insecticide efficacy</a> can be a major blow to malaria control efforts. </p>
<p>Levels of malaria incidence can change very quickly. This was the case during a epidemic between <a href="http://www.samj.org.za/index.php/samj/article/view/7441/5461">1996-2000</a> which was caused by a combination of insecticide resistance and anti-malarial drug resistance.</p>
<p>Insecticide resistance is a growing threat to malaria control efforts globally. In South Africa, indoor residual spraying is the cornerstone of the malaria elimination efforts. Hence, it is important to keep a close eye on vector mosquito populations in affected areas. </p>
<p>A concerted effort on the part of the government ensured that malaria infection rates were brought down again. Our research suggests there needs to be extra vigilance to ensure there isn’t another spike.</p>
<h2>Resistance</h2>
<p>Our research was done as part of ongoing malaria surveillance in the country. Malaria surveillance is essential for provincial control and elimination programmes. These surveillance activities include collecting mosquitoes, identifying them and testing their sensitivity to insecticides. The aim is to provide important information on vector mosquito populations in affected areas, such as their feeding, breeding and resting behaviours and their susceptibilities to insecticide. </p>
<p>In our <a href="https://sajs.co.za/article/view/11755">paper</a> we looked at <em>Anopheles</em> with special emphasis on <em>Anopheles arabiensis</em>, which is the primary vector of malaria in the northern Kwa-Zulu Natal. </p>
<p>We collected <em>Anopheles</em> specimens from Mamfene, Jozini, northern KwaZulu-Natal between November 2019 and April 2021. We conducted standard insecticide susceptibility tests. These showed resistance to DDT, permethrin, deltamethrin, and bendiocarb, as well as full susceptibility to pirimiphos-methyl. These are classes of insecticides that are approved for indoor residual spraying. </p>
<p>The levels of resistance we detected are still low, with an average survival rate of 12%. But they’re nevertheless concerning.</p>
<p>If insecticide resistance becomes widespread it can result in operational failure. This would mean that the current insecticide-based mosquito control strategies would not be effective. This, in turn, can lead to mosquito numbers growing as <a href="https://www.nature.com/articles/nature15535">parasite densities</a> increase.</p>
<p>It is, therefore, essential that control is maintained and strengthened by adopting suitable strategies to prevent the development of <a href="https://irac-online.org/about/resistance/management/">insecticide resistance</a>. </p>
<p>South Africa is aware of the problem, which is why it has adopted malaria control programmes that use at least two different insecticides in a mosaic spraying pattern. This approach has proved highly successful. This is like using a multi-drug approach to combat resistance in bacteria and viruses. It will slow down the development of insecticide resistance compared to using a single insecticide. </p>
<h2>No time for complacency</h2>
<p>South Africa’s low number of cases mean that the country is a candidate for malaria elimination. But this is not the time for complacency. The spike in malaria cases in South Africa in <a href="https://malariajournal.biomedcentral.com/articles/10.1186/s12936-019-3001-x">2017</a> shows how quickly the progress can be undone. </p>
<p>Various countries have relegated malaria to history. China is the latest country to achieve this, which is significant due to the size of its population and geographical area. </p>
<p>South Africa could join this list, with KwaZulu-Natal province at the forefront of the charge towards elimination. Yet, the province is also a reminder of what could happen if the country lets its guard down.</p>
<p>Malaria is a dynamic disease, and mosquitoes do not respect borders. The epidemics of 1996-2000 and the spike in cases in 2017 should be a stark warning of what can happen, especially if complacency steps in.</p><img src="https://counter.theconversation.com/content/181618/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Shüné Oliver receives funding from the NHLS Research Trust, the National Research Foundation of South Africa and . the Wits Chancellor’s Female Academic Leaders Fellowship.</span></em></p><p class="fine-print"><em><span>Basil Brooke and Givemore Munhenga 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>Insecticide resistance is a growing threat to malaria control efforts globally. It is, thus, important to keep a close eye on vector mosquito populations in affected areas.Shüné Oliver, Medical scientist, National Institute for Communicable DiseasesBasil Brooke, Associate Professor at the Wits Research Institute for Malaria in the Faculty of Health Sciences, University of the WitwatersrandGivemore Munhenga, Senior Medical Scientist, National Institute for Communicable DiseasesLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1755142022-01-27T03:08:06Z2022-01-27T03:08:06ZTest all students and staff twice a week, or only close contacts? States have different school plans – here’s what they mean<figure><img src="https://images.theconversation.com/files/442860/original/file-20220127-16-14ndxyz.jpg?ixlib=rb-1.1.0&rect=51%2C0%2C5760%2C3837&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/mother-testing-her-child-covid-home-1956075829">Shutterstock</a></span></figcaption></figure><p>Schools will open for term one across Australia next week – except in Queensland which has <a href="https://www.abc.net.au/news/2022-01-10/qld-delayed-school-start-angers-some-parents/100746942">delayed the start of the school year</a>.</p>
<p>As the country battles a wave of Omicron infections, states have introduced a comprehensive suite of measures to help reduce school outbreaks, as well as disruptions. Testing plans rely on regular use of rapid antigen tests (RATs), which the government will provide to schools and parents. They are a very important additional tool in providing a safe school environment.</p>
<p><a href="https://www.coronavirus.vic.gov.au/rapid-antigen-testing-schools">Victoria</a> and <a href="https://education.nsw.gov.au/covid-19/advice-for-families">New South Wales</a> strongly recommend primary and secondary staff and students do a RAT twice a week on school days for the first four weeks of term. Because of the greater risk associated with COVID for some students with disabilities, Victoria’s recommendation for specialist school staff and teachers is testing five days a week. </p>
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<p>Children who test positive will be required to stay home along with household members for seven days in Victoria.</p>
<p>Regular testing of asymptomatic cases as in NSW and Victoria is known as a “surveillance strategy” and the <a href="https://www.canberratimes.com.au/story/7591943/what-you-need-to-know-about-the-acts-back-to-school-plan/">ACT has similar plans</a>. But while <a href="https://indaily.com.au/news/2022/01/21/back-to-school-office-plans-announced-amid-six-more-deaths-3023-new-cases/">South Australia recommends</a> early education and care staff test several times per week for surveillance, the state’s schools strategy is different and is known as “<a href="https://www.education.sa.gov.au/sites/default/files/preschool-early-childhood-settings-testing-isolating-and-qurantining-a3-placemat.pdf">test-to-stay</a>”. Here, close contacts will need to do a RAT every day for seven days and can attend school if they test negative.</p>
<p>NSW and Victoria will also allow close contacts to attend school as long as they report a negative RAT test.</p>
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<p>Both strategies, surveillance and test to stay, have been implemented in several jurisdictions in the United States, Canada and Europe, all of which reopened schools during Omicron outbreaks. But why do different Australian states have different plans, and what is the evidence for these testing measures?</p>
<h2>Surveillance and testing to stay: the evidence</h2>
<p>Twice-weekly testing for surveillance is voluntary in NSW, Victoria and the ACT, so not everyone will be following the guidelines perfectly. But modelling by the <a href="https://www.doherty.edu.au/uploads/content_doc/Synthesis_DohertyModelling_FinalReport__NatCab05Nov.pdf">Doherty Institute</a> (using Delta parameters) found detecting infections in school early – such as with surveillance – and high vaccine coverage in the community markedly reduce outbreak risk even if the testing uptake is only 50%. </p>
<p>The modelling also found twice-weekly screening of asymptomatic students in areas at risk of outbreaks can result in even fewer infections and <a href="https://www.doherty.edu.au/uploads/content_doc/Synthesis_DohertyModelling_FinalReport__NatCab05Nov.pdf">fewer in-person teaching days lost</a>. </p>
<p>The Doherty report also found allowing close contacts to attend school if they test negative, through a test-to-stay strategy, contains an outbreak as effectively as requiring close contacts to quarantine at home. </p>
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<p>Doherty’s findings reproduce the outcomes seen in a <a href="https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(21)01908-5/fulltext">real-world study when the Delta variant was dominant</a>, which compared standard quarantine to test-to-stay in England. There was no difference in transmission between schools where bubbles were sent into home isolation for ten days versus those where daily contact testing (<a href="https://www.ox.ac.uk/news/2021-07-23-daily-contact-covid-19-testing-students-effective-controlling-transmission-schools">test-to-stay</a>) was implemented.</p>
<p>Another impressive study from <a href="https://www.cdc.gov/mmwr/volumes/70/wr/mm7021e2.htm?s_cid=mm7021e2_w">Utah</a> of 13 high schools (November 2020 to March 2021) found using test-to-stay detected an additional 90 infections and saved 109,752 in-person learning days.</p>
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Read more:
<a href="https://theconversation.com/when-will-this-covid-wave-be-over-4-numbers-to-keep-an-eye-on-and-why-174533">When will this COVID wave be over? 4 numbers to keep an eye on and why</a>
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<p>In Massachusetts, the test-to-stay program found that of 503,312 tests conducted (up to 9 January 2022), <a href="https://www.doe.mass.edu/covid19/testing/default.html#webinar">only 1.4% were positive</a>, which was lower than the statewide rate of positive tests. Additionally, secondary transmission rates were found to be low in schools using this strategy and ranged from <a href="https://www.doe.mass.edu/covid19/testing/default.html#webinar">0.7%</a> to <a href="https://www.cdc.gov/coronavirus/2019-ncov/science/science-briefs/transmission_k_12_schools.html">2.9%</a>. These studies were done before the emergence of Omicron.</p>
<h2>So, which one is better?</h2>
<p>The surveillance strategy will help identify any positive cases early, before symptoms develop, and help prevent introducing infections into schools and the broader community.</p>
<p>The test-to-stay strategy minimises the need for children who are not infectious to stay at home unnecessarily, helps reduce days of lost learning and staffing issues, and minimises disruption from quarantine requirements.</p>
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Read more:
<a href="https://theconversation.com/schools-can-expect-a-year-of-disruption-here-are-7-ways-they-can-help-support-the-well-being-of-students-and-staff-174886">Schools can expect a year of disruption. Here are 7 ways they can help support the well-being of students and staff</a>
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<p>The decision on which strategy to take depends on context, including workforce issues and the level of community transmission, and the availability of sufficient quantity of RATs. </p>
<p>When there is a case in the class, test-to-stay should be done daily for close contacts for seven days. But when community transmission is high, it’s best to add surveillance screening twice weekly for staff and students aged five and above (and 3-5 year olds if tolerated).</p>
<p>The Doherty modelling found a synergistic benefit of combining twice weekly surveillance screening with a test to stay policy. The greatest number of face-to-face teaching days gained using this approach occurs when community transmission is highest. </p>
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<p>States employing a surveillance strategy will need to revisit this in four weeks, including the uptake and acceptance of testing – specifically the impact of children having regular testing for an infection that has little direct harm to them. There must be a clear off-ramp as the outbreak may also be almost complete and children will be tired of having nasal swabs. </p>
<h2>What’s likely to happen when schools open</h2>
<p>The number of new cases surveillance detects will always be biased towards the age groups and settings most tested. As schools open, the number of infections will increase, but they will appear to increase even more because intensive testing will find many more mild and asymptomatic cases.</p>
<p>Mobility patterns also change after the school holidays. Because more people are moving around, there will inevitably be an increase in infections in early childhood and school settings. But these will be relatively short-lived and mild, given the overseas experience. States that delay opening schools may simply postpone trouble and lengthen the outbreak. Moreover, there is <a href="https://www.thelancet.com/journals/lanchi/article/PIIS2352-4642(20)30095-X/fulltext">little evidence closing schools controls infection rates</a> and transmission in the broader community during outbreaks.</p>
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Read more:
<a href="https://theconversation.com/we-shouldnt-delay-the-start-of-school-due-to-omicron-2-paediatric-infectious-disease-experts-explain-174330">We shouldn't delay the start of school due to Omicron. 2 paediatric infectious disease experts explain</a>
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<p>Ongoing surveillance <a href="https://www.rivm.nl/en/coronavirus-covid-19/children-and-covid-19/research-results-ggd-data">in the Netherlands</a> has found adults are the most common source of infection. As children grow older, they are more likely to become the source but still less likely than adults. The study also found teaching staff during the Omicron period up until the time of publication of this article had slightly <a href="https://www.rivm.nl/en/coronavirus-covid-19/children-and-covid-19/research-results-ggd-data">fewer infections</a> than the general adult population.</p>
<p>COVID vaccination in children is effective at preventing severe disease, but has <a href="https://theconversation.com/we-shouldnt-delay-the-start-of-school-due-to-omicron-2-paediatric-infectious-disease-experts-explain-174330">minimal impact</a> on mild Omicron infections. Any preventive effect against infection may wane quite quickly.</p>
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<p>It is understandable <a href="https://www.smh.com.au/national/schools-must-be-last-to-close-and-first-to-open-science-confirms-they-re-the-safest-place-for-children-20220126-p59r9k.html">many parents will be feeling anxious</a> about schools opening. But it is important to remember COVID in <a href="https://theconversation.com/we-shouldnt-delay-the-start-of-school-due-to-omicron-2-paediatric-infectious-disease-experts-explain-174330">healthy children is generally a mild illness</a>, akin to influenza, so unvaccinated and partially vaccinated children can return safely to school. Although hospitalisation does occur, it is <a href="https://www.ft.com/content/28be9d3f-0b12-4c33-bda9-fbff375c0b7e">less frequent</a> than other common childhood respiratory viruses. </p>
<p>RATs are an important tool in helping to provide a safe working and learning environment and we strongly encourage school staff and parents to test as recommended.</p>
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<p><em>Correction: This article previously said a child in NSW who tests positive could return to school when symptoms resolve and they record two days of negative tests. This is incorrect and has been removed. We have also clarified the Netherlands study period.</em></p><img src="https://counter.theconversation.com/content/175514/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Fiona Russell receives funding from NHMRC, the Wellcome Trust, DFAT and the World Health Organization. </span></em></p><p class="fine-print"><em><span>Robert Booy consults to all vaccination companies in Australia and works one day a week for Vaxxas. He has received funding from NHMRC and ARC in relation to vaccine research.</span></em></p>States are using 2 main school testing strategies: testing everyone regularly, known as surveillance, having close contacts test daily for 7 days and come to school if negative, known as test to stay.Fiona Russell, Senior Principal Research Fellow; paediatrician; infectious diseases epidemiologist; vaccinologist, The University of MelbourneRobert Booy, Infectious Disease Paediatrician and Senior Professorial Fellow, National Centre for Immunisation Research and Surveillance, University of SydneyLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1666252021-08-25T15:11:11Z2021-08-25T15:11:11ZIt’s been a year since Africa was declared polio free. But a threat remains<figure><img src="https://images.theconversation.com/files/417566/original/file-20210824-13-18fxv99.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A child gets a dose of the oral polio vaccine.</span> <span class="attribution"><span class="source">Simon Maina/AFP via Getty Images</span></span></figcaption></figure><p>The <a href="https://www.who.int/news/item/25-08-2020-global-polio-eradication-initiative-applauds-who-african-region-for-wild-polio-free-certification">25th of August marks</a> the first anniversary of a milestone that took over 30 years to achieve. Africa being free from polio – a disease that has caused death and paralysis throughout recorded history.</p>
<p>Polio is a viral illness that can cause sudden weakness, permanent paralysis, or death in people who were previously healthy and had no risk factors or comorbidities. It usually affects children. The virus is spread by faecally contaminated food and water or close contact.</p>
<p>But the outbreaks of this fearful disease have become a thing of the past, told to us by our grandparents. The reason for the disappearance? Vaccination.</p>
<p>The <a href="https://polioeradication.org/">Global Polio Eradication Initiative</a> was launched in 1988. In that year, more than 350,000 people were paralysed. Polio cases were reported from at least 125 countries.</p>
<p>The initiative set an original target of the year 2000 for polio eradication. It introduced polio vaccines into health programmes around the globe and ensured birth cohorts of children were routinely vaccinated. This drive reduced the number of polio cases to only 22 in 2017. </p>
<p>Only <a href="https://polioeradication.org/polio-today/polio-now/wild-poliovirus-list/">two cases</a> of polio from paralysed individuals have been recorded so far in 2021. This is the lowest number ever. But an additional 62 detections of polio have been identified in wastewater treatment plants or surface water downstream of large populations in Pakistan and Afghanistan. So the case number may be artificially low due to poor surveillance or weak health systems.</p>
<p>Despite the efforts of health programmes around the world, there is still a threat that polio could spread again. Even one case would constitute an international event.</p>
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Read more:
<a href="https://theconversation.com/why-eradicating-polio-everywhere-has-been-so-hard-to-crack-105405">Why eradicating polio everywhere has been so hard to crack</a>
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<p>Africa has had a long history with polio. <a href="https://www.news24.com/news24/analysis/barry-d-schoub-africa-is-now-polio-free-with-south-africa-playing-a-pivotal-role-20200831">South Africa</a> used crowd-funding in the <a href="https://www.africakicksoutwildpolio.com/timeline/">1960s</a> to raise funds for a research facility to develop a polio vaccine, <a href="https://www.news24.com/news24/analysis/barry-d-schoub-africa-is-now-polio-free-with-south-africa-playing-a-pivotal-role-20200831">in collaboration with international researchers</a>. The facility originated as the Poliomyelitis Research Foundation and developed into the <a href="https://www.nicd.ac.za/">National Institute for Communicable Diseases</a>, which has more recently played a leading role in the fight against COVID-19, listeria, and other pathogens. </p>
<p>Polio is still a large part of <a href="https://www.gov.za/faq/health/why-should-i-have-my-child-vaccinated">routine childhood vaccinations</a> in South Africa. </p>
<p>No wild polio, that is polio cases caused by the natural ‘wild type’ form of the virus, has been detected in Africa since 2016. On 25 August 2020, the continent was declared free of wild poliovirus. This leaves only two countries on the globe – Pakistan and Afghanistan – where wild polio is found. A weak healthcare system and vaccine hesitancy have allowed the sustained transmission of polioviruses, and the unfortunate consequence: paralysis or death. </p>
<h2>Poliovirus biology and vaccines</h2>
<p>Polioviruses occur in three serotypes (types 1, 2 and 3). It is <a href="https://www.who.int/news-room/fact-sheets/detail/poliomyelitis">estimated</a> that less than one in 100 infected individuals become paralysed. Others may be asymptomatic or have varying degrees of flu-like illness. Thus, when one paralysed case has been detected, there are likely 99 other asymptomatically infected individuals, making it challenging to control the spread. </p>
<p>There have been two vaccines used since the 1960s to prevent polio: the Salk vaccine, which is an inactivated vaccine, and the Sabin vaccine, which is a live attenuated vaccine. A live vaccine contains a weakened version of the natural ‘wild type’ virus. </p>
<p>Both vaccines are excellent at preventing paralysis. The two vaccines differ, however, in their ability to control asymptomatic poliovirus transmission. </p>
<p>The inactivated polio vaccine is an injectable vaccine that induces antibodies in the blood that prevent paralysis should the person later come into contact with wild polio. If a person later encounters wild poliovirus, the wild virus may still replicate in the person’s gastrointestinal tract and shed in their stool, potentially transmitting asymptomatically to others in the community. The inactivated polio vaccine is excellent for personal protection against paralysis. But it’s not effective at controlling outbreaks, as it does not effectively prevent asymptomatic polio transmission. </p>
<p>The Sabin vaccine is a live, orally-administered, weakened vaccine strain given as drops. It produces good intestinal immunity. This means that, should the vaccinated individual come into contact years later with wild poliovirus, the wild poliovirus won’t be shed in the person’s faeces. Thus, in addition to preventing paralysis, the oral polio vaccine can prevent shedding of wild poliovirus in stool. It is therefore very effective at controlling polio outbreaks. This benefit has been instrumental in decreasing polio transmission and bringing polio to the brink of eradication.</p>
<p>The oral polio vaccine is very effective. But if the population vaccination coverage is low, then people who get the live vaccine can transmit this virus to those who are not immunised. Over weeks to months, this transmission among the community has the benefit of immunising susceptible people. Yet, over a long period of more than six months to years, mutations can arise in the virus genome that can turn it back into a disease-causing virus. This is called a vaccine-derived poliovirus. </p>
<p>Vaccine-derived polio is extremely rare. But it has arisen in multiple <a href="https://www.africanews.com/2021/08/17/uganda-confirms-polio-outbreak//">countries</a> over the past decades. </p>
<p>To combat this phenomenon, a new live vaccine has just been developed. This vaccine is called the novel oral polio vaccine, serotype 2 (nOPV2). This vaccine received <a href="https://www.who.int/news/item/13-11-2020-first-ever-vaccine-listed-under-who-emergency-use">emergency use listing</a> in November 2020, just before the SARS-CoV-2 vaccines, and has already been used in seven African countries. Novel oral polio vaccines against serotypes 1 and 3 are currently in development.</p>
<h2>Maintaining efforts</h2>
<p>The development of nOPV2 is a game-changer in the war against polio. The current target for polio eradication has been <a href="https://polioeradication.org/wp-content/uploads/2021/06/polio-eradication-new-Strategy-2022-26-Executive-Summary.pdf">extended to 2026</a>. </p>
<p>To meet this deadline, three things must happen. </p>
<ul>
<li><p>Health systems around the world need to keep vigilant; </p></li>
<li><p>vaccination coverage need to be kept high; and </p></li>
<li><p>we need to keep developing new vaccines to counteract evolving viruses.</p></li>
</ul><img src="https://counter.theconversation.com/content/166625/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Melinda Suchard has received speaker honoraria from Sanofi Pasteur. She manages grants from the World Health Organisation for polio surveillance.</span></em></p><p class="fine-print"><em><span>Wayne Howard 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>Outbreaks of polio have become a thing of the past, told to us by our grandparents, only because of vaccination.Wayne Howard, Medical Scientist, National Institute for Communicable DiseasesMelinda Suchard, Head, Centre for Vaccines and Immunology, National Institute for Communicable DiseasesLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1652012021-08-01T09:26:29Z2021-08-01T09:26:29ZNigeria isn’t ready to deal with rising COVID-19 cases<figure><img src="https://images.theconversation.com/files/413520/original/file-20210728-13-auulbi.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Nigeria must increase its testing capacity to deal with rising COVID-19 cases </span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/health-worker-takes-a-swab-from-a-man-during-a-community-news-photo/1210354602?adppopup=true">Olukayode Jaiyeola/NurPhoto via Getty Images </a></span></figcaption></figure><p><em>With <a href="https://punchng.com/covid-19-nigeria-records-10-cases-of-delta-variant-ncdc/?utm_source=auto-read-also&utm_medium=web&">rising cases</a> of the Delta variant of the SARS-CoV-2 virus in Nigeria, there is heightened concern about how well the country is prepared to deal with them. The Conversation Africa’s Wale Fatade asked public health expert Doyin Odubanjo what Nigeria should do.</em> </p>
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<h2>What makes the Delta variant different from other COVID-19 variants?</h2>
<p>The variant has now become the main one of concern <a href="https://www.reuters.com/business/healthcare-pharmaceuticals/delta-covid-variant-now-dominant-worldwide-drives-surge-us-deaths-officials-2021-07-16/">globally</a> and is believed to be the cause of the <a href="https://www.bbc.com/news/world-57907681">recent surge</a> in cases seen in Asia and Africa. It is also believed to be behind the rise in cases even in places with good population vaccination rates such as <a href="https://www.usnews.com/news/top-news/articles/2021-07-26/how-the-delta-variant-upends-assumptions-about-the-coronavirus">Israel and the United Kingdom</a>. </p>
<p>The Delta variant, from all available evidence, has mutations that makes it <a href="https://www.yalemedicine.org/news/5-things-to-know-delta-variant-covid">more contagious</a>. It also replicates very quickly, resulting in high viral loads. This can lead to severe illness requiring <a href="https://www.gavi.org/vaccineswork/five-things-we-know-about-delta-coronavirus-variant-and-two-things-we-still-need">hospitalisation</a> and may take longer to clear and achieve a negative COVID-19 test result. </p>
<p>The combination of higher <a href="https://www.gavi.org/vaccineswork/five-things-we-know-about-delta-coronavirus-variant-and-two-things-we-still-need">transmissibility</a> – more people get infected faster – and higher viral load – <a href="https://www.hackensackmeridianhealth.org/HealthU/2021/07/14/3-things-you-need-to-know-about-the-delta-variant/">people get more sick</a> – means that the variant causes more cases per day. Thus it has the tendency to overwhelm the healthcare system, which could run out of bed spaces, oxygen and other essentials.</p>
<h2>How bad is the situation in Nigeria as regards the Delta variant?</h2>
<p>Unfortunately, it is difficult to say. This is because we are failing where surveillance for COVID-19 is concerned. Recent reports show that <a href="https://punchng.com/covid-19-testing-stops-in-13-states-delta-variant-hitting-unvaccinated-nigerians/">13 states </a> have stopped testing for COVID-19 while others are increasingly relying on private laboratories to do the tests at a higher cost. It is impossible to monitor the disease spread or progression without testing.</p>
<p>To make matters worse, to know the impact of the Delta variant, there is a need to go beyond the <a href="https://my.clevelandclinic.org/health/diagnostics/21462-covid-19-and-pcr-testing">polymerase chain reaction</a> (PCR) tests being done or reported. There is a need to do genomic studies – this is a study of what makes up the virus – on the positive cases to know what variant they may be and even monitor the development of new variants. Such genomic studies are not yet being done systematically.</p>
<h2>How prepared is Nigeria to deal with it?</h2>
<p>Nigeria is not in any way prepared to deal with a serious rise in COVID-19 cases as our health system is more challenged than it was before the pandemic. The staff morale is very low and <a href="https://www.dw.com/en/nigeria-saving-lives-amid-the-health-care-crisis/av-57318575">health worker migration</a> is increasing at an alarming rate. Added to that are <a href="https://www.globalcitizen.org/en/content/nigeria-doctors-strike-COVID-19-health-care/?template=next">strike actions</a> or threats. And, perhaps due to the state of the economy, the political will and leadership required to manage the COVID-19 outbreak is fading away.</p>
<p>Worse still, we have not succeeded in engaging the public effectively and consequently have a politically charged environment with a gulf widening between the government and the people. This means that non-pharmaceutical measures like the use of face masks, social distancing and lockdowns may be even more difficult to implement now as people are less likely to cooperate. Attempts to enforce such measures may even result in civil disturbances.</p>
<p>So, Nigeria cannot afford another wave of COVID-19 cases and definitely nothing on the scale of what the Delta variant has caused in <a href="https://www.washingtonpost.com/world/2021/07/21/coronavirus-latest-updates/">other countries</a>.</p>
<h2>What should be done to keep it at bay?</h2>
<p>I do not know if we can talk of keeping it at bay as the Delta variant has already been identified in parts of Nigeria. So, we need to monitor and manage its spread in the country. We must also keep a close watch on our borders to ensure that new cases are not imported. To monitor it will require that our testing capacity is maintained as a public service and is not just left to private laboratories, which will exclude many people because of cost. We must also go the extra mile of doing genomic studies systematically as part of our surveillance.</p>
<p>We must explore community engagement strategies more than ever to get people to make COVID-19 prevention a personal responsibility.</p><img src="https://counter.theconversation.com/content/165201/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Doyin Odubanjo 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>Nigeria must increase its testing capacity and do more genomic studies to deal effectively with the Delta variant of COVID-19.Doyin Odubanjo, Executive Secretary, Nigerian Academy of ScienceLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1644252021-07-22T14:56:00Z2021-07-22T14:56:00ZWe created a tool to help predict COVID-19 increases in African countries<figure><img src="https://images.theconversation.com/files/412108/original/file-20210720-27-15gx2d2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">shutterstock</span> </figcaption></figure><p>One of the obstacles if you are trying to guide policy and protect people from COVID-19 is the bewildering amount of data available every day. We are awash in information, but everyone wants to distil insight that makes sense from this. </p>
<p>Policymakers need to make sense of the data so as to predict and manage what’s happening. To address this need, we developed a data-driven disease surveillance framework to track and predict country-level COVID-19 cases. </p>
<p>We are an international team of scientists working on novel ways of <a href="https://reporter.nih.gov/search/DJPw96zywUeRgRvjBN83-w/project-details/10006784">predicting</a> diagnosis when presented with a serious infection. We start with model-based prediction of infectious diseases. Ultimately we are interested in improving treatment when the infectious agent is unknown. But for COVID-19, our methods are valuable for understanding and predicting the infection at the population level. </p>
<p>Our focus has been on infant infections in East Africa and in Southeast Asia. For over 15 years, we’ve <a href="https://news.psu.edu/video/602235/2019/12/17/research/liveb1g-infectious-disease-forecasting">worked</a> with Ugandan hospitals, healthcare providers, planners, economists, engineers and policymakers on predictive mapping of infant infections and birth defects. </p>
<p>Early in 2020 we began discussing ways to use our skills to contribute to the fight against the novel SARS‑CoV‑2, the virus causing COVID-19. We tapped into a wide network of experts, organisations and local authorities. They helped us adapt our approach to generate predictions for week-ahead COVID-19 case numbers.</p>
<p>We <a href="https://www.pnas.org/content/118/28/e2026664118">created a set</a> of visualisation tools and graphs that are very easy to interpret. We worked closely with the Ugandan planners and economists to be sure that what we created together could be implemented. We built on a proven method that was already in use in the UK and several European countries, adapting it to the whole of the African continent.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/411930/original/file-20210719-19-115uf3p.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Layered map of the African continent, with layers displaying case numbers, humidity, rainfall, population, and temperature." src="https://images.theconversation.com/files/411930/original/file-20210719-19-115uf3p.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/411930/original/file-20210719-19-115uf3p.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=565&fit=crop&dpr=1 600w, https://images.theconversation.com/files/411930/original/file-20210719-19-115uf3p.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=565&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/411930/original/file-20210719-19-115uf3p.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=565&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/411930/original/file-20210719-19-115uf3p.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=710&fit=crop&dpr=1 754w, https://images.theconversation.com/files/411930/original/file-20210719-19-115uf3p.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=710&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/411930/original/file-20210719-19-115uf3p.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=710&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">The model used in this study integrates multiple sets of data to predict COVID-19 transmission. Layers, from top to bottom: COVID-19 case counts, specific humidity, rainfall, population, and temperature.</span>
<span class="attribution"><span class="source">Andrew Geronimo</span></span>
</figcaption>
</figure>
<h2>How the model is built</h2>
<p>We used a relatively simple model, by mathematical standards, to base the computer codes. We incorporated the daily case reports from each country, as well as the characterisation of the Human Development Index for each country, population, the stringency of social measures to control the infection, and meteorological data. We took into account the cases in neighbouring countries, as well as whether the country is landlocked.</p>
<p>Our model used the case numbers reported up to and including the previous week, to predict the case numbers in the week ahead. </p>
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<em>
<strong>
Read more:
<a href="https://theconversation.com/predicting-covid-19-what-applying-a-model-in-kenya-would-look-like-134675">Predicting COVID-19: what applying a model in Kenya would look like</a>
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<p>The model included past weather observations of temperature, rainfall, and specific humidity. Some of these environmental factors have been <a href="https://theconversation.com/research-shows-coronavirus-thrives-in-dry-air-and-august-is-coastal-australias-least-humid-month-144508">implicated</a> in COVID-19 transmission outside of Africa. We modified the weather data for each country by adjusting for population. In Algeria, for example, where much of the population lives along the cooler, wetter coast, we emphasise or weight the weather data in proportion to where people live (and ignore weather data over unpopulated desert). </p>
<p>We took into account cross-border flow of goods and commerce, since for landlocked African countries, this is their lifeline for goods and services. </p>
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Read more:
<a href="https://theconversation.com/how-covid-19-affected-informal-cross-border-trade-between-uganda-and-drc-160124">How COVID-19 affected informal cross-border trade between Uganda and DRC</a>
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<p>It is difficult to obtain population mobility data for Africa, so we used the cases in all other countries to test whether those cases were associated with the next week’s cases in nearby countries. This proved very effective.</p>
<p>We factored in the economics of different countries, as well as the evolution of real-time governmental stringency policies such as lockdowns and border closures. </p>
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<em>
<strong>
Read more:
<a href="https://theconversation.com/kenya-responded-fast-to-ebola-scare-but-cross-border-risk-remains-high-119173">Kenya responded fast to Ebola scare, but cross-border risk remains high</a>
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<p>And then we needed to see if we could get an understandable summary of the current state of the pandemic in Africa, and whether predictions a week or so ahead were accurate compared with the actual measured case numbers.</p>
<h2>From predictions to policy</h2>
<p>The predictions were much more accurate than we had anticipated. We employed a rigorous way of scoring predictions for each country. Only for a few countries were these predictions inaccurate (Burundi, Cameroon, Somalia, and Botswana). To visualise these predictions, we created a set of tools and graphs that are very easy to interpret. A policy person needs to see what the present situation is, how that current state got there from past events, and what will happen in the future. The <a href="http://146.186.149.88:3838/current/COVID19-HHH4-Africa/">websites</a> we created will enable anyone to use a computer mouse to select their country, or the continent, and see the results of the model. No math or PhD required. </p>
<p>For the technical scientists in other countries or the global agencies, we are sharing our full code. We wrote this code in free open-source software, and all the data that the model uses is from free open-source websites, so that there are no barriers to implementation for anyone. Our methods stress data that is predictive, and automatically ignores data that is not contributing to an understanding of the cases next week. This is an old trick in economics, and we found that it works very well in predicting infectious cases. </p>
<p>The <a href="https://www.pnas.org/content/118/28/e2026664118">publication</a> contains links to computer code that runs the model, and to the graphical display of these findings, for anyone to use.</p>
<p>Our colleagues in Uganda are <a href="https://www.facebook.com/UgandaMediaCentre/videos/1210133216076390/?app=fbl">finding this model useful</a> in predicting cases a week ahead. They are using it to help inform social policies and lockdowns as they track the effect on cases, and plan for reopening as case pressure eases. Because the effect of control measures is delayed by a period of weeks, prediction enables better policy planning. But like so many things in nature, such as the weather, predictions beyond two weeks are often very uncertain. </p>
<h2>Looking ahead</h2>
<p>One of the clear implications from our findings is that pandemics are crises that no country can best manage on its own. We encourage neighbouring African countries to share data and cooperate on travel and border management. </p>
<p>This pandemic will end through massive vaccinations in Africa. Until billions of additional safe and effective SARS-CoV-2 vaccines <a href="https://www.nature.com/articles/s41577-021-00579-y">become available for Africa</a>, predictive methods such as this to help inform policy will be needed.</p><img src="https://counter.theconversation.com/content/164425/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Steven J. Schiff receives funding from the US National Institutes of Health (R01-AI145057-01).</span></em></p><p class="fine-print"><em><span>Andrew Geronimo receives funding from the National Institutes of Health (R01-AI145057-01)</span></em></p><p class="fine-print"><em><span>Claudio Fronterre receives funding from the National Institutes of Health (R01-AI145057-01). </span></em></p><p class="fine-print"><em><span>Paddy Ssentongo receives funding from the National Institutes of Health (R01-AI145057-01)</span></em></p>Policymakers need to make sense of the data so as to predict and manage what’s happening. To address this need, we developed a visualisation tool to track and predict country-level COVID-19 cases.Steven J. Schiff, Brush Chair Professor of Engineering, Departments of Neurosurgery, Engineering Science and Mechanics, and Physics, Penn StateAndrew Geronimo, Assistant Research Professor, Department of Neurosurgery, Penn StateClaudio Fronterre, Lecturer in Biostatistics, Centre for Health Informatics, Computing, and Statistics, Lancaster UniversityPaddy Ssentongo, Assistant Research Professor, Center for Neural Engineering, Department of Engineering Science and Mechanics, Penn StateLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1604292021-06-01T13:02:02Z2021-06-01T13:02:02ZThe next pandemic is already happening – targeted disease surveillance can help prevent it<figure><img src="https://images.theconversation.com/files/401991/original/file-20210520-19-yuhq7i.jpeg?ixlib=rb-1.1.0&rect=0%2C0%2C7000%2C3919&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Sustained surveillance for disease outbreaks at global hot spots may be the key to preventing the next pandemic.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/photo/rendering-futuristic-world-map-interactive-royalty-free-image/1216889103?adppopup=true">MR.Cole_Photographer/Getty Images</a></span></figcaption></figure><p>As more and more people around the world are getting vaccinated, one can almost hear the collective sigh of relief. But the next pandemic threat is likely already making its way through the population right now. </p>
<p>My research as an infectious disease epidemiologist has found that there is a simple strategy to mitigate emerging outbreaks: proactive, real-time surveillance in settings where animal-to-human disease spillover is most likely to occur. </p>
<p>In other words, don’t wait for sick people to show up at a hospital. Instead, monitor populations where disease spillover actually happens.</p>
<h2>The current pandemic prevention strategy</h2>
<p>Global health professionals have long known that pandemics fueled by <a href="https://www.news-medical.net/health/What-is-a-Spillover-Event.aspx">zoonotic disease spillover</a>, or animal-to-human disease transmission, were a problem. In 1947, the World Health Organization established a global network of hospitals to <a href="https://www.who.int/influenza/gip-anniversary/en/">detect pandemic threats</a> through a process called <a href="https://www.cdc.gov/nssp/overview.html">syndromic surveillance</a>. The process relies on standardized symptom checklists to look for signals of emerging or reemerging diseases of pandemic potential among patient populations with symptoms that can’t be easily diagnosed.</p>
<p>This clinical strategy relies both on infected individuals coming to <a href="https://apps.who.int/iris/bitstream/handle/10665/259884/9789241513623-eng.pdf">sentinel hospitals</a> and medical authorities who are <a href="https://www.bbc.com/news/world-asia-china-51364382">influential and persistent</a> enough to raise the alarm. </p>
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<figcaption><span class="caption">Sentinel surveillance recruits select health institutions and groups to monitor potential disease outbreaks.</span></figcaption>
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<p>There’s only one hitch: By the time someone sick shows up at a hospital, an outbreak has already occurred. In the case of <a href="https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it">SARS-CoV-2, the virus that causes COVID-19</a>, it was likely widespread long before it was detected. This time, the clinical strategy alone failed us.</p>
<h2>Zoonotic disease spillover is not one and done</h2>
<p>A more proactive approach is currently gaining prominence in the world of pandemic prevention: viral evolutionary theory. This theory suggests that <a href="https://doi.org/10.3390/v13040637">animal viruses become dangerous human viruses</a> incrementally over time through frequent zoonotic spillover. </p>
<p>It’s not a one-time deal: An “intermediary” animal such as a civet cat, pangolin or pig may be required to mutate the virus so it can make initial jumps to people. But the final host that allows a variant to become fully adapted to humans may be humans themselves.</p>
<p>Viral evolutionary theory is playing out in real time with the rapid development of <a href="https://www.cdc.gov/coronavirus/2019-ncov/transmission/variant.html">COVID-19 variants</a>. In fact, an international team of scientists have proposed that undetected human-to-human transmission after an animal-to-human jump is the likely <a href="https://doi.org/10.1038/s41591-020-0820-9">origin of SARS-CoV-2</a>.</p>
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<figcaption><span class="caption">Viruses jump species through a process of random mutations that allow them to successfully infect their hosts.</span></figcaption>
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<p>When novel zoonotic viral disease outbreaks like Ebola first came to the world’s attention in the 1970s, research on the extent of disease transmission relied on <a href="https://www.cdc.gov/coronavirus/2019-ncov/testing/serology-overview.html">antibody assays</a>, blood tests to identify people who have already been infected. Antibody surveillance, also called <a href="https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/geographic-seroprevalence-surveys.html">serosurveys</a>, test blood samples from target populations to identify how many people have been infected. Serosurveys help determine whether diseases like Ebola are circulating undetected.</p>
<p>Turns out they were: Ebola antibodies were found in more than <a href="https://doi.org/10.1016/S0769-2617(82)80028-2">5% of people tested in Liberia in 1982</a>, decades before the West African epidemic in 2014. These results support viral evolutionary theory: It takes time – sometimes a lot of time – to make an animal virus dangerous and transmissible between humans. </p>
<p>What this also means is that scientists have a chance to intervene.</p>
<h2>Measuring zoonotic disease spillover</h2>
<p>One way to take advantage of the lead time for animal viruses to fully adapt to humans is long-term, repeated surveillance. Setting up a <a href="http://dx.doi.org/10.2471/BLT.16.175984">pandemic threats warning system</a> with this strategy in mind could help <a href="https://doi.org/10.3390/v13040637">detect pre-pandemic viruses</a> before they become harmful to humans. And the best place to start is directly at the source.</p>
<p>My team worked with <a href="https://www.scientificamerican.com/article/how-chinas-bat-woman-hunted-down-viruses-from-sars-to-the-new-coronavirus1/">virologist Shi Zhengli</a> of the Wuhan Institute of Virology to develop a human antibody assay to test for a very distant cousin of SARS-CoV-2 found in bats. We established proof of zoonotic spillover in a small 2015 serosurvey in Yunnan, China: <a href="https://doi.org/10.1007/s12250-018-0012-7">3% of study participants living near bats</a> carrying this SARS-like coronavirus tested antibody positive. But there was one unexpected result: None of the previously infected study participants reported any harmful health effects. Earlier spillovers of SARS coronaviruses – like the first SARS epidemic in 2003 and Middle Eastern Respiratory Syndrome (MERS) in 2012 – had caused high levels of illness and death. This one did no such thing. </p>
<p>Researchers conducted a larger study in Southern China between 2015 and 2017. It’s a region home to bats known to carry SARS-like coronaviruses, including the one that caused the <a href="https://doi.org/10.1038/nature12711">original 2003 SARS pandemic</a> and the one <a href="https://doi.org/10.1038/s41586-020-2012-7">most closely related to SARS-CoV-2</a>.</p>
<p>Fewer than 1% of participants in this study tested antibody positive, meaning they had been previously infected with the SARS-like coronavirus. Again, none of them reported negative health effects. But syndromic surveillance – the same strategy used by sentinel hospitals – revealed something even more unexpected: An additional <a href="https://doi.org/10.1016/j.bsheal.2019.10.004">5% of community participants</a> reported symptoms consistent with SARS in the past year.</p>
<p>This study did more than just provide the biological evidence needed to establish proof of concept to measure zoonotic spillover. The pandemic threats warning system also picked up a signal for a SARS-like infection that couldn’t yet be detected through blood tests. It may even have detected early variants of SARS-CoV-2. </p>
<p>Had surveillance protocols been in place, these results would have triggered a search for community members who may have been part of an undetected outbreak. But without an established plan, the signal was missed.</p>
<h2>From prediction to surveillance to genetic sequencing</h2>
<p>The lion’s share of pandemic prevention funding and effort over the past two decades has focused on discovering wildlife pathogens, and predicting pandemics before animal viruses can infect humans. But this approach has not predicted any major zoonotic disease outbreaks – including H1N1 influenza in 2009, MERS in 2012, the West African Ebola epidemic in 2014 or the current COVID-19 pandemic.</p>
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<figcaption><span class="caption">Gregory Gray and his team at Duke University recently discovered a novel canine coronavirus at a global “hot spot” through surveillance and genetic sequencing.</span></figcaption>
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<p>Predictive modeling has, however, provided robust heat maps of the <a href="https://doi.org/10.1038/s41467-017-00923-8">global “hot spots”</a> where zoonotic spillover is most likely to occur. </p>
<p>Long-term, regular surveillance at these “hot spots” could detect spillover signals, as well as any changes that occur over time. These could include an uptick in antibody-positive individuals, increased levels of illness and demographic changes among infected people. As with any proactive disease surveillance, if a signal is detected, an outbreak investigation would follow. People identified with <a href="https://doi.org/10.1038/d41586-018-05373-w">symptoms that can’t be easily diagnosed</a> can then be screened using genetic sequencing to characterize and identify new viruses.</p>
<p>This is exactly what Greg Gray and his team from Duke University did in their search for <a href="https://doi.org/10.1093/cid/ciaa347">undiscovered coronaviruses</a> in rural Sarawak, Malaysia, a known “hot spot” for zoonotic spillover. Eight of 301 specimens collected from pneumonia patients hospitalized in 2017-2018 were found to have a canine coronavirus never before seen in humans. Complete viral genome sequencing not only suggested that it had recently jumped from an animal host – it also harbored the same mutation that made both SARS and SARS-CoV-2 so deadly.</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>Let’s not miss the next pandemic warning signal</h2>
<p>The good news is that surveillance infrastructure in global “hot spots” already exists. The <a href="https://www.cordsnetwork.org/">Connecting Organisations for Regional Disease Surveillance</a> program links six regional disease surveillance networks in 28 countries. They pioneered “participant surveillance,” partnering with communities at high risk for both initial zoonotic spillover and the gravest health outcomes to contribute to prevention efforts.</p>
<p>For example, Cambodia, a country at risk of pandemic avian influenza spillover, established a free national hotline for community members to report animal illnesses directly to the Ministry of Health in real time. Boots-on-the-ground approaches like these are key to a timely and coordinated public health response to stop outbreaks before they become pandemics.</p>
<p>It is easy to miss warning signals when global and local priorities are tentative. The same mistake need not happen again.</p><img src="https://counter.theconversation.com/content/160429/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Maureen Miller received funding from USAID that was used to develop the pandemic-threats surveillance warning system discussed in this article. </span></em></p>A more coordinated effort by scientists, stakeholders and community members will be required to stop the next deadly virus that’s already circulating in our midst.Maureen Miller, Adjunct Associate Professor of Epidemiology, Columbia UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1575402021-03-31T12:17:36Z2021-03-31T12:17:36ZGenomic surveillance: What it is and why we need more of it to track coronavirus variants and help end the COVID-19 pandemic<figure><img src="https://images.theconversation.com/files/392394/original/file-20210329-19-1jea5af.jpg?ixlib=rb-1.1.0&rect=0%2C422%2C6377%2C4044&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Sequencing the genetic code of virus samples taken from COVID-19 patients reveals how SARS-CoV-2 is spreading and changing.</span> <span class="attribution"><span class="source">Nate Langer/UPMC</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p>“You can’t fix what you don’t measure” is a maxim in the business world. And it holds true in the world of public health as well.</p>
<p>Early in the pandemic, the United States <a href="https://theconversation.com/making-coronavirus-testing-easy-accurate-and-fast-is-critical-to-ending-the-pandemic-the-us-response-is-falling-far-short-142366">struggled to meet the demand to test people for SARS-CoV-2</a>. That failure meant officials didn’t know the true number of people who had COVID-19. They were left to respond to the pandemic without knowing how quickly it was spreading and what interventions minimized risks.</p>
<p>Now the U.S. faces a similar issue with a different type of test: genetic sequencing. Unlike a COVID-19 test that diagnoses infection, genetic sequencing decodes the genome of SARS-CoV-2 virus in samples from patients. Knowing the genome sequence helps researchers understand two important things – how the virus is mutating into variants and how it’s traveling from person to person.</p>
<p>Before the COVID-19 pandemic, this kind of genomic surveillance was reserved mainly for conducting small studies of antibiotic-resistant bacteria, investigating outbreaks and monitoring influenza strains. As <a href="https://scholar.google.com/citations?user=dcezvIQAAAAJ&hl=en&oi=ao">genomic</a> <a href="https://scholar.google.com/citations?user=v88WxTwAAAAJ&hl=en&oi=ao">epidemiologists</a> and <a href="https://scholar.google.com/citations?user=pWTer_MAAAAJ&hl=en&oi=ao">infectious disease</a> experts, we perform these kinds of tests every day in our labs, working to puzzle out how the coronavirus is evolving and moving through the population.</p>
<p>Particularly now, as new coronavirus variants of concern continue to emerge, genomic surveillance has an important role to play in helping bring the pandemic under control.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/392402/original/file-20210329-13-2kcaj2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="woman in PPE inserts specimens into lab equipment" src="https://images.theconversation.com/files/392402/original/file-20210329-13-2kcaj2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/392402/original/file-20210329-13-2kcaj2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/392402/original/file-20210329-13-2kcaj2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/392402/original/file-20210329-13-2kcaj2.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/392402/original/file-20210329-13-2kcaj2.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/392402/original/file-20210329-13-2kcaj2.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/392402/original/file-20210329-13-2kcaj2.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 load patient sample specimens into a robotic liquid handler to prepare them for sequencing.</span>
<span class="attribution"><span class="source">Nate Langer/UPMC</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Tracking virus’s travels and changes</h2>
<p>Genome sequencing involves deciphering the order of the nucleotide molecules that spell out a particular virus’s genetic code. For the coronavirus, that genome contains a string of around 30,000 nucleotides. Each time the virus replicates, errors are made. These mistakes in the genetic code are called mutations.</p>
<p>Most mutations do not significantly change the function of the virus. Others may be important, particularly when they <a href="https://doi.org/10.1038/d41586-021-00031-0">encode vital elements, such as the coronavirus spike protein</a> that <a href="https://doi.org/10.1038/s41401-020-0485-4">acts as a key to enter human cells</a> and cause infection. <a href="https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html">Spike mutations may influence</a> how infectious the virus is, how severe the infection may become, and how well current vaccines protect against it.</p>
<p>Researchers are particularly on the lookout <a href="https://doi.org/10.1038/d41586-020-02544-6">for any mutations</a> that distinguish virus specimens from others or match known variants.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/392306/original/file-20210329-15-1g76nbr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="phylogenetic tree of SARS-CoV-2 from COVID-19 patients" src="https://images.theconversation.com/files/392306/original/file-20210329-15-1g76nbr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/392306/original/file-20210329-15-1g76nbr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=418&fit=crop&dpr=1 600w, https://images.theconversation.com/files/392306/original/file-20210329-15-1g76nbr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=418&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/392306/original/file-20210329-15-1g76nbr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=418&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/392306/original/file-20210329-15-1g76nbr.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=525&fit=crop&dpr=1 754w, https://images.theconversation.com/files/392306/original/file-20210329-15-1g76nbr.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=525&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/392306/original/file-20210329-15-1g76nbr.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=525&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Researchers can build what are essentially family trees for SARS-CoV-2, called phylogenetic trees, that map out how closely related various virus samples are. The red dots here denote patients who are part of a single outbreak, while the others are COVID-19 patients with unrelated strains.</span>
<span class="attribution"><span class="source">Lee Harrison</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Scientists can use the genetic sequences to track how the virus is being transmitted in the community and in health care facilities. For example, if two people have viral sequences with zero or very few differences between them, it suggests the virus was transmitted from one to the other, or from a common source. On the other hand, if there are a lot of differences between the sequences, these two individuals did not catch the virus from each other.</p>
<p>This kind of information lets public health officials tailor interventions and recommendations for the public. Genomic surveillance can also be important in health care settings. <a href="https://doi.org/10.1093/cid/ciaa512">Our hospital, for example</a>, <a href="https://doi.org/10.1093/cid/ciaa1887">uses genomic surveillance</a> to <a href="https://doi.org/10.1017/ice.2018.343">detect outbreaks</a> that <a href="https://doi.org/10.1093/cid/ciz666">otherwise are missed</a> <a href="https://doi.org/10.1016/j.jbi.2019.103126">by traditional methods</a>.</p>
<h2>Surveillance can provide a warning</h2>
<p>But how do researchers know if variants are emerging and if people should be concerned?</p>
<p>Take the B.1.1.7 variant, first detected in the United Kingdom, which has strong genomic surveillance in place. Public health investigators discovered that a certain sequence with multiple changes, including the spike protein, was <a href="https://www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201">on the rise in the U.K.</a> Even amid a national shutdown, <a href="https://www.medrxiv.org/content/10.1101/2020.12.24.20248822v3">this version of the virus was spreading rapidly</a>, more so than its predecessors.</p>
<p>Scientists looked further into this variant’s genome to determine how it was overcoming the distancing recommendations and other public health interventions. They found particular mutations in the spike protein – with names like ∆69-70 and N501Y – that made it easier for the virus to infect human cells. Preliminary research suggests these mutations translated into a higher rate of transmission, meaning that <a href="https://www.medrxiv.org/content/10.1101/2020.12.24.20248822v3">they spread much more easily</a> from person to person than prior strains.</p>
<p>Vaccine developers and other scientists then used this genetic information to test whether the new variants change how well the vaccines work. Fortunately, preliminary research that has not yet been peer-reviewed found that the B.1.1.7 variant <a href="https://www.medrxiv.org/content/10.1101/2021.02.02.21250799v1">remains susceptible to current vaccines</a>. More worrisome are other variants such as P.1. and B.1.351, first discovered in Brazil and South Africa, respectively, that <a href="https://doi.org/10.1038/s41591-021-01318-5">can evade some antibodies produced by the vaccines</a>. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/392654/original/file-20210330-23-1ogrjdh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="doctor checking on a COVID-19 patient in a hospital bed" src="https://images.theconversation.com/files/392654/original/file-20210330-23-1ogrjdh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/392654/original/file-20210330-23-1ogrjdh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/392654/original/file-20210330-23-1ogrjdh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/392654/original/file-20210330-23-1ogrjdh.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/392654/original/file-20210330-23-1ogrjdh.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/392654/original/file-20210330-23-1ogrjdh.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/392654/original/file-20210330-23-1ogrjdh.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 strong surveillance system would sequence a set proportion of those tested for COVID-19.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/medical-director-of-the-intensive-care-unit-dr-thomas-news-photo/1230420715">Apu Gomes/AFP via Getty Images</a></span>
</figcaption>
</figure>
<h2>Setting up a genomic surveillance system</h2>
<p>Detecting variants of concern and developing a public health response to them requires a robust genomic surveillance program. That translates to scientists sequencing virus samples from about 5% of the total number of COVID-19 patients, selected to be representative of the populations most at risk from the disease. Without this genomic information, new variants may spread rampantly and undetected through the country and globally.</p>
<p>So how is the U.S. performing in the <a href="https://www.cdc.gov/amd/what-we-do/amd-at-cdc.html">area of genomic surveillance</a>? Not very well, and <a href="https://www.sciencemag.org/news/2021/02/us-rushes-fill-void-viral-sequencing-worrisome-coronavirus-variants-spread">well behind other developed countries</a>, coming in 34th in the <a href="https://covidcg.org/?tab=global_sequencing#">number of SARS-CoV-2 genomes sequenced per number of cases</a>. Even within the U.S., there is <a href="https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/genomic-surveillance-dashboard.html">large variation among states</a> for genomes sequenced per number of cases, ranging from Tennessee at 0.09% to Wyoming at 5.82%.</p>
<p>But this is about to change. The Centers for Disease Control and Prevention, in conjunction with other agencies of the federal government, is partnering with private labs, state and local public health labs, academia and others <a href="https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance.html">to increase genomic surveillance capacity in the U.S.</a></p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/392406/original/file-20210329-23-rv2t7f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Masked woman and man, pointing at computer screen, with a map of genetic relationships" src="https://images.theconversation.com/files/392406/original/file-20210329-23-rv2t7f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/392406/original/file-20210329-23-rv2t7f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/392406/original/file-20210329-23-rv2t7f.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/392406/original/file-20210329-23-rv2t7f.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/392406/original/file-20210329-23-rv2t7f.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/392406/original/file-20210329-23-rv2t7f.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/392406/original/file-20210329-23-rv2t7f.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">Author Lee Harrison and a colleague surmise the relationship between various virus samples based on their genomic sequences.</span>
<span class="attribution"><span class="source">Nate Langer/UPMC</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<p>Reaching the new <a href="https://www.nytimes.com/2021/02/17/health/coronavirus-variant-sequencing.html">national goal of 5% set by the White House</a> is not as simple as footing a hefty bill for a laboratory to perform the tests, though. Laboratories must collect the samples, often from different sources: public health labs, hospitals, clinics, private testing labs. Once the sequencing test is performed, bioinformaticians use advanced programs to identify important mutations. Next, public health professionals merge the genomic data with the epidemiological data to determine how the virus is spreading. All of this requires investment in training people to perform these tasks as a team.</p>
<p>Ultimately, to be useful, a successful genomic surveillance program must be fast and the data needs to be made publicly available immediately to inform real-time decision-making by public health officials and vaccine manufacturers. Such a program is one of the public health tools that will help bring the current pandemic under control and set up the U.S. to be able to respond to future pandemics.</p>
<p>[<em>Get the best of The Conversation, every weekend.</em> <a href="https://theconversation.com/us/newsletters/weekly-highlights-61?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=weeklybest">Sign up for our weekly newsletter</a>.]</p><img src="https://counter.theconversation.com/content/157540/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Lee Harrison receives funding from the National Institutes of Health for his research on the genomic epidemiology of hospital outbreaks. He has presented this work at a scientific advisory board meeting of Infectious Diseases Connect. </span></em></p><p class="fine-print"><em><span>Vaughn Cooper is co-founder of and consultant for Microbial Genome Sequencing Center, LLC. He has received support from the National Institutes of Health for his study of how microbes evolve during infection.</span></em></p><p class="fine-print"><em><span>Alexander Sundermann 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 US lags in testing coronavirus samples from COVID-19 patients, which can help track the spread of the virus and the emergence of new variants. But labs are ramping up this crucial surveillance.Alexander Sundermann, Assistant Professor of Infectious Diseases, University of PittsburghLee Harrison, Professor of Epidemiology, Medicine, and Infectious Diseases and Microbiology, University of PittsburghVaughn Cooper, Professor of Microbiology and Molecular Genetics, University of PittsburghLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1573182021-03-18T01:32:42Z2021-03-18T01:32:42ZWhat is Mycoplasma genitalium, the common STI you’ve probably never heard of<figure><img src="https://images.theconversation.com/files/390232/original/file-20210317-21-14e4lym.jpg?ixlib=rb-1.1.0&rect=0%2C1%2C998%2C661&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/close-man-hands-holding-his-crotch-769304695">from www.shutterstock.com</a></span></figcaption></figure><p><em><a href="https://www.fpv.org.au/for-you/sexually-transmissible-infections-blood-borne-viruses/mycoplasma-genitalium">Mycoplasma genitalium</a></em> (MG) is a sexually transmitted infection (STI) with many of the hallmarks of its better-known counterpart, <a href="https://www.betterhealth.vic.gov.au/health/conditionsandtreatments/chlamydia">chlamydia</a>.</p>
<p>You can have MG without knowing it, or have symptoms; it can affect men and women, and it can be treated with antibiotics. </p>
<p>However, unlike chlamydia, we only have a limited number of antibiotics to treat it, due to a quirk in its cellular structure and the growing threat of antibiotic resistance. The antibiotics we need to use with resistant MG can also, uncommonly, have serious side-effects.</p>
<p>Here’s what you need to know about this common STI.</p>
<h2>What is it? How do I get it? How common is it?</h2>
<p>MG can affect both men and women, and is passed from person to person via their body fluids when they have sex. That can be via penile-vaginal sex or via penile-anal sex. Transmission via oral sex isn’t thought to be a big factor.</p>
<p>Several studies tell us MG is common, perhaps as common as chlamydia.</p>
<p>UK and US <a href="https://pubmed.ncbi.nlm.nih.gov/26534946/">data</a> <a href="https://pubmed.ncbi.nlm.nih.gov/33560093/">show</a> 1-2% of the adult population have it (making it about <a href="https://pubmed.ncbi.nlm.nih.gov/31794495/">as common as chlamydia</a>), and it is as common in men as in women. </p>
<p>In research yet to be published, when we tested women who walked through the door of our sexual health service in Melbourne, 6% had MG, which was as common as chlamydia (7%) in women in the same study. Of women with MG, roughly the same number had symptoms compared to no symptoms. When we tested <a href="https://pubmed.ncbi.nlm.nih.gov/30882306/">gay men without symptoms</a> who attended our service, 10% had MG.</p>
<p>However, we’re not entirely sure how many people are infected with MG throughout Australia. That’s because Australia has yet to set up a formal surveillance network (we’re in the middle of setting that up at the moment). MG is also not a notifiable disease yet. That means doctors or laboratories don’t have to tell health authorities when they have a case.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/390234/original/file-20210317-21-1ghrluf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Mycoplasma genitalium, as 3D rendered image" src="https://images.theconversation.com/files/390234/original/file-20210317-21-1ghrluf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/390234/original/file-20210317-21-1ghrluf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=300&fit=crop&dpr=1 600w, https://images.theconversation.com/files/390234/original/file-20210317-21-1ghrluf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=300&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/390234/original/file-20210317-21-1ghrluf.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=300&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/390234/original/file-20210317-21-1ghrluf.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=377&fit=crop&dpr=1 754w, https://images.theconversation.com/files/390234/original/file-20210317-21-1ghrluf.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=377&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/390234/original/file-20210317-21-1ghrluf.jpg?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">Mycoplasma genitalium is a sexually transmitted infection that affects men and women.</span>
<span class="attribution"><a class="source" href="https://www.shutterstock.com/image-illustration/bacteria-mycoplasma-genitalium-3d-illustration-causative-1415788364">from www.shutterstock.com</a></span>
</figcaption>
</figure>
<h2>How do I know if I have it?</h2>
<p>If you do have symptoms, these can resemble those of chlamydia. So the best thing is to go to your GP or sexual health clinic for a checkup, as the treatments are different.</p>
<p>If you’re a man with symptoms, they can vary from mild to moderate and include:</p>
<ul>
<li><p>mild irritation, an itch, or a burning sensation when urinating</p></li>
<li><p>a penile discharge, which may be clear or more like pus.</p></li>
</ul>
<p>For women, symptoms may include:</p>
<ul>
<li><p>a vaginal discharge</p></li>
<li><p>bleeding or pain with sex</p></li>
<li><p>abdominal pain (which may be a sign of <a href="https://www.betterhealth.vic.gov.au/health/healthyliving/pelvic-inflammatory-disease-pid">pelvic inflammatory disease</a>).</p></li>
</ul>
<p>For men or women who have anal sex, symptoms may include:</p>
<ul>
<li>an itch or pain inside the anus, anal discharge and sometimes anal bleeding.</li>
</ul>
<p>Your doctor will take a urine sample for men and a vaginal swab for women. For men or women who have anal sex, they will take a rectal swab, or you will be instructed how to take it yourself. Samples will then be sent for laboratory testing.</p>
<h2>How is it treated?</h2>
<p>Once diagnosed, you’ll be treated with a course of oral antibiotics for about two weeks. Unfortunately, you may need several courses to cure the infection due to <a href="https://pubmed.ncbi.nlm.nih.gov/32622378/">increasing antibiotic resistance</a>. And some of these antibiotics can have side-effects. Occasional, but serious, side-effects include an abnormal heart rhythm, rupture of tendons and nerve damage.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/health-check-im-taking-antibiotics-when-will-they-start-working-107528">Health Check: I’m taking antibiotics – when will they start working?</a>
</strong>
</em>
</p>
<hr>
<h2>What happens if I leave it untreated?</h2>
<p>If the infection is left untreated in women, it can cause similar complications to chlamydia. Some women go on to develop <a href="https://pubmed.ncbi.nlm.nih.gov/32701123/">pelvic inflammatory disease</a>, although less commonly than with chlamydia. Pelvic inflammatory disease could, in turn, lead to infertility. If you’re pregnant, it can, uncommonly, lead to premature birth or miscarriage.</p>
<p>If left untreated in men there are no apparent complications but the main risk is men can infect new partners and reinfect treated partners. And for gay men, there’s <a href="https://pubmed.ncbi.nlm.nih.gov/19194271/">some data</a> to suggest a link between MG and HIV, although further studies are needed.</p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/how-to-make-your-next-sexual-health-check-less-erm-awkward-72498">How to make your next sexual health check less, erm ... awkward</a>
</strong>
</em>
</p>
<hr>
<h2>Can I still be tested even if I don’t have symptoms?</h2>
<p>Current guidelines both <a href="http://www.sti.guidelines.org.au/sexually-transmissible-infections/mycoplasma-genitalium">in Australia</a> and <a href="https://www.bashhguidelines.org/current-guidelines/urethritis-and-cervicitis/mycoplasma-genitalium-2018/">internationally</a> recommend testing people with symptoms, or sexual contacts of known cases. They <a href="https://www.thelancet.com/action/showPdf?pii=S2589-5370%2821%2900059-6">don’t recommend doctors screen</a> people <a href="https://www.theguardian.com/australia-news/2021/mar/17/gps-urged-not-to-test-gay-men-for-sti-super-bug-over-fears-it-will-become-more-antibiotic-resistant">without symptoms</a>.</p>
<p><div data-react-class="Tweet" data-react-props="{"tweetId":"1371870337932132352"}"></div></p>
<p>When you screen, you have to be confident you have access to highly effective treatments, the treatments do not cause more harm than the condition itself and you have a good understanding of how often the condition progresses to cause complications.</p>
<p>For MG that balance is against screening currently. That’s because there are often no symptoms and we don’t yet fully understand how often the infection progresses to cause harm, although it seems to do so less often than chlamydia. The microorganism has also rapidly become so resistant to antibiotics we are having to use stronger and stronger ones, and multiple courses, to cure. This contrasts to chlamydia, which is easy to cure. </p>
<p>Not only do many antibiotics have side-effects, they affect the bacteria in people’s gut. These bacteria are important to keep us healthy, and if we bombard them with antibiotics it can affect our health and also lead to antibiotic resistance in a whole range of other bacteria, not just MG.</p>
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Read more:
<a href="https://theconversation.com/we-know-why-bacteria-become-resistant-to-antibiotics-but-how-does-this-actually-happen-59891">We know _why_ bacteria become resistant to antibiotics, but _how_ does this actually happen?</a>
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<img src="https://counter.theconversation.com/content/157318/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Catriona Bradshaw receives funding from the NHMRC and ARC (government funding). Melbourne Sexual Health Centre has also received research support from Speedx Pty Ltd and Hologic Pty Ltd which are manufacturers of diagnostic assays for Mycoplasma genitalium. </span></em></p>You can have this STI without knowing it, or have symptoms, it can affect men and women, and it can be treated with antibiotics. Left untreated, it may cause complications.Catriona Bradshaw, Professor, Head of Research Translation and Head of the Genital Mycoplasma and Microbiota Group, Monash UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1551532021-03-14T09:06:04Z2021-03-14T09:06:04ZFirst ever national survey shows the extent of South Africa’s TB problem<figure><img src="https://images.theconversation.com/files/388535/original/file-20210309-13-19yndw4.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The WHO recommends that TB prevalence surveys be done in high burden countries. </span> <span class="attribution"><span class="source">Spencer Platt/Getty Images</span></span></figcaption></figure><p>South Africa’s long-awaited <a href="https://www.knowledgehub.org.za/system/files/elibdownloads/2021-02/A4_SA_TPS%20Short%20Report_10June20_Final_highres.pdf">tuberculosis (TB) prevalence survey</a> results were recently released. This is the first national prevalence survey of its kind for TB in South Africa. </p>
<p>TB prevalence surveys are difficult and expensive to do, and so are not carried out routinely, but have been done in many high burden countries following a World Health Organisation (WHO) <a href="https://www.who.int/publications/i/item/9789241598828">recommendation in 2007</a>. In the absence of prevalence survey data, TB estimates are based on the reported numbers of people treated for TB, adjusted to take account of the estimated number of people who have TB but don’t access treatment.</p>
<p>The results show that South Africa has a far higher number of people with TB than previously thought. And many people are living with TB who have not been diagnosed or treated. </p>
<p>It shows that prevalence of TB in South Africa in 2018 was 737 per 100,000. Prevalence was lowest in younger people (15-24 years) and peaked in those between the ages of 35 abd 44, and adults older than 65. </p>
<p>The survey was conducted between 2017 and 2019 by the South African Medical Research Council, Human Sciences Research Council and the National Institute for Communicable Diseases on behalf of the Department of Health. South Africa, along with other countries, routinely reports to the WHO the number of people who attend clinics and start TB treatment. But this regularly reported number misses many other people who have TB. </p>
<p>To be included in the TB statistics reported to the <a href="https://www.who.int/publications/i/item/9789240013131">WHO</a>, someone has to have visited the clinic for care, had their sputum tested, received a positive result and started TB treatment. People can be lost at any step in this process and their number may not be reflected in the national statistics. </p>
<p>People with TB who are missed or whose treatment is delayed may suffer prolonged ill-health. They may be unable to undertake normal daily activities, and be unable to work, resulting in economic hardship for themselves and their families. In addition, the longer a person has untreated TB, the more likely they are to pass the infection to other people and continue the cycle. </p>
<p>TB prevalence surveys like this one are important because they give a truer picture of the burden of disease. They are conducted in a random sample of people, selected from clusters that represent all provinces and socio-demographic groups in South Africa. </p>
<h2>New burden</h2>
<p>More than 35,000 people participated in this survey. This is a massive undertaking and the only way to get a more accurate picture of how many people in the country truly have TB.</p>
<p>This knowledge is critical because TB remains one of the leading causes of death in South Africa. It claims more lives annually than the <a href="https://sacoronavirus.co.za/">COVID-19 pandemic</a> has so far. This is despite TB being a curable disease. </p>
<p>The more accurate data that is now available indicates that there were 360,000 new cases of TB in 2019 – a good deal higher than the previous estimate of 301,000 TB cases in 2018.</p>
<p>Based on the new prevalence data, the WHO estimates that in 2019, <a href="https://tbfacts.org/tb-statistics-south-africa/">58,000</a> people died of TB in South Africa and <a href="https://apps.who.int/iris/bitstream/handle/10665/337538/9789240016095-eng.pdf">1.4 million people</a> died from TB globally. </p>
<p>TB is airborne and highly infectious. It spreads when an infected person coughs, sneezes, or even speaks, and people nearby breathe in the bacteria. It is important to understand what the levels of infection are in the country, especially because some people live with TB for a long time before they start treatment. This can be months or even years. Some people never get a diagnosis and never start treatment. They may be infectious and pass TB on to other people. They may also have damage to their lungs that is not picked up but may have long-term health consequences. By understanding the true rate of TB in South Africa, we can come up with better ways to find and treat all the people who have TB.</p>
<p>The prevalence survey also flags some important trends. Most of the people whose TB disease was “missed” are men and are HIV-negative. This is similar to <a href="https://pubmed.ncbi.nlm.nih.gov/27598345/">findings</a> from other countries in Africa. It is also backed by preliminary results from <a href="https://pubmed.ncbi.nlm.nih.gov/32802963/">Vukuzazi</a>, a large-scale community health screening survey we conducted in northern KwaZulu-Natal. </p>
<p>Our <a href="https://www.abstractserver.com/TheUnion2018/TheUnion2018_Abstracts_Web.pdf#page=605">previous research</a> has also shown that HIV-negative men are less likely than HIV-positive people or HIV-negative women to attend clinics for health checks. More effort needs to be put into finding and treating people with active TB. In particular, there is an urgent need for research to figure out how to reach HIV-negative men who rarely visit clinics.</p>
<p>An important finding of the national TB prevalence survey is that most of the people found to have TB in the survey did not report having the <a href="https://tbfacts.org/tb/">classic symptoms</a> of TB. These include cough, fever, night sweats and weight loss. This means that we need new diagnostic tools for TB that can help screen large numbers of people, even those who don’t have symptoms. The Department of Health has emphasised the use of chest X-rays for screening for TB. Because of the logistics involved, this will be challenging to implement, especially in under-served, rural areas of the country. Research into new, accurate and mobile diagnostics should be a priority.</p>
<h2>The COVID-19 impact</h2>
<p>COVID-19 has had a devastating impact on the number of people getting tested and treated for TB. According to <a href="http://www.samj.org.za/index.php/samj/article/view/13137">new research</a>, testing rates for TB have dropped by up to 50% in the year since South Africa’s COVID-19 lockdown. </p>
<p>Additionally, far fewer people have accessed treatment for TB since March 2020. </p>
<p>Unfortunately, this means that current rates of TB are likely to be even higher than those identified during the pre-COVID-19 era. </p>
<p>Even in light of the economic and health challenges presented by COVID-19, the South African health community must maintain a focus on finding and treating TB. The national TB prevalence survey provides very useful information to guide how to do this.</p><img src="https://counter.theconversation.com/content/155153/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Emily Wong and members of her laboratory receive funding from the National Institute of Allergy and Infectious Diseases and the Fogarty International Center of the National Institutes of Health, the Bill and Melinda Gates Foundation, the South African Medical Research Council and the African Academy of Sciences.</span></em></p><p class="fine-print"><em><span>Alison Grant receives funding from Economic and Social Research Council (UK), National Institute of Allergy and Infectious Diseases (USA), Bill and Melinda Gates Foundation, Wellcome Trust. </span></em></p>South Africa’s long-awaited TB prevalence survey results were recently released. They reveal that the country has a much higher burden of TB than previously thought.Emily B. Wong, Assistant Professor, Africa Health Research Institute (AHRI)Alison Grant, Professor of International Health at LSHTM and Member of Faculty, Africa Health Research Institute (AHRI)Licensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1564672021-03-11T13:29:23Z2021-03-11T13:29:23ZSewage-testing robots process wastewater faster to predict COVID-19 outbreaks sooner<figure><img src="https://images.theconversation.com/files/388904/original/file-20210310-23-9z2neq.jpg?ixlib=rb-1.1.0&rect=35%2C17%2C5955%2C3970&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Sewage samples mixed with magnetic beads and loaded onto the liquid-handling robot for viral concentration</span> <span class="attribution"><span class="source">C. H. Sheikhzadeh @ HOMA Photographic Art</span></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>By using a sewage-handling robot, our laboratory has been able to <a href="https://doi.org/10.1128/mSystems.00045-21">detect coronavirus in wastewater 30 times faster</a> than nonautomated large-scale systems. This advance, published in the microbiology journal mSystems, provides even more lead time to communities monitoring their wastewater for early warning about local cases of COVID-19.</p>
<p>When clinical studies emerged showing that people who test positive for SARS-CoV-2 <a href="https://doi.org/10.1002/jmv.25825">shed the virus in their stool</a>, the sewer seemed like an obvious place to look for it. <a href="https://theconversation.com/covid-19-clues-in-a-communitys-sewage-4-questions-answered-about-watching-wastewater-for-coronavirus-144255">Wastewater surveillance can be used at the community level</a> to see potential outbreak clusters before clinical diagnosis, especially in areas where COVID-19 prevalence rates far exceed testing rates.</p>
<p>The problem is that the virus is heavily diluted in the waste stream because of how many people’s bathrooms drain into it, not to mention all the other junk they flush. Surveillance depends on concentrating the viral particles from the wastewater to detect these low levels. This viral concentration step is typically the <a href="https://doi.org/10.1016/j.scitotenv.2020.141245">major bottleneck in wastewater analyses</a> because it’s laborious and time-consuming. Our robot system takes a different, quicker approach.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/388643/original/file-20210309-23-tc2oee.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="aerial view of Point Loma Wastewater Treatment Plant" src="https://images.theconversation.com/files/388643/original/file-20210309-23-tc2oee.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/388643/original/file-20210309-23-tc2oee.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=477&fit=crop&dpr=1 600w, https://images.theconversation.com/files/388643/original/file-20210309-23-tc2oee.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=477&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/388643/original/file-20210309-23-tc2oee.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=477&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/388643/original/file-20210309-23-tc2oee.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=600&fit=crop&dpr=1 754w, https://images.theconversation.com/files/388643/original/file-20210309-23-tc2oee.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=600&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/388643/original/file-20210309-23-tc2oee.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=600&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 treatment plants can be the front lines for coronavirus detection in a community.</span>
<span class="attribution"><span class="source">San Diego County</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>Why it matters</h2>
<p><a href="https://theconversation.com/testing-sewage-can-give-school-districts-campuses-and-businesses-a-heads-up-on-the-spread-of-covid-19-149593">Cities, schools and businesses</a> around the country are using wastewater surveillance to find coronavirus in their midst. </p>
<p>Wastewater surveillance is especially useful as an early-alert system for high-risk areas, such as communities where undocumented residents may be cautious about individual testing.</p>
<p>The most commonly used <a href="https://doi.org/10.1016/j.scitotenv.2020.139960">viral concentration technique uses filters</a> and can take anywhere from six to eight hours to transform a couple dozen sewage specimens into samples that can then be tested for the presence of SARS-CoV-2. Our new protocol concentrates 24 samples in a single 40-minute run.</p>
<p>We repurposed gear that usually performs microbiology or cell biology tasks in the lab to deal with sewage instead. By miniaturizing and automating our system, we eliminate a bunch of labor-intensive steps, resources and associated costs. And our hands-free process is much quicker.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/388665/original/file-20210309-19-hztqwq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Gloved researchers open an autosampler to remove a bottle of liquid." src="https://images.theconversation.com/files/388665/original/file-20210309-19-hztqwq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/388665/original/file-20210309-19-hztqwq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/388665/original/file-20210309-19-hztqwq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/388665/original/file-20210309-19-hztqwq.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/388665/original/file-20210309-19-hztqwq.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/388665/original/file-20210309-19-hztqwq.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/388665/original/file-20210309-19-hztqwq.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">Researchers gather a liter of sewage collected over the course of the day from a sewer line connected to a UC San Diego building.</span>
<span class="attribution"><span class="source">C.H. Sheikhzadeh</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>How we do this work</h2>
<p>We gather sewage from autosamplers at <a href="https://www.sandiego.gov/public-utilities/customer-service/water-wastewater-facilities/point-loma">San Diego’s main wastewater treatment plant</a>, as well as from those we’ve deployed at over 100 manholes on the campus of the University of California, San Diego, which collect sewer samples every 30 minutes through the day.</p>
<p>Then, back in the lab, instead of relying on multiple filter steps, we <a href="https://www.ceresnano.com/viruscapture">use tiny magnetic beads to enrich the viral particles</a>. We purchase these nanomagnetic beads that are designed to bind to a variety of respiratory viruses. The sewage-handling robot is equipped with a specialized magnetic head that <a href="https://doi.org/10.1038/s41598-020-78771-8">snags the magnetic beads, with viruses attached</a>. It preferentially fishes out viral particles, leaving behind the rest of the junk in the sewage sample.</p>
<p>Using a robot to automate the sewage concentration process lets us concentrate 24 samples in 40 minutes for each robot. Then the same robot can extract the viral RNA, processing 96 samples in 36 minutes. Finally, we use a polymerase chain reaction to search for the signature genes of SARS-CoV-2, much like a clinical diagnostic test that a lab would run on a patient’s nasal swab.</p>
<p>Overall, our system can process 96 samples in 4.5 hours, dramatically reducing the time from specimen to result.</p>
<h2>What’s next</h2>
<p>So far, ours is the only coronavirus wastewater study we’re aware of <a href="https://www.covid19wbec.org/covidpoops19">that uses an automated process</a>.</p>
<p>We’re using this technique as a part of our <a href="https://returntolearn.ucsd.edu/dashboard/index.html">large-scale wastewater surveillance on campus</a> and sampling over 100 locations daily. <a href="https://ucsdnews.ucsd.edu/feature/uc-san-diego-and-san-diego-county-test-covid-19-early-alert-system-in-schools">San Diego school districts are also using it</a> as an early-alert system.</p>
<p>We’re now using the viral genome sequencing part of our system to track the emergence of new SARS-CoV-2 variants.</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><img src="https://counter.theconversation.com/content/156467/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>A community’s wastewater can predict coronavirus cases that haven’t yet been diagnosed. The quicker that information is known, the better.Smruthi Karthikeyan, Postdoctoral Research Associate in Pediatrics, University of California, San DiegoRob Knight, Professor of Pediatrics and Computer Science and Engineering, University of California, San DiegoLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1543172021-03-08T13:36:16Z2021-03-08T13:36:16Z5 strategies to prepare now for the next pandemic<figure><img src="https://images.theconversation.com/files/388110/original/file-20210305-13-82k3mw.jpg?ixlib=rb-1.1.0&rect=134%2C0%2C5856%2C3925&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Stacked disasters – like a winter storm that damages a water system during a pandemic – can provide lessons for the next time around.</span> <span class="attribution"><a class="source" href="https://newsroom.ap.org/detail/WinterWeatherWaterWoes/c3bfa8a4505c4ce6a0f01d6049eb3089/photo?boardId=d7f2514f50804466b15dfb81ed00d9cd&st=boards&mediaType=audio,photo,video,graphic&sortBy=&dateRange=Anytime&totalCount=33&currentItemNo=0">AP Photo/Rogelio V. Solis</a></span></figcaption></figure><p>While the world is still reeling from the COVID-19 pandemic, public health and emergency management experts are already preparing for the next one. After all, biologists are certain <a href="https://www.who.int/medicines/ebola-treatment/WHO-list-of-top-emerging-diseases/en/">another dangerous new pathogen will emerge</a> sooner or later.</p>
<p>We are public health researchers engaged in both leading <a href="https://public-health.tamu.edu/directory/clendenin.html">public health disaster response</a> and <a href="https://scholar.google.com/citations?user=me4Q9y4AAAAJ&hl=en">evaluating emergency management</a>.</p>
<p>Here are five strategies that will give the world a head start – and maybe even help prevent the next outbreak or epidemic from blowing up into a pandemic.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/388113/original/file-20210305-21-1i9k9ru.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="masked man's arm is prepped for injection outdoors" src="https://images.theconversation.com/files/388113/original/file-20210305-21-1i9k9ru.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/388113/original/file-20210305-21-1i9k9ru.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=390&fit=crop&dpr=1 600w, https://images.theconversation.com/files/388113/original/file-20210305-21-1i9k9ru.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=390&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/388113/original/file-20210305-21-1i9k9ru.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=390&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/388113/original/file-20210305-21-1i9k9ru.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=490&fit=crop&dpr=1 754w, https://images.theconversation.com/files/388113/original/file-20210305-21-1i9k9ru.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=490&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/388113/original/file-20210305-21-1i9k9ru.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=490&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 public health response in Guinea was swift when new cases of Ebola virus disease were identified in February 2021.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/health-worker-from-the-guinean-ministry-of-health-cleans-a-news-photo/1231345676?adppopup=true">Carol Valade/AFP via Getty Images</a></span>
</figcaption>
</figure>
<h2>1. Shore up the systems already in place</h2>
<p>The identification in February 2021 of <a href="https://www.who.int/csr/don/17-february-2021-ebola-gin/en/">a new outbreak of Ebola in Guinea</a> showed how critical surveillance and reporting are for rapidly responding to and containing infectious disease. </p>
<p>The process generally works like this: Once an astute clinician diagnoses a disease that is <a href="https://wwwn.cdc.gov/nndss/conditions/notifiable/2020/">on the watch list</a> of the World Health Organization and the Centers for Disease Control and Prevention, she reports the case to local health authorities to investigate. The information gets passed up the chain to the state, federal and international levels.</p>
<p>Clinicians, public health practitioners and labs all around the world send disease reports to groups like the WHO’s <a href="https://extranet.who.int/goarn/">Global Outbreak Alert and Response Network</a>. It aggregates all that data and helps identify outbreaks of new infectious diseases and their pandemic potential.</p>
<p>If a pathogen does make it past local monitors and starts to spread, governments have <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/incident-command-system">emergency management systems in place to respond</a>. These incident command structures provide a framework to respond to crises that range from infectious disease to natural disaster to terrorist attack.</p>
<p>In the U.S., various federal agencies have different responsibilities. They monitor emerging infectious diseases, establish a strategic national stockpile of resources and support the states in their preparedness and response. Responsibility for the emergency response lies with each state – that’s in the U.S. Constitution – so they have flexibility in how they implement everything on a local level.</p>
<p>One practical way to be prepared for a future pandemic is to ensure that all these systems and structures remain stable. That means <a href="https://www.kff.org/coronavirus-covid-19/fact-sheet/the-u-s-government-and-the-world-health-organization/">maintaining funding</a>, training and personnel for a rapid global response even when no pandemic threats are visible on the horizon.</p>
<h2>2. Prepare the public to do its part</h2>
<p>Effective pandemic response requires a clear, consistent voice and an actionable message that reflects best practices based on sound science. Messaging and data that clearly explain how each individual has an important role in curbing the pandemic – and that it might evolve as the pandemic unfolds over time – are critical.</p>
<p>The message to stay home and “<a href="https://www.nytimes.com/article/flatten-curve-coronavirus.html">flatten the curve</a>” to avoid overwhelming health care resources with COVID-19 cases was an essential early <a href="https://www.cdc.gov/coronavirus/2019-ncov/daily-life-coping/personal-social-activities.html">public health message</a> that resonated with many Americans who were not designated as essential workers. However, once initial shutdown orders were lifted and new treatments emerged, there was general confusion about the safety of public gatherings, particularly since <a href="https://theconversation.com/covid-19-messes-with-texas-what-went-wrong-and-what-other-states-can-learn-as-younger-people-get-sick-141563">guidance varied by state or locality</a>.</p>
<p>Guidance is also most effective if it’s tailored to different audiences. In the South, distrust of testing and vaccination efforts by government and health care providers is directly linked to <a href="https://www.countyhealthrankings.org/learn-from-others/webinars/responding-to-crisis-in-the-latino-population-with-an-equity-lens">language barriers and immigration concerns</a>. One strategy to reach diverse and often underserved populations is to rely on leaders in the local faith community to <a href="https://www.globalhealthnow.org/2020-08/fix-us-coronavirus-response-start-culture">help deliver public health messages</a>.</p>
<p>Preparedness requires an “<a href="https://www.fema.gov/emergency-managers/national-preparedness/goal">all of community approach</a>” that engages everyone in the planning stages, especially those from underserved or vulnerable populations. Building relationships now can improve access to information and resources when the next disaster strikes, helping ensure equity and agility in response.</p>
<p>Science and risk communication scholars have started talking about the best ways people can <a href="https://www.who.int/news-room/events/detail/2020/06/30/default-calendar/1st-who-infodemiology-conference">manage the flood of information during a pandemic</a>. Lessons from what’s been called the infodemic of COVID-19 news – some trustworthy but some certainly not – can inform new strategies for sharing reliable info and fostering trust in science.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/388105/original/file-20210305-13-2kxz15.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="a" src="https://images.theconversation.com/files/388105/original/file-20210305-13-2kxz15.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/388105/original/file-20210305-13-2kxz15.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=189&fit=crop&dpr=1 600w, https://images.theconversation.com/files/388105/original/file-20210305-13-2kxz15.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=189&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/388105/original/file-20210305-13-2kxz15.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=189&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/388105/original/file-20210305-13-2kxz15.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=238&fit=crop&dpr=1 754w, https://images.theconversation.com/files/388105/original/file-20210305-13-2kxz15.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=238&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/388105/original/file-20210305-13-2kxz15.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=238&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Participants at a tabletop exercise in Texas that envisioned an Ebola virus disease outbreak.</span>
<span class="attribution"><span class="source">The USA Center for Rural Health Preparedness</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span>
</figcaption>
</figure>
<h2>3. Get coordinated and practice</h2>
<p>Emergency managers and health care leaders have long recognized that a <a href="https://doi.org/10.3201/eid1906.121478">coordinated response by diverse teams</a> is critical for public health emergencies.</p>
<p><a href="https://www.ready.gov/exercise">Tabletop exercises</a> that simulate real emergencies help officials prepare for crises of all types. Like a fire drill, they bring together community stakeholders to walk through a hypothetical disaster scenario and hash out roles and responsibilities. These practice sessions include people who work in public health, emergency management and health care, as well as federal, tribal, state and local front-line responders.</p>
<p>Practice scenarios must also include the reality of “stacked disasters,” like a hurricane or winter storm that puts even more stress on the disaster response system.</p>
<p>These exercises enable a community to test parts of the overall emergency management plan and determine gaps or areas to strengthen. Ongoing testing and training to the plan ensures everyone is as ready as they can be.</p>
<p>Beyond this training, health care professionals could be cross-trained to <a href="https://www.cidrap.umn.edu/news-perspective/2020/11/covid-related-nursing-shortages-hit-hospitals-nationwide">back up specialized clinical staff</a>, who may need support over the course of a long pandemic.</p>
<p>The COVID-19 pandemic delivered lessons about <a href="https://www.ama-assn.org/delivering-care/public-health/new-hope-fixing-supply-chain-problems-ppe-tests-vaccines">infrastructure and supply chains</a>. Strategic investments can <a href="https://www.whitehouse.gov/briefing-room/presidential-actions/2021/01/21/executive-order-a-sustainable-public-health-supply-chain/">shore up existing strategic national stockpiles</a> of supplies and vaccinations for the future. If necessary, the president can use <a href="https://www.cfr.org/in-brief/what-defense-production-act">the Defense Production Act</a> to order private companies to prioritize federal orders.</p>
<h2>4. Polish the playbook</h2>
<p>After every major disaster response, all of the different groups involved – law enforcement, EMS, fire, emergency management, public health, search and rescue and so on – conduct what are called “after action reviews.” They can improve plans for the next time around.</p>
<p>For instance, after the <a href="https://www.cdc.gov/flu/pandemic-resources/2009-h1n1-pandemic.html">2009 influenza pandemic</a>, the Department of Health and Human Services found that while CDC communication efforts were widely successful, some non-English-speaking populations missed important messages. The <a href="https://www.gao.gov/products/GAO-11-632">after action review noted</a> that distrust in the government increased when vaccine supplies did not meet public expectations. In turn, officials could plan exercises to <a href="https://www.cdc.gov/cpr/readiness/healthcare/documents/PIEET_Cleared_9_5.docx">test and tweak approaches for next time</a>.</p>
<p>A thorough review of the response to the current COVID-19 pandemic at all levels will identify gaps, challenges and successes. Those “After Action” findings need to be integrated into future planning to improve preparedness and response for the next pandemic.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/388111/original/file-20210305-13-575k7d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="seated operators in front of telephone switchboard" src="https://images.theconversation.com/files/388111/original/file-20210305-13-575k7d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/388111/original/file-20210305-13-575k7d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=451&fit=crop&dpr=1 600w, https://images.theconversation.com/files/388111/original/file-20210305-13-575k7d.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=451&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/388111/original/file-20210305-13-575k7d.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=451&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/388111/original/file-20210305-13-575k7d.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=567&fit=crop&dpr=1 754w, https://images.theconversation.com/files/388111/original/file-20210305-13-575k7d.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=567&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/388111/original/file-20210305-13-575k7d.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=567&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 previous pandemic hastened the end of switchboard operators. Which technologies will get a boost after this one?</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/telephone-operators-receive-long-distance-calls-from-news-photo/3302030?adppopup=true">Stevens/Topical Press Agency/Hulton Archive via Getty Images</a></span>
</figcaption>
</figure>
<h2>5. Build on the new normal</h2>
<p>Back when the <a href="https://www.govexec.com/management/2021/02/1918-pandemic-provides-warning-about-covid-19s-future/172078/">1918 H1N1 influenza pandemic unfolded</a>, few Americans had a telephone. Quarantine rules led more households to <a href="https://www.egi.co.uk/news/what-can-1918-teach-us-about-post-pandemic-tech-adoption/">use phones and hastened research</a> that reduced reliance on human telephone operators. Similarly, no doubt COVID-19 triggered some rapid changes that will last and help the U.S. be ready for future events. </p>
<p>It’s been easier to adapt to the necessary lifestyle changes due to this pandemic thanks to the ways technology has changed the workplace, the classroom and the delivery of health care. Business analysts predict the quick move to video teleconferencing and remote work for offices in 2020 will <a href="https://www.mckinsey.com/featured-insights/future-of-work/the-future-of-work-after-covid-19#">be lasting legacies of COVID-19</a>. A multidisciplinary team here at Texas A&M is tracking how robotics and automated systems are being used in pandemic response in clinical care, public health and public safety settings.</p>
<p>Some of the sudden, dramatic changes to norms and behaviors, like the use of face masks in public, may be among the easiest strategies to keep in place to fend off a future pandemic from a respiratory virus. Just as telephone systems continued to improve over the last 100 years, ongoing innovation that builds on rapid adoption of technologies around COVID-19 will help people adjust to sudden lifestyle changes when the next pandemic strikes.</p>
<p>[<em><a href="https://theconversation.com/us/newsletters/the-daily-3?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=experts">Expertise in your inbox. Sign up for The Conversation’s newsletter and get expert takes on today’s news, every day.</a></em>]</p><img src="https://counter.theconversation.com/content/154317/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>Shoring up surveillance and response systems and learning lessons from how the COVID-19 pandemic unfolded will help the world be ready the next time around.Tiffany A. Radcliff, Associate Dean for Research and Professor of Health Policy and Management, Texas A&M UniversityAngela Clendenin, Instructional Assistant Professor of Epidemiology and Biostatistics, Texas A&M UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1518322021-01-13T13:20:18Z2021-01-13T13:20:18ZThe scent of sickness: 5 questions answered about using dogs – and mice and ferrets – to detect disease<figure><img src="https://images.theconversation.com/files/378085/original/file-20210111-15-1b5qelp.jpg?ixlib=rb-1.1.0&rect=18%2C6%2C2026%2C1355&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Moose, a mixed-breed dog from the Nebraska Humane Society, trains in odor-detection work. </span> <span class="attribution"><span class="source">Bill Cotton/CSU</span>, <a class="license" href="http://creativecommons.org/licenses/by-nd/4.0/">CC BY-ND</a></span></figcaption></figure><p><em>Editor’s note: As COVID-19 continues to spread worldwide, scientists are analyzing new ways to track it. One promising approach is <a href="https://doi.org/10.1038/d41586-020-03149-9">training dogs to detect people who are infected</a> by smelling samples of human urine or sweat. Research scientist Glen Golden, who has trained dogs and ferrets to detect avian flu in birds, explains why certain animals are well suited to sniff out sickness.</em></p>
<h2>1. Which species have a nose for disease?</h2>
<p>Some animals have highly developed senses of smell. They include rodents; dogs and their wild relatives, like wolves and coyotes; and <a href="https://www.britannica.com/topic/list-of-mustelids-2058294">mustelids</a> – carnivorous mammals such as weasels, otters and ferrets. These species’ brains have three or more times more functional olfactory receptor neurons – nerve cells that respond to odors – than species with less keen smelling abilities, including humans and other primates. </p>
<p>These neurons are responsible for detecting and identifying volatile olfactory compounds that send meaningful signals, like smoke from a fire or the aroma of fresh meat. A substance is volatile if it changes readily from liquid to gas at low temperatures, like the acetone that gives nail polish remover its fruity smell. Once it vaporizes, it can spread rapidly through the air.</p>
<p>When one of these animals detects a meaningful odor, the chemical signal is translated into messages and transported throughout its brain. The messages go simultaneously to the olfactory cortex, which is responsible for identifying, localizing and remembering odor, and to other brain regions responsible for decision-making and emotion. So these animals can detect many chemical signals over great distances and can make rapid and accurate mental associations about them. </p>
<h2>2. How do researchers choose a target scent?</h2>
<p>In most studies that have used dogs to detect cancer, the dogs have identified physical samples, such as skin, urine or breath, from patients who either have been diagnosed with cancer or have <a href="https://doi.org/10.1016/j.applanim.2004.04.008">undiagnosed cancer at an early stage</a>. Scientists don’t know what odor cue the dogs use or whether it varies by type of cancer.</p>
<p>The U.S. Department of Agriculture’s <a href="https://www.aphis.usda.gov/aphis/ourfocus/wildlifedamage/programs/nwrc">National Wildlife Research Center</a> in Colorado and the <a href="https://monell.org/">Monell Chemical Senses Center</a> in Pennsylvania have trained mice to detect <a href="https://doi.org/10.1371/journal.pone.0075411">avian influenza in fecal samples from infected ducks</a>. Bird flu is hard to detect in wild flocks, and it <a href="https://www.cdc.gov/flu/avianflu/avian-in-humans.htm">can spread to humans</a>, so this work is designed to help wildlife biologists monitor for outbreaks. </p>
<p>The Kimball lab at Monell taught the mice to get a reward when they smelled a confirmed positive sample from an infected animal. For example, mice would get a drink of water when they traveled down the arm of a Y-shaped maze that contained feces from a duck infected with avian influenza virus. </p>
<p>By chemically analyzing the fecal samples, researchers found that the concentration of volatile chemical compounds in them changed when a duck became infected with bird flu. So they inferred that this altered smell profile was what the mice recognized.</p>
<figure>
<iframe width="440" height="260" src="https://www.youtube.com/embed/0UxLt3yugUA?wmode=transparent&start=0" frameborder="0" allowfullscreen=""></iframe>
<figcaption><span class="caption">Members of the mustelid family, such as ferrets, badgers and otters, have highly developed senses of smell. Here a wolverine sniffs out frozen meat buried deep in the snow.</span></figcaption>
</figure>
<p>Building on that work, we’ve trained ferrets and dogs to detect avian influenza in fowl, such as wild ducks and domestic chickens, in a collaborative study between Colorado State University and the National Wildlife Research Center that is currently under review for publication.</p>
<p>With ferrets, we started by training them to alert, or signal that they had detected the target odor, by scratching on a box that contained high ratios of those volatile compounds and to ignore boxes that contained low ratios. Next we showed the ferrets fecal samples from both infected and noninfected ducks, and the ferrets immediately began alerting to the box containing the fecal sample from an infected duck. </p>
<p>This approach is similar to the way that dogs are trained to detect known volatile odors in explosives or illegal drugs. Sometimes, though, we have to let the detector animal determine the odor profile that it will respond to.</p>
<h2>3. Can animals be trained to detect more than one target?</h2>
<p>Yes. To avoid confusion about what a trained animal is detecting, we can teach it a different behavioral response for each target odor. </p>
<p>For example, the dogs in the U.S. Department of Agriculture’s <a href="https://www.aphis.usda.gov/aphis/ourfocus/wildlifedamage/programs/nwrc/sa_spotlight/sniffing+out+disease">Wildlife Services Canine Disease Detection Program</a> respond with an aggressive alert, such as scratching, when they detect a sample from a duck infected with bird flu. When they detect a sample from a white-tailed deer infected by the prion that causes <a href="https://www.cdc.gov/prions/cwd/index.html">chronic wasting disease</a>, they respond with a passive alert such as sitting down.</p>
<p>Research at the University of Auburn has shown that dogs can remember and respond to <a href="https://doi.org/10.1007/s10071-020-01362-7">72 odors during an odor memory task</a>. The only limitation is how many ways a dog can communicate about different odor cues. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/378089/original/file-20210111-21-8ff0si.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Sign showing images of a dog and the SARS-CoV-2 virus." src="https://images.theconversation.com/files/378089/original/file-20210111-21-8ff0si.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/378089/original/file-20210111-21-8ff0si.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/378089/original/file-20210111-21-8ff0si.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/378089/original/file-20210111-21-8ff0si.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/378089/original/file-20210111-21-8ff0si.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=502&fit=crop&dpr=1 754w, https://images.theconversation.com/files/378089/original/file-20210111-21-8ff0si.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=502&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/378089/original/file-20210111-21-8ff0si.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">A sign notifies travelers about a pilot study at Helsinki airport that offers free coronavirus tests using dogs to detect infections by smell.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/airport-signs-illustrate-the-new-covid-19-canine-test-news-photo/1228704590">Shoja Lak/Getty Images</a></span>
</figcaption>
</figure>
<h2>4. What kinds of factors can complicate this process?</h2>
<p>First, any organization that trains animals to detect disease needs the right type of laboratory and equipment. Depending on the disease, that could include personal protection equipment and air filtering. </p>
<p>Another concern is whether the pathogen might infect the detection animals. If that’s a risk, researchers may need to inactivate the samples before they expose the animals. Then they need to see whether that process has altered the volatiles that they are teaching the animals to associate with infection. </p>
<p>Finally, handlers have to think about how to reinforce the desired response from detection animals in the field. If they are working in a population of mostly noninfected people – for example, in an airport – and an animal doesn’t get a chance to earn a reward, it may lose interest and stop working. We look for animals that have a strong drive to work without stopping, but working for a long time without reward can be challenging for even the most motivated animal. </p>
<p><div data-react-class="Tweet" data-react-props="{"tweetId":"1254696791003541505"}"></div></p>
<h2>5. Why not build a machine that can do this?</h2>
<p>Right now we don’t have devices that are as sensitive as animals with well-developed senses of smell. For example, a dog’s sense of smell is <a href="https://doi.org/10.1016/j.applanim.2005.07.009">at least 1,000 times more sensitive than any mechanical device</a>. This could explain why dogs have detected cancer in tissue samples that have been <a href="https://doi.org/10.1016/j.applanim.2004.04.008">medically cleared as not cancerous</a> </p>
<p>We also know that ferrets can detect avian flu infection in fecal samples before and after laboratory analysis shows that the virus has stopped shedding. This suggests that for some pathogens, there may be changes in volatiles in individuals who are infected but are asymptomatic. </p>
<p>As scientists learn more about how mammals’ sense of smell works, they’ll have a better chance of creating devices that are as sensitive and reliable in sniffing out disease.</p><img src="https://counter.theconversation.com/content/151832/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Glen Golden receives funding from the United Stated Department of Agriculture.</span></em></p>Scientists are experimenting with using dogs to sniff out people infected with COVID-19. But dogs aren’t the only animals with a nose for disease.Glen J. Golden, Research Scientist/Scholar I, Colorado State UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1489282020-11-04T14:42:11Z2020-11-04T14:42:11ZSouth Africa is testing digital technology to detect outbreaks of respiratory diseases<figure><img src="https://images.theconversation.com/files/367159/original/file-20201103-15-s7q2sv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">shutterstock</span> </figcaption></figure><p>Global mobility has increased and the world has become more connected. But this comes with a greater risk of the spread of respiratory diseases, particularly pneumonia, which is a leading <a href="https://www.who.int/news-room/fact-sheets/detail/children-reducing-mortality">cause of death</a> in children under the age of five and the elderly. Real-time and more accurate data about respiratory diseases are critical for public health response – especially during an outbreak. </p>
<p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030548/">Pneumonia</a> is a lower respiratory tract infection. It’s caused by very small organisms that cause the air sacs in the lungs to fill up with fluid. This makes breathing difficult and may lead to death. Data from respiratory disease surveillance programmes help public health officials to detect potential clusters that may lead to widespread outbreaks and implement strategies to minimise the impact. </p>
<p>Information collected in clinics and hospitals doesn’t provide the full picture of an illness. This information depends on people actually going to health facilities, which doesn’t always happen. Some people may not be severely ill, or may not be able to get to the health facility. And there may not be adequate laboratory capacity to run tests.</p>
<p>Relying on facilities for information about illnesses makes it difficult to detect an outbreak or seasonal increase as it happens – and hard to estimate the total case numbers. There can be a delay and under-reporting, which makes the public health response less effective. The sooner a cluster of cases is detected, the better it can be managed.</p>
<p>These days there are other ways to collect information about illnesses, using technology. They fall under the description of <a href="https://www.researchgate.net/publication/263742723_Public_health_for_the_people_Participatory_infectious_disease_surveillance_in_the_digital_age">digital participatory surveillance</a>. These are platforms that allow people to routinely report their own symptoms via the internet, on a mobile application or through social media <a href="https://pubmed.ncbi.nlm.nih.gov/24350723/">surveys</a>. They can also record questions about health-seeking behaviour. Health authorities can then analyse the digitally collected data, obtain a bigger picture of how prevalent a disease is in a population, and see trends that allow the health system to prepare and manage better.</p>
<p>The National Institute for Communicable Diseases in South Africa is planning a pilot phase of a digital participatory surveillance platform. The aim is to assess the feasibility and inform its structure, before incorporating it into the existing facility-based surveillance programmes. In particular, this pilot phase will be used to survey respiratory diseases such as influenza and potentially COVID-19.</p>
<p>Influenza is a vaccine preventable disease and one of the causes of pneumonia. It causes an estimated <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692552/">11,000 deaths</a> every year in South Africa. With regard to COVID-19, which can also cause pneumonia, the pilot phase may potentially assist in detecting a big increase in cases at an early stage.</p>
<p>The success of a digital participatory surveillance programme depends on the consistent participation of the population.</p>
<p>South Africa already has another technological tool designed to combat the pandemic: the COVID-19 Alert app. But that is intended for contact tracing, by helping the user ascertain whether they have been in close proximity to a confirmed COVID-19 case. It’s different from digital participatory surveillance apps that are intended for long-term surveillance of respiratory diseases beyond COVID-19, and do not serve contact tracing purposes. </p>
<h2>Digital surveillance</h2>
<p>Digital participatory surveillance is relatively low-cost and easily scaleable to any disease of public health significance. Users report on a weekly basis whether they have experienced symptoms related to respiratory illness or not. This allows for real-time estimation of cases without relying on access to medical care or testing capacity. This data can also be used to <a href="https://www.researchgate.net/publication/315869302_Using_Participatory_Web-based_Surveillance_Data_to_Improve_Seasonal_Influenza_Forecasting_in_Italy">forecast</a> how outbreaks might spread in a community. </p>
<p>To date, digital participatory surveillance has not been widely used on the African continent, despite its potential value. But it’s been used in other parts of the world.</p>
<p>The first platform of this kind was launched in Europe in the 2003/2004 influenza season and they are now used in several countries, where they have been able to <a href="https://pubmed.ncbi.nlm.nih.gov/28076411/">detect flu outbreaks earlier</a>. The <a href="https://flunearyou.org/#!/">USA</a>, <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294562/">Australia</a> and Mexico have their own digital participatory surveillance programmes. Today, 11 European countries have established a continent-based digital participatory surveillance network called <a href="https://pubmed.ncbi.nlm.nih.gov/26616039/">InfluenzaNet</a>. This allows for a comparison of trends within and between countries in Europe. </p>
<p>Countries in Europe, and the US and Australia have increased and sustained participation on these platforms through media campaigns and public health messaging. The National Institute for Communicable Diseases is employing similar strategies through public relations and media in South Africa.</p>
<p>South Africa’s digital participatory surveillance will face some important challenges, though. </p>
<p>Firstly, information and communications technology is <a href="https://www.researchgate.net/publication/285593353_ICT_Adoption_in_South_Africa_-_Opportunities_Challenges_and_Implications_for_national_development">limited</a>. Some parts of the country may not have internet connectivity. </p>
<p>Secondly, the <a href="https://www.tandfonline.com/doi/full/10.1080/1369118X.2015.1065285?scroll=top&needAccess=true">digital divide</a> within a population means segments of the demographic may not be fully represented, because not everyone has access to smartphones or internet connectivity. </p>
<p>There may be some concerns and scepticism around <a href="https://sigmapubs.onlinelibrary.wiley.com/doi/full/10.1111/j.1741-6787.2012.00243.x">social media</a> and mobile apps with regard to data confidentiality and privacy. These are longstanding challenges that both government and various industries need to address.</p>
<h2>Moving forward</h2>
<p>As the digital world evolves, there is an opportunity to use technology to solve critical problems in public health. </p>
<p>Digital participatory surveillance allows the community to share in the responsibility of disease surveillance and contribute to the control and prevention of respiratory disease outbreaks.</p><img src="https://counter.theconversation.com/content/148928/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Cheryl Cohen receives funding from United States Centres for Disease Control and Prevention and Wellcome Trust UK. </span></em></p><p class="fine-print"><em><span>Mvuyo Makhasi is currently the project lead for digital participatory surveillance that will be launched by the National Institute for Communicable Diseases</span></em></p><p class="fine-print"><em><span>Sibongile Walaza 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>Digital participatory surveillance allows the community to share in the responsibility of disease surveillance and contribute to the control and prevention of respiratory disease outbreaks.Cheryl Cohen, co-head of the Centre for Respiratory Disease and Meningitis, National Institute for Communicable DiseasesSibongile Walaza, Medical Epidemiologist at the National Institute of Communicable Diseases and Lecturer at the School of Public Health, University of the WitwatersrandLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1488572020-11-03T14:11:31Z2020-11-03T14:11:31ZHow ending polio in Africa has had positive spinoffs for public health<figure><img src="https://images.theconversation.com/files/366076/original/file-20201028-21-9w8mqn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">The polio eradication programme in Africa directly combated a severe debilitating disease. </span> <span class="attribution"><span class="source">Yasuyoshi Chiba / AFP via Getty Images</span></span></figcaption></figure><p><a href="https://theconversation.com/africa-is-within-reach-of-being-declared-a-polio-free-region-44786">Polio</a> is a highly infectious disease. It’s caused by a virus that enters the body through the mouth. The virus then multiplies in the intestine and attacks the central nervous system – causing paralysis. </p>
<p>Polio was one of the most dreaded diseases in the world in the 20th century. Four decades ago, an estimated 350,000 people were paralysed each year by the poliovirus in <a href="https://www.who.int/news-room/fact-sheets/detail/poliomyelitis">more than 125 countries</a>. This led the World Health Assembly in 1988 to adopt a resolution for the worldwide eradication of polio, drawing inspiration from the eradication of <a href="https://www.who.int/health-topics/smallpox#tab=tab_1">smallpox</a>. </p>
<p>The global programme to <a href="http://polioeradication.org/">eradicate polio</a> is spearheaded by a number of actors. These include national governments, the World Health Organisation (WHO), multiple development agencies, and healthcare workers. </p>
<p>The <a href="https://theconversation.com/africa-is-within-reach-of-being-declared-a-polio-free-region-44786">strategy</a> involves widespread vaccination as part of routine healthcare services as well as mass vaccination campaigns. Sensitive surveillance to detect and rapidly respond to polio cases is also key.</p>
<p>This initiative has been extremely successful. The number of people paralysed by polio decreased by 99.9% – from 350,000 in 1988 to 175 in 2019. During the same period, the number of polio endemic countries fell from more than 125 to only two: Afghanistan and Pakistan. A country is endemic when there’s widespread circulation of polio. </p>
<p>The latest WHO region to be certified polio free is Africa. The region was certified on <a href="https://www.afro.who.int/news/africa-eradicates-wild-poliovirus">25 August 2020</a>. The certification came four years after the last case of poliovirus on the continent. </p>
<p>The polio eradication programme in Africa directly combated a severe debilitating disease. But it also provided a platform for <a href="https://theconversation.com/the-legacy-benefits-from-africas-fight-against-polio-45688">broader healthcare services on the continent</a>. Polio eradication created renewed demand for vaccination services and innovative ways to deliver healthcare services. </p>
<h2>What does it take to eradicate a disease?</h2>
<p>It takes a combination of multiple biological and non-biological factors to eradicate a disease. Only one disease, smallpox, has so far been eradicated. </p>
<p>Polio viruses only survive for a very short time in the environment and there are no animal or insect reservoirs that carry polio viruses. More importantly, effective vaccines exist against polio. Beyond these biological features of polio, the eradication of polio from Africa required sound leadership. </p>
<p>In 1996 African heads of state resolved to stamp polio out of Africa. Then South African President Nelson Mandela launched the “Kick Polio out of Africa” campaign. Thereafter, <a href="https://theconversation.com/the-legacy-benefits-from-africas-fight-against-polio-45688">all-of-society collaborations</a> supporting widespread polio vaccination sprang up across African countries. These involved government departments, the private sector, the civil society, and the community at large to ensure eradication of <a href="https://www.afro.who.int/health-topics/polio">polio from the continent</a>. </p>
<p>Within national governments in Africa, public service departments worked across portfolio boundaries, formally and informally, to achieve the shared goal of polio eradication. All these efforts culminated, 14 years later, in the certification of the eradication of polio from Africa. </p>
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<a href="https://theconversation.com/africa-is-within-reach-of-being-declared-a-polio-free-region-44786">Africa is within reach of being declared a polio free region</a>
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<p>Certification is based on evidence that <a href="https://dictionary.cambridge.org/dictionary/english/certification">something has been achieved</a>. In the case of polio eradication, a region only gets certified when all the countries in the area demonstrate the absence of poliovirus transmission for at least three consecutive years in the presence of extremely sensitive surveillance. </p>
<p>Polio surveillance refers to a disease detection system that involves both community and laboratory components. </p>
<p>Surveillance in the community is done by the general public and healthcare workers. Healthcare workers need to report all cases of children who experience abrupt weakness of the limbs. Community members need to report any newly paralysed children in their communities to healthcare services. In the laboratory, the polio virus responsible for any case of polio paralysis is identified and its source determined. Without such high-quality surveillance it would be difficult to locate where and exactly how the polio virus is circulating or to confirm when its transmission has <a href="https://theconversation.com/africa-is-within-reach-of-being-declared-a-polio-free-region-44786">been eradicated</a>.</p>
<p>Twenty years ago, Africa was close to polio eradication; then <a href="https://theconversation.com/africa-is-within-reach-of-being-declared-a-polio-free-region-44786">misinformation surfaced in northern Nigeria</a> about the effectiveness and safety of polio vaccines. This misinformation led some people in the area to refuse or delay polio vaccines. Vaccination coverage dropped, resulting in widespread polio outbreaks in northern Nigeria and beyond. Such misinformation has gained traction on <a href="https://gh.bmj.com/content/5/10/e004206">social media</a>. </p>
<p>Avoiding vaccination even when it’s available is referred to as <a href="https://www.thinkglobalhealth.org/article/vaccine-hesitancy-escalating-danger-africa">vaccine hesitancy</a>. Polio vaccine hesitancy poses significant risks not only for the hesitant people, but also the wider community. It could prevent African communities from reaching thresholds of vaccination coverage necessary to keep polio out of Africa. If a single child remains infected with polio virus in any part of the world, children in all countries are at risk of contracting the disease.</p>
<h1>Long-term rewards</h1>
<p>Africa’s health systems are much stronger because of the investments made. Countries were supported to make life-saving gains. These included increasing access to health care in the most remote places, strengthening routine vaccination systems, and ensuring strong disease surveillance. </p>
<p>Polio’s legacy must be built on to achieve <a href="https://www.africakicksoutwildpolio.com/the-legacy-of-polio-eradication-in-africa/">other major health goals</a>.</p><img src="https://counter.theconversation.com/content/148857/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Charles Shey Wiysonge 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 polio eradication programme in Africa directly combated a severe debilitating disease. But it also provided a platform for broader healthcare services on the continent.Charles Shey Wiysonge, Director, Cochrane South Africa, South African Medical Research CouncilLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1442552020-08-31T12:22:15Z2020-08-31T12:22:15ZCOVID-19 clues in a community’s sewage: 4 questions answered about watching wastewater for coronavirus<figure><img src="https://images.theconversation.com/files/355438/original/file-20200830-17-1k9o7wc.jpg?ixlib=rb-1.1.0&rect=31%2C116%2C2914%2C1868&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Germs flushed down the drain can be detected at water treatment plants.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/portlad-water-district-public-relations-manager-michelle-news-photo/585540652">Derek Davis/Portland Portland Press Herald via Getty Images</a></span></figcaption></figure><p><em>Researchers around the world are testing wastewater for the SARS-CoV-2 virus, in hopes that what goes down the drain can act as an early warning system for COVID-19 infections in communities.</em></p>
<p><em><a href="https://scholar.google.com/citations?user=CXpAqu8AAAAJ&hl=en&oi=ao">Environmental engineer Kyle Bibby</a> is coordinating a nationwide research network sponsored by the National Science Foundation that aims to help scientists pool their work in this area. Here he explains the sewage-virus connection and how researchers hope to eventually translate raw measurements into useful public health information.</em></p>
<h2>How do you monitor wastewater for germs?</h2>
<p>This idea has gotten a lot of attention recently, but it’s not new. Scientists have been searching sewage for pathogens <a href="https://doi.org/10.1146/annurev.mi.49.100195.002333">since at least the 1940s</a>, <a href="https://theconversation.com/sewage-surveillance-is-the-next-frontier-in-the-fight-against-polio-105012">most notably for poliovirus</a>.</p>
<p>The overall concept is pretty straightforward. Infected individuals excrete the pathogen, which gets flushed down the toilet or washed down the drain. The pathogen – or fragments of its genes – then travel through a community’s sewage system to a treatment plant, where careful sampling can detect its presence.</p>
<p>About two-thirds of people infected with SARS-CoV-2 <a href="https://www.nature.com/articles/s41586-020-2196-x">excrete the coronavirus in their stool</a>. A treatment facility can monitor wastewater for the virus’ RNA using molecular tools.</p>
<p>There’s no real standard yet, but most approaches involve concentrating the wastewater sample to some degree to make it more likely that you’ll be able to detect any RNA. We’re not looking for a whole, intact genome, but a small sequence of a single SARS-CoV-2 gene.</p>
<p>The RNA fragments that we’re measuring are too small to physically capture directly. So we use other tricks to snag them, usually by what we call electrostatic interaction – getting the RNA to stick to something like a filter, or using other chemicals to get it to clump together.</p>
<p>Then we quantify how much of the viral RNA is in the sample.</p>
<p>It’s important to recognize that we can’t directly extrapolate from what’s measured in the wastewater to how many people in the community have the coronavirus – at least not yet.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/355440/original/file-20200830-14-or0vbz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="huge tank of wastewater at a treatment plant" src="https://images.theconversation.com/files/355440/original/file-20200830-14-or0vbz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/355440/original/file-20200830-14-or0vbz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=399&fit=crop&dpr=1 600w, https://images.theconversation.com/files/355440/original/file-20200830-14-or0vbz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=399&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/355440/original/file-20200830-14-or0vbz.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=399&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/355440/original/file-20200830-14-or0vbz.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=502&fit=crop&dpr=1 754w, https://images.theconversation.com/files/355440/original/file-20200830-14-or0vbz.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=502&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/355440/original/file-20200830-14-or0vbz.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>
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<span class="caption">Millions of households’ wastewater can flow to one treatment plant.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/huge-tank-full-of-wastewater-is-seen-at-dc-waters-blue-news-photo/499524598">Nicholas Kamm/AFP via Getty Images</a></span>
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<h2>What does the presence of coronavirus tell you?</h2>
<p>We can have three related goals when we’re looking for viral RNA in the wastewater. First is direct surveillance. Essentially is the virus there, yes or no. That probably has the most promise within small confined communities, schools, dorms, prisons, long-term care facilities and so on. This would require sampling directly from the sewer at the facility. For instance, the University of Arizona <a href="https://tucson.com/news/arizona_news/university-of-arizonas-wastewater-testing-halts-potential-surge-in-covid-19-cases-at-dorm/article_e29a25ef-b1d2-5da7-8b8d-1ea3b3f166ea.html">detected the presence of asymptomatic infected students</a> by testing wastewater from on-campus housing.</p>
<p>The next potential application could be monitoring for trends. Is the apparent concentration of the virus increasing? That may indicate that infections within the community are increasing as well.</p>
<p>And the third application – which we’re probably the furthest away from – is directly applying our measurements to estimate the number of infected individuals in the community.</p>
<p>There’s a lot of uncertainty associated with how much of this virus an infected individual excretes, and how long they excrete it for – reports seem to suggest that it varies a lot. You could have one person sick with COVID-19 excreting 100 copies of the coronavirus genome per gram of feces. Another individual could be excreting 100 million copies per gram of feces, a big difference. </p>
<p>The overall vision is that wastewater monitoring could inform all sorts of public health intervention and disease surveillance programs. It could complement clinical surveillance, which often lags behind the true disease level in the community.</p>
<h2>Is the wastewater itself a contamination risk?</h2>
<p>Wastewater surveillance has typically been used to detect a pathogen that spreads via the fecal-oral route – not the respiratory route apparently responsible for SARS-CoV-2 infections. There’s debate about <a href="https://doi.org/10.1016/S2468-1253(20)30048-0">whether or not the coronavirus can be spread via water</a>. I would say it’s plausible, though it certainly isn’t a dominant transmission route and it hasn’t been demonstrated yet.</p>
<p>While there are some reports of infectious virus being excreted in stool, the vast <a href="https://doi.org/10.3201/eid2608.200681">majority appears to be inactivated</a> once it leaves a patient’s body. So I really don’t believe coronavirus in wastewater should be a significant concern for the general public.</p>
<p>It’s possibly a bigger concern to a wastewater worker. But the consensus is that standard personal protective equipment for dealing with wastewater is adequate for controlling the coronavirus. Remember – outside of the pandemic, wastewater can contain other infectious pathogens at any time.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/355442/original/file-20200830-24-1vmst9s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="water flows into a river from a pipe connected to a treatment plant" src="https://images.theconversation.com/files/355442/original/file-20200830-24-1vmst9s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/355442/original/file-20200830-24-1vmst9s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=363&fit=crop&dpr=1 600w, https://images.theconversation.com/files/355442/original/file-20200830-24-1vmst9s.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=363&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/355442/original/file-20200830-24-1vmst9s.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=363&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/355442/original/file-20200830-24-1vmst9s.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=456&fit=crop&dpr=1 754w, https://images.theconversation.com/files/355442/original/file-20200830-24-1vmst9s.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=456&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/355442/original/file-20200830-24-1vmst9s.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=456&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">Researchers believe treated wastewater is not a coronavirus threat.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/water-flows-into-the-minnesota-river-from-a-pipe-connected-news-photo/1156753616">Jerry Holt/Star Tribune via Getty Images</a></span>
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<p>But imagine swimming at a beach downstream of a treatment plant. You don’t really need to worry about any bits of broken up viral genome left in the water. The concern is infectious virus and we just haven’t seen any infectious virus make it all the way to a sewage treatment plant, much less through the wastewater treatment and disinfection process.</p>
<h2>What are the challenges to be worked out?</h2>
<p>It’s a misconception to think this technique is ready to go right off the shelf. There’s still a lot of unsettled science about how to do it well.</p>
<figure class="align-right zoomable">
<a href="https://images.theconversation.com/files/355443/original/file-20200831-17-cwdi5l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="medical worker points swab toward patient's nostril" src="https://images.theconversation.com/files/355443/original/file-20200831-17-cwdi5l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=237&fit=clip" srcset="https://images.theconversation.com/files/355443/original/file-20200831-17-cwdi5l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=695&fit=crop&dpr=1 600w, https://images.theconversation.com/files/355443/original/file-20200831-17-cwdi5l.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=695&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/355443/original/file-20200831-17-cwdi5l.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=695&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/355443/original/file-20200831-17-cwdi5l.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=873&fit=crop&dpr=1 754w, https://images.theconversation.com/files/355443/original/file-20200831-17-cwdi5l.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=873&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/355443/original/file-20200831-17-cwdi5l.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=873&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 screening serves a different purpose than testing individuals for SARS-CoV-2.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/medical-worker-shows-the-process-for-rapid-coronavirus-news-photo/1269132586">Spencer Platt/Getty Images North America via Getty Images</a></span>
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<p>It’s also not quite right to think of this as like testing every single person in the community for COVID-19. There are a variety of issues with detection limits, getting composite samples that grab wastewater from throughout the day, and of course just the fact that many sick people might not excrete viral RNA for us to detect. A negative wastewater result does not in fact mean that zero people in the area have the coronavirus. So wastewater surveillance is subtly different from a clinical diagnosis tool.</p>
<p>I worry about a city’s department of health getting wastewater data from a contract lab and all of a sudden either thinking everything is safe and the coronavirus cases are low in their area or else overextrapolating that cases are high. It’s not like we couldn’t get to the ability to use this tool in this way pretty quickly. We’re just not there yet today.</p>
<p>My colleagues and I are trying to help establish a framework to translate this information to a usable format for communities, so municipalities can use wastewater monitoring to help make tough decisions that affect people’s lives and the economy. We also have projects looking at the persistence of this infectious virus in wastewater.</p><img src="https://counter.theconversation.com/content/144255/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Kyle Bibby receives funding from the National Science Foundation and the Alfred P. Sloan Foundation.</span></em></p>Sewage surveillance is one technique that can alert authorities to the presence of a pathogen in the community. An environmental engineer explains the state of the science when it comes to SARS-CoV-2.Kyle Bibby, Associate Professor of Environmental Engineering, University of Notre DameLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1394282020-06-18T12:16:04Z2020-06-18T12:16:04ZTracing homophobia in South Korea’s coronavirus surveillance program<figure><img src="https://images.theconversation.com/files/341862/original/file-20200615-65961-1g8k0ol.jpg?ixlib=rb-1.1.0&rect=0%2C24%2C5481%2C3870&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Korean health workers offer coronavirus testing in the Itaewon nightlife district of Seoul.</span> <span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/medical-staff-members-wearing-protective-clothing-guide-news-photo/1212731196">Jung Yeon-Je/AFP via Getty Images</a></span></figcaption></figure><p>Many people around the world have looked to South Korea’s so-called <a href="https://thediplomat.com/2020/03/a-democratic-response-to-coronavirus-lessons-from-south-korea">“democratic” response</a> to the coronavirus pandemic as a <a href="https://talkingpointsmemo.com/edblog/pay-close-attention-to-south-koreas-apparent-success">template</a> for other nations to follow. That response is often contrasted with China’s <a href="https://www.scmp.com/week-asia/health-environment/article/3075164/south-koreas-coronavirus-response-opposite-china-and">“draconian measures”</a> of forced lockdown in people’s homes.</p>
<p>Key to this global interest is South Korean citizens’ willing participation in <a href="https://theconversation.com/coronavirus-south-koreas-success-in-controlling-disease-is-due-to-its-acceptance-of-surveillance-134068">mass surveillance technologies and techniques</a>, ranging from mandatory testing and financial data collection to cellphone GPS tracking and social media analyses.</p>
<p>Yet my research reveals that widespread homophobia in South Korea is <a href="http://blog.castac.org/2019/04/the-surveillance-cyborg/">getting in the way</a> of a more effective public health response and may put South Koreans at greater risk of contracting the coronavirus. This was particularly evident in the government’s response to a May 2020 outbreak of coronavirus infections in the country’s queer communities.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/341347/original/file-20200611-80766-o5wilx.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/341347/original/file-20200611-80766-o5wilx.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/341347/original/file-20200611-80766-o5wilx.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/341347/original/file-20200611-80766-o5wilx.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/341347/original/file-20200611-80766-o5wilx.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/341347/original/file-20200611-80766-o5wilx.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/341347/original/file-20200611-80766-o5wilx.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/341347/original/file-20200611-80766-o5wilx.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">Anti-gay activists demonstrate outside the Korea Queer Culture Festival in Seoul in June 2019.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/anti-same-sex-marriage-activists-attend-the-rally-next-to-news-photo/1153030333">Chung Sung-Jun/Getty Images</a></span>
</figcaption>
</figure>
<h2>Recent cases of homophobia</h2>
<p>Homosexuality is not illegal in South Korea, but there is a <a href="https://doi.org/10.1353/jks.2014.0018">strong social stigma against it</a>, including decades of discrimination against people living with HIV/AIDS. </p>
<p>For many years, some hospitals <a href="https://medium.com/@benkwagner/south-korean-patients-have-nowhere-to-go-as-world-gathers-to-discuss-hiv-aids-cdaece9e64c9">have refused to treat people living with HIV/AIDS</a>. Politicians, influential conservative Christian leaders and even doctors have <a href="https://thediplomat.com/2016/09/aids-in-south-korea-out-of-sight-out-of-mind/">incorrectly claimed</a> that homosexuality causes AIDS. And the government has <a href="https://www.eastasiaforum.org/2018/02/17/government-policies-fuel-south-koreas-hiv-epidemic/">criminalized HIV transmission</a> and conducts strict surveillance on people who test positive.</p>
<p>Homophobia is also rife in the <a href="https://www.academia.edu/42098216/Ripples_of_Trauma_Queer_Bodies_and_the_Temporality_of_Trauma_in_the_South_Korean_Military">South Korean military</a>, where all men are required to serve for roughly two years. As recently as 2017, the activist organization Military Human Rights Center reported on a <a href="https://koreaexpose.com/military-witch-hunt-gay-soldiers/">“gay witch-hunt”</a> in which the chief of staff of the Korean army coerced soldiers into using gay dating apps, in an effort to identify soldiers who might be queer. Those who came under suspicion through this scheme were charged under the military’s anti-sodomy law, a law that ostensibly makes homosexuality illegal in the military. Some soldiers were also <a href="https://www.nytimes.com/2017/05/24/world/asia/south-korea-gay-soldier-military-court.html?_r=0">imprisoned</a>.</p>
<p>In 2015 that discrimination intersected with a rapidly spreading disease, during the Middle East respiratory syndrome outbreak. Conservative Christians began spreading rumors nationwide – including in <a href="https://www.yna.co.kr/view/MYH20150625001400038">Korean news media</a> – that there was a so-called “super virus” combining AIDS and MERS.</p>
<p>The resulting fears about HIV/AIDS and the perceived dangers of queer people brought droves of anti-LGBTQ protesters to a queer culture festival in Seoul in June 2015. When I spoke there to one male protester, he gestured to festival-goers across the street, saying they had the so-called “super virus,” but explained that the people with him were protected by the Holy Spirit.</p>
<p>That year, South Koreans suffered the worst MERS outbreak outside the Middle East and largely <a href="https://www.theregreview.org/2020/05/14/oh-south-korea-success-against-covid-19/">blamed an ineffective government response</a> for the illnesses and deaths. In the wake of that epidemic, the current South Korean government remade its pandemic plans, which added unprecedented levels of public information and testing. But in the move toward transparency, queer communities that rely on anonymity to protect against homophobia are facing renewed discrimination.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/341866/original/file-20200615-65956-yqssjv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/341866/original/file-20200615-65956-yqssjv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/341866/original/file-20200615-65956-yqssjv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=389&fit=crop&dpr=1 600w, https://images.theconversation.com/files/341866/original/file-20200615-65956-yqssjv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=389&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/341866/original/file-20200615-65956-yqssjv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=389&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/341866/original/file-20200615-65956-yqssjv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=488&fit=crop&dpr=1 754w, https://images.theconversation.com/files/341866/original/file-20200615-65956-yqssjv.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=488&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/341866/original/file-20200615-65956-yqssjv.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=488&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 man wearing a mask walks through the Itaewon district of Seoul, South Korea.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/man-wearing-a-face-mask-walks-in-the-popular-nightlife-news-photo/1212436029">Jung Yeon-Je/AFP via Getty Images</a></span>
</figcaption>
</figure>
<h2>Coronavirus outbreak in queer communities</h2>
<p>During the week of April 27, 2020, Korean bars and clubs were allowed to reopen after the government eased some nightlife restrictions. On May 1, a Korean <a href="http://www.koreaherald.com/view.php?ud=20200507000634">man in his late 20s visited a series of bars</a> and clubs in the Itaewon district of Seoul. The following day he felt ill and tested positive for the coronavirus.</p>
<p>At that time, the Korean Center for Disease Control and Prevention began trying to figure out who might have come in contact with the man. The agency used records of financial transactions from those clubs and bars, GPS tracking of mobile phones in the area and direct interviews with potentially affected people.</p>
<p>Some of the media reports included the names of the establishments the man had been to; <a href="http://www.koreaherald.com/view.php?ud=20200508000751">others specifically identified them as gay clubs</a>. That led to queer Koreans and their lifestyles <a href="https://www.washingtonpost.com/world/asia_pacific/tracing-south-koreas-latest-virus-outbreak-shoves-lgbtq-community-into-unwelcome-spotlight/2020/05/11/0da09036-9343-11ea-87a3-22d324235636_story.html">being blamed</a> for 79 new cases appearing in May 2020.</p>
<p>Many queers feared that contact tracing would <a href="https://www.pinknews.co.uk/2020/05/11/south-korea-coronavirus-second-wave-gay-dating-doxxing-homophobia-itaewon/">forcibly out them</a>, especially since some Korean media outlets took to <a href="https://www.theguardian.com/world/2020/may/11/south-korea-struggles-to-contain-new-outbreak-amid-anti-lgbt-backlash">reporting the identities</a> of the venues’ customers and where they worked. Queer South Koreans are <a href="https://www.theguardian.com/world/2020/may/08/anti-gay-backlash-feared-in-south-korea-after-coronavirus-media-reports#maincontent">withdrawing from social media and dating apps</a>, fearful that they might be trapped into being outed live online.</p>
<p>All of that homophobia has made it harder for public health officials to track down and test the thousands of people who visited the bars and clubs.</p>
<p>To ease the fear of being outed, the government instituted <a href="http://english.hani.co.kr/arti/english_edition/e_national/944663.html">anonymous testing</a> for those connected to the most recent outbreak. But that doesn’t solve the problem. </p>
<p>The process of contact tracing includes talking to the friends, relatives, co-workers and other close connections with a person who may have been exposed to the coronavirus. In South Korea, the latest outbreak is so closely linked to queer communities that any mention of a possible exposure – much less a positive test result – is, effectively, the same as being outed at home, at work and in private social life. The surveillance technologies themselves are the problem.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/341348/original/file-20200611-80789-14u4aa9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="" src="https://images.theconversation.com/files/341348/original/file-20200611-80789-14u4aa9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/341348/original/file-20200611-80789-14u4aa9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/341348/original/file-20200611-80789-14u4aa9.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/341348/original/file-20200611-80789-14u4aa9.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/341348/original/file-20200611-80789-14u4aa9.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/341348/original/file-20200611-80789-14u4aa9.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/341348/original/file-20200611-80789-14u4aa9.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 scene from a pride parade in Seoul, South Korea, in June 2019.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/participants-march-during-a-pride-event-in-support-of-lgbt-news-photo/1147211830">Ed Jones/AFP via Getty Images</a></span>
</figcaption>
</figure>
<h2>The problem with surveillance</h2>
<p><a href="https://doi.org/10.1177/0306312716648403">Surveillance</a> has <a href="https://muse.jhu.edu/book/46525">historically been used in South Korea</a> to weed out suspected communists and individuals considered to be immoral or violating social norms. In addition, some of the specific techniques have been used in crime prevention and policing – like collecting and analyzing <a href="http://english.hani.co.kr/arti/english_edition/e_national/729695.html">social media data</a> and <a href="https://www.nytimes.com/2015/04/03/opinion/south-koreas-invasion-of-privacy.html">cellphone subscriber information</a>. That means public health can come at the expense of people’s privacy and livelihoods.</p>
<p>One man who visited Seoul’s gay district <a href="https://www.theguardian.com/world/2020/may/11/south-korea-struggles-to-contain-new-outbreak-amid-anti-lgbt-backlash">told the Guardian</a> that he felt “trapped and hunted down” by the government because it required his credit card company to report his financial transactions in the area: “If I get tested, my company will most likely find out I’m gay. I’ll lose my job and face a public humiliation. I feel as if my whole life is about to collapse.”</p>
<p>South Korea’s coronavirus surveillance program is alerting the public about new disease outbreaks, but at the expense of marginalized communities that rely on anonymity and privacy. A coalition of 23 groups, calling itself “<a href="https://www.queer-action-against-covid19.org/">Queer Action Against Covid-19</a>,” is conducting a survey to see how widespread these problems are – in hopes of finding effective ways to protect public health that also respect the privacy of Korea’s queer communities and other vulnerable populations.</p>
<p>[<em>Get the best of The Conversation, every weekend.</em> <a href="https://theconversation.com/us/newsletters/weekly-highlights-61?utm_source=TCUS&utm_medium=inline-link&utm_campaign=newsletter-text&utm_content=weeklybest">Sign up for our weekly newsletter</a>.]</p><img src="https://counter.theconversation.com/content/139428/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Timothy Gitzen has received funding from the Korean Foundation, but no longer receives funding from them. </span></em></p>South Korea’s mass surveillance to curb the coronavirus pandemic uses technologies and techniques that are grounded in anti-LGBTQ discrimination.Timothy Gitzen, Postdoctoral Fellow, Society of Fellows in the Humanities, University of Hong KongLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1364272020-04-19T08:12:36Z2020-04-19T08:12:36ZAfrica joins the race to trace COVID-19 with genomics<figure><img src="https://images.theconversation.com/files/328328/original/file-20200416-192725-1wje33n.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Genomic sequencing can help in understanding viruses.</span> <span class="attribution"><span class="source">Gio.tto/Shutterstock</span></span></figcaption></figure><p>One important aspect of managing emerging infections is identifying chains of transmission and assigned cases to clusters of infection. A case in point is South African trade union leader Zwelinzima Vavi, who spent a few days in hospital with the new coronavirus disease. He <a href="https://citizen.co.za/news/covid-19/2264324/zwelinzima-vavi-released-from-hospital-after-admission-for-covid-19/">stated</a> that he “had no idea” where he may have contracted the virus and was scrutinising his travel history for clues. </p>
<p>This experience is hardly unusual, and would be more so for South Africans using public transport and living in crowded circumstances. To ensure that scientists can trace people’s contacts, stronger systems of disease surveillance are needed – ones that draw on genome sequencing.</p>
<p>The first two SARS-CoV-2 virus sequences from the African continent were published by <a href="http://virological.org/t/first-african-sars-cov-2-genome-sequence-from-nigerian-covid-19-case/421">ACEGID</a> in Ede, Nigeria and <a href="https://inrb.net/">INRB</a> in Kinshasa, Democratic Republic of the Congo, in early March. These labs have played significant roles in research on and fighting Ebola. With strong research links to the US, they represent both African success stories and outposts of a “health security” regime focused on emerging pathogens “over there” (in Africa) that might threaten the lives “over here” (in the US). The global health security model is based on this flow of disease. However, COVID-19 has reversed the narrative.</p>
<p>The US and Europe, rather than African countries, are among the epicentres of the pandemic. If the <a href="https://journals.sagepub.com/doi/10.1177/030631270203200507">global health security model</a> monitors disease trajectories along the lines of networks of exchange, the model has worked largely as designed. Information and techniques have been shared, especially between Western scientists and health authorities, in an unprecedented fashion since the start of 2020.</p>
<p>In South Africa, the National Bioinformatics Institute (<a href="https://www.sanbi.ac.za/">SANBI</a>) recently collaborated with the National Institute for Communicable Disease (<a href="https://www.nicd.ac.za/">NICD</a>) to produce the first SARS-CoV-2 viral genome collected in South Africa. Soon after this the Kwazulu-Natal Research Innovation and Sequencing Platform (<a href="https://www.krisp.org.za/">KRISP</a>) published five further genomes. </p>
<p>The variation captured in these genomes, when compared to genomes sampled elsewhere, provides a fingerprint that might be associated with a particular virus – and so, a patient with a particular cluster of transmission.</p>
<p>The first use of this kind of finger printing, more formally known as genomic epidemiology, was to trace the source of the anthrax used in the <a href="https://www.fbi.gov/history/famous-cases/amerithrax-or-anthrax-investigation">2001 anthrax letter attacks</a> in the US. In South Africa similar techniques were used to identify the source of a 2017-2018 <a href="https://www.ncbi.nlm.nih.gov/pubmed/31062992">listeriosis</a> outbreak.</p>
<p>Worldwide, genomic surveillance techniques are proving useful in tracking the spread of COVID-19 and South Africa is well positioned to adopt them within its public health system response.</p>
<h2>How it works</h2>
<p>All six SARS-CoV-2 genomes produced in South Africa thus far have been submitted to the <a href="https://www.gisaid.org/">GISAID</a> data repository and from there incorporated in the <a href="https://nextstrain.org/ncov">Nextstrain</a> platform. Nextstrain uses both sequence data and sample metadata to produce a phylogenetic tree and map of the virus’ global spread. Figure 1 shows the phylogenetic tree with African and, in particular South African, sequences highlighted.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/328058/original/file-20200415-153302-1597il6.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/328058/original/file-20200415-153302-1597il6.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=395&fit=crop&dpr=1 600w, https://images.theconversation.com/files/328058/original/file-20200415-153302-1597il6.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=395&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/328058/original/file-20200415-153302-1597il6.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=395&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/328058/original/file-20200415-153302-1597il6.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=497&fit=crop&dpr=1 754w, https://images.theconversation.com/files/328058/original/file-20200415-153302-1597il6.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=497&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/328058/original/file-20200415-153302-1597il6.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=497&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px">
<figcaption>
<span class="caption">Figure 1.</span>
<span class="attribution"><span class="source">Nextstrain</span></span>
</figcaption>
</figure>
<p>In reading the phylogenetic tree remember that the SARS-CoV-2 virus has a genetic code of about 29000 letters of RNA. This RNA is essential to describing the virus’ proteins and is replicated millions of times as the virus spreads within a person and transmits to a new host. While SARS-CoV-2 is assisted in its replication by a “proofreading” exonuclease, mutations accumulate in the virus at a rate <a href="http://virological.org/t/phylodynamic-analysis-176-genomes-6-mar-2020/356">estimated</a> at 0.8x10<sup>3</sup> per nucleotide site per year. </p>
<p>These mutations can involve the addition, removal or rearrangement of parts of the genome sequence. But single nucleotide variations – the change, for example of a guanine (G) to a cytosine (C), are the most informative for current phylogenetic techniques.</p>
<p>The evolution represented by the Nextstrain phylogeny is all considered with regards to the “reference” sequence of SARS-CoV-2, derived from a sequence collected on 26 December 2019 in Wuhan, China. The South African R03006-2 <a href="http://virological.org/t/whole-genome-sequence-of-the-severe-acute-respiratory-syndrome-coronavirus-2-sars-cov-2-obtained-from-a-south-african-coronavirus-disease-2019-covid-19-patient/452">sequence</a> differs from the reference sequence at six positions that bear some similarity to virus sequences collected in Europe.</p>
<p>While this is a relatively modest signal and must not be <a href="https://www.medrxiv.org/content/10.1101/2020.03.16.20034470v1">over-interpreted</a>, it is clear from the phylogenetic tree that the South African virus sequences are found in four different places with regards to the global distribution of virus. This indicates multiple imports of COVID-19 into the country. </p>
<p>The situation with R03006-2, KRISP_011 and KRISP_007 is more difficult to discern: are they part of a transmission chain? Figure 2 presents a closer look.</p>
<figure class="align-center ">
<img alt="" src="https://images.theconversation.com/files/328077/original/file-20200415-153313-1omc3mc.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/328077/original/file-20200415-153313-1omc3mc.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=470&fit=crop&dpr=1 600w, https://images.theconversation.com/files/328077/original/file-20200415-153313-1omc3mc.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=470&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/328077/original/file-20200415-153313-1omc3mc.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=470&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/328077/original/file-20200415-153313-1omc3mc.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=590&fit=crop&dpr=1 754w, https://images.theconversation.com/files/328077/original/file-20200415-153313-1omc3mc.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=590&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/328077/original/file-20200415-153313-1omc3mc.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=590&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">Figure 2: a closer view of the Nextstrain phylogenetic tree, branches scaled by time.</span>
<span class="attribution"><span class="source">Nextstrain</span></span>
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</figure>
<p>The R03006 sample was collected on 7 March, and the KRISP samples three weeks later, on 1 April. The sequences are very similar and there could be a link, but the small number of sequenced samples (six out of 1380 cases reported in South Africa by 1 April, and 8000 sequenced out of nearly 2 million cases worldwide) hampers our ability to draw conclusions. Perhaps R03006 and the KRISP samples illustrate transmission from another person whose virus is not present in the data. </p>
<p>Genomic epidemiology can aid in understanding disease transmission, but it is not enough on its own. It needs to be combined with field epidemiological data for correct interpretation. The more sequences we have to work with, the more bioinformaticians can assist their colleagues in understanding transmission and the structure of the COVID-19 disease outbreak.</p>
<h2>What’s missing</h2>
<p>Surveying SARS-CoV-2 sequencing on the African continent reveals a weakness. Of the first 87 virus genomes published, 86 emerged from research institutes. While many of these have strong links with national health systems, they also reflect both the <a href="https://www.nature.com/articles/d41586-018-07418-6">weakness</a> of African governments’ investment in science and a disconnect between genomic science and public health. <a href="https://theconversation.com/why-its-time-african-researchers-stopped-working-in-silos-59539">Silos</a> also exist between national initiatives, while the continent faces a singular disease threat. </p>
<p>In this context, the launch of a Pathogen Genomics Intelligence Institute (<a href="https://africacdc.org/africa-cdc-institutes/africa-cdc-pathogen-genomics-intelligence-institute/">PGII</a>) by the Africa CDC in 2019 was prescient. </p>
<p><a href="https://www.tandfonline.com/eprint/4y485eC9CkUGt45XkidU/full?target=10.1080/17441692.2019.1614645">Surveillance</a> is part of the ‘hardware’ of health systems’ preparedness for emerging infectious diseases. The South African response to COVID-19 clearly aligns with this vision, but it is crucial that virus sequencing and genomic epidemiology be deployed within the public health response to understand and counter disease transmission in the coming months.</p><img src="https://counter.theconversation.com/content/136427/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Peter van Heusden works for the South African National Bioinformatics Institute.</span></em></p>The variation captured in these genomes, when compared to genomes sampled elsewhere, provides a fingerprint that might be associated with a particular virus and a particular cluster of transmission.Peter van Heusden, Researcher, University of the Western CapeLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1315922020-02-19T08:27:31Z2020-02-19T08:27:31ZWhy it’s important to study coronaviruses in African bats<figure><img src="https://images.theconversation.com/files/315497/original/file-20200214-11011-rhfu2i.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Viral sequences related to known human coronavirus outbreaks have been identified in horsehoe bats.</span> <span class="attribution"><span class="source">Dr. Low de Vries</span>, <span class="license">Author provided</span></span></figcaption></figure><p>The current outbreak of a new coronavirus disease, <a href="https://www.who.int/health-topics/coronavirus">named COVID-19</a>, raises the question of where diseases like this come from and where the risks lie. By the middle of February almost <a href="https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200218-sitrep-29-covid-19.pdf?sfvrsn=6262de9e_2">2000</a> people had died in this outbreak, which has also had a global economic impact. </p>
<p>It is clear that the virus may have an animal reservoir. In other words, it may be permanently found in a host species of animal, where it does not normally cause disease. Viruses can spill over from the host to other animals and humans. Evidence <a href="https://www.nature.com/articles/d41586-020-00020-9">points</a> to a possible initial spillover of the virus into humans and other animals in an animal market in Wuhan in China.</p>
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Read more:
<a href="https://theconversation.com/a-clue-to-stopping-coronavirus-knowing-how-viruses-adapt-from-animals-to-humans-130790">A clue to stopping coronavirus: Knowing how viruses adapt from animals to humans</a>
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<p>Bats are prone to act as reservoir for viruses. Chinese populations of the horseshoe bat genus (<em>Rhinolophus</em>) have already been <a href="https://www.nature.com/articles/s41586-020-2012-7">found</a> to host viruses similar to the new coronavirus. This suggests that it’s important to watch out for related viruses in this genus of bats elsewhere, including <a href="https://doi.org/10.1111/jzo.12769">African countries</a>.</p>
<p>Scientists on the continent do keep a watch by doing bio-surveillance and specifically looking for pieces of coronavirus genomes in bat species. If these are found, the researchers can determine the genome sequence and analyse how it is related to other animal and human coronaviruses. </p>
<p>If it’s closely related, it may be an indication of where the spillover of new viruses came from and whether it poses a risk of a disease outbreak. </p>
<p>The horseshoe bat genus is found around the world and there are 40 species in Africa. But so far no viruses related to the cause of COVID-19 disease have been reported from African bat species.</p>
<h2>The lesson from SARS</h2>
<p>Global surveillance for coronavirus diversity in bats has expanded rapidly in the past two decades because of a previous novel coronavirus disease <a href="https://www.ncbi.nlm.nih.gov/pubmed/25757061">outbreak</a>, severe acute respiratory syndrome (SARS), in China in 2002. This virus resulted in significant illness and death <a href="https://www.mdpi.com/1999-4915/7/3/996">(10%)</a> among human populations. It also spread globally due to travel. The virus appeared to have <a href="https://www.nature.com/articles/s41579-018-0118-9">originated in animals</a> and “jumped” to humans for the first time. </p>
<p>At first, it was thought that masked palm civets and raccoon dogs were the <a href="https://www.ncbi.nlm.nih.gov/pubmed/12958366">animal hosts</a> for the SARS virus. But it later appeared that they were probably infected by another reservoir source. The horseshoe bat genus hosted viruses similar to SARS but these were sufficiently different to rule out a direct spillover from bats.</p>
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<img alt="" src="https://images.theconversation.com/files/315491/original/file-20200214-10985-d6uca5.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/315491/original/file-20200214-10985-d6uca5.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=450&fit=crop&dpr=1 600w, https://images.theconversation.com/files/315491/original/file-20200214-10985-d6uca5.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=450&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/315491/original/file-20200214-10985-d6uca5.JPG?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=450&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/315491/original/file-20200214-10985-d6uca5.JPG?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=566&fit=crop&dpr=1 754w, https://images.theconversation.com/files/315491/original/file-20200214-10985-d6uca5.JPG?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=566&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/315491/original/file-20200214-10985-d6uca5.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">
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<span class="caption">No SARS related coronaviral sequences have been detected in bats in Southern Africa.But surveillance must be improved.</span>
<span class="attribution"><span class="source">Dr. Low de Vries, University of Pretoria</span>, <span class="license">Author provided</span></span>
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<p>Still, the similarity gave rise to a lot of research into Chinese <a href="https://jvi.asm.org/content/90/6/3253">horseshoe bat</a> species. After 11 years of <a href="https://www.ncbi.nlm.nih.gov/pubmed/24172901">continued surveillance</a>, viruses were identified that were nearly identical to human SARS. They were also capable of using the same binding receptor as human SARS coronavirus. This indicated the potential for direct infection from bats to humans – a feature that most bat-borne SARS-related viruses were lacking. </p>
<p>These viruses in bats weren’t directly linked to the human outbreak. But it did indicate that spillover of these viruses circulating in bat populations was possible when opportunities for contact occurred. No new cases of SARS have been reported since 2004 but the continued presence of various SARS-related strains in horseshoe bat populations makes re-emergence possible. </p>
<p>Thanks to all the efforts to identify the potential reservoir of SARS, many coronavirus viral sequences have been detected in bats globally. </p>
<h2>Studying African bats</h2>
<p>Work done in South Africa by <a href="https://www.up.ac.za/centre-for-viral-zoonoses">our group</a> has not detected any viruses related to SARS or the COVID-19 disease in local bats.</p>
<p>Coronavirus <a href="https://doi.org/10.1111/jzo.12769">surveillance studies</a> in bats in other African countries have been mostly one-off studies and haven’t included all the species or considered seasonal shedding of viruses. Highly diverse and novel <a href="https://academic.oup.com/ve/article/3/1/vex012/3866407">coronavirus sequences</a> were reported in cases where surveillance studies were performed. This contributed to the hypothesis that bats were the original evolutionary source. </p>
<p>Viral sequences distantly related to SARS were identified in <a href="https://www.ncbi.nlm.nih.gov/pubmed/31269631">horseshoe bats</a> collected in <a href="https://link.springer.com/article/10.1007%2Fs10393-019-01458-8">Rwanda</a> and Uganda and the free-tailed bat (<em>Chaerephon</em>) genus in <a href="https://www.ncbi.nlm.nih.gov/pubmed/19239771">Kenya</a>. Because SARS-related viruses are so strongly associated with horseshoe bats, though, the free-tailed bat is not considered an important host for transmission. </p>
<p>The sequences found in Rwanda, Uganda and Kenya are not SARS, though they have some genetic relatedness. They do not pose a direct spillover risk and haven’t been shown to be able to infect human cells. There have not been any human outbreaks of SARS or other coronaviruses linked to bats on the continent.</p>
<p>Most countries in Africa do not have active programmes in place to watch for corona- and other bat-borne viruses in bats and to understand their epidemiology and ecology. We do know that bat coronaviruses are excreted in faecal material, which makes it easier to transmit them through bat populations and creates opportunities for exposure to other species. </p>
<h2>Novel coronaviruses</h2>
<p>No outbreaks of coronaviruses with a link to bats have been reported in Africa. But we still need to be vigilant. </p>
<p>Coronaviruses are known to have a high mutation rate and can recombine with other coronaviruses, creating new virus variants with the potential to emerge as outbreak viruses in humans. The emergence of novel coronaviruses is also strongly <a href="https://academic.oup.com/ve/article/3/1/vex012/3866407">linked</a> to a high diversity present in host populations and to contact between bats, humans and other animals, creating opportunities for spillover. </p>
<p>Understanding viral presence and diversity is the first step. And further understanding of the many factors that may play a role in the spillover of pathogens from bats to humans requires systematic surveillance of bat populations through a variety of disciplines. </p>
<p>This is particularly needed on the African continent in view of high species diversity and other pressures.</p><img src="https://counter.theconversation.com/content/131592/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Wanda Markotter receives funding from the National Research Foundation. She is affiliated with the NGO, AfricanBats. </span></em></p>Understanding the many factors that may play a role in spillover of pathogens from bats to humans requires systematic surveillance of bat populations.Wanda Markotter, Professor/Director Centre for Viral Zoonoses/ DST-NRF South African Research Chair, University of PretoriaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1147682019-04-22T08:41:47Z2019-04-22T08:41:47ZHow higher temperatures and pollution are affecting mosquitoes<figure><img src="https://images.theconversation.com/files/269955/original/file-20190418-28100-hd3kcv.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Three species of immature mosquito: the common house mosquito, and the malaria vectors An. arabiensis and An. funestus.</span> <span class="attribution"><span class="source">Supplied</span></span></figcaption></figure><p>In 2017, malaria killed <a href="https://www.who.int/health-topics/news-room/fact-sheets/detail/malaria">435 000</a> people around the world. The vast majority of these deaths – 403 000 – were on the African continent. Most malaria cases are in <a href="https://www.who.int/health-topics/news-room/detail/19-11-2018-who-and-partners-launch-new-country-led-response-to-put-stalled-malaria-control-efforts-back-on-track">sub-Saharan Africa</a>.</p>
<p>My colleagues and I at the <a href="http://www.nicd.ac.za/centres/centre-for-emerging-zoonotic-and-parasitic-diseases/">National Institute for Communicable Diseases</a> track malaria cases and mosquito behaviour in South Africa. </p>
<p>As part of our research we have looked at three key aspects. One is the effect of human activity on mosquito biology. Here we <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0192551">looked at</a> the effects of heavy metal pollution on various life history traits as well as the expression of insecticide resistance in <em>Anopheles arabiensis</em>, which is one of the mosquito species that transmits malaria.</p>
<p>We also did <a href="https://malariajournal.biomedcentral.com/articles/10.1186/s12936-018-2250-4">research</a> into what impact changes in climate are having on the efficacy of insecticides aimed at malaria vectors.</p>
<p>And, finally, we looked at what the effect of <a href="https://malariajournal.biomedcentral.com/articles/10.1186/s12936-017-1720-4">higher temperatures</a> is on the major malaria vector, <em>An. arabiensis</em>. </p>
<p><em>An. arabiensis</em> is extremely difficult to control. Besides already reported insecticide resistance, they are prone to avoiding insecticide treated nets and walls. These mosquitoes also tend to bite people outdoors, where little can be done for protection. </p>
<p>Our work aims to understand the biology of this complex mosquito to track how changes in the environment are affecting the behaviour of this animal. This will hopefully inform malaria control strategies and bring us closer to eliminating the disease. </p>
<h2>Toxins</h2>
<p>The larval stage of the mosquito is aquatic. This vulnerable stage is crucial for the well-being of adult mosquitoes, in the same way that the health of a human baby will determine an adult’s future health. </p>
<p>Many larval environmental factors have a profound effect on the well-being of the adult mosquito. These include the environmental temperature, the level of crowding and access to nutrition. Human activity, however, has resulted in increased levels of water pollution, and mosquito larvae being exposed to more toxins.</p>
<p>This has a big impact on malaria transmitting mosquitoes. These insects usually breed in clean water, but have adapted to breeding in polluted water. This means that malaria vectors can now potentially increase their range to areas where malaria didn’t usually occur. </p>
<p>Our <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0192551">research</a> shows that polluted water sources are becoming a breeding ground for mosquitoes that are tolerant to a range of toxins. We found that adult mosquitoes that were exposed to metal during the larval stage developed insecticide resistance. </p>
<p>Currently we do not know whether insecticide-resistant or susceptible mosquitoes are better at transmitting malaria. But polluting activities are resulting in range expansion and changes in selection procedures in mosquitoes. </p>
<h2>Temperature on insecticides and mosquitoes</h2>
<p>Further research we did suggests that high temperatures also affect the efficacy of certain <a href="https://malariajournal.biomedcentral.com/articles/10.1186/s12936-018-2250-4">insecticides</a>. </p>
<p>Insecticides are commonly used as public health interventions against malaria vectors in some African countries including South Africa, Cameroon and Kenya. They are an important part of malaria control policies and strategies to eliminate the disease. </p>
<p>Our findings are important in efforts to determine the efficacy of insecticides currently used. But our study was based in a laboratory under controlled conditions, so our findings must still be tested in a real-life setting. This is because different temperatures could have different effects. Environmental conditions also vary and could have an impact on the efficacy of insecticides.</p>
<p>When it comes to mosquitoes, our research showed that temperature can have a significant impact on the life cycle of these insects. For example, climate change may affect the distribution of malaria vectors. We studied how rising temperatures affected major malaria vectors. We focused specifically on how insecticide-resistant vectors were affected versus vectors that are susceptible to insecticide. </p>
<p>Mosquitoes that develop resistance are <a href="https://malariajournal.biomedcentral.com/articles/10.1186/s12936-017-1720-4">more tolerant</a> of high temperatures than those that aren’t resistant. This means that as temperatures rise, so do the survival odds of insecticide-resistant mosquitoes. This will complicate malaria control. </p>
<h2>Why we should be worried</h2>
<p>Human activities are driving mosquito evolution. Polluting activities are resulting in malaria-transmitting mosquitoes expanding into regions where they previous weren’t. Adaptation to water pollution results in increased tolerance to pesticides.</p>
<p>Insecticide resistant or tolerant mosquitoes cope better with more toxic pollutants. Currently it is not known if these mosquitoes are more likely transmit malaria than insecticide susceptible mosquitoes. </p>
<p>Scientists are only beginning to unravel what this could mean for the elimination of malaria.</p><img src="https://counter.theconversation.com/content/114768/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Shüné Oliver receives funding from the National Research Foundation and the National Health Laboratory Service Research Trust. </span></em></p>Researchers are only beginning to understand the impact of pollution and increased temperatures on the biology of mosquitoes.Shüné Oliver, Medical scientist, National Institute for Communicable DiseasesLicensed as Creative Commons – attribution, no derivatives.