tag:theconversation.com,2011:/us/topics/infectious-disease-surveillance-64826/articlesInfectious disease surveillance – The Conversation2023-10-16T12:48:25Ztag:theconversation.com,2011:article/2153012023-10-16T12:48:25Z2023-10-16T12:48:25ZWho tracked UK COVID infections the best at the height of the pandemic? A new study provides the answer<p>At the height of the COVID pandemic everybody, from health ministers to Joe public, wanted to know two things: how many infected people are there in the country? And is this number going up or down?</p>
<p>There were many sources for these figures, from the Office for National Statistics to the Zoe app. We wanted to know which of these methods was the most reliable during the first two years of the pandemic. Our results have just been published in <a href="https://www.thelancet.com/journals/lanpub/article/PIIS2468-2667(23)00219-0/fulltext">The Lancet Public Health</a>.</p>
<p>In judging the effectiveness of the various surveillance methods, we looked at three criteria. First, to what degree did the method reflect whether cases were rising or falling? Second, how accurate was it in giving estimates of the actual infection numbers? And, third, was the data available swiftly enough for control measures, such as enhanced contact tracing, to be rapidly put in place? </p>
<p>The gold standard surveillance was the Office for National Statistics (ONS) COVID survey. This tested a random sample of people every two weeks and reported both the number of <a href="https://theconversation.com/the-ons-has-published-its-final-covid-infection-survey-heres-why-its-been-such-a-valuable-resource-202589">people likely to test positive</a> and the number of new infections occurring every day. </p>
<p>The other big advantage of the ONS survey is that it picked up all infections, whether or not the person had symptoms (and you probably recall that many people were asymptomatic). But, by the time their results were reported, the data was usually a week or two out of date. Not good if you needed to quickly introduce new control measures. </p>
<p>The ONS survey was also very expensive, as it involved visiting tens of thousands of people each week to take swabs. </p>
<p>The number of new cases reported each day by the Department of Health on the <a href="https://coronavirus.data.gov.uk/">COVID dashboard</a> was much more up to date, being published within a couple of days of the swabs being taken. This data tracked the ONS estimates very closely, though the reported numbers were usually only about 45% of the ONS data. So a little less than half of all infections were being picked up by mass screening.</p>
<p>The <a href="https://zoe.com/learn/category/covid">Zoe app</a> also tracked the ONS survey estimates closely and was a good estimate of whether infections were rising or falling. But, at times, the Zoe estimates were too high. Sometimes, it was also slow at spotting a fall in case numbers. </p>
<p>The Zoe app estimates were periodically adjusted to fit closer to the ONS survey estimates, raising the question of how good it would have been if it wasn’t for the ONS data to calibrate its estimates.</p>
<p>For influenza surveillance, the UK relies heavily on <a href="https://www.gov.uk/government/statistics/national-flu-and-covid-19-surveillance-reports-2023-to-2024-season">GPs</a> reporting people with influenza-like illness. However, for COVID this data source was very poor, not correlating at all with infection counts. </p>
<p>Using data on computer searches such as found in Google Trends has been used to track infectious diseases, especially <a href="https://www.nature.com/articles/nature07634">Google Trends and influenza</a>. Here again, there was very little correlation between infection numbers and Google Trend searches for either “COVID” or “coronavirus”.</p>
<p>The number of people calling NHS 111 with COVID symptoms performed only slightly better. </p>
<p>We also examined use of the <a href="https://111.nhs.uk/">NHS 111 website</a> to identify potential COVID cases, the number of patients suspected of having COVID at <a href="https://www.gov.uk/government/publications/emergency-department-weekly-bulletins-for-2023">emergency departments</a>, and <a href="https://coronavirus.data.gov.uk/details/cases?areaType=nation&areaName=England">hospital admissions</a>. These were all moderately correlated with the ONS estimates. </p>
<p>Hospital admissions data tended to lag about a week behind changes in infection numbers, so did not provide timely information.</p>
<p>Wastewater surveillance, where assumptions are made about infection numbers in the population based on <a href="https://www.thelancet.com/journals/lanplh/article/PIIS2542-5196(21)00230-8/fulltext">testing sewage for the presence of the virus</a>, received a lot of interest during the COVID pandemic. </p>
<p>Testing of wastewater for <a href="https://theconversation.com/polio-was-recently-detected-in-sewage-in-the-uk-heres-what-else-scientists-look-for-in-our-wastewater-185799">poliovirus has a long history</a>. But for poliovirus, detecting any circulating virus is enough to raise the alarm. For COVID, the question was can wastewater testing indicate how much infection is present in the population? In our analysis, we found that counts in wastewater were moderately correlated with the prevalence of COVID in the population. </p>
<h2>Useful additional insights</h2>
<p>No single surveillance method was ideal in England. But the most timely and consistent approach was reporting the results of routine testing on the COVID dashboard. </p>
<p>Other surveillance methods were unable to improve on this routine approach for timeliness and detection of trends. </p>
<p>Even so, the other approaches provided useful additional insights. For example, the Zoe app provided some of the earliest evidence that <a href="https://health-study.zoe.com/post/is-loss-of-smell-or-taste-a-symptom-of-covid-19">loss of the sense of smell</a> was an important symptom of COVID. </p>
<hr>
<p>
<em>
<strong>
Read more:
<a href="https://theconversation.com/covid-killed-your-sense-of-smell-heres-how-experts-train-people-to-get-theirs-back-150989">COVID killed your sense of smell? Here's how experts train people to get theirs back</a>
</strong>
</em>
</p>
<hr>
<p>The hospital admissions data and emergency department attendance methods provided important information on how the pandemic was affecting health services. NHS 111 call and website data provided useful information early in the pandemic, before other surveillance methods were established. </p>
<p>Although wastewater surveillance did little to increase our understanding of the course of the pandemic in England, this surveillance method may be useful in countries that don’t have easy access to human testing. </p>
<p>Overall, the best indication of the course of the pandemic came not from relying on a single surveillance method but from considering the outputs from all available data sources.</p><img src="https://counter.theconversation.com/content/215301/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Paul Hunter consults for the World Health Organization. He receives funding from National Institute for Health Research, the World Health Organization and the European Regional Development Fund.</span></em></p><p class="fine-print"><em><span>Iain Lake receives funding from the UK National Institute for Health and Care Research.</span></em></p>ONS, Zoe app, Google Trends … there were many ways to keep an eye on COVID cases during the pandemic. Here’s how they fared.Paul Hunter, Professor of Medicine, University of East AngliaIain Lake, Professor of Environmental Epidemiology, University of East AngliaLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/1807752022-05-04T12:33:48Z2022-05-04T12:33:48ZWastewater monitoring took off during the COVID-19 pandemic – and here’s how it could help head off future outbreaks<figure><img src="https://images.theconversation.com/files/460684/original/file-20220502-23-iuraw7.jpg?ixlib=rb-1.1.0&rect=0%2C416%2C5067%2C3284&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">Sampling wastewater can be time-intensive.</span> <span class="attribution"><span class="source">John Eisele/Colorado State University</span></span></figcaption></figure><p><em>A community’s sewage holds clues about its COVID-19 burden. Over the course of the pandemic, wastewater surveillance has become an increasingly popular way to try to understand local infection trends.</em></p>
<p><em>Microbiologists <a href="https://scholar.google.com/citations?user=NXca5vEAAAAJ&hl=en&oi=ao">Susan De Long</a> and <a href="https://scholar.google.com/citations?user=Flb9Tp8AAAAJ&hl=en&inst=6416714965532506866">Carol Wilusz</a> met and became wastewater aficionados in April 2020 when a grassroots group of wastewater treatment plant operators asked them to develop and deploy a test to detect SARS-CoV-2 in samples from the sewers of Colorado. De Long is an environmental engineer who studies useful bacteria. Wilusz’s expertise is in RNA biology. Here they describe how wastewater surveillance works and what it could do in a post-pandemic future.</em></p>
<h2>How is wastewater monitored for SARS-CoV-2?</h2>
<p>Wastewater surveillance takes advantage of the fact that many human pathogens and products of human drug metabolism end up in urine, feces or both. The SARS-CoV-2 virus that causes COVID-19 shows up in surprisingly <a href="https://doi.org/10.1186/s12879-021-06443-7">large quantities in feces of infected people</a>, even though this is not a major route of disease transmission.</p>
<p>To figure out whether any pathogens are present, we first need to collect a representative sample of wastewater, either directly from the sewer or at the point where what engineers call “influent” enters a treatment plant. We can also use solids that have settled out of the wastewater.</p>
<p>Technicians then need to remove large particles of fecal matter and concentrate any microbes or viruses. The next step is extracting their nucleic acids – the DNA or RNA that holds the pathogens’ genetic information.</p>
<p>The sequences contained in the DNA or RNA act as unique bar codes for the pathogens present. For instance, if we detect genes that are unique to SARS-CoV-2, we know that the coronavirus is in our sample. We use PCR-based approaches, similar to those <a href="https://theconversation.com/whats-the-difference-between-a-pcr-and-antigen-covid-19-test-a-molecular-biologist-explains-170917">used in clinical diagnostic tests</a>, to detect and quantify SARS-CoV-2 sequences.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="masked lab worker with glassware and lab equipment" src="https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/460685/original/file-20220502-14-3ao8tu.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">A lab technician prepares to process wastewater samples for SARS-CoV-2 detection at Colorado State University.</span>
<span class="attribution"><span class="source">John Eisele/Colorado State University</span></span>
</figcaption>
</figure>
<p>Characterizing the nucleic acid sequence in more detail can provide information about viral strains – for instance, <a href="https://doi.org/10.1016/j.scitotenv.2022.153171">it can identify variants</a> like omicron BA.2. </p>
<p>Currently, the vast majority of wastewater surveillance efforts are focused on SARS-CoV-2, but the same techniques work with other pathogens, including <a href="https://doi.org/10.3390/v11090775">poliovirus</a>, <a href="https://doi.org/10.1101/2022.02.15.22271027">influenza</a> and <a href="https://doi.org/10.1111/j.1365-2672.2012.05231.x">noroviruses</a>. </p>
<p>Before the pandemic, one application was <a href="https://theconversation.com/sewage-surveillance-is-the-next-frontier-in-the-fight-against-polio-105012">monitoring for rare poliovirus outbreaks</a> in areas where polio vaccination is ongoing. Wastewater can also be monitored for signs of various drugs to give insights into the <a href="https://doi.org/10.1016/j.scitotenv.2020.138376">level and type of drug use in a population</a>.</p>
<h2>Where does the data go?</h2>
<p>During the pandemic, the U.S. Centers for Disease Control and Prevention developed the <a href="https://www.cdc.gov/healthywater/surveillance/wastewater-surveillance/wastewater-surveillance.html">National Wastewater Surveillance System</a> specifically to track SARS-CoV-2 across the country. <a href="https://covid.cdc.gov/covid-data-tracker/#wastewater-surveillance">Over 800 sites report data</a> to this NWSS system, but not all states and counties are currently represented.</p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="Map of U.S. with dots for sites that report to NWSS" src="https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=375&fit=crop&dpr=1 600w, https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=375&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=375&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=471&fit=crop&dpr=1 754w, https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=471&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/460802/original/file-20220502-18-4i6hkd.png?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=471&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">More than 800 sites that cover populations of various sizes report COVID-19 wastewater numbers to the CDC.</span>
<span class="attribution"><a class="source" href="https://covid.cdc.gov/covid-data-tracker/?ACSTrackingID=USCDC_2145-DM80954&ACSTrackingLabel=4.29.2022%20-%20COVID-19%20Data%20Tracker%20Weekly%20Review&deliveryName=USCDC_2145-DM80954#wastewater-surveillance">CDC COVID Data Tracker</a>, <a class="license" href="http://creativecommons.org/licenses/by/4.0/">CC BY</a></span>
</figcaption>
</figure>
<p>Many state agencies, like the <a href="https://cdphe.maps.arcgis.com/apps/dashboards/d79cf93c3938470ca4bcc4823328946b">Colorado Department of Public Health and Environment</a>, and cities, like <a href="https://covid19.tempe.gov/pages/indicators#Wastewater%20Dash">Tempe, Arizona</a>, have their own dashboards for reporting data. Some companies performing wastewater analysis report data <a href="https://biobot.io/data/">on their own dashboards</a>, too.</p>
<p>In our opinion, the NWSS represents an exciting first step in monitoring population health through wastewater. Similar systems are being established in other countries, <a href="https://www.health.nsw.gov.au/Infectious/covid-19/Pages/sewage-surveillance.aspx">including Australia</a> and <a href="https://www.esr.cri.nz/our-expertise/covid-19-response/wastewater-testing-results/">New Zealand</a>.</p>
<h2>What does wastewater data really show?</h2>
<p>SARS-CoV-2 levels in wastewater from large populations are an excellent indicator of the infection level in a community. The system automatically monitors everyone who lives in the sewershed, so it’s anonymous, unbiased and equitable. Importantly, it is also impossible to track the infection back to a particular person, household or neighborhood without taking additional samples.</p>
<p>Wastewater surveillance doesn’t rely on the availability of clinical tests or people reporting their test results. It also picks up asymptomatic and pre-symptomatic cases of COVID-19; this is critical because people who are <a href="https://doi.org/10.1038/s41591-020-0869-5">infected but don’t feel sick can still spread COVID-19</a>.</p>
<p>In our opinion, wastewater testing is increasingly important as more COVID-19 tests are done at home. And because vaccination has also led to <a href="https://academic.oup.com/cid/article/74/7/1275/6345339">more mild and asymptomatic cases of COVID-19</a>, people may be infected without getting tested at all. These factors mean that clinical case data are less informative than earlier in the pandemic, while wastewater data remains a consistent indicator of community infection level. </p>
<figure class="align-center zoomable">
<a href="https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=1000&fit=clip"><img alt="COVID-19 rapid tests for home use on a pharmacy shelf" src="https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&fit=clip" srcset="https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=600&h=400&fit=crop&dpr=1 600w, https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=600&h=400&fit=crop&dpr=2 1200w, https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=600&h=400&fit=crop&dpr=3 1800w, https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=754&h=503&fit=crop&dpr=1 754w, https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=30&auto=format&w=754&h=503&fit=crop&dpr=2 1508w, https://images.theconversation.com/files/461038/original/file-20220503-25-b6tyjm.jpg?ixlib=rb-1.1.0&q=15&auto=format&w=754&h=503&fit=crop&dpr=3 2262w" sizes="(min-width: 1466px) 754px, (max-width: 599px) 100vw, (min-width: 600px) 600px, 237px"></a>
<figcaption>
<span class="caption">Wastewater surveillance doesn’t rely on people reporting a positive home test or even being aware of their infections.</span>
<span class="attribution"><a class="source" href="https://www.gettyimages.com/detail/news-photo/take-home-covid-19-testing-kit-is-displayed-on-the-shelf-of-news-photo/1360415081">Spencer Platt/Getty Images News</a></span>
</figcaption>
</figure>
<p>So far, you can’t accurately predict the number of infected individuals in a community based on the level of virus in its wastewater. The stage of someone’s infection, how their body responds to the virus, the viral variant, how far a person was from where the wastewater sample was taken, even the weather can all <a href="https://doi.org/10.1016/j.jhazmat.2021.127456">affect the amounts of SARS-CoV-2 measured in sewage</a>. </p>
<p>But scientists can infer relative changes in infection rates. Watching viral levels go up and down in sewage provides a glimpse of whether cases are rising or falling in the community as a whole.</p>
<p>Because SARS-CoV-2 can be detected in wastewater days or even weeks before outbreaks occur, wastewater monitoring can provide an early warning that public health measures may be warranted. And trends in the signal are important – <a href="https://twitter.com/drericding/status/1468627450049540099?lang=en">if you know levels are rising</a>, it may be a good time to reinstitute a mask mandate or recommend working from home. At present, public health officials use wastewater monitoring data <a href="http://dx.doi.org/10.15585/mmwr.mm7030e2">along with other information</a> like test positivity rates and the number of clinical cases and hospitalizations in the community to make these kinds of decisions.</p>
<p>Data from sequencing can also help detect new variants and monitor their levels, allowing health responses to take into account the characteristics of the variant present.</p>
<p>In smaller populations, such as in college dormitories and nursing homes, wastewater monitoring can detect a small number of infected people. That can sound the alarm that targeted clinical testing is in order to identify infected people for isolation. Early detection, targeted testing and quarantining are <a href="https://doi.org/10.1126/science.abc5798">effective at preventing outbreaks</a>. Rather than using clinical testing for routine monitoring, administrators can reserve disruptive clinical tests for times when SARS-CoV-2 is detected in the wastewater.</p>
<h2>What will monitoring look like in the future?</h2>
<p>Widespread and routine use of wastewater monitoring would give public health officials access to information about the levels of a range of potential infections in U.S. communities. This data could guide decisions about where to provide additional resources to communities, like holding testing or vaccination clinics in places where infection is on the rise. It could also help determine when interventions like masking or school closures are necessary.</p>
<p>In the best case, wastewater monitoring might catch a new virus when it first arrives in a new area; an early shutdown in the very localized area could potentially prevent a future pandemic. Interestingly, researchers have detected SARS-CoV-2 in <a href="https://www.reuters.com/article/health-coronavirus-italy-sewage/italy-sewage-study-suggests-covid-19-was-there-in-december-2019-idINL1N2DV2XE">archived wastewater samples collected before</a> anyone had been diagnosed with COVID-19. If wastewater monitoring had been part of the established public health infrastructure back in late 2019, it could have provided an earlier warning that SARS-CoV-2 was becoming a global threat.</p>
<p>For now, though, establishing and operating a national wastewater surveillance system, particularly one that includes building-level monitoring at key locations, is still too costly and labor-intensive.</p>
<p>Ongoing research and development efforts are trying to simplify and automate wastewater sampling. On the analysis side, adaptation of PCR and sequencing technologies to detect other pathogens, including novel ones, will be vital to take full advantage of such a system. Ultimately, wastewater surveillance could help support a future in which pandemics are far less deadly and have less social and economic impact.</p>
<p>[<em>Research into coronavirus and other news from science</em> <a href="https://memberservices.theconversation.com/newsletters/?nl=science&source=inline-science-corona-research">Subscribe to The Conversation’s new science newsletter</a>.]</p><img src="https://counter.theconversation.com/content/180775/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>Susan De Long receives funding from Colorado Department of Public Health and Environment, the Anschutz Foundation, the National Science Foundation, and the Department of Energy.</span></em></p><p class="fine-print"><em><span>Carol Wilusz receives funding from Colorado Department of Public Health & Environment and the Anschutz Foundation. </span></em></p>Over 800 sites across the US report coronavirus data from sewage to the CDC. Here’s how this kind of surveillance system works and what it can and can’t tell you.Susan De Long, Associate Professor of Civil and Environmental Engineering, Colorado State UniversityCarol Wilusz, Professor of Microbiology, Immunology and Pathology, Colorado State UniversityLicensed as Creative Commons – attribution, no derivatives.tag:theconversation.com,2011:article/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>
<hr>
<p>
<em>
<strong>
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>
</strong>
</em>
</p>
<hr>
<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/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/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>
<figcaption>
<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>
</figcaption>
</figure>
<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>
<figcaption>
<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>
</figcaption>
</figure>
<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>
</figcaption>
</figure>
<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/1088382019-01-13T09:21:42Z2019-01-13T09:21:42ZDNA sequencing can help fight epidemics – but there are privacy risks<figure><img src="https://images.theconversation.com/files/251225/original/file-20181218-27767-1de19kn.jpg?ixlib=rb-1.1.0&q=45&auto=format&w=496&fit=clip" /><figcaption><span class="caption">A portable DNA sequencer in action.</span> <span class="attribution"><span class="source">UGA CAES/Extension/Flickr</span></span></figcaption></figure><p>The Democratic Republic of Congo is battling an <a href="https://www.sciencemag.org/news/2018/12/ebola-vaccine-having-major-impact-outbreak-may-still-explode-west-africa">Ebola outbreak</a>. As is the case with any disease caused by pathogenic viruses – like Zika or influenza – Ebola spreads dangerously and unpredictably. This makes tracking the movement of viruses around the world a major challenge.</p>
<p>Researchers have increasingly turned to DNA sequencing to help identify and track these sorts of diseases. They use portable DNA sequencers, which are the size of a USB and can be easily carried for use in the field. One such sequencer, the <a href="https://nanoporetech.com/products/minion">MinION</a> from Oxford Nanopore Technologies <a href="http://www.zibraproject.org/about/">was used</a> during the 2016 Zika virus epidemic in Brazil. It’s also being used <a href="https://www.nature.com/articles/s41579-018-0130-0">to track</a> the DRC’s Ebola outbreak.</p>
<p>Some researchers hope it will soon be possible to combine sequencing data collected in this way with other information to tell us even more about disease outbreaks. Integrating different kinds of data into a global infectious disease surveillance system that continuously scans for new epidemics might make it possible to detect outbreaks and sequence viruses as they emerge, allowing public health responses to be suggested in real time.</p>
<p>There’s no doubt these efforts are driven by good intentions. But, as we argue in <a href="https://rgs-ibg.onlinelibrary.wiley.com/doi/full/10.1002/geo2.66">our new research</a>, this technology – which supporters hope will become increasingly available to <a href="https://www.theatlantic.com/science/archive/2016/04/this-technology-will-allow-anyone-to-sequence-dna-anywhere/479625/">members of the public</a> – could have serious privacy implications. </p>
<p>Metagenomic data – the kind that could be collected on a sequencer such as MinION or others such as the <a href="https://www.czbiohub.org/">Chan Zuckerberg Biohub’s</a> new platform IDSeq – contains an enormous amount of information about who we are and how we live. In combination with other widely available information someone could potentially use that data to work out where you live, or with whom you have a close relationship. </p>
<p>The reality is that, as improvements in data analysis methods allow us to extract new insights from old data (or <a href="https://www.theregister.co.uk/2015/10/02/s_korean_anonymised_health_data_sharing_a_breach_in_waiting/">de-anonymise anonymised data</a>), it’s impossible to be absolutely sure what the potential uses of data will be. </p>
<h2>Signing away your data</h2>
<p>Imagine having an app on your smart phone that allows you to analyse samples from the world around you. You could use it to sequence your pet cat’s DNA, or to figure out whether the mould growing in your shower is dangerous.</p>
<p>Sound far-fetched? It’s not. The technology required is already here. For example, the Chan Zuckerberg Biohub recently announced <a href="https://idseq.net/">IDSeq</a>, a new platform and database for infectious disease surveillance where registered users <a href="https://medium.com/czi-technology/a-platform-for-infectious-disease-detectives-253753026fe8">can upload</a> their metagenomic sequencing data to have it analysed for free.</p>
<p>There’s just one catch, as there would be with any sequencing app: you have to sign over permissions to the data. Most people will do this unthinkingly. Author Jamie Susskind <a href="https://www.theguardian.com/books/2018/dec/05/future-politics-by-jamie-susskind-review-when-life-changing-decisions-are-made-by-machines">has called</a> this pervasive and common arrangement “the data deal”: people accept whatever a company asks so they can use an app or product, and worry about the implications later.</p>
<p>This is the case with IDSeq. Initially enthusiastic researchers became <a href="https://twitter.com/firefoxx66/status/1052610954767331330">concerned</a> when they realised the platform’s terms and conditions contained a clause granting the Chan Zuckerberg Initiative “perpetual” permission to “use”, reproduce, distribute, display and create derivative works" from the data. </p>
<p>The current justification given for this clause is that it’s intended to permit users’ research data to be used for improving IDSeq. However, in principle the data could later be shared with <a href="https://assets.idseq.net/Privacy.pdf">“any third party that purchases”</a> part of the assets or organisation. </p>
<h2>A world of information</h2>
<p>So why does it matter if you share metagenomic data from your everyday life? Quite simply, because the data from that cat hair or mould sample might contain more information than you realise – and far more than you intended to sign away. </p>
<p>It could contain not only the DNA you wanted to sequence, but also DNA from your fingers when you loaded the sample, from the bacteria on your skin from the last person you hugged, or from the gardens your cat visited last night. In short, that data contains vital information about your <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426293/">microbiome</a> – the vast collection of microorganisms that live on and in our bodies. And your microbiome can tell someone an awful lot about you.</p>
<p>As we learn more about our microbiomes, we are beginning to understand how much they are personalised. Even if we could filter out the human DNA sequences from datasets, our microbiomes could <a href="http://doi.org/10.1073/pnas.1423854112">theoretically</a> still be used to identify us. </p>
<p>The microbiome contains information not only about our lifestyles, like our diet and drug intake, but also our social relationships, such as who we live with. That’s a lot of information to work with, in a world where we already share a great deal of data about ourselves via platforms like Facebook and Instagram, or personal fitness trackers. This data could feasibly be merged with metagenomic data, making it even more powerful. </p>
<p>There are ever more surprising examples of incidental data being used in dramatic and unexpected ways that are far removed from the original reasons for collecting it. Data from a murder victim’s Fitbit was <a href="https://www.nytimes.com/2018/10/03/us/fitbit-murder-arrest.html">used</a> to convict her killer. And data from users of the fitness app Strava inadvertently <a href="https://www.theguardian.com/world/2018/jan/28/fitness-tracking-app-gives-away-location-of-secret-us-army-bases">revealed</a> the location of secret US army bases. </p>
<p>There is every reason to believe that data from portable sequencers collected primarily for disease surveillance would contain information that could be used in similarly surprising, and concerning, ways. Metagenomic sequencing data is highly personalised. It contains implicit information about who we interact with and where we go, which makes it commercially valuable. </p>
<p>These concerns shouldn’t (and won’t) stop portable sequencers being used for infectious disease surveillance. Corporations and governments will promise great benefits from the use of this technology. For example, the IDSeq privacy notice justifies data collection by <a href="https://assets.idseq.net/Privacy.pdf">appealing</a> to “legitimate interest in investigating and stopping the spread of infectious diseases and promoting global health”. </p>
<p>We need to continue scrutinising these organisations to make sure we understand exactly what’s being done with our data. The consequences of widespread portable sequencing, like emerging infectious diseases themselves, will be highly unpredictable.</p><img src="https://counter.theconversation.com/content/108838/count.gif" alt="The Conversation" width="1" height="1" />
<p class="fine-print"><em><span>The authors do not work for, consult, own shares in or receive funding from any company or organisation that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.</span></em></p>Researchers have increasingly turned to DNA sequencing to help identify and track diseases like Ebola.Liam Shaw, Computational biologist, University of OxfordNicola C. Sugden, PhD Researcher, University of ManchesterLicensed as Creative Commons – attribution, no derivatives.