The Key To Tracking Covid19 And Other Ailments Should Start With Sewers
Potty and sewage surveillance could help scientists predict new outbreaks. The Key To Tracking Covid19 And Other Ailments Should Start With Sewers
We won’t have to shelter from the new coronavirus forever. In fact, we may be able to briefly return to public life this summer, according to The Atlantic. But several predictors of Covid-19 outbreaks suggest the virus could be seasonal, returning with fury in the fall. It is likely that several periods of social distancing will be necessary for containing the virus until a vaccine for SARS-CoV-2, the virus that causes Covid-19, is widely available, which could take a year or more.
How will folks know when it’s safe to come out and when to go back indoors? There may be clues in our sewage.
Dozens of scientists across the globe are sampling poo to find tiny shreds of the coronavirus that can serve as an early warning of outbreaks. In theory, if viral levels reach a certain threshold, health experts can tell more people to stay home. When viral loads abate, they can tell people it’s okay to fraternize.
Last week, Dutch scientists announced a first-of-its-kind method for detecting SARS-CoV-2 in wastewater. The team, from KWR Water Research Institute, took samples of wastewater from six Dutch cities as well as Amsterdam’s airport in February 2020, weeks before the Netherlands announced its first case of Covid-19. They collected new samples and repeated the experiment in the first and third weeks of March.
After running the sewage samples through a centrifuge, the scientists looked for four genetic signatures of SARS-CoV-2. Three were from the nucleocapsid (N) gene, which builds proteins that make up the core of the virus. The remaining gene encodes the envelope (E) protein, which the virus uses to reproduce.
Our Sewage Offers A Crude—But Anonymous—Picture Of What People Are Consuming, From Caffeine To Opioids. Researchers Are Now Turning Their Focus To The Covid-19 Pandemic. Regular Sewage Sampling Could Give Public Health Officials An Early Warning That The Coronavirus Is On The Rise In Their Communities.
In the February samples, the researchers found no sign of coronavirus. But by early March, some of the results came back positive. All but one of the samples taken in the third week of March samples came back positive, with bits of the N and E genes.
In the city of Amersfoort, the team was able to detect SARS-CoV-2 before any cases had been announced locally. These results were published before peer review on MedRxiv.
Detecting the virus through sewage is only the first step toward using poo analysis as an early outbreak warning system, according to Krista Wigginton, an associate professor at the University of Michigan’s civil and environmental engineering department.
She is leading a joint project between UM and Stanford University using a $200,000 grant from the National Science Foundation to study how the coronavirus worms through our pipes.
“You’re looking for a needle in the haystack,” Wigginton tells OneZero, adding that while the Dutch team has found the virus, the next stage is correlating that data in a way that corresponds with the population level.
“It’s very preliminary, but it’s a great proof of concept. We can go out and detect it, but now we need to do a lot of work to be like, ‘Okay, what level was it at and how many people in the community does that correspond to?’” Wigginton explains. “I don’t think we’re able to say yet what we can do with this tool.”
“If you could sequence the coronaviruses in wastewater, you have a much better idea of how the virus is mutating and possibly where the virus came from in your community.”
In other words, counting the pieces of a virus is one thing — but how do you know how many people might be infected when those pieces are mushed together within a smelly mess? It will take analyzing tons of wastewater to find out, which usually means waiting for it to pass through the point of the sewage treatment process in which solids separate from the liquid, which Wigginton says could still be months away.
“It’ll take some time and a lot of research to know how the levels in wastewater compare to the other indicators in a community,” Wigginton says. “But we think it’s quite possible that this could be at least as sensitive as these other indicators like using thermometer data and Google searches to figure out when communities are starting to have an uptick. This just seems like another tool.”
Wigginton has been studying ways to detect coronavirus in wastewater for several years. When Covid-19 was declared a pandemic, she says she wasn’t shocked that another virus like SARS or MERS had emerged but was stunned by how fast it spread.
Much of the focus on the novel coronavirus distribution has centered on airborne transmission. But coronaviruses, like the one that caused the 2003 SARS outbreak in Hong Kong, can also reproduce in the gastrointestinal tract.
At Amoy Gardens, a housing estate in Kowloon, SARS jumped from one patient to hundreds via diarrhea that became airborne after flushing, spreading a distance of around 200 meters. According to a report in Nature, SARS-CoV-2 may be broadcast the same way.
In Palo Alto, California, Wigginton and her colleagues have been collecting local sewage samples for weeks to build accurate tools for testing. Her team is also exploring whether ultraviolet light and sunlight can disinfect the virus. The Bay Area was one of the earliest places to report a Covid-19 outbreak in the United States and still has some of the highest numbers of cases in the country, so the region will likely have a high volume of viral particles in the waste stream.
Finding new ways to track the coronavirus is especially important because many cases appear to be asymptomatic and the United States has a limited number of tests. Not everyone who gets a Covid-19 infection gets severely sick, sees a doctor, or gets tested, but they can still spread the virus. Surveilling sewage gives health experts a bigger picture of the pandemic’s scope.
“Another thing it can do is give you an idea of the diversity of the virus in the community,” Wigginton says. “If you could sequence the coronaviruses in wastewater, you have a much better idea of how the virus is mutating and possibly where the virus came from in your community because it might match with viruses that came from a certain city somewhere else. So I think there’s other valuable tools in this approach as well.”
Wigginton and the Dutch team are not the only ones monitoring our excrement for coronaviruses. Researchers at the University of Arizona Water and Energy Sustainable Technology Center and the Norwegian Institute for Water Research (NIVA) are doing similar research. “The future of public health surveillance depends on developing innovative bioanalytical approaches,” Jose Antonio Baz Lomba, a research scientist at NIVA said in a press release.
Sewage surveillance is already used to monitor public health in several ways, including monitoring for polioviruses and pathogens that have evolved to have antimicrobial resistance. Wastewater surveillance is even used to track the use of cocaine and meth. As the planet continues to be reshaped by this novel coronavirus, tracking Covid-19 by sifting through fecal matter will likely become an important, lifesaving tool.
This Smart Toilet Recognizes Your Butt And Analyzes Poo For Diseases
An experimental toilet out of Stanford University identifies users by their finger and anal prints while gathering data for urine and stool analysis, a new study reports.
Going to the bathroom could end up relieving your health anxieties as well as your bladder. Researchers have created a smart toilet that can analyze feces and urine for various diseases and some forms of cancer. The experimental toilet can also identify users by both their unique fingerprints, and even their anal prints. Yes, those exist.
The researchers from Stanford University published their findings in a new study in Nature Biomedical Engineering science journal on Monday. Twenty-one participants tested the smart toilet over the course of several months.
“The smart toilet is the perfect way to harness a source of data that’s typically ignored, and the user doesn’t have to do anything differently,” lead study researcher Sanjiv Gambhir said in a statement.
The toilet used for the study was actually a basic toilet with high-tech motion-sensing tools attached inside the bowl. The toilet records video of the user’s urine and feces which is then processed by algorithms that can determine urine stream time and volume, as well as a stool sample’s viscosity.
The experimental toilet also uses uranalysis strips to measure the urine’s white blood cell count and detect levels of proteins that best determine if the user is healthy or suffering from bladder infections, cancers, diabetes or possible kidney failure.
The collected toilet data is stored in a cloud-based system for doctors to access later.
One of the more unusual features of this smart toilet is a built-in identification system that reads the user’s fingerprints on the toilet flush handle, and even weirder… an anus-recognition system.
“The whole point is to provide precise, individualized health feedback, so we needed to make sure the toilet could discern between users,” Gambhir said. “We know it seems weird, but as it turns out, your anal print is unique.”
The anal and fingerprint scans enable users to be matched to their specific data, which comes in handy if more than one person is using the same smart toilet. While the toilet does take scans of the anal print, it does not share those images to the user’s cloud or doctors.
What’s next? More participants in the study and the ability to integrate molecular features into stool analysis.
“That’s a bit trickier,” said Gambhir, “but we’re working toward it.”
Your Poop Might Be Key For Predicting The Next Pandemic
Looking for the new coronavirus in wastewater could give us a heads up about where the outbreak is spreading—and when it has started to dissipate.
On March 5, there had not yet been a clinical diagnosis of COVID-19 in Amersfoort, a Dutch city of more than 150,000 people to the east of Amsterdam. But underneath Amersfoort’s streets, dotted with Medieval buildings, the sewage pipes containing people’s fecal matter told another story.
In early March, researchers at KWR, an independent water research institute, detected viral fragments from SARS-CoV-2, the virus that causes COVID-19, in wastewater collected from the nearby wastewater treatment plant. Their findings, published on a preprint server without peer review, indicated that the virus had in fact arrived.
Their work also revealed the promise of wastewater sampling as a public health tool—both to monitor the spread of the current COVID-19 pandemic, as well as detect its reappearance in the future.
In Boston, a company called Biobot, in collaboration with researchers at MIT, just completed a similar study. On Tuesday, they published (also in a preprint paper) the stunning fact that the amount of virus they observed in wastewater was much higher than they expected it to be based on the number of confirmed cases in the Boston area.
The amount of virus they saw would suggest that about 5 percent of all fecal samples were positive for the virus, while the reported number of infections was only at .026 percent of the population during the same period. As the researchers told STAT, this amounts to an expected 2,300 people infected around the treatment facility, when there have only been 446 confirmed cases.
Our pee and poop contain a lot of information, Mariana Matus, the CEO and co-founder of Biobot, said, and could be a critical factor—in tracking the true number of COVID-19 infections, which areas are most affected, and deciphering when the virus has actually disappeared from our communities.
“It’s an invaluable source of information about human health, because we’re all using the toilet on a daily basis,” she said.
Wastewater has been used to detect other viruses before. In 2013, a poliovirus outbreak in Israel was detected by surveillance of the sewage system before any cases were reported. The surveillance system was set up in 1989 by the Israeli health department, where samples were automatically collected weekly.
Epidemiologists usually detect polio, which is highly contagious, by reports of the physical symptoms in people, namely the acute flaccid paralysis (AFP) it can cause—but by that point, it’s usually too late. “It’s just the tip of the iceberg – one case of AFP indicates substantial underlying polio transmission in a population,” a team of epidemiologists wrote in The Conversation in 2018.
By finding the virus early on, before any AFP cases, Israel was able to begin a polio vaccine campaign, and the virus disappeared again from the wastewater before a larger outbreak took hold. Sewage surveillance has also been shown to be a tool for early warnings of Hepatitis A and norovirus outbreaks.
Before the COVID-19 pandemic, Matus and her colleagues at Biobot were focusing on using wastewater to track opioid use. But when studies from March found that the new coronavirus could be shed through feces, she and her team shifted gears.
KWR and Biobot both find the virus in the wastewater by looking for different genes that are specific to SARS-CoV-2. They’re not alone: Nature reported that more than a dozenresearch groups around the world will be analyzing wastewater for SARS-CoV-2 as well.
Frederic Béen, a scientific researcher at KWR, said that his colleagues tested sewage samples from seven cities and the Amsterdam Schiphol airport. They started early: February 6—which was three weeks before the first reported clinical case of COVID-19, February 27. At that date, they didn’t find any of the virus yet.
On March 5, however, they found the first viral fragment. By March 15 and 16, at least one viral fragment was found in six of the wastewater treatment plants—matching the rise of the outbreak in the country.
Matus said that in the U.S., having a system like this in place would have helped push for a faster response. “Imagine if we already had this platform at scale in the country and then when the outbreak happened in China in January?” she said. “And we started testing for SARS-CoV-2 right away.
We might have had a better response, because today we only raise the alarm when we reach enough clinical cases. With technology like this, the idea is that you can respond quickly and just have that data that is naturally being generated by people’s bodies.”
Even though it’s too late for an early warning, this kind of data can be useful at different points in the pandemic too— it could track the progression of infection, especially since widespread COVID-19 testing has been difficult to access, and an unknown number of people have mild symptoms or are asymptomatic—but are still potentially transmitting the disease to the virus to others.
“It would be a more accurate sense of the total number of cases, and not just those confirmed through the hospital system,” Matus said. “Not to mention all of the people who lack access to healthcare. There’s just many steps at which people can fall off and not be taken into account.”
Biobot hopes to use the data from the wastewater to model the actual number of infected people in a given area. Wastewater provides a large snapshot, since it can tell you about the entirety of the area that the facility services.
“The beauty of wastewater monitoring is that by collecting just a few hundred milliliters of wastewater, flowing into the wastewater treatment plant, you obtain a sample that represents thousands, like a small village, or hundreds of thousands of people, like a city the size of Amsterdam or New York,” Béen said.
About two thirds of the U.S. population is covered by wastewater infrastructure; many of the rest use septic tanks. This technology would be available only to those who are connected to wastewater facilities, for now.
To get more granular information, Matus said that Biobot has developed portable testing devices that can look at smaller neighborhoods. For now, they haven’t done that because they are too busy—it requires having people go into manholes in those communities.
Matus said that their next step is to learn more about if different people shed different amounts of the virus, and at what points in their illness, so that they can get even more accurate, detailed information from their data.
Biobot is a private company that is collaborating with researchers at MIT, Harvard, and Brigham and Women’s Hospital —but is currently doing this work pro bono. It announced on Twitter that it would accept sewage samples from wastewater treatment facilities across the U.S., and they were booked up within about a week. They’re now testing wastewater from 30 different states, and their goal is to be able to test up to 10,000 samples per week by June.
As the pandemic eventually subsides, wastewater testing could provide a peace of mind that testing individuals cannot: It could help confirm that the virus isn’t present anymore in the community— critical knowledge that could inform when social distancing measures can be alleviated.
And if COVID-19 turns out to be seasonal, returning in the fall, wastewater could be an indicator to tell if the outbreaks are starting to climb back up.
“Down the line, once we start seeing a decrease in the clinical cases, getting a sense of if this is actually contained or not will be hugely invaluable,” Matus said.
In Sewage, Scientists Find Not Just Waste, But Coronavirus Clues
Traces of the new virus in wastewater can potentially bolster surveillance efforts as countries look to end lockdowns.
In search of an early-warning system for the new coronavirus, Eric Alm spends most mornings handling sewage that has been flushed down toilets in Massachusetts.
He first opens a tube filled with 40 milliliters of raw sewage from an urban treatment plant that captures wastewater from households in the state. Samples are then analyzed at the Massachusetts Institute of Technology. If Prof. Alm and his team of scientists are successful, they quickly find traces of the genetic signature of the coronavirus.
“The flu is pretty tricky to test in wastewater,” said Prof. Alm, co-director of MIT’s Center for Microbiome Informatics and Therapeutics. “For Covid-19, we’re fortunate that it is excreted in large enough amounts.”
Scientists around the world have long used the technique, known as wastewater-based epidemiology, to track social scourges such as drug use or chemical spills with the aim of guiding policy decisions. An outbreak of polio in Israel in 2013 was detected by the monitoring of sewage.
Now, scientists are hopeful that sewage can bolster surveillance efforts for the coronavirus as countries look to end lockdowns that have hobbled their economies. Unlike clinical tests such as nasal swabs that return results only of individuals, they believe wastewater samples can provide information on hundreds of thousands of people or more in one hit.
The Massachusetts program found traces of the coronavirus in sewage around the time that the first patients were confirmed as positive in clinical tests in the state. In the Netherlands, a separate study found no traces on Feb. 8 but got a positive result on March 15, a week after the first person with the virus was reported in the country. Studies in France and Australia also have made positive findings.
“The sweet spot is being able to detect a resurgence of cases early,” said Kara Nelson, a professor in civil and environmental engineering at the University of California, Berkeley, who specializes in studying pathogens that can be transmitted through water pipes.
For public health bodies, a major blind spot is people who are infected with the coronavirus but display no symptoms. Ending lockdowns would free asymptomatic people to move around communities, risking fresh outbreaks.
There is no approved treatment or vaccine for Covid-19, the disease caused by the virus, in the U.S. Drugmakers and U.S. public-health officials are hoping a drug to treat symptoms of the disease could clear testing and be approved for widespread use within months, and a vaccine by early 2021.
“We’ll be looking for second and third waves until…we have vaccines available,” said Dr. Paul Bertsch, land and water science director at Australia’s Commonwealth Scientific and Industrial Research Organisation. “Getting an early warning protection system in place will be very important.”
Dr. Bertsch, who helped run a study in Australia analyzing sewage from a catchment area of some 600,000 people, said the coronavirus had shown up in feces around three days after infection. That is shorter than it typically takes a person to display symptoms, which can be five days or more, he said.
Scaling up sewage-monitoring programs won’t be easy. “It will take mobilizing different resources and a stronger role from the public sector. Most of our wastewater treatment plants are managed by public agencies,” Prof. Nelson said of the U.S.
Also, scientists aren’t sure how much of the virus is excreted by individuals. That creates a high degree of uncertainty when scientists try to determine the size of an outbreak. Calibrating data from the earliest studies has thrown up wide ranges, often out of sync with clinical estimates.
Meanwhile, public-health bodies are focusing resources on expanding clinical-testing programs. Capacity in laboratories is already tight.
“My main concern is that the time we need to do this is longer than the time we have for it to be useful,” said Prof. Nelson, who isn’t involved in the programs to trace the coronavirus in sewage.
Still, she thinks wastewater testing could be implemented at a fraction of the cost of clinical testing and some other measures being considered by governments, such as contact tracing.
Scientists believe more data will yield more accurate results and help to build a formula that policy makers can use when deciding to end or extend quarantines. Wastewater sampling can be reviewed in tandem with results from clinical tests.
Prof. Alm said his team now can gather information from sewage-treatment plants in 150 U.S. cities covering 10% of the population, and he hopes to expand to 1,000 cities in about a month.
In Australia, Dr. Bertsch said one option is to develop a national program by tapping expertise at the Australian Criminal Intelligence Commission, which used wastewater from 58 treatment plants as a tool to measure drug use last year.
“If you’re in New York City, you can go to the grocery store and test people and you’ll know the disease prevalence whereas in places where prevalence is low it’s much harder to get a positive test,” Prof. Alm said. “That’s where the sewage-based estimates are useful.”
China’s Zero-Tolerance Covid Tactics Now Include Anal Swabs
Scientists have found that some Covid-19 patients have active and prolonged gut viral infection, even if they don’t manifest gastrointestinal symptoms. For such people, stool samples often test positive even a week after their respiratory samples have gone negative, researchers from the Chinese University of Hong Kong found.
China is ramping up efforts to neutralize the coronavirus as new outbreaks challenge its already stringent pandemic strategy, with another weapon added to an arsenal of border curbs, mass testing and hard lockdowns: anal swabs.
While there’s no nationwide policy on use of the technique, some residents in China’s northern regions — where more than 1,700 cases have emerged — have been subjected to the swabs with little warning. The method involves the insertion of a saline-soaked cotton swab about two-to-three centimeters into the anus, with the sample then tested for active traces of the virus.
More than 1,000 schoolchildren and teachers in Beijing were given anal, throat and nose swabs last week, along with a separate antibody test, after one asymptomatic virus case was detected on campus, according to local officials.
On Monday, passengers on a flight from Changchun, the capital city of Jilin province, to Beijing were told to disembark after officials discovered that someone from an area deemed as high risk for virus transmission was on board. They were then brought to a hotel where health workers took nose and anal swabs, said a passenger who asked to be identified only by his last name, Wang.
Some people arriving into Beijing are being asked to undertake anal swabs as well, with one traveler who came from Hong Kong a few weeks ago telling Bloomberg News she was told to do the swab herself while in mandatory hotel quarantine. The person, who didn’t want to be identified citing privacy concerns, also had to do three nose and throat tests, one blood test and her hotel room has been tested twice.
Use of the new detection technique is based on research that traces of the virus found in the anus can last longer than in the respiratory tract, Li Tongzeng, deputy director of the respiratory and infectious disease department of Beijing You An Hospital said in an interview with state television last week. Anal swabs could be more accurate than throat and nose tests, especially in detecting asymptomatic cases, he said, adding they were only being used on at-risk groups, including at quarantine sites.
Still, there’s no evidence that virus transmission is any more common among patients who test positive in the anus area, and anal swabbing has not been conducted in other places that have successfully achieved near-elimination of the pathogen, like New Zealand.
Since quelling its original outbreak in the central city of Wuhan last year, China has mounted a relentless drive to stamp out the coronavirus within its vast population, often deploying resources and powers that wouldn’t be viable or even countenanced in other countries.
While Western nations like the U.S. and U.K. still struggle with adequate virus testing, China is not just testing entire city populations every week, but also millions of frozen food imports and the containers that they arrive in every day for minute traces of the pathogen.
That zeal, driven in part by local government officials concerned about repercussions should their cities become the next Wuhan, has worked at keeping outbreaks in check, but the use of techniques like anal swabbing is being questioned by some experts — even in the country’s state-run media. So far, it appears to be only being used consistently in the north, including the capital.
“I don’t understand why Beijing added anal swabs. It’s not like poking the throat. You need a certain place and the risk of such transmission routes is lower,” said Jiang Qingwu, a professor of epidemiology at the School of Public Health at Shanghai’s Fudan University. “Maybe they want to find remnants? It’s true that the virus can be detected there.”
While more research is needed to determine how effective anal swabs are, stool testing has been “grossly underutilized” in the pandemic, said Francis Chan, dean of the university’s faculty of medicine and director of its Centre for Gut Microbiota Research. The virus was still actively replicating in the feces of at least half of the study participants after they’d cleared it from their lungs, he said.
China’s capacity to endure disruption to business and everyday life in its ferocious fight against the coronavirus is a hallmark of its approach.
It’s the only country that has repeatedly detected traces of the virus on frozen food imports, with efforts that include disinfecting packaging adding to delays at ports, where containers of produce have been piling up. Local consumers are shunning foreign food for fear of infection, and China’s meat imports are projected to plunge as much as 30% this year from a record in 2020.
China’s lockdowns are also getting tougher, rivaling the severity of curbs placed on Wuhan a year ago even as case levels pale in comparison to elsewhere. China has reported just two Covid-19 deaths since April, and new infections at the height of the current flare-up number around 100 a day, compared with hundreds of thousands in the U.S.
Covid Lockdowns Are Spreading A Year After China Shocked World
In Tonghua, a city of 2 million people in Jilin province bordering North Korea, all residents have been banned from leaving their homes since Jan. 21 after 100 infections were detected. Some have complained on social media of insufficient food supplies after the sudden order, prompting an apology from local officials.
There are signs that the central government is trying to encourage some moderation.
An editorial from the Xinhua state news agency said Jan. 16 that local authorities should cease using the phrase “wartime measures” to describe their containment efforts. Such slogans could cause unnecessary panic, “paralyze people’s minds” and affect normal activities, the editorial said.
But with the Lunar New Year holiday approaching in mid-February, when officials expect 1.7 billion trips to be taken despite pleas for people to stay home, the wartime footing is likely to continue. The country is also doubling down on vaccination, with plans to inoculate 50 million people by the holiday with locally-developed vaccines.
“We don’t tolerate the virus circulating. Once we find it, we immediately quash it and outbreaks are not allowed,” said Lu Hongzhou, an infectious disease physician who advises both the central and Shanghai governments on Covid-19 treatment.
“Our country has always pursued this strategy and it can’t be adjusted.”
MIT Offshoot That Detects Virus In Wastewater Raises $20 Million
Biobot Analytics, a pandemic-era leader on testing to detect levels of the coronavirus in wastewater, has raised $20 million in funding.
The company is planning to begin testing for influenza as well as SARS-CoV-2 before year-end, and will bring back its initial focus, detecting levels of opioid use, said co-founder and Chief Executive Officer Mariana Matus.
The funding round drew high interest from investors, and the company is considering another one, Matus said. Founded in 2017 by two women affiliated with the Massachusetts Institute of Technology, Matus and architect Newsha Ghaeli, Biobot now employs 40 people. It says it has tested wastewater in more than 700 locations, including under contracts with the U.S. government and the World Bank.
Biobot is also researching use of its wastewater analysis techniques to identify and track coronavirus variants, making it “more of a tool to catch new threats before we know about them,” Matus said.
The company is currently analyzing wastewater weekly at 130 sites, she said, and is adding a service for workplaces.
Thursday Ventures led the funding round, with participation from existing investors including The Engine and American Family Insurance Institute for Corporate and Social Impact. They were joined by new investors including Plum Alley Investments; Anne Wojcicki, CEO of genomics company 23andMe Inc.; and Ginkgo Bioworks Inc. co-founder Tom Knight.
“This past year, wastewater epidemiology changed from being an obscure niche area of science to becoming a central pillar of the response to the Covid-19 pandemic,” Matus said. “And now, in the later stages of the pandemic, it’s becoming a central pillar of preparing for the next pandemic.”
Covid Infections Are Down In South Africa’s Capital, Wastewater Shows
* Omicron Was First Identified In The Capital, Pretoria * Cases Are Rising Across At Least Seven Of Nine Provinces
Covid-19 infections are falling in the municipal area that includes South Africa’s capital, Pretoria, according to analyses of wastewater samples, indicating that the omicron wave may have peaked in the city where it was first found in the country.
The findings align with comments by Health Minister Joe Phaahla on Friday that the omicron-driven wave may be peaking in Gauteng, where Pretoria and Johannesburg are situated.
Still, national daily cases hit a record this week and the incidence of the virus appears to be rising in at least seven of the nation’s nine provinces. Gauteng accounted for 27% of the just under 25,000 new infections confirmed on Thursday, down from 72% of the about 16,000 found on Dec. 3.
“Early indications are that we might have reached the peak in Gauteng,” Phaahla told an online media briefing. “But there is a corresponding, rapid increase of cases in the other big provinces.”
Gauteng is home to a quarter of South Africa’s 60 million people. Cases are also rising fast in KwaZulu-Natal, the second-most populous province, and the Western Cape, where Cape Town is located.
South Africa announced the discovery of omicron on Nov. 25, and daily cases since then have risen at a far faster pace than in any of the country’s three previous infection waves.
The declining incidence of the disease in Pretoria points to sharply rising, but shorter, waves of infection as omicron spreads across South Africa and the world. Studies have shown that the variant is far more transmissible than earlier strains such as delta.
The volume of virus particles shed by people with Covid-19 has declined for two successive weeks at the Daaspoort wastewater treatment plant, which drains central Pretoria, the council said in a report on Friday for the week ended Dec. 10. Elsewhere in Tshwane, the municipal area that includes Pretoria, treatment plants appear to be showing a decrease in virus particles, but more tests are needed, the council said.
While the particles are not infectious, they provide an indication of the prevalence of the disease. Still, the concentration of virus particles is increasing in Johannesburg, and across the four other provinces where samples were analyzed.
Where Will We Find The Next Covid Outbreak? Check The Sewers
Sewage surveillance isn’t new, but it has a critical role to play in fighting health crises — if only policy makers would make better use of it.
Israeli scientists monitoring samplings of sewage water in 2013 made a startling discovery: an outbreak of paralyzing polio was imminent. A national vaccination campaign was quickly mobilized and no cases appeared. That same year, Swedish scientists provided public officials with an early warning for outbreaks of hepatitis A and norovirus using the same methods.
If we are to regain, and retain, normal living, we’ll need the same kind of early warning system for future variants and pandemics. Fortunately, we’re getting closer to having that.
Monitoring sewage systems is now one of the hottest areas of pandemic research, as viral RNA is shed through feces. (Those squeamish about the scatological, consider yourselves warned.) Used properly, this approach could help public health authorities build resilience against virus outbreaks.
Already wastewater surveillance has provided authorities with a picture of rising omicron rates. Britain has wide-scale wastewater surveillance (sampling covers 70% of the population of England) — no small feat given the age of the sewage system. Monitoring was ramped up during the pandemic under the U.K. Health Security Agency.
Omicron found in wastewater has aligned with clinical trends observed across the country since the beginning of December.
Slushing through sewage for insights into public health is hardly new. London doctor John Snow traced cholera outbreaks in the mid-19th century to contaminated water. For decades, scientists have looked for viral pathogens and other biomarkers, including illicit drugs, in the water we flush from hospitals, homes and businesses.
And yet, prior to the SARS-CoV-2 pandemic, most sewage monitoring was relatively small-scale, often focused on retrospective samples analyzed largely for academic or broad public health purposes.
The Netherlands was one of the first countries to demonstrate that SARS-CoV-2 could be picked up in sewer systems. Ever since, research funding has poured into the area. Surveillance systems were cobbled together, scaled up and made to work faster. Some countries have sophisticated public-facing dashboards.
Federal agencies in the U.S. set up the National Wastewater Surveillance System to inform and coordinate the patchwork of state and local efforts. Scientists at the University of California Merced have helpfully created a sweeping CovidPoops19 dashboard to post information on global wastewater testing, currently covering efforts in 58 countries.
Such systems may be our best leading indicator, at least if those doing the sampling know what they are looking for. Scientists at the University of Barcelona tested archival wastewater samples (which had been frozen) and found the presence of SARS-CoV-2 dating back to mid-January 2020, 41 days before the announcement of the first case on Feb. 25.
Sewage sampling in Paris in 2020 revealed viral RNA that anticipated the shape of the infection curve. In certain contained settings, such as schools, care homes or airports, wastewater sampling can provide critical time for health authorities to mobilize clinical testing or other policies. In one study in Britain, Covid was detected in the sewage system of 80% of schools studied a week before community tests provided confirmation.
“When we are at the peak of a wave like in the spring of 2020, you know you are in a pandemic. But when you are in the present situation, where the virus has reappeared and new variants are showing up, then it’s very important to have this early warning system,” says Albert Bosch, professor of microbiology at the University of Barcelona and head of the Enteric Virus Laboratory, which conducts Spain’s surveillance program. His team found omicron in Madrid the same week it was reported in South Africa.
Such systems offer a relatively cost-effective way to look for the presence of the virus and spot trends. The results of wastewater monitoring are unaffected by lack of access to testing or whether people even bother to get a test. All of this can help authorities identify where to target resources, which should mean both quicker reactions and fewer restrictions for most people.
And yet it’s also harder than it sounds. Differences in methodology, conditions and sampling analysis can make comparisons across areas difficult, there’s still a poor understanding in many places of how to interpret and use surveillance data for public health purposes.
The technology for wastewater surveillance is in some ways very basic, but there are complexities that can get in the way of getting accurate readings or using them for policy. Unlike the viral RNA found on a nose or throat swab, wastewater contains a great many biological and chemical substances that can muddy the picture. Changes in the physical and chemical composition of sewage mean it’s inherently less stable than your standard nasal swab.
The simplest technique is what’s known as a grab sample — pretty much a ladle dipped in sewage water. But samples can be affected by any number of factors from the time of day (most people use the bathroom in the mornings) to the weather (heavy rainfall can impact things). More sophisticated surveillance, known as composite sampling, uses programmable pumps to draw water at regular intervals.
The effects of dilution, hydraulic action in sewage systems, water chemistry and other factors mean the viral signal can vary significantly between test sites, making comparison difficult. Samples also need to be refrigerated during transport. And interpreting data requires both epidemiological expertise and experts on statistical methodology and wastewater specialists.
Then the onus is on authorities to put the information to good use. That seems to be happening at the community level in some places. A team of researchers at the University of Kentucky has developed a new technology for extracting the viral RNA from wastewater using magnetic beads and partnered with the owners of nursing homes and long-term care facilities to use wastewater surveillance to get an early warning of infections there.
James Keck, assistant professor of medicine and research lead at the university, says the big challenge is not gathering and analyzing samples but interpreting data, decision making and communication. “It’s a relatively new science — how you communicate the results and to whom are not easy and public health officials are not used to using that kind of data.”
Indeed, U.K. health authorities view such surveillance as supplementary information; it’s not clear how exactly it’s used for decision making or what the thresholds are for triggering a policy response. Belgium uses three “alerting indicators” based on viral concentration levels and the speed and trend of increase in wastewater and publishes its findings, which at least adds transparency.
If we are to build more resilient response systems to future variants and pandemics, then governments need to direct more resources to wastewater surveillance methods, infrastructure and training (including in rural areas and developing countries where testing isn’t widely available). Increased sewage monitoring could even play an essential role in what may be the next major health crisis we face — antimicrobial resistance.
As we hopefully emerge from omicron, it’s nice to know that some smart people have their heads in the gutter.
Omicron’s Spread Through U.S. Cities Is Shown In Wastewater Study
* Sewage Tests Found Related Mutations Before Human Cases * Testing Could Help Health Officials Get Ahead Of Outbreaks
Signs of the omicron variant that’s fueling a worldwide surge in Covid-19 cases were present in the U.S. a week or more before it first appeared in California, and spread widely in the weeks afterwards, according to a study showing the power of wastewater analysis for tracking outbreaks.
Evidence of omicron appeared in U.S. sewage samples collected as early as Nov. 21, state and local health officials from California, Colorado, Houston and New York City said in a study published by the U.S. Centers for Disease Control and Prevention.
The first infection in a U.S. patient was confirmed on Dec. 1 in California.
“The findings give strong early evidence that the omicron variant was likely present or more widely distributed in these communities than originally indicated by clinical testing alone,” the authors said in CDC’s Morbidity and Mortality Weekly Report. The four health authorities were the first to find signs of the variant in their wastewater, according to the study.
New variants like omicron, first seen in South Africa and Botswana, pose a risk because their genetic changes may increase their contagiousness or virulence. They may also be less recognizable to the human immune system, raising the possibility of reinfections or breakthrough cases in vaccinated people.
Analyzing wastewater containing human feces can be an important way to look for warning signs of new mutations, as well as track those already spreading to determine how long existing surges will last.
SARS-CoV-2 infects a wide variety of human tissues along with the lungs, including the gut, and is frequently excreted by infected people. Dutch researchers reported in March 2020 that they were able to find genetic material from the virus in wastewater before Covid-19 cases were reported in the population.
The technique “gives you a heads-up because people may not want to pick up the phone for surveys, but everybody poops,” said Gigi Gronvall, an immunologist at the John Hopkins Center for Health Security. “And it’s so unbiased because everybody uses the same sewer system.”
Houston; New York
Variants occur as the virus’s genome evolves, sometimes giving rise to new versions with features that make them able to spread faster or infect cells more efficiently. Researchers can look for these mutations in pieces of the viral genome that persist in sewage.
About two days before Houston’s first omicron case was detected, the city’s health department collected wastewater containing six coronavirus mutations that turned out to be associated with the variant. That was followed over the next two weeks by increasing detection of mutations related to omicron, the report said.
In New York City, the warnings of omicron came even earlier. The city’s Department of Environmental Protection found omicron-associated mutations in a sewage samples collected about 10 days before the first case of the variant was seen in the community.
Separately, New York Governor Kathy Hochul proposed spending $5 million annually from 2023 through 2025 to expand the state’s wastewater surveillance program for coronavirus markers.
The CDC funds 43 health departments for the National Wastewater Surveillance System that provides data on Covid’s presence and trends in water systems.
CDC To Expand Wastewater Monitoring To Help Track Coronavirus Trends
The agency plans to use the system to find other deadly pathogens
The Centers for Disease Control and Prevention plans to expand a system that detects the coronavirus in wastewater to better predict surges and declines of the virus and, eventually, wants to harness the network’s early-warning power to find other deadly pathogens and control outbreaks of food-borne disease.
Research suggests that 40 to 80 percent of people infected with the coronavirus shed viral genetic material in their feces even if they don’t have symptoms. It’s one of the first signs of an infection.
Increases in wastewater virus levels generally take place four to six days before health officials see a corresponding rise in case counts or hospitalizations.
“These data are uniquely powerful because they capture the presence of infections from people with and without symptoms and are not affected by access to health care or availability of clinical testing,” Amy Kirby, who leads the agency’s wastewater surveillance system, said during a briefing Friday.
Wastewater surveillance can be used to track other diseases and health concerns, Kirby said. Officials are working to expand surveillance to gather data on other pathogens by the end of the year, with targets including antibiotic-resistant bacteria, norovirus, influenza, a deadly fungal pathogen called Candida auris and food-borne infections caused by E. coli and salmonella.
The CDC gets data from about 400 testing sites that measure the coronavirus in wastewater. Some health departments are also able to conduct advanced genetic sequencing to track variants of concern. California, Colorado, New York City and Houston were the first to detect evidence of the omicron variant in community wastewater.
Participating states have used wastewater data to make public health decisions, Kirby said, such as directing mobile testing to certain vaccination sites and readying additional equipment and other resources for hospitals in communities where cases are forecast to increase.
Universities, colleges, states and cities, and commercial testing companies collect samples from sewage pipes to monitor the spread of the virus. Cities including Boston were able to identify impending case surge and conclude that the omicron variant had peaked.
The CDC until 2020 did not have a national system to track infectious diseases through wastewater. The agency has since provided money to 37 states, four cities and two territories for utilities to collect sewage samples, for laboratories to get those samples tested and for state officials to send the data to the CDC. Many of these states are still implementing their systems.
On Friday, the CDC said it was making public on its website the data it has received from 28 states and the District of Columbia. Some states have that data available on their websites, but the CDC data allows consumers to compare data across states.
More than 34,000 samples have been collected from communities representing about 53 million people. The CDC plans to add 255 testing sites in the next few weeks and additional sites during the next few months, expanding the reach of the program “to look into most states” and territories and tribal communities, Kirby said.
Kirby said her team is working with the rest of the agency’s coronavirus response to “find ways that wastewater surveillance can help provide situational awareness for what’s going on in the community, as well as serving as that early warning system that a new increase may be coming in a community.”
In Ohio, a color-coded map on the state health department’s website shows the increase or decrease in virus levels in wastewater for an area. Substantial increases in virus levels trigger an email notification to health districts, utilities and community health leaders, according to a CDC report last fall.
In Utah, wastewater data is one of the main components of a ranking system to determine where to dispatch mobile testing teams.
Out of 255 surveillance systems with data, 70 percent showed a decline in the virus over the past 15 days, while the remainder reported increases. No clear patterns emerged from the data, and in many cases treatment plants showing increases are next to plants with decreases.
The U.S. Is Expanding Its Hunt For Early Warnings Of Covid In Sewage
The samples stink, but the data are good.
U.S. public health officials are expanding their monitoring of Covid-19 in sewage, which has become a crucial early warning for surges of new cases.
The Centers for Disease Control and Prevention this week began sharing virus wastewater trends on its public-facing Covid data website. And the agency is in the midst of expanding the number of places from which raw sewage gets monitored for rising or falling waves of disease, adding hundreds of new sites in the coming months.
The U.S. struggle to track Covid in real-time has been one of the biggest frustrations of the pandemic. Early on, testing capabilities were only a fraction of what was needed. At-home tests, now more plentiful, mostly don’t get reported to health authorities. And even when local health departments and health care providers do get data, consolidating it for real-time analysis has been a challenge.
But with wastewater, the sewage – and the data it contains – keeps flowing.
Paying attention to that data can alert health officials to prepare medical surge teams, send out mobile testing units and to arrange for adequate supplies. It’s also a useful tool for health officials to help confirm what they’re seeing from other sources.
State and local health departments have been using, and publishing, the data since relatively early in the pandemic. The CDC has been monitoring it as well with Kirby’s program watching for SARS-CoV-2 signs in wastewater since 2020. Many cities track and publish the data on their own: Boston, Miami and dozens of others all make at least some data available.
To help get more places watching their wastewater, the CDC has convened working groups with state and local health officials who already use wastewater to track Covid levels. And they’re offering guidance and information sharing to help bring new sites online. As of Friday, the agency has begun posting wastewater data from 255 towns, cities, municipalities and other places.
The CDC has also contracted with a company called LuminUltra to collect wastewater data from 500 sites; about 200 are online so far. Kirby said the agency has identified hundreds more sites that it wants to enroll.
Trends, Not Totals
The data have limits. They can tell health officials whether the trend of cases in the community is increasing or decreasing, often days ahead of nasal-swab test results. But it can’t tell who’s sick, or how many cases there are.
About 80% of U.S. households are connected to a sewer system, according to the agency, limiting its use in some rural regions that rely on well-water and septic systems. Wastewater tests only capture information from what’s known as a sewershed.
That’s the network of pipes and drains that make up a sewer network. Those often don’t match perfectly with county boundaries, especially in parts of the U.S. such as the Northeast where systems can be far older and more convoluted.
“It’s a hyperlocal type of data; it’s most useful in the communities it’s being collected,” Kirby said.
In Missouri, there are more than 100 monitoring sites across the state. Since May 2020, the data have helped the health department predict where cases are heading.
To pull the sewage, a machine called an auto-sampler takes small volumes of sewage every 15 minutes for 24 hours. (And yes, it smells.) A one-liter sample is shipped by courier to a lab that spins down the liquid into a solid pellet. Then it’s analyzed for signs of virus. In total, it takes about 3-4 days from sewer to result, though running genetic analysis to identify variants can take longer.
It’s an evolving science. The state is working on ways to use the data to estimate how many people might be infected, not just identifying a rising or falling wave. The system has also had to compensate for events like heavy rain, which can dilute samples and skew the data.
But it’s proven helpful. During one of Missouri’s last waves, it let the state predict where the outbreak was headed, said Jeff Wenzel, chief of the Bureau of Environmental Epidemiology of the Missouri Department of Health and Senior Services.
“We were able to anticipate the trend and the time to get to a peak and come back down,” he said in an interview.
The data’s as useful as the samples are unglamorous.
“It’s just a dingy fluid,” Wenzel said.
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