PHOTO ILLUSTRATION BY EMILY SHERER / GETTY IMAGES
As COVID-19 testing sites close and experts warn that the number of cases captures a small proportion of infections, many public health experts are turning to a newer source who can tell us what is happening to the virus: our stools.
In the last two years, scientists have developed systems that can detect COVID-19 in our wastewater. This is a great early warning system, as the virus can appear in people’s waste days before they start experiencing symptoms or can be tested. It is also less biased than the case data: not everyone can find a test for COVID-19 and not every positive result will be reported … but everyone poops.
However, as with so many other indicators for COVID-19, interpreting wastewater data is not as simple as it seems. Prior to COVID-19, this type of data was not used to track respiratory viruses. This means that the Centers for Disease Control and Prevention have little infrastructure to build on. The agency is trying to standardize reporting from researchers across the country, many of whom have different methods of water sampling. In addition, state and local health officials who cite wastewater as a potential substitute for underestimated case numbers are not accustomed to interpreting environmental data, which has unique warnings and requires a learning curve for those accustomed to looking at numbers from hospitals and health clinics.
The COVID-19 Documentation Project surveyed 19 state and local health agencies, as well as scientists working on wastewater sampling, to learn about the challenges they face. We found that many states are months, if not more, away from being able to use wastewater data to guide public health decisions, even when the rise of the omicron sub-option is looming, BA.2. Meanwhile, the CDC’s much-shared wastewater monitoring panel is in the works and difficult to interpret for consumers who can hope to keep up with trends in their fields.
“People are saying, ‘We can’t believe this.’ [PCR] testing data now and moving to more reliance on wastewater data, said Steve Balog, a researcher at the Metropolitan Council, a local agency in the twin cities, Minnesota, a metro area that began monitoring wastewater in late 2020.
But health services can’t just snap a switch – or look at the bottom of a toilet bowl – and suddenly get a comprehensive trend for COVID-19 from wastewater. It takes time to adjust the sampling technology, to understand the environment around the wastewater site and to gather enough data to easily interpret the trends.
Some universities and their public health partners in California began investing in sewage control at the start of the pandemic. San Diego, for example, began sewage sampling in the fall of 2020 as part of efforts to reopen the campus for the University of California, San Diego, said Smruti Kartikeyan, a postdoctoral fellow working on surveillance. It was later extended to other parts of the city, including sites selected to monitor COVID-19 in local public school districts.
The Karthikeyan team uses machines called “autosamplers” that are placed in a sewer system and are programmed to collect small amounts of water over time. These machines slowly collect a certain amount of water for 24 hours, which is a more in-depth method than capturing this volume at once, as it captures waste from all day. Researchers then typically take a small portion of the wastewater, dilute it with other chemicals to preserve the genetic material in the sample, and perform PCR tests for COVID-19 to determine if the virus is present. They can also conduct tests to look for specific options, such as omicron. The Karthikeyan team uses robots to automate these analysis steps and reduce errors; other researchers have more human-driven processes.
UCSD now processes about 200 wastewater samples a day, Kartikeyan said. When signs of COVID-19 appear in the wastewater of a particular site, another automated system warns residents or workers of that site that they must perform a PCR test. These signals help limit outbreaks on the UCSD campus while minimizing testing costs.
“People who receive the signals” feel they have a reason to be tested, “Kartikeyan said. “And we get 98 percent compliance when we send these emails to students.” Other colleges and universities have similarly used wastewater to conduct targeted tests.
The San Diego Wastewater Monitoring Network also directs COVID-19 safeguards to the UCSD health system, with multi-level guidelines based on wastewater data (and several other indicators) that tell workers when to disguise themselves. reduce their personal working hours or take other precautions. In March, just one week after the health system began using this guide, wastewater trends led to a return to mandatory camouflage.
But many places do not have the same resources for establishing wastewater monitoring – or linking public health actions to data – as San Diego. Asked if he knew of any other institutions that use wastewater to manage their safety measures, UCSD Health Chief Medical Officer Dr. Christopher Longhurst said no: “I can’t point you to one.”
In recent months, California scientists have expanded their wastewater monitoring to more rural parts of the state with the support of the state’s Department of Public Health. This poses new challenges: public health officials are often unaccustomed to looking at data from outpatient hospitals or health clinics, and there are many logistical obstacles to sampling in new locations, combined with difficulties in interpreting data from less populated areas where Wastewater monitoring is highly sensitive to changes in the distribution of COVID-19.
A document from the Stanford University Coronavirus Warning Network (SCAN) describes how genetic material dumped by someone with COVID-19 can change: during infection, from person to person, and depending on measurement techniques. the weather, the influx of spring breakers or even local business practices. For example, Modesto, a city in California’s central valley, had a lot of canned fruit in its sewers. This industrial flow may have blocked the signal of coronavirus genetic material, which has affected scientists’ ability to isolate it in PCR testing, said Colleen Notton, a professor of environmental engineering at the University of California, Merced, who works on wastewater monitoring. this region. .
The Maine Centers for Disease Control and Prevention is facing similar problems as it extends surveillance from Portland, the state’s main urban center, to more rural communities, said Michael Abbott, who heads the agency’s wastewater screening.
One of Portland’s treatment plants is a long-standing collection site for Biobot, a wastewater monitoring company based in Cambridge, Massachusetts. In Portland, a city of nearly 70,000 people, a “really significant increase” in the prevalence of COVID-19 is needed to start raising sewage virus levels, Abbott said. So when wastewater rises, the trend is easy to interpret.
But in rural areas of the state, some of which began to observe during the Omicron jump, “data tends to jump up and down more than follow a fairly smooth curve,” Abbott said. A small number of cases can have a huge impact on wastewater levels, especially when these cases involve outside tourists who go to small towns, as is common in Maine.
While public health officials are learning to navigate wastewater data, public health agencies in several countries have told us that they still do not see the system as a reliable source for political decision-making – at least not in isolation. A recent report by the Rockefeller Foundation found that many local agencies, especially those serving rural areas, do not have the internal capacity to include wastewater data as they deal with budget cuts and incineration.
The Minnesota Department of Health is working to expand wastewater sampling, agency spokesman Gary Bowman said in an email. But it will take weeks or months for this extension to become useful data, long after Minnesota PCR test numbers have become completely unreliable. And even if Minnesota expands wastewater monitoring to cover the entire state, the agency is unsure whether the federal government will continue funding, Bowman said.
However, it would be difficult to say that these local wastewater challenges exist, if we look at the CDC’s wastewater dashboard. Highly publicized after it was added to the agency’s COVID Data Tracker in February, the dashboard shows only one indicator until early April: color dots representing an increase or decrease in coronavirus levels found on each site over the past two weeks. There was no context for the actual spread of the virus or how recent trends compare to longer time frames.
If a site measures “virus undetected” (meaning no COVID-19) for three consecutive weeks and then measures a relatively low level of COVID-19, the CDC dashboard will show a 100% increase, he said. Zuzana Bohrerova, an environmental scientist at Ohio State University who works on the Ohio Observation Program. A red dot on the dashboard can be a serious warning or it can be insignificant – the original presentation of the CDC made it difficult to say.
“I think they were trying to be simpler,” Notton told the CDC board. “They did not want to release all the concentration data because they thought it was difficult for people to understand.
On April 8, the agency updated this dashboard, adding new metrics and the option to click on a specific site for …
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