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Testing poop to predict Miami’s COVID-19 trends? It has been a messy process so far



MIAMI – In March, when it became clear that the United States was facing an unprecedented pandemic, Miami-Dade County began sampling its wastewater as a potential tool to measure the extent of COVID-19 infections. The hope was that testing the county’s poop for coronavirus could serve as an early warning indicator of a dreaded second wave expected in the fall.

Now that cases rising across the state and Florida are experiencing a steady rise to levels not seen since August, what does the wastewater say?

The short answer: Not much, at least not yet. The process got off to a slow, messy start, but they have cleared the data and there are still some who promise it will work.

For months, the county has paid $ 3,600 a week to see if testing wastewater could help estimate coronavirus infection trends in the population. Miami-Dade̵

7;s water and sewer department sends samples from its three sewage plants to a special laboratory in Boston called Biobot.

The results were intended to help former mayor Carlos Gimenez and public health experts get ahead of the virus and potentially save lives by better preparing the hospital’s infrastructure for surges. After all, everyone jaws and wastewater reflects all individuals in a community, whether they have COVID-19 symptoms and access to testing or not.

Because coronavirus appears in human waste only a day or two after infection, mining wastewater for COVID-19 data emerged as another COVID-19 meter. Used in conjunction with other data, it can help provide a sense of where the COVID curve may be heading.

But while cities like Paris and Boston have integrated wastewater test results into their COVID-19 control strategies, WASD says test delivery results are not yet fast enough to make it a Miami-Dade planning tool.

“We need to have more confidence in the data. The results at this point mimic test data coming to us from the state, ”said WASD Director Kevin Lynskey.

Miami-Dade Water and Sewer takes weekly samples from its Virginia Key treatment plant as part of a COVID-19 test program.

Lynskey said the Biobot data is still mostly a look back at the COVID curve rather than forward for trend indication. For example, recent Biobot analysis of Dade’s wastewater shows that the number of estimates of cases began to develop around mid-October, but no data is available yet after October 27 due to county delays, Lynskey said.

Problems have arisen at both ends of the process – the collection of samples from the county’s three large sewer systems and the analysis of it at Biobot.

When sampling began in March, the results were unreliable with spikes and droplets that made no sense when analyzed against the clinical and test data from COVID-19 patients tracked by the Florida Department of Health, Lynskey said. Biobot admits that its methods were necessary after it launched the test program in March.

Until August, Biobot’s algorithm assessed the presence of the virus, or how widespread the disease was in the population. Because the lab was still fine-tuning its technology, the results took up to two weeks to come back, and the test program was considered an ongoing work, Lynskey said.

So in August, Biobot revised its model. It included more information in its analysis, including new research on how the virus behaves in wastewater, and began producing results that showed the occurrence of new cases that could point to trends rather than just the proportion of cases in the population at a particular moment. And the company also started processing data much faster and turned the tests on in a few days.

“We have been working with hundreds of communities for several months, so we are in a very different place today in terms of our understanding of laboratory methods, data analysis pipelines to the virus just because of the data set we have collected,” said Newsha Ghaeli, President of Biobot. and co-founder. “Our sensitivity levels have changed and improved.”

Back in March and April, Biobot would deliver data back to communities two weeks after sampling, a result that could not be traded at all, she said. Now Biobot can test samples in one day and send the results the next day.

So why does Miami-Dade not benefit from this faster turnaround? There have been delays with its own sampling over the last three weeks, so there were no tests through Biobot or data after October 27th. WASD said there were delays in receiving sets from Biobot and it is working to get the test program back on track.

In Boston, the water and sewer company makes the data available and encourages officials and the public to use it along with other information to make decisions about the pandemic.

In July, the Massachusetts Water Resources Authority began publishing the results of COVID testing at its Deer Island treatment plant on its website. The results are shared with staff from the Department of Public Health, the Department of Environmental Protection, the Executive Office of Health and Human Services and the Executive Office of Energy and Environmental Affairs, according to the MWRA.

“It is important to note that this is a pilot for a science under development,” the website said. “The results of this study will be used by public health officials as an additional tool for the Commonwealth to track how the pandemic is trending in Massachusetts, along with data from clinical trials, admissions, etc.”

Some wastewater sampling programs are also implemented by other states. Since July, the Wisconsin State Laboratory of Hygiene in partnership with the University of Wisconsin, Milwaukee and the State Department of Natural Resources has been testing samples from sewage treatment plants once a week for approx. 20 counties with 75% of the population. Universities like Yale and the Massachusetts Institute of Technology are also testing their wastewater to track the COVID pandemic in their communities. The University of Miami is also launching its own program that tests wastewater from various collection points on its campuses.

It is not clear if Florida is working on a state-funded program because neither the Department of Health nor the government’s Ron DeSantis’ office responded to requests for comment.

At the national level, the Centers for Disease Control and Prevention and the U.S. Department of Health and Human Services announced last month that they are launching the National Wastewater Monitoring System to generate data to “help public health officials better understand the extent of COVID-19 infections in communities.” ”

The CDC is currently developing a portal for state, tribal, local and territorial health departments to submit wastewater test data into a national database to be used for public health actions.

Data from wastewater testing is not intended to replace existing COVID-19 monitoring systems, but is intended to supplement them by providing data to communities where timely COVID-19 clinical trials are underutilized or unavailable, the CDC said.

Meanwhile, Biobot uses poop data from cities to conduct all sorts of epidemiological studies. For example, the laboratory discovered that people with COVID threw a greater viral load into their poop in the first few days of infection. So if sewer samples show a significant increase in viral load, that means an increase in numbers could happen in a week or so, Ghaeli said.

Statistically, when people are infected with the virus, they are likely to show symptoms on day four or five. They would probably like to be tested, and if the system is not overwhelmed, test results would probably be available in two or three days. So the test result would follow the onset of the infection by about a week or more.

If poop testing is performed effectively, it can give public health officials a warning of trends in advance.

Lynskey said the county may decide to conduct more targeted wastewater testing to identify hot spots and get a more detailed overview of infection trends.

“We could test individual grid points in our system. We can perform more localized tests rather than sampling at the treatment plant, ”he said. “We could make them from more focused pools and start polishing where infections are more problematic.”

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(c) 2020 Miami Herald

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