How poop can predict the next coronavirus hotspots

coronavirus hotspots


Public health experts around the country are using every tool at their disposal to track the spread of COVID-19 in their area. For some cities and states, one of those tools is poop from the sewage water. The virus shows up reliably in the feces of sick people before they start to show symptoms. 


All that ends up where feces usually ends up, sewage plants like this one in Brooklyn, New York. A lot less gross than I thought it would be. The amount of virus swirling around in the plant is a good indicator of how many people are infected. 


How poop can predict the next coronavirus hotspots


It's an early window into how much illness is on the horizon and is helping the city to code the future of the pandemic. Early, like March, April, there were so many people said, I want your sewage tested for COVID. 


I want your sewage. And I'm like, what are you gonna do with it? What is your method like? Who are you? -  Pam Elardo leads the Bureau of WastewaterTreatment here in New York City. It's the largest municipal wastewater utility in North America. 


It includes 14 separate wastewater treatment plants spread through the city.  The largest plant processes waste for a million people. - On a dry day, treats about300 million gallons a day. When it rains, it takes stormwater from the streets. 

And when that happens, it can be over a 700million gallons in a day. Early on in the pandemic, scientists started to get interested in testing sewage for the virus to track the spread of the disease. Private companies and research labs from across the country began reaching out to wastewater plants like this one. - 


They felt that there might be, it might be traceable. The method hadn't been refined yet but there was a lot of interest in it. Pam thought the idea was worthwhile but didn't want to outsource. They felt like, and their leadership team felt like, they need to be in charge of it and control the process. 


So they quickly were able to repurpose part of their laboratories, their existing biological, microbiology laboratory here at Newtown Creek, to be able to do what they did in a short period. Like literally weeks, is amazing. 

To see what this all looks like, we took a short tour of the plant. The first stop, screening for all the stuff people shouldn't flush. - 80% of this is the stuff that is not human waste. We don't want to see anything except pee, puke, toilet paper, only toilet paper, not any other kind of paper and poop. 


That's it. This is what the plant's for. Then we tagged along on a sample collection And that was sewage. First, plant employees drop a metal contraption holding plastic bottles down into the incoming stream of liquid sewage. 


covid19 update


Nice and slow. So this is gonna go to the lab where they will analyze it for traces of the coronavirus. So the fecal samples arrive in the coolers every day, 365 days a year, and they process them  Analyzing this sample is more involved than the usual swab COVID tests. 


Dimitri Katehis leads the lab's efforts. So they take samples, influent samples, twice a week from the influent to all 14 facilities. That gives them a snapshot of the genetic material from the virus. So not an infectious virus, but rather just its genetic snippets. What this does is effectively allow us to develop a sort of early warning system.  

The team uses a technique called PCR, which magnifies tiny traces of genetic material until it can be detected by a machine. The less time it takes to magnify to a detectable level, the more material there was, to begin with. 


That lets them roughly quantify the amount of virus in the sewage.  When you go and you take a clinical test, you are basically, the question is, are you positive or are you negative? Here the question is, how much genetic material is there?  Can you translate that at all to the number of people who might be sick in that area? No is the short answer because the shedding rates vary. 


As an individual gets sick, they shed viral material at different rates, whether they're symptomatic or asymptomatic, or frankly how ill that individual is. The shedding rates are not adequately characterized yet to allow them to take this information and back-calculate an estimate as to how many people are ill.  


What they can do is track whether the amount of virus is rising or falling and the relative size of the outbreak. Do you have a sense of what, what concentration tends to correlate with like, a big outbreak versus a small outbreak?  


They have, unfortunately, because we were starting to see that. And what they are seeing is that values on the order of about 10 to 20,000 copies of RNA per liter indicate a brewing condition. And then when they start seeing values over 40 to50,000 copies per liter, there's a significant cluster and there's a significant response in the community.  

Using this system, Dimitri and his team were able to predict a recent hotspot in Coney Island. And they helped sound an early alarm on Staten Island. The city started noticing that there's possibly an increase in Staten Island, which had been very quiet up to that point. And they asked them, are you seeing anything? they were just wrapping up that sample that Saturday morning, and lo and behold they saw a significant spike in both Port Richmond as well as at Oakwood Beach, there two plants that serve Staten Island. 


And so they were able to provide that feedback and they, in turn, were able to increase the clinical testing.  This tool is still new. And even though it's worked well so far, the team is trying to refine and expand it. 

Right now, for example, it takes about three days to analyze each sample. They are purchasing some automated equipment to try to cut that down to two days and give them one more day. In what they are doing here, unfortunately, every day counts. Sewage monitoring on its own can't solve a pandemic. It has to be paired with other disease surveillance systems like data on testing, hospitalizations, and symptoms. 

Now, the city has a model that brings in, like as I said, a lot of data streams, everything from ambulance runs in the neighborhood to prescriptions being utilized, and so forth. And then they can make assessments whether they need to direct more clinical testing resources in certain neighborhoods, in certain areas, or whether they need to, God forbid, do more social distancing or enhanced enforcement. 


They do a little bit of that as well. - They will never know exactly, definitively how many people have COVID-19 at one particular time. Everything is an estimate, but each strategy estimates in a slightly different way. 


So by combining them, they get the best idea of what's happening. Eventually, the team hopes they can use this method to track other viruses and to monitor other health threats to the city. their basis is public health protection. 


That's how their industry got started. And so all of that means they should be contributing where they can in terms of how the sewage system, how the sewage information contributes to this pandemic, and any kind of future issues that they may come up against. 


In the last 10 years, they have seen a tenfold increase in the number of wipes coming there, because the manufacturer puts the word flushable on the box. We spend over $20 million a year of your money, if you live in New York City, throwing this stuff out. It belongs in the trash can. Trash it, don't flush it. 

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