Poop alert: Sewage could signal impending burst of COVID-19 cases

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Around the country and the world, coronavirus lockdowns and stay-at-home orders are being lifted as the rate of new infections begins to slow. That shouldn’t be interpreted as humans having suddenly beaten the virus; local outbreaks of SARS-CoV-2 are going to be something we contend with until there’s an effective vaccine or widespread immunity. For public health officials, having as much notice as possible about those outbreaks will be vital. And it’s possible that sewage sludge might be able to provide that notice.

The idea is pretty simple. We know that infected humans shed SARS-CoV-2 viral RNA in feces, so you can take samples of sewage sludge, look for the virus’s genetic materials, and thereby get an idea of the viral load of the pooping population.

In fact, the idea of using our sewers for biosurveillance isn’t a new one. I first heard the concept at the Advances in Genome Biology and Technology meeting in 2011, when biotechnology companies like PacBio and Oxford Nanopore proposed using their advanced new platforms to sequence the DNA in sewage for public health intelligence. But the idea was old hat even then—Israel has been monitoring sewage for signs of polio outbreaks since 1989, and it detected outbreaks in 1991, 2002, and 2013.

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