It All Comes Out in the Wash: COVID-19 Tracked in Wastewater


A CDC program examines wastewater to get a jump on COVID-19 eruptions, and also to detect new variants, some of which may have been hatched in animals.

COVID-19 hospitalizations rates plummet in recent weeks, and while infection and mortality rates continue to remain high, they’re also expected to decline most experts believe, suggesting that we may be approaching Omicron’s plateau, followed by a quick decline. Normal will be back. Unless a new troublesome variant surfaces from our wastewater.

The United States reported 356,658 new COVID-19 cases and 2441 deaths last Friday, according to the Johns Hopkins Coronavirus Resource Center. There’s been a decrease in new daily cases of COVID-19 by almost 50% in the last 2 weeks, feeding the hope that we may be able to live lives that approximate the way we lived before COVID-19 even though death rates have increased by 35%, according to the New York Times tracker. Death rates are seen as a lagging indicator.

Meanwhile public policy officials keep their guard up, looking for new variants even in unexpected places—such as wastewater. Back in October 2020, Infection Control Today® (ICT®) reported on how wastewater might offer clues as to how certain communities fair against COVID-19. In a Q&A with ICT®, Sean Norman, MS, PhD, an associate professor and the director of the molecular microbial ecology laboratory at the University of South Carolina, said that “oftentimes sewage provides a leading indicator. We actually know ahead of time what’s going to be happening in the community, because we get numbers from asymptomatic individuals.”

In that interview, Norman mentioned that he was working in partnership with the Centers for Disease Control and Prevention (CDC) “to really try to understand the prevalence of the virus and identify trends: upward trends and downward trends.”

While Norman spoke of examining wastewater to track COVID-19 viral shedding from human beings, wastewater may also offer clues on whether animals host the virus and to what degree.

Norman’s efforts may be what Amy Kirby, PhD, MPH, had in mind last Friday when she said at a press conference about the CDC’s National Wastewater Surveillance System (NWSS) that “what started as a grassroots effort by

Amy Kirby, PhD, MPH, Centers for Disease Control and Prevention

Amy Kirby, PhD, MPH, Centers for Disease Control and Prevention

academic researchers and wastewater utilities has quickly become a nationwide surveillance system with more than 34,000 samples collected representing approximately 53 million Americans.”

Kirby is a senior service fellow in the Waterborne Disease Prevention Branch at CDC. Since its launch in September 2020, the NWSS has grown so that the CDC partners with 37 states, four cities and two territories to help build wastewater surveillance systems in their communities. More than 400 testing sites around the country engage in wastewater surveillance.

As Norman pointed out to ICT®, wastewater surveillance can act as an early warning system for COVID-19 surges: “We get the numbers.”

Kirby also touched on how monitoring of wastewater might help spot new COVID-19 variants whether they spring from human beings or animals. Kirby says that “many of our states are sequencing their wastewater samples and that data will be coming into CDC within the next few weeks…. [This] is a very powerful method for tracking variants of concern in wastewater and we’re … to monitor … new variants of concern entering our communities….”

Medical experts believe that Omicron, which did not evolve from Delta, had been incubated in either an immunocompromised person, or rodents. The fact that COVID-19 can incubate and mutate in animals and reinfect humans raises concerns among some medical experts.

A study published last week in Nature Communications shows that investigators found COVID-19 mutations with what the investigators describe as “cryptic lineages.” They could have emerged from humans or animals. The mutations have been circulating for about a year and show no sign of challenging either the Delta or Omicron variants for dominance. Some of the investigators believe that the mutations come from humans, quite possibly incubating in long-term care facilities. 

“Since January 2021, the lineages have remained geographically constrained over many months in the sewersheds we sampled, which is not consistent with a contagious human pathogen,” the study states.

However, because the lineages stayed put, so to speak, and did not move around the city as would human-carried variants, it’s very possible that animals incubated them.

“While the origins of these cryptic lineages have not been determined, we have demonstrated that they have expanded receptor tropism which is consistent with expansion to an animal reservoir,” the study states. “Other SARS-CoV-2 animal reservoirs have been identified. However, no single animal was strongly represented in all our rRNA sequencing analysis, which raises doubts that a single animal reservoir is the source of all the cryptic lineages.”

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