NYC wastewater shows link between cryptic COVID variants and worse phases of the pandemic

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NYC wastewater shows link between cryptic COVID variants and worse phases of the pandemic


In a new study, Columbia University researchers have identified coronavirus mutations in New York City wastewater that seem to appear when severe disease rates begin to rise. The findings may pinpoint subtle, understated variants in the pandemic that are affecting day-to-day outcomes, including hospitalization and death, without doctors noticing.

“Wastewater is a pooled sample,” said Archana Anand, a postdoctoral researcher at Columbia who worked on the study, which includes data from fall 2020 through winter 2022. By collecting genetic information from these wastewater samples, researchers can study the virus strains circulating among hundreds of thousands of people at once, rather than gathering this information one PCR test swab at a time.

To identify potential leads on what those novel mutations do, Anand linked the wastewater data with data on cases, hospitalizations and deaths from the New York City and New Jersey health departments. By connecting COVID-19 patterns in ZIP codes served by the north Manhattan plant and in Bergen County, New Jersey to the mutations present in these sewersheds, she found some mutations that may be helping the coronavirus move faster and evade people’s immune systems.

For example, she identified three mutations on the N protein — a piece of the virus that protects its genetic material, along with serving other functions. When these mutations were present in the wastewater, hospitalization, mortality, and test positivity rates were higher.

The Columbia team is led by engineering professor and wastewater expert Kartik Chandran. Prior to the pandemic, Chandran tracked microbial communities in wastewater, leading his lab to easily pivot to the coronavirus.

Most wastewater surveillance in the US focuses on measuring how much coronavirus is present in a given sewershed. But Chandran is interested in answering more complex questions.

“It’s not just the ‘who’ and ‘how many,'” he said. “It’s the function and activity.”

In other words: it’s not just how much coronavirus is in the sewage, but which variants, and what those variants are capable of.

Tracking variants through wastewater rather than PCR tests is “more comprehensive,” said Marc Johnson, a professor of microbiology and immunology at the University of Missouri who leads the state’s wastewater surveillance program and was not involved with the Columbia study.

“It tells you about everyone,” he said, including people “who don’t even know they’re sick.” Wastewater surveillance has become more widespread over the past year, thanks in part to funding from the Centers for Disease Control and Prevention. But setting up sewage testing — and incorporating variant tracking — can be logistically difficult for health departments.

Anand and her colleagues flagged specific coronavirus mutations that they say deserve further attention as potential drivers of increased transmission or severity. The study, which has not yet been peer-reviewed, may be a starting point for identifying the next major variant of concern in New York City, or even for designing variant-specific treatments and vaccines.

The Documenting COVID-19 project, which partnered with Gothamist to publish this article, explored this study’s implications through interviews with its authors and outside experts as part of its ongoing research into wastewater surveillance for COVID-19. The Documenting COVID-19 project is partially supported by Columbia University’s Brown Institute for Media Innovation, which is not affiliated with the lab that conducted this study.



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