Cryptic Variant Found in NYC’s Sewers

River D'Almeida, Ph.D
2 min readFeb 8, 2022

A rat strain? Or the next Omicron?

Image via Pexels

Article via LabRoots

Viral experts are still unsure where and how the Omicron variant originated, but one thing is clear: it has overtaken prior SARS-CoV-2 variants and wreaked havoc. As of the end of January 2022, the Omicron variant was responsible for 96.4% of global COVID cases.

While some scientists are focusing their efforts on developing therapies and vaccines to stop COVID variants from emerging for good, others are looking for clues on the variants’ origins in an unlikely place — the sewers.

Between 40 and 80 percent of individuals infected with COVID-19 are shedding trace amounts of SARS-CoV-2 RNA every time they flush. This makes wastewater surveillance an essential tool to track the spread of the virus across communities. The Centers for Disease Control and Prevention (CDC) recently announced plans to expand their current monitoring program (that spans 400 sites) in an effort to keep a closer eye on infection trends throughout the U.S.

Now a team of virologists studying variants in New York City’s wastewater samples has reported strange sequences not linked to any of the known circulating strains.

The research was reported in the journal Nature Communications.

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River D'Almeida, Ph.D

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