What a CUNY Professor Is Learning About Omicron and Its Mutations From New York’s Sewers

February 3, 2022

“Our lab found the earliest known evidence of the presence of omicron in the U.S.,” Professor John Dennehy said.

John Dennehy Wastewater
John Dennehy

By Lida Tunesi

Since June 2020, Professor John Dennehy (GC/Queens, Biology) has been working with New York City to gather data on COVID-19 from a place that harbors many biological secrets: the sewers. 

Monitoring coronavirus levels and looking for variants in the wastewater is cost-effective, Dennehy previously told the Graduate Center. It also catches data that clinics miss, either from people who are asymptomatic and don’t get tested or those who test positive at home and don’t report their results.

“Our lab found the earliest known evidence of the presence of omicron in the U.S.,” Dennehy said. The first case of omicron in the U.S. was reported on December 1, 2021, but Dennehy’s group found genetic mutations unique to omicron in a wastewater sample collected on November 21.

In 2021, Dennehy and his collaborators, including Professor Monica Trujillo at Queensborough Community College, also started to see genetic material in wastewater that didn’t match up with omicron, delta, or any other variant of concern. Because the lab only looks at one region of the viral genome and not the entire thing, they refer to these new players as lineages, rather than variants.

In a paper published in Nature Communications, Dennehy, Trujillo, and other co-authors  picked four of these lineages, found in three New York City sewersheds, to examine more closely. This initial study’s mix of results and unresolved puzzles shows the strains are worth researching further for the sake of public health.

When tested in the lab, each of the four lineages showed some resistance to monoclonal antibody treatments, and total resistance in some cases. The researchers also tested blood plasma from vaccinated patients and previously infected patients. Plasma from both groups showed some ability to fight off the lineages, but in varying amounts.

However, it’s not clear that the mystery lineages are infecting humans. Over several months, the four stayed constrained to a certain number of sewersheds, whereas people moved around fairly freely in 2021. The researchers found evidence that these lineages might be able to infect rat and mouse cells, but they cautioned that this is not enough information to definitively point to an animal source.

What they can say is that each of the lineages also shared many genetic mutations with the omicron variant, suggesting the possibility of convergent evolution.

“Viruses adapting locally all ‘converge’ on the same mutations that increase their fitness in humans,” Dennehy said. “We see the same mutations pop up in variants all over the world because, despite geographic separation, the virus faces the same selection pressures, i.e., the ability to infect humans and to transmit between humans.”

This does not point to a definitively good or bad outcome, though.

“What do I predict?” Dennehy said. “After [omicron], who knows? Maybe another variant that evades antibody-mediated neutralization. Maybe it dies down to more manageable levels.”

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