New York City wastewater shows links between puzzling COVID variants and worsening stages of the pandemic.

This article was produced in partnership with Gothamist.

In a new study, researchers at Columbia University identified a coronavirus mutation in New York City wastewater. This seems to emerge when the rate of severe disease starts to rise.The findings point to subtle, understated variants of the pandemic that are affecting day-to-day outcomes such as hospitalizations and deaths, without doctors even realizing it. may identify.

“Wastewater is a pooled sample,” said Archana Anand, a postdoctoral fellow at Columbia University who worked on the study, which includes data from fall 2020 to winter 2022. Instead of gathering this information in one PCR test swab at a time, she’s targeting hundreds of thousands of people at a time.

To identify potential clues about what these new mutations do, Anand linked the wastewater data with data on cases, hospitalizations, and deaths from health departments in New York City and New Jersey. . By linking her COVID-19 pattern in her Manhattan factory and Bergen County zip code to mutations present in these sewers, she suggests that the coronavirus travels faster and evades people’s immune systems. I’ve discovered some mutations that might help.

Table showing a heatmap of the function and incidence intensity of the most frequently occurring COVID-19 amino acid mutations in order of decreasing incidence from top to bottom. A darker color indicates a higher frequency of occurrence of the mutation.
Table showing a heatmap of the function and incidence intensity of the most frequently occurring COVID-19 amino acid mutations in order of decreasing incidence from top to bottom. A darker color indicates a higher mutation frequency.Anand Archana, Chenfa Long, Kartik Chandran

For example, she identified three mutations in the N protein. The N protein is part of the virus, protecting its genetic material and serving other functions. Hospitalization, mortality, and positive test rates were higher when these mutations were present in the effluent.

The Colombian team is led by engineering professor and drainage expert Kartik Chandran. Before the pandemic, Chandran tracked microbial communities in wastewater, leading his lab to easily redirect to coronavirus.

Most wastewater monitoring in the United States is focused on measuring how much coronavirus is present in a particular sewer system.

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

In other words, not just how much coronavirus is in the sewage, but what subspecies have what capabilities.

Mark Johnson, a professor of microbiology and immunology at the University of Missouri who heads the state’s wastewater monitoring program and was not involved in the Columbia study, traced the mutant via wastewater rather than PCR testing. It is said that it is “more comprehensive” to

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

Anand and her colleagues flagged a specific coronavirus mutation. They say more attention needs to be paid to potential factors for increased infection or severity. The study, which has yet to be peer-reviewed, could be a starting point for identifying the next major subspecies of concern in New York City, as well as for designing variant-specific therapies and vaccines. It can also be a starting point.

The Documenting COVID-19 project, which published this article in partnership with Gothamist, explored the implications of this study through interviews with the authors and outside experts as part of an ongoing study on wastewater monitoring for COVID-19. did. The Documenting COVID-19 project is supported in part by the Brown Institute for Media Innovation at Columbia University. This laboratory is not affiliated with the lab that conducted this study.

Identification of new mutations

Chandran’s team is analyzing wastewater samples from a Columbia University building and two wastewater treatment plants. They are the North River Wastewater Treatment Plant in Upper Manhattan and the Little Ferry Wastewater Treatment Plant in Bergen County, New Jersey. Each plant serves approximately 500,000 people.

By sequencing these samples, researchers were able to track various subspecies that New Yorkers have known all too well over the past year and a half. Alpha and Iota (the “New York variant”) take control of the sewage treatment plant in his early 2021, followed by Delta and Omicron.

Johnson acknowledges that many of the mutations reported in the study are “some of the variants of concern” that are considered more harmful by public health agencies.

Chandran and his team did more than just identify these variants by analyzing all parts of the coronavirus genome. This is the part that attaches to human cells and allows them to enter.

Given the vital role of the spike protein, it is probably the best-studied part of the coronavirus. Our immune system also tries to block the spike, creating selective pressure that forces the virus to adapt. increase. According to Johnson, more mutations occur in the spike protein than in any other part of the virus.

However, other less-studied segments of the coronavirus may play a role in how it spreads.

“We didn’t mean to limit ourselves to spike proteins,” Chandran said. “The same way you look at cholesterol and blame heart disease, you look at a single biomarker.”

Search function

About 60% of the mutations reported in the new study occur in parts of the virus other than the spike protein, Anand said. In addition, her analysis found “several mutations whose functional implications we do not yet understand.”

Further research is needed to solidify these connections. Tying specific mutations to specific viral properties can be difficult. This is usually done in the laboratory, in Petri dishes or in animal models of disease.

“It’s important to first discount the likelihood that the prevalence of any mutation is not due to being ‘inherited’ by another mutation,” says variant-tracking firm Helix’s bioinformatics and infection said Shishi Luo, associate director of disease. In a situation like this, two mutations that happened to evolve together could turn out to be a surprising subspecies, but only one of them actually gives the virus a meaningful advantage.

Columbia’s study did not include an animal model that actively tested which mutations were dangerous and which were simply introduced. hopes to follow up on their research.

New York City is so big and dense, Johnson said, that it’s the perfect place to track the coronavirus through its wastewater. You can test millions of people. But the work should be done elsewhere, he added.

Luo hopes that variants will be tracked across the country and linked to other types of data.

“If we can conduct certain analyzes of this preprint in real time, it would be a great first step towards an early warning system,” she said.

Such an alert system could flag new mutations and determine how they would change the severity of the pandemic.

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