New COVID-19 Variant Spreading in New York

A new way of coronavirus It is spreading rapidly in New York City and carries a worrisome mutation that can weaken the effectiveness of vaccines, two teams of researchers have found. The new variant, called B.1.526, first appeared in samples collected in the city in November. As of the middle of this month, it represented about one in four viral sequences that appear in a database shared by scientists. A study of the new variant, led by a Caltech group, was published online Tuesday. The other, conducted by researchers at Columbia University, is not yet public. None of the studies have been peer-reviewed or published in a scientific journal. But the consistent results suggest that the spread of the variant is real, experts said.

“It’s not particularly happy news,” said Dr. Michel Nussenzweig, an immunologist at Rockefeller University who was not involved in the new research. “But knowing is good, because then maybe we can do something about it.”

Nussenzweig said he was more concerned about the variant in New York than the one that is spreading rapidly in California. Yet another new contagious variant, discovered in Britain, now accounts for around 2,000 cases in 45 states. It is expected to become the most prevalent form of coronavirus in the United States at the end of March.

Researchers have been analyzing the genetic material of the virus to see how it might be changing. They examine the genetic sequences of the virus taken from a small proportion of infected people to trace the appearance of new versions.

The Caltech researchers discovered the B.1.526 increase by looking for mutations in hundreds of thousands of viral gene sequences in a database called GISAID. “There was a pattern that was recurring and a group of isolates concentrated in the New York region that I hadn’t seen,” said Anthony West, a computational biologist at Caltech.

He and his colleagues found two versions of the coronavirus increasing in frequency: one with the E484K mutation seen in South Africa and Brazil, which is believed to help the virus partially bypass vaccines; and another with a mutation called S477N, which can affect how strongly the virus binds to human cells.

As of mid-February, the two together accounted for about 27 percent of New York City’s viral sequences deposited in the database, West said. (At the moment, both are grouped as B.1.526).

Researchers at Columbia University took a different approach. They sequenced 1,142 patient samples at their medical center. They found that 12 percent of people with coronavirus had been infected with the variant containing the E484K mutation.

Patients infected with the virus-carrying this mutation were on average about six years older and more likely to have been hospitalized. While most of the patients were found in neighborhoods close to the hospital, particularly Washington Heights and Inwood, there were several other cases scattered throughout the metropolitan area, said Dr. David Ho, director of the Aaron Diamond AIDS Research Center.

“We see cases in Westchester, in the Bronx and Queens, in lower Manhattan and in Brooklyn,” Ho said. “So it seems to be very widespread. It is not a single outbreak. ”

The team also identified six cases of the variant that struck Britain, two infections with a variant identified in Brazil, and one case of the variant that gripped South Africa. The latter two had not been reported before in New York City, Ho said.

Researchers at the university have alerted authorities in New York state and the city, as well as the Centers for Disease Control and Prevention, Ho said. He and his colleagues plan to sequence around 100 viral genetic samples a day to monitor the rise invariants.

Other experts said that the sudden appearance of coronavirus variants was worrying.

“Given the involvement of E484K or S477N, combined with the fact that the New York region has a lot of permanent immunity against the spring wave, this is definitely one to watch,” said Kristian Andersen, a virologist at the Scripps Research Institute in San Diego, who was not involved in the new research efforts.

The E484K mutation has appeared independently in many different parts of the world, an indication that it offers the virus a significant advantage.

“Variants that have an advantage are going to increase quite quickly in frequency, especially when the numbers are going down overall,” said Andrew Read, an evolutionary microbiologist at Penn State University.

Ho’s team reported in January that monoclonal antibodies made by Eli Lilly and one of the monoclonal antibodies in a cocktail made by Regeneron are powerless against the variant identified in South Africa.

And several studies have now shown that variants containing the E484K mutation are less susceptible to vaccines than the original form of the virus. The mutation interferes with the activity of a class of antibodies that almost everyone makes, Nussenzweig said.

“People who have recovered from coronavirus or those who have been vaccinated have a high probability of being able to combat this variant, there is no doubt about that ”, he said. But “they can get a little sick.”

They can also infect others and keep the virus circulating, which could delay herd immunity, he added.

But other experts were a bit more optimistic. “These things are a little less controlled by the vaccine, but they are not orders of magnitude lower, which would terrify me,” Read said.

As the virus continues to evolve, vaccines will need to be adjusted, “but in the scheme of things, those are not huge concerns compared to not having a vaccine,” Read said. “I would say the glass is three-quarters full, compared to where we were last year.”