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A new form of coronavirus is spreading rapidly in New York City and carries a disturbing mutation that could weaken the effectiveness of vaccines, two teams of researchers have found.
The new variant, called B.1.526, first appeared in samples taken in the city in November. As of the middle of this month, it represented about one in four viral streaks appearing in a database shared by scientists.
A study of the new variant, conducted by a group at Caltech, was posted online Tuesday. The other, by researchers at Columbia University, has been submitted to a pre-print server but is not yet public.
No 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 Michel Nussenzweig, an immunologist at Rockefeller University who was not involved in the new research. “But just knowing that is good, because then maybe we can do something about it.”
Dr Nussenzweig said he was more concerned with the variant in New York City than the one rapidly spreading in California. Another contagious new variant, discovered in Britain, now accounts for around 2,000 cases in 45 states. It is expected to become the most common form of the coronavirus in the United States by the end of March.
Researchers looked at the virus’s genetic material to see how it might change. They examine the genetic sequences of viruses taken from a small proportion of infected people to trace the emergence of new versions.
Caltech researchers discovered the increase in B.1.526 by looking for mutations in hundreds of thousands of viral genetic sequences in a database called GISAID. “There was a pattern that was recurring, and a cluster of isolates concentrated in the New York City area that I hadn’t seen,” said Anthony West, a computational biologist at Caltech.
He and his colleagues have 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 avoid vaccines; and another with a mutation called S477N, which can affect the way the virus binds to human cells.
As of mid-February, the two together accounted for about 27% of the New York City viral sequences deposited in the database, Dr West said. (For now, the two are grouped together as B.1.526.)
Columbia University researchers took a different approach. They sequenced 1,142 patient samples at their medical center. They found that 12% of people with the 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 the majority of patients were found in areas close to the hospital – particularly in Washington Heights and Inwood – there were several other cases scattered throughout the metro area, said Dr David Ho, director of Aaron Diamond. AIDS Research Center.
“We are seeing cases in Westchester, Bronx and Queens, lower Manhattan and Brooklyn,” Dr. Ho said. “So this seems to be prevalent. It is not a single epidemic.
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 took over in South Africa. The latter two had not been reported in New York before, Dr Ho said.
University investigators have alerted New York state and city officials, as well as the Centers for Disease Control and Prevention, Dr. Ho said. He and his colleagues plan to sequence about 100 viral genetic samples per day for monitor the increase in variants.
Other experts said the sudden appearance of coronavirus variants was concerning.
“Considering the involvement of E484K or S477N, combined with the fact that the New York area has a lot of lifelong spring wave immunity, this is definitely one to watch out for,” said Kristian Andersen, virologist at Scripps. Research Institute in San Diego, which did not participate in the new research efforts.
The E484K mutation has emerged independently in many parts of the world, indicating that it gives the virus a significant advantage.
“The variants that have an advantage will increase in frequency quite quickly, especially when the numbers go down overall,” said Andrew Read, evolutionary microbiologist at Penn State University.
Dr Ho’s team reported in January that the 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 was. The mutation interferes with the activity of a class of antibodies that almost everyone makes, said Dr Nussenzweig.
“People who have recovered from the coronavirus or who have been vaccinated are very likely to be able to fight this variant, there is no doubt,” he said. But “they can get a little sick”.
They can also infect other people and keep the virus circulating, which could delay the herd’s immunity, he added.
But other experts were slightly more optimistic. “These things are a little less well controlled by the vaccine, but they are not orders of magnitude smaller, which would terrify me,” Dr Read said.
As the virus continues to evolve, vaccines will need to be changed, “but in the scheme of things, those aren’t big concerns about not having a vaccine,” Dr Read said. “I would say the glass is three-quarters full, compared to where we were last year.”
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