A new form of the coronavirus is spreading rapidly in New York City and carries a worrying mutation that could weaken vaccine effectiveness, two teams of researchers have found.
The new variant, called B.1.526, first appeared in samples collected in the city in November. In the middle of this month, it was responsible for about one in four viral sequences that appeared in a database shared by scientists.
A study of the new variant, led by a Caltech group, was posted online on Tuesday. The other, by researchers at Columbia University, was submitted to a prepress server, but is not yet public.
No study has been examined by peer review or published in a scientific journal. But consistent results suggest that the spread of the variant is real, experts said.
“It is not particularly happy news,” said Michel Nussenzweig, an immunologist at Rockefeller University who was not involved in the new research. “But knowing about it is good, because then maybe we can do something about it.”
Dr. Nussenzweig said he was more concerned with the variant in New York than with the one that is spreading rapidly in California. Another new contagious variant, discovered in Britain, now accounts for about 2,000 cases in 45 states. It is expected to become the most prevalent form of coronavirus in the United States by the end of March.
The researchers have examined the virus’s genetic material to see how it may be changing. They examine genetic sequences of viruses taken from a small proportion of infected people to map the emergence of new versions.
The Caltech researchers found the increase in B.1,526 by scanning for mutations in hundreds of thousands of viral genetic sequences in a database called GISAID. “There was a recurring pattern and group of isolates concentrated in the New York area that I hadn’t seen,” said Anthony West, a computer 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 appears to help the virus partially dodge vaccines; and another with a mutation called S477N, which can affect how tightly the virus binds to human cells.
In mid-February, the two together accounted for about 27% of New York City’s viral streams deposited in the database, West said. (Both are currently grouped 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 were infected with the variant that contains the E484K mutation.
Patients infected with the virus that carries this mutation were about six years older, on average, and were more likely to have been hospitalized. Although most patients were found in neighborhoods close to the hospital – particularly Washington Heights and Inwood – there were several other cases spread throughout the metropolitan area, said Dr. David Ho, director of the Aaron Diamond AIDS Research Center.
“We see cases in Westchester, the Bronx and Queens, lower Manhattan and Brooklyn,” said Ho. “So it seems to be widespread. It is not a single outbreak. “
The team also identified six cases of the variant that hit Britain, two infections with one variant identified in Brazil and one case of the variant it took in South Africa. The last two had not been reported in New York City before, he said. Ho.
University investigators have alerted authorities in New York state and the city, as well as the Centers for Disease Control and Prevention, said Dr. Ho. He and his colleagues plan to sequence about 100 viral genetic samples a day to monitor the increase in variants.
Other experts said the sudden appearance of coronavirus variants was worrying.
“Given the involvement of E484K or S477N, combined with the fact that the New York area has great permanent immunity against the spring wave, this is definitely a place to watch,” said Kristian Andersen, virologist at Scripps Research Institute in San Diego, which was not involved in the new research efforts.
The E484K mutation emerged independently in many different parts of the world, an indication that it offers the virus a significant advantage.
“Variants that have an advantage will increase very quickly in frequency, especially when the numbers are decreasing,” said Andrew Read, an evolutionary microbiologist at Penn State University.
Dr. Ho’s team reported in January that the monoclonal antibodies produced 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, said 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 about that,” he said. But “they can get a little sick from it”.
They can also infect other people and keep the virus circulating, which can delay the herd’s immunity, he added.
But other experts were a little more optimistic. “These things are a little less controlled by the vaccine, but they are not orders of magnitude down, which would terrify me,” said Dr. Read.
As the virus continues to evolve, vaccines will need to be adjusted, “but in the scheme of things, these are not major concerns compared to not having a vaccine,” said Dr. Read. “I would say the glass is three-quarters full, compared to where we were last year.”