Most New York Coronavirus Cases Came From Europe, Genomes Show

The Four Percent


New research indicates that the coronavirus began to circulate in the New York area by mid-February, weeks before the first confirmed case, and that travelers brought in the virus mainly from Europe, not Asia.

“The majority is clearly European,” said Harm van Bakel, a geneticist at Icahn School of Medicine at Mount Sinai, who co-wrote a study awaiting peer review.

A separate team at N.Y.U. Grossman School of Medicine came to strikingly similar conclusions, despite studying a different group of cases. Both teams analyzed genomes from coronaviruses taken from New Yorkers starting in mid-March.

The research revealed a previously hidden spread of the virus that might have been detected if aggressive testing programs had been put in place.

Sophisticated computer programs can then figure out how all of those mutations arose as viruses descended from a common ancestor. If they get enough data, they can make rough estimates about how long ago those ancestors lived. That’s because mutations arise at a roughly regular pace, like a molecular clock.

In January, as the scope of the catastrophe in China became clear, a few countries started an aggressive testing program. They were able to track the arrival of the virus on their territory and track its spread through their populations.

As new cases arose in other parts of the country, other researchers set up their own pipelines. The first positive test result in New York came on March 1, and after a couple of weeks, patients surged into the city’s hospitals.

“I thought, ‘We need to do this for New York,’” Dr. Heguy said.

Dr. Heguy and her colleagues found some New York viruses that shared unique mutations not found elsewhere. “That’s when you know you’ve had a silent transmission for a while,” she said.

Dr. Heguy estimated that the virus began circulating in the New York area a couple of months ago.

And researchers at Mount Sinai started sequencing the genomes of patients coming through their hospital. They found that the earliest cases identified in New York were not linked to later ones.

“Two weeks later, we start seeing viruses related to each other,” said Ana Silvia Gonzalez-Reiche, a member of the Mount Sinai team.

Dr. Gonzalez-Reiche and her colleagues found that these viruses were practically identical to viruses found around Europe. They cannot say on what particular flight a particular virus arrived in New York. But they write that the viruses reveal “a period of untracked global transmission between late January to mid-February.”

So far, the Mount Sinai researchers have identified seven separate lineages of viruses that entered New York and began circulating. “We will probably find more,” Dr. van Bakel said.

Sidney Bell, a computational biologist working with the Nextstrain team, cautions people not to read too much into these new mutations themselves. “Just because something is different doesn’t mean it matters,” Dr. Bell said.

Mutations do not automatically turn viruses into new, fearsome strains. They often don’t bring about any change at all. “To me, mutations are inevitable and kind of boring,” Dr. Bell said. “But in the movies, you get the X-Men.”

Peter Thielen, a molecular biologist at the Johns Hopkins Applied Physics Laboratory, likes to think of the spread of viruses like a dandelion seed landing on an empty field.

The flower grows up and produces seeds of its own. Those seeds spread and sprout. New mutations arise over the generations as the dandelions fill the field. “But they’re all still dandelions,” Mr. Thielen said.

While the coronavirus mutations are useful for telling lineages apart, they don’t have any apparent effect on how the virus works.

That’s good news for scientists working on a vaccine.

Vaccine developers hope to fight Covid-19 by teaching our bodies to make antibodies that can grab onto the virus and block its entry into cells.



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