The New York Times looks at two different batches of genetic data which both indicate that shutting down travel from China didn’t actually affect the spread of the virus in New York, since that strain almost definitely arrived in the Big Apple from Europe:
“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.
People were just oblivious,” said Adriana Heguy, a member of the N.Y.U. team.
Dr. Heguy and Dr. van Bakel belong to an international guild of viral historians. They ferret out the history of outbreaks by poring over clues embedded in the genetic material of viruses taken from thousands of patients.
Viruses invade a cell and take over its molecular machinery, causing it to make new viruses.
The process is quick and sloppy. As a result, new viruses can gain a new mutation that wasn’t present in their ancestor. If a new virus manages to escape its host and infect other people, its descendants will inherit that mutation.
Tracking viral mutations demands sequencing all the genetic material in a virus — its genome. Once researchers have gathered the genomes from a number of virus samples, they can compare their mutations.
Maciej Boni of Penn State University and his colleagues recently used this method to see where the coronavirus, designated SARS-CoV-2, came from in the first place. While conspiracy theories might falsely claim the virus was concocted in a lab, the virus’s genome makes clear that it arose in bats.
The most closely related coronavirus is in a Chinese horseshoe bat, the researchers found. But the new virus has gained some unique mutations since splitting off from that bat virus decades ago.
In January, a team of Chinese and Australian researchers published the first genome of the new virus. Since then, researchers around the world have sequenced over 3,000 more. Some are genetically identical to each other, while others carry distinctive mutations.
As new genomes come to light, researchers upload them to an online database called GISAID. A team of virus evolution experts are analyzing the growing collection of genomes in a project called Nextstrain. They continually update the virus family tree.
The deepest branches of the tree all belong to lineages from China. The Nextstrain team has also used the mutation rate to determine that the virus probably first moved into humans from an animal host in late 2019.
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.