The new coronavirus began spreading in New York weeks before the first confirmed case and came to the area via travelers from Europe, not China, new research suggests.
Two separate teams of scientists studying the genetics of the SARS-CoV-2 virus in the region came to similar conclusions: People were spreading the virus in New York as early as late January, before more widespread testing began, and it came mostly from Europe, not Asia.
“We know with certainty that these were coming from European strains,” Adriana Heguy, director of the Genome Technology Center at NYU Langone Health, told USA TODAY.
Harm van Bakel, a geneticist at Icahn School of Medicine at Mount Sinai, told the New York Times: “The majority is clearly European.”
The teams, whose research is still in early stages, looked at genomes of the virus taken from different groups of patients beginning in mid-March and found community spread of the virus before then.
The first case of the new coronavirus confirmed in New York came March 1. More than a month earlier President Donald Trump said he would increase restrictions on traveling from China. But it wasn’t until March 11 that Trump said he was restricting travel from Europe.
In New York, more than 7,000 people have died due to complications from COVID-19, Gov. Andrew Cuomo said Thursday. Almost 150,000 people have confirmed positive tests for the virus, according to the state’s health department.
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As a researcher, Heguy normally focuses on other diseases like cancer and cardiovascular disease. She said she was looking at work done on sequencing the virus from the University of Washington in Seattle when she got a call from her colleague, Matthew Maurano.
“It’s obvious that this is going to explode and we have no idea where all of these strains are coming from,” Heguy said she thought one morning. “The same morning, (Maurano) picks up the phone … and he said, ‘Adriana, I think we need to jump on this thing immediately.'”
The first patient NYU Langone team studied had no travel history, indicating they were infected by someone in the community. When Heguy and Maurano compared the genetic data of the virus from that patient to other’s in an international database, it was clear that strain came from England.
“That our first case was community acquired gave us the hint that of course this has been going around for a while and it was just undetected because there was no testing happening before,” Heguy said.
Since then, the team has tested more than 90 samples and counting from the New York area to better track from which strain of the virus the region’s cases are originating.
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Heguy and the team have pinpointed strains originating from European countries, including France, Austria and the Netherlands, in two-thirds of the patients they’ve conducted genetic sequencing of the virus. Other strains have come from countries in Asia and the West Coast of the U.S., but taken with the results from the Mount Sinai research, Heguy said it’s clear that New York’s outbreak largely originated from European strains.
The team has also shared its data and relied on results from scientists around the world to determine where the strains are originating through GISAID and Nextstrain, which are building a database and phylogenetic tree of the virus.
As the coronavirus passes from one person to another, it can mutate, or change its genetic information slightly, Heguy said. By tracking those mutations, scientists are able to locate from what region that strain of the virus originated.
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The Mount Sinai study looked at 90 SARS-CoV-2 genomes from 84 confirmed COVID-19 cases in its health system in New York and found “multiple, independent but isolated introductions mainly from Europe and other parts of the United States from January through early March 2020,” the researchers wrote.
Van Bakel told the Times that his team identified seven distinct lineages of the virus circulating in New York.
“We will probably find more,” he added.
Without early testing and then sequencing of the virus, though, public health officials weren’t able to know where the virus was coming from and who could be at risk before it grew to its current levels, Heguy said.
“Every single case of strange pneumonias here in New York, they could have been testing earlier and then do immediately the contact tracing,” she said.
Heguy said continuing to collect data and build out a larger sample size will be a next step in the research. Scientists are also hoping to understand the clinical implications of the different strains of the virus. Sequencing the virus’ genetic information now will also help in case a second wave were to occur, she said.
“We want to be ready with all the sequences and the mutations in terms of when there’s a second wave so that we can effectually do surveillance,” Heguy said.
Follow USA TODAY’s Ryan Miller on Twitter @RyanW_Miller