Most New York Coronavirus Cases Came From Europe, Genomes Show - The New York Times - 0 views
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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.
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The research revealed a previously hidden spread of the virus that might have been detected if aggressive testing programs had been put in place.
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It would not be until late February that Italy would begin locking down towns and cities, and March 11 when Mr. Trump said he would block travelers from most European countries. But New Yorkers had already been traveling home with the virus.
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While conspiracy theories might falsely claim the virus was concocted in a lab, the virus’s genome makes clear that it arose in bats.
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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.
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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.
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already, the genomes of the virus are revealing previously hidden outlines of its history over the past few months.
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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.
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Dr. Boni said that ancestral virus probably gave rise to a number of strains that infected horseshoe bats, and perhaps sometimes other animals.
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It’s entirely possible, Dr. Boni said, in the past 10 or 20 years, a hybrid virus arose in some horseshoe bat that was well-suited to infect humans, too. Later, that virus somehow managed to cross the species barrier.
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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.
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Dr. Boni and his colleagues found that the genome of the new virus contains a number of mutations in common with strains of coronaviruses that infect bats.
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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.
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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.
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But the United States fumbled in making its first diagnostic kits and initially limited testing only to people who had come from China and displayed symptoms of Covid-19.“It was a disaster that we didn’t do testing,”
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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.
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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,”
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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,”
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Dr. Gonzalez-Reiche and her colleagues found that these viruses were practically identical to viruses found around Europe.
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hey write that the viruses reveal “a period of untracked global transmission between late January to mid-February.”
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Dr. van Bakel and his colleagues found one New York virus that was identical to one of the Washington viruses found by Dr. Bedford and his colleagues. In a separate study, researchers at Yale found another Washington-related virus. Combined, the two studies hint that the coronavirus has been moving from coast to coast for several weeks.
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While the coronavirus mutations are useful for telling lineages apart, they don’t have any apparent effect on how the virus works.
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Some viruses evolve so quickly that they require vaccines that can produce several different antibodies. That’s not the case for Covid-19. Like other coronaviruses, it has a relatively slow mutation rate compared to some viruses, like influenza.