Post by Admin on Apr 10, 2020 8:20:22 GMT
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.
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,” Dr. Heguy said.
A few cases came to light starting at the end of January. But it was easy to dismiss them as rare imports that did not lead to local outbreaks.
The illusion was dashed at the end of February by Trevor Bedford, an associate professor at the Fred Hutchinson Cancer Research Center and the University of Washington, and his colleagues.
Using Nextstrain, they showed that a virus identified in a patient in late February had mutation shared by one identified in Washington on Jan. 20.
The Washington viruses also shared other mutations in common with ones isolated in Wuhan, suggesting that a traveler had brought the coronavirus from China.
With that discovery, Dr. Bedford and his colleagues took the lead in sequencing coronavirus genomes. Sequencing more genomes around Washington gave them a better view of how the outbreak there got started.
“I’m quite confident that it was not spreading in December in the United States,” Dr. Bedford said. “There may have been a couple other introductions in January that didn’t take off in the same way.”
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.
The coronavirus genomes are also revealing hints of early cross-country travel.
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.
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.”
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,” Dr. Heguy said.
A few cases came to light starting at the end of January. But it was easy to dismiss them as rare imports that did not lead to local outbreaks.
The illusion was dashed at the end of February by Trevor Bedford, an associate professor at the Fred Hutchinson Cancer Research Center and the University of Washington, and his colleagues.
Using Nextstrain, they showed that a virus identified in a patient in late February had mutation shared by one identified in Washington on Jan. 20.
The Washington viruses also shared other mutations in common with ones isolated in Wuhan, suggesting that a traveler had brought the coronavirus from China.
With that discovery, Dr. Bedford and his colleagues took the lead in sequencing coronavirus genomes. Sequencing more genomes around Washington gave them a better view of how the outbreak there got started.
“I’m quite confident that it was not spreading in December in the United States,” Dr. Bedford said. “There may have been a couple other introductions in January that didn’t take off in the same way.”
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.
The coronavirus genomes are also revealing hints of early cross-country travel.
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.
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.”