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Early transmission SARS-CoV-2 reconstructed using genomics

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News of infections caused by a new coronavirus and the daily use of the names SARS-CoV-2 and COVID-19, became widespread around February. But the question of how long the virus was already present in the United States before this time has remained unknown. Now, a team of researchers has reconstructed some of the earliest transmissions of the virus. By analyzing the genomic sequences of SARS-CoV-2 samples from infected patients in Washington state, they suggest that most early SARS-CoV-2 infections stem from a single entry in late January or early February, causing the rapid transmission of the virus to the community went undetected for several weeks before this spread of the community became apparent.

This work has been published in science on paper, Covert transmission of SARS-CoV-2 in the state of Washington.

The team, led by Trevor Bedford, PhD, associate professor of vaccines and infectious diseases at Fred Hutch and colleagues at the University of Washington in Seattle, analyzed the genetic sequences of 453 SARS-CoV-2 genomes from the Washington State blast assembled between 19 January and 15 March.

The first confirmed case of SARS-CoV-2 in the United States was identified in Washington state on Jan. 19 in an individual returning from Wuhan. The team genomic analysis revealed that 84% of the genomes in their study fall into a group closely related to the first case. This group is called the Washington State outbreak and is derived from viruses circulating in China. The authors wrote that the Washington State eruption has a very comb-like structure, indicative of rapid exponential growth.

The findings also suggest that most of the early SARS-CoV-2 cases in the state came from a single introduction of the virus, probably between January 22nd and February 10th.

The first case of community outbreak was discovered on 28 February. To better understand the chain of transmission that led him, Bedford and colleagues analyzed more than 10,000 specimens collected as part of the Seattle Flu Study between January 1 and March 15. They found evidence for SARS-CoV-2 a few days before the first previously reported community case in Washington. Refining the time and geographical origin of entry into the state of Washington will require a combination of previous samples and samples from other geographic locations, the authors said.

They also noted that other states in the United States have shown different genetic histories from the State of Washington, with a majority of SARS-CoV-2 sequences from New York and Connecticut clustered within European lines, for example.

In addition to the 384 viruses from the State of Washington identified in the Washington State outbreak, they observed 12 viruses from elsewhere, including California, Connecticut, Minnesota, New York, North Carolina, Virginia, Utah, Australia and the Grand Cruise Ship. Princess.

The authors wrote that in January and February, the screening for SARS-CoV-2 in the United States was aimed at travelers with fever, cough, and shortness of breath, with the starting point expanding after new outbreaks were identified but specifying travel to China until on February 24th. Their analysis shows that at least one plaque of SARS-CoV-2 had been circulating in the Seattle area for 36 weeks at the time the virus was first detected in a non-traveler on February 28th. Until then, variants within this category accounted for the majority of confirmed infections in the region (84%). Several factors may have contributed to the delayed detection of the alleged community outbreak, including limited testing among non-travelers or the presence of asymptomatic or mild illness.

Their results highlight the critical need for extensive oversight of SARS-CoV-2 transmission in the community, even after the pandemic is brought under control, the authors said. They noted that several factors may have contributed to the delayed detection of the alleged community outbreak in Washington, including limited testing among non-travelers.

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