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Researchers track how COVID-19 infiltrated California, spread in Bay Area communities

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SAN FRANCISCO, Calif. (KRON) — COVID-19 researchers have traced how the coronavirus originally infiltrated Northern California and then began spreading through communities.

“Transmission of (coronavirus) in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage,” a manuscript of the study released this week states.

For the study, virus genomes were sampled from 29 patients diagnosed with COVID-19 infection, between Feb. 3-March 15. “Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state,” the study says.

The study was conducted by researchers and data from the University of California San Francisco, the CDC, the California Department of Public Health, and the Santa Clara Public Health Department. One key researcher is microbiologist Charles Chiu, an infectious disease specialist who has been toiling away inside UCSF’s Viral Diagnostics and Discovery Center ever since the COVID-19 pandemic broke out.

The study concluded that rapid testing, contact tracing, social distancing, and travel restrictions will help flatten the curve in California, and keep it from spiking out of control.

“I am cautiously optimistic that Governor Gavin Newsom and Mayor London Breed’s foresightful “shelter-in-place” policies may have helped to flatten the curve,” Chiu said.

If Californians continue to stay home and follow shelter-in-place orders, “We can avoid what is devastating my colleagues and friends in New York right now,” Chiu said.

California’s stay-at-home order has been extended through May 3.

Twenty-four hours a day, a genetic sequencing machine is running inside Chiu’s laboratory at UCSF. The machine is sequencing genomes of viruses that have infected COVID-19 patients around the Bay Area. When a virus spreads as rapidly as the coronavirus, speed is crucial to saving lives. Luckily, this machine, the NextSeq 550, is one of the fastest of its kind.

“We will be running this 24 hours a day. I see no reason why we can’t sequence the genomes of every case,” Chiu told the San Francisco Chronicle.

The first confirmed case of coronavirus in the United States occurred in Washington state. A man who lives near Seattle traveled to Wuhan, China at the same time people were mysteriously becoming ill with a pneumonia-like illness there. The man was not diagnosed with COVID-19 until after he had already returned home to Washington.

Chiu found a link between Washington’s strain and the strain that infected passengers on the Grand Princess cruise ship as it voyaged from San Francisco to Mexico.

covid plane
(Getty Images) – Medical Personnel help load passengers from the Grand Princess cruise ship onto airplanes in Oakland, on March 10.

The study says, “Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington state, including the WA1 genome representing the first reported case in the United States on January 19.”

A different strain that made its way into California infected a San Benito County resident who had recently traveled to China.

“Until late Feb 2020, the majority of infections identified in the United States were related
to travelers returning from high-risk countries, repatriated citizens under quarantine, or close
contacts of infected patients,” the study found.

A recent model released by the Institute for Health Metrics and Evaluation at the University of Washington projects the number of COVID-19 cases and deaths throughout the United States. The model projects California will reach its peak of COVID-19 cases by April 26. The study also predicts California will have an estimated 4,306 total deaths due to COVID-19 by Aug. 4.

MORE: California COVID-19 cases to peak by Apr. 26, study predicts

Researchers said now that the virus exists in every San Francisco Bay Area county, the most important factor to flatten California’s curve is social distancing.

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