Genetic sleuths flesh out the story of how coronavirus got its start in Washington

An epidemiological “family tree” shows how different strains of the coronavirus that causes COVID-19 spread out across different regions of the world. The red circle highlights WA1, the first confirmed case reported in Washington state and the United States. Click on the image for a larger view. (Nextstrain Graphic)

Detailed genetic analyses of the strains of virus that cause COVID-19 suggest that the outbreak took hold in Washington state in late January or early February, but went undetected for weeks.

That’s the upshot of two studies published by the journal Science, based on separate efforts to trace the genetic fingerprints of the coronavirus known as SARS-CoV-2.

The studies draw upon analyses of more than 10,000 samples collected in the Puget Sound region as part of the Seattle Flu Study during the early weeks of the outbreak, plus thousands more samples from other areas of the world.

One of the studies was conducted by a team including Trevor Bedford, a biologist at Seattle’s Fred Hutchinson Cancer Research Center who has been issuing assessments of the virus and its spread since the earliest days of the outbreak. The first version of the team’s paper went online back in March and was revised in May, months in advance of today’s peer-reviewed publication.

The other study comes from researchers led by the University of Arizona’s Michael Worobey, who also published a preliminary version of their results in May.

There are subtle differences between the two analyses. For example, Bedford and his colleagues say it’s most likely that the majority of the infections in Washington state arose from a single case that was introduced in late January or early February.

Worobey’s team, however, suggests multiple travelers returning from China during that time frame may have brought the virus to Washington and California.

Transmission map — This schematic map shows early and apparently “dead-end” introductions of SARS-CoV-2 to Europe and the U.S. (dashed arrows). Successful dispersals between late January and mid-February are shown with solid arrows: from Hubei Province, China, to Northern Italy; from China to Washington state; and later, from Europe (as the Italian outbreak spread more widely) to New York City and from China to California. (Credit: Andrew Rambaut / University of Edinburgh and Jeffrey Joy / University of British Columbia)

Bedford and his colleagues say there’s not yet enough evidence to rule out the hypothesis that the community spread of coronavirus started with the first reported case, known as WA1, which dates to Jan. 19. But the other team’s analysis, which involved running simulations of the virus’ spread, argues against that scenario.

Worobey and his colleagues also argue against the possibility that the virus came to Washington state via British Columbia, which was an alternate scenario suggested by the data. Instead, they say it’s more likely that the virus made the jump directly from China.

At the time, foreign travelers were barred from coming to the U.S. from China, but tens of thousands of U.S. citizens and visa holders continued to make the trip even after the ban took effect. Worobey and his co-authors say a similar scenario led to separate introductions of the virus to the U.S. East Coast from China via Europe.

Both studies suggest that closer surveillance of COVID-19 cases, based on the model established by the Seattle Flu Study, could have lessened the impact of the pandemic in the U.S. But in a news release, Worobey said there’s a silver lining to the researchers’ gloomy conclusions.

“Our research shows that when you do early intervention and detection well, it can have a massive impact, both on preventing pandemics and controlling them once they progress,” Worobey said. “While the epidemic eventually slipped through, there were early victories that show us the way forward: Comprehensive testing and case identification are powerful weapons.”

Trevor Bedford, Alex Greninger, Pavitra Roychoudhury, Lea Starita and Michael Famulare are the lead authors of “Cryptic Transmission of SARS-CoV-2 in Washington State.” Jay Shendure and Keith Jerome are the senior authors — and there are scores of co-authors, including investigators with the Seattle Flu Study.

In addition to Worobey, the authors of “The Emergence of SARS-CoV-2 in Europe and North America” include Jonathan Pekar, Brendan Larsen, Martha Nelson, Verity Hill, Jeffrey Joy, Andrew Rambaut, Marc Suchard, Joel Wertheim and Philippe Lemey.

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