Coronavirus: How Did It Get to the West?

Combining virus genomics with epidemiologic simulations and travel records offers some clues.

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Photo by Louis Maniquet on Unsplash

In late 2019 we saw the emergency of SARS-CoV-2 (the cause of COVID019), setting off a global pandemic linked to more than 900,000 deaths globally. Following the initial outbreak in China’s Hubei province, the virus spread worldwide, prompting isolation, contract tracing, and travel restrictions.

I live in the Seattle area, the site of the first outbreak in the United States. Indeed, I work at the hospital that had the first significant outbreak in the USA. A traveler had returned from the disease epicenter (Wuhan, China) on January 15, 2020.

Now comes a new and exciting study that combines genomics from coronavirus with detailed travel records and computer simulations of epidemics. Researchers aim to reconstruct, in sufficient detail, the spread of the virus across the globe. How did the pandemic develop in space in time?

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The novel coronavirus, Covid-19. Photo by CDC on Unsplash

University of Arizona researcher Michael Worobey led scientists from 13 institutions in North American and Europe. They based their analysis on viral genome sequencing findings, ones that are available to the general public.

Did the first arrivals of affected individuals traveling from Chia to the USA and Europe explode into outbreaks across the continent? No, instead, public health officials controlled the disease via tracing and containment. Now, back to that first Washington state patient, “WA1.” He became the first in the USA to have sequencing of his SARS-CoV-2 genome.

Researchers soon understood that he was not the only case — several cases developed in the state, genetically similar to the virus of WA1. Remarkably, however, the genome sequences of these subsequent cases appeared different from WA1. The study authors conclude that the viral jump from China to the US probably occurred around February 1.

Can we blame our Canadian neighbors? No.

The answer appears to be no. The researchers found that the Canadian viral genomes were not ancestral to our Washington state ones. The new study points to China to USA direct transmission. Across the pond, a similar scenario unfolded. On January 20, a German gentleman returned from a business trip in Shanghai, China, unwittingly transporting the virus to Bavaria. Rapid testing and isolation proved successful. The German outbreak did not serve as the seed for the explosion in Northern Italy that soon enveloped Europe before heading to New York City.

How did it spread? Using computer simulations

Testing, contact tracing, and isolation (along with quarantining of affected individuals) enabled Seattle and Germany to contain the early outbreaks in January this year. Riffing on that observation, the scientists created computer simulations of the epidemiology and evolution of the virus.

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Seattle. Photo by Ben Dutton on Unsplash

Did WA1 start the outbreak in Washington state? If we believe the answer is yes, let’s run that epidemic through the simulator repeatedly. When we sample patients, and the viral genome is analyzed, do we see the simulator’s patterns match real-life findings?

It turns out that WA1 did not serve as the seed for the local outbreak. The investigators found similarly for European episodes: German patient #1 did not seed the Italy cluster of cases. Molecular epidemiology is an excellent tool for discovering SARS-CoV-2 transmission patterns.

I find it fascinating that we can use the viral family tree, detailed travel histories, and simulations to understand how the novel coronavirus spread so quickly worldwide. Early intervention appears to have had great success in limiting the disease, but eventually, it slipped through.

Written by

I have degrees from Harvard, Yale, and Penn. I am a radiation oncologist in the Seattle area. You may find me regularly posting at

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