In a new study, researchers combined evolutionary genomics from coronavirus samples with computer-simulated epidemics and detailed travel records to reconstruct the spread of COVID-19 across the world in unprecedented detail.
They found an extended period of missed opportunity when intensive testing and contact tracing might have prevented COVID-19 from becoming established in North America and Europe.
The study also challenges suggestions that linked the earliest known cases of COVID-19 on each continent in January to outbreaks detected weeks later.
The research was conducted by a team at the University of Arizona and elsewhere.
The team based their analysis on results from viral genome sequencing efforts, which began immediately after the virus was identified.
These efforts quickly grew into a worldwide effort unprecedented in scale and pace and have yielded tens of thousands of genome sequences, publicly available in databases.
Contrary to widespread narratives, the first documented arrivals of infected people traveling from China to the U.S. and Europe did not snowball into continental outbreaks, the researchers found.
Instead, swift and decisive measures aimed at tracing and containing those initial incursions of the virus were successful and should serve as model responses directing future actions and policies by governments and public health agencies.
So how did the virus arrived in the U.S. and Europe?
A Chinese national flying into Seattle from Wuhan, China on Jan. 15 became the first patient in the U.S. shown to be infected with the novel coronavirus and the first to have a SARS-CoV-2 genome sequenced.
This patient was designated ‘WA1.’ It was not until six weeks later that several additional cases were detected in Washington state.
The team tested the prevailing hypothesis suggesting that patient WA1 had established a transmission cluster that went undetected for six weeks.
Although the genomes sampled in February and March share similarities with WA1, they are different enough that the idea of WA1 establishing the ensuing outbreak is very unlikely, they determined.
The researchers’ findings indicate that the jump from China to the U.S. likely occurred on or around Feb. 1 instead.
The results also put to rest speculation that this outbreak, the earliest substantial transmission cluster in the U.S., may have been initiated indirectly by dispersal of the virus from China to British Columbia, Canada, just north of Washington State, and then spread from Canada to the U.S.
Multiple SARS-CoV-2 genomes published by the British Columbia Center for Disease Control appeared to be ancestral to the viral variants sampled in Washington State, strongly suggesting a Canadian origin of the U.S. epidemic.
However, the present study revealed sequencing errors in those genomes, thus ruling out this scenario.
Instead, the new study implicates a direct-from-China source of the U.S. outbreak, right around the time the U.S. administration implemented a travel ban for travelers from China in early February.
The nationality of the “index case” of the U.S. outbreak cannot be known for certain because tens of thousands of U.S. citizens and visa holders traveled from China to the U.S. even after the ban took effect.
A similar scenario marks the first known introduction of coronavirus into Europe.
On Jan. 20, an employee of an automotive supply company in Bavaria, Germany, flew in for a business meeting from Shanghai, China, unknowingly carrying the virus, ultimately leading to the infection of 16 co-workers.
In that case, too, an impressive response of rapid testing and isolation prevented the outbreak from spreading any further, the study concludes.
Contrary to speculation, this German outbreak was not the source of the outbreak in Northern Italy that eventually spread widely across Europe and eventually to New York City and the rest of the U.S.
The researchers also show that this China-to-Italy-US dispersal route ignited transmission clusters on the East Coast slightly later in February than the China-to-US movement of the virus that established the Washington State outbreak.
The Washington transmission cluster also predated small clusters of community transmission in February in California, making it the earliest anywhere in North America.
The team says intensive interventions, involving testing, contact tracing, isolation measures, and a high degree of compliance of infected individuals, who reported their symptoms to health authorities and self-isolated in a timely manner, helped Germany and the Seattle area contain those outbreaks in January.
To reconstruct the pandemic’s unfolding, the scientists ran computer programs that carefully simulated the epidemiology and evolution of the virus, in other words, how SARS-CoV-2 spread and mutated over time.
Other methods were then combined with the data from the virtual epidemics, yielding exceptionally detailed and quantitative results.
The research shows that when people do early intervention and detection well, it can have a massive impact, both on preventing pandemics and controlling them once they progress.
While the epidemic eventually slipped through, there were early victories that show the way forward: Comprehensive testing and case identification are powerful weapons.
One author of the study is Michael Worobey.
The study is published in Science.
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