The Genetic Evolutionary Tree of the US COVID Outbreak

Some new and very interesting information from the Bedford Lab in Washington State. I’ve mentioned Bedford’s work a few times. He runs a research lab at the Fred Hutchinson Center where he studies viral genomes. It was his work that initially revealed that in late February that COVID19 had been spreading in Washington state for some six weeks. He just posted another Twitter thread in which he says there is now a critical mass of genomic sequencing data from different parts of the United States and the world that allows us to construct a preliminary map of how the disease spread across the United States.

Was there a single patient zero from whom the US epidemic originated or were there multiple separate introductions from different parts of the world? Or what was the mix of the two?

The key findings largely match expectations and some points have been revealed in individual studies which have already received press attention. The disease was introduced early from China in Washington State and California. These early introductions were then compounded with follow-on introductions from outside. The virus was introduced to New York not from China but from Europe. The outbreak started mid-February and grew rapidly and spread from there to other parts of the country. Some other states had highly focused introduction points (Louisiana) and other seemed to be seeded from multiple places.

With these studies it is important to remember that as in all history, viral genomic history is written by the winning viruses. It’s entirely possible – indeed it seems very probable given the scale of international travel – that COVID was introduced earlier to New York directly from China. But for whatever reason it didn’t take hold or didn’t effectively propagate itself. A mid-February introduction from Europe must have been connected to a super-spreading event which allowed it to take hold, flourish and – if recent antibody studies are broadly accurate – infect more than 1.5 million New York City residents in about ten weeks.

You can see Bedford’s Twitter thread starting here and a detailed interactive map of the genomic evolution and geographical spread here at the NextStrain website.

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