SNOHOMISH CASE - gene sequencing The team at the @seattleflustudy have sequenced the genome the #COVID19 community case reported yesterday from Snohomish County, WA, and have posted the sequence publicly to http://gisaid.org. There are some enormous implications here.
This case, WA2, is on a branch in the evolutionary tree that descends directly from WA1, the first reported case in the USA sampled Jan 19, also from Snohomish County, viewable here: https://nextstrain.org/ncov?f_division=Washington.
This strongly suggests that there has been cryptic transmission in Washington State for the past 6 weeks.
It's possible that this genetic similarity is a coincidence and these are separate introductions. However, I believe this is highly unlikely. The WA1 case had a variant at site 18060. This variant is only present in 2/59 viruses from China.
I'd assess the p-value for this coincidence at 2/59=0.03 and so is statistically significant. Additionally, these two cases are geographically proximal, both residing in Snohomish County.
I believe we're facing an already substantial outbreak in Washington State that was not detected until now due to narrow case definition requiring direct travel to China.
We will be working closely with @KCPubHealth and @WADeptHealth to investigate the full extent of the outbreak.
We're hoping to update soon with better estimates of the number of infections in Washington State using available data.
Thank you to the @seattleflustudy team, and particularly to @lea_starita, for exceptionally fast turnaround from diagnostic assay at @WADeptHealth to sequenced genome.
An update, because I see people overly speculating on total outbreak size. Our best current expectation is a few hundred current infections. Expect more analyses tomorrow.
https://twitter.com/trvrb