A small update on genomic epidemiology of the #COVID19 epidemic in Washington State (where we have lots of data) and elsewhere in the US (where data is sparse). 1/8
By sequencing the genome of the #SARSCoV2 / #HCoV19 virus, we can see which infections are connected to which other infections. See here for background nextstrain.org/help/general/h… and @nextstrain nextstrain.org/ncov for latest analysis. 2/8
Thanks to sequencing by @UWVirology, @CDCgov and @seattleflustudy we have genomes for 39 viruses sampled from WA. Importantly 35 of these 39 viruses (90%) fall into a single genetic cluster indicating a single ~Jan introduction from China and subsequent local spread. 3/8 
The other four viruses appear as one-off introductions of either immediate travel cases, or as recent steps in a newly arrived transmission chain. Given genetic proximity, these appear to be related to viruses from Europe and Iran. 4/8
Thus, for WA state new introductions from outside the US appear to be driving many fewer new infections than local transmission. 5/8
Other states have fewer recently sequenced viruses. NY has two, one with direct travel history to Iran (and which has a genome consistent with this travel history) and another that appears to be a recent travel introduction from Europe. 6/8
San Diego County has a virus that appears to be a recent introduction from Europe, and besides the two Grand Princess-associated cases, the remaining genome from Minnesota also appears to be a recent European import clustering closely with viruses sampled in the Netherlands. 7/8
I don't know exactly how to square the finding of a large community cluster in Washington State with these 4 apparently recently introduced viruses in other states. My strong suspicion is that more sequencing will reveal growing community clusters elsewhere in the US as well. 8/8
