One of the most powerful aspects of genomic data for #COVID19 is the ability to make connections between seemingly disparate outbreaks. This is a thread describing one such possible connection. Please keep in mind this is only a hypothesis and not proven fact. 1/9
Thanks to rapid work by @UWVirology and @seattleflustudy we now have 13 #HCoV19 genomes from Washington State. All 12 of the genomes from community cases have grouped into an emerging outbreak clade. 2/9
This figure shows the genetic relationships among these viruses, where all the WA viruses are closely related. Given this shared ancestry pattern, it looks like the large majority of current cases in WA derive from a single introduction event. nextstrain.org/ncov?label=cla… 3/9 
I believe this introduction event was likely mid-Jan (bedford.io/blog/ncov-cryp…), but even if it wasn't WA1 that introduced the virus, this level of genetic diversity alongside frequent positive specimens () argues for a sizable outbreak. 4/11
Another indication of outbreak size is seeing offshoots of an outbreak arrive elsewhere in the world. For example, international travel cases were an early indication of how sizable the outbreak in Wuhan really was (). 5/11
Absolutely stellar work by @cychiu98 at @UCSF alongside @CAPublicHealth has revealed a community case in California which may have been acquired on the Grand Princess cruise ship in Feb. 6/11
The virus "CA-CDPH-UC1" appears to nest within genetic diversity of the Washington State outbreak. This suggests a scenario in which an individual infected in WA travelled to California / Grand Princess and instigated a chain of transmission that led to this case. 7/11
The exact circumstances of this possible transmission from WA to CA cannot be known from the genetic data alone. But the occurrence of spread from WA to CA is another indicator of the size of the WA outbreak. 8/11
That said, given that we still only have the one transmission chain and a putative origin in mid-Jan, our best estimate for the number of active infections remains as described here: 9/11
We're doing our best to dial in these numbers for WA and @cychiu98 and @CAPublicHealth are actively investigating the genomics of cases on board the Grand Princess. More to follow. 10/11
Huge thanks to @cychiu98, @CAPublicHealth @UCSF for this important finding. And also thanks to the folks in WA: @debnick60, @mjonasrieder, @HelenChuMD, @lea_starita, @JShendure, @famulare_mike, @KiraNewmanMDPhD, @trs, @databae_, @pavitrarc, @GreningerLab 11/11
