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Follow the World Health Organization's instructions to reduce your risk of infection. Avoid the three Cs: Crowded places, Close Contact Settings & Confined spaces. Airborne aerosols play an important role in transmitting COVID-19.

- Avoid crowded places and limit time in enclosed spaces

- Apply social distance

- Air rooms by opening windows & doors

- Keep hands and surfaces clean, cover coughs & sneezes

- Wear a mask when you are not at home or when physical distancing is not possible

Trevor Bedford
+ Your AuthorsArchive @trvrb Scientist @fredhutch, studying viruses, evolution and immunity. Collection of #COVID19 threads here: bedford.io/misc/twitter/ May. 12, 2020 2 min read

We now have enough #SARSCoV2 genomic data from different states to make some broad conclusions about how the #COVID19 epidemic has unfolded in the US. 1/14

We see a spectrum where some states had single (early) introductions that fueled the majority of the epidemic, while in others the epidemic appears to be driven by a larger number of separate introductions. 2/14

This analysis shows relationships from sequencing viral genomes. The main thing to pay attention to is how cases (dots colored by state) cluster. Patches of cases from the same state indicate local transmission. All figures from @nextstrain:  https://nextstrain.org/ncov/north-america?c=division&f_country=USA&r=division  3/14

These analyses depend on comparison of sequenced viruses and so equitable sampling over geography and time is necessary to make reliable conclusions. This sampling has improved recently, but there are still gaps in sequencing and caution in interpretation is warranted. 4/14

If we look at New York, we see that most infections appear to derive from an introduction from Europe in mid-February (node on the tree labeled "NY"). This introduction rapidly grew to a substantial epidemic focused in NYC, but frequently introduced to other locations. 5/14

While if we look at Washington we see an introduction of a lineage from China that drove much of the early outbreak, but then multiple introductions from the NY clade fueling further transmission chains in March. 6/14

California is interesting in that like WA, much of the outbreak is fueled by an early introduction of a lineage from Asia and then later cases derived from repeated introductions from elsewhere in the US. 7/14

Contrast this with Wisconsin, in which the outbreak appears driven by a large number of separate introductions from elsewhere in the US and Europe. It lacks the early successful introduction seen in NY, WA and CA. 8/14

Louisiana has a remarkably focused outbreak in which most sequenced cases appear to derive from a couple closely related introduction events. This outbreak nests within the genetic diversity seen in NY suggesting a possible transmission route. 9/14

Part of the Texas outbreak groups closely with this clade from LA, while other samples from Texas reveal a large number of separate introductions to the state. 10/14

Overall, we see substantial mixing of transmission chains across states. This mixing largely occurred during Feb and early March. I'd expect moving forward for there to be more geographically focused transmission chains given reduced travel in the US. 11/14

I see continued genetic sequencing as potentially illuminating sources of infection and whether further cases within a state are largely the result of local transmission or of repeated introductions from outside the state. 12/14

These inferences are the result of rapid sequencing and sharing by a large number of groups. A huge thank you to @GISAID, @mason_lab, @HealthNYGov, @nyulangone, @MountSinaiNYC, @KATarinambraun, @GageKMoreno, @tcflab, @dho_lab, @PKennyLab, @gundersenhealth, @Tulane, 13/14

@MiGScenter, @AmyFeehan3, @OchsnerHealth, @czbiohub, @cychiu98, @K_G_Andersen, @scrippsresearch, @gkay92, @MethodistHosp, @HMethodistMD, @UWVirology, @seattleflustudy and many others. 14/14


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