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There is a lot of Twitter chatter surrounding a rumor that circulation of #COVID19 in California in fall 2019 has resulted in herd immunity. This is empirically not the case. COVID-19 was first introduced into the USA in Jan/Feb 2020. 1/18
We have a couple good sources of evidence here: (1) direct testing of @seattleflustudy samples collected in Jan and Feb 2020 and (2) phylogenetic evidence showing genetic relationships of sequenced viruses. 2/18
For (1), the @seattleflustudy has gone back and tested retrospective samples collected between Jan 1 and March 10 in our research assay. These samples were collected as part of our study of respiratory infections in the Seattle area. 3/18
All samples were from individuals suffering acute respiratory infection with a subset having influenza-like illness. Individuals with undiagnosed COVID-19 should be picked up with these symptom criteria. 4/18
We tested 3600 samples collected in Jan 2020 for COVID-19 status and found zero positives. We tested 3308 samples collected in Feb 2020 and found a first positive on Feb 21 with a total of 10 samples testing positive in Feb. 5/18pic.twitter.com/Jcx0qzdfx8
Additionally, we confirmed that these samples from acute respiratory infections from Oct 2019 through Feb 2020 contained a variety of different viruses including influenza, RSV, rhinovirus, metapneumovirus and seasonal coronavirus. 6/18pic.twitter.com/rjPEWFROjg
As you may know, seasonal coronaviruses are responsible for ~30% of common colds and are easily distinguished from #SARSCoV2 (the virus responsible for COVID-19) in molecular assays. There is no chance of confusion between these in our assay. 7/18
It's empirically true that the Seattle flu season in Oct through Jan was not the result of COVID-19. We would have seen it in these data. Given travel connections between WA and CA there is no way that COVID-19 was widely circulating in CA, but we see zero cases in WA. 8/18
For (2), the genetic relationships among sequenced viruses reveals their transmission history as described here https://nextstrain.org/help/general/how-to-read-a-tree …. #SARSCoV2 accumulates genetic changes at about 2 per month along a transmission chain (https://nextstrain.org/ncov/global?l=clock …). 9/18pic.twitter.com/9r1jLJqC20
We can use the number of genetic changes observed in a viral lineage to estimate the date of its common ancestor. 10/18
There have been hundreds of viruses sequenced from infections in the USA. We can use these sequences to date the arrival of the epidemic. Doing so, we see that there were multiple introductions driving the US epidemic and the earliest was in Jan. https://nextstrain.org/ncov/global?f_country=USA … 11/18pic.twitter.com/r2uylqcH2D
There were multiple paths the virus took to reach the US. There was a direct introduction from China that occurred in late Jan and there were multiple introductions from the European epidemic that occurred during the course of Feb. 12/18
If we restrict to viruses sampled in California (highlighted here as larger yellow dots) we see that they fall in with the rest of the US epidemic. There is no chance SARS-CoV-2 was circulating in California in fall 2019. Circulation in CA started in Jan or Feb 2020. 13/18pic.twitter.com/oZR8paTaOh
Estimating total number of infections is difficult without serology (see this thread: https://twitter.com/trvrb/status/1247609734896607232 …), but I'd guess that we're catching between 1 in 10 to 1 in 20 infections as a confirmed case. 14/18
This would give 5-10 million infections in the US or about 2-3% cumulative prevalence. This is a long way from the 50% (R0 of 2) to 66% (R0 of 3) we'd need for herd immunity. 15/18
I see #TestTraceIsolate as the only real solution to the problem we're facing (see recent thread from @firefoxx66 https://twitter.com/firefoxx66/status/1248939530939490304 …), alongside non-economically disruptive distancing and broad use of masks. 16/18
Huge thanks to the @seattleflustudy team, including @debnick60, @mjonasrieder, @seattleflustudy, @HelenChuMD, @lea_starita, @BrotmanBaty, @JShendure, @famulare_mike, @KiraNewmanMDPhD, @trs, @databae_ 17/18
And thank you to the groups from all over the US and the world who have generously shared sequence data via @GISAID to be analyzed with @nextstrain. 18/18
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