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I wanted to respond to news of #COVID19 death in Santa Clara County on Feb 6. This is an interesting, if slightly puzzling, data point. 1/9
We know that there is very little genetic diversity in global samples of SARS-CoV-2, which points to emergence in ~Nov 2019 in Wuhan, China. We know that once community spread is established it ramps quickly in the absence of social distancing. 2/9
Rate of increase in confirmed cases as well as genomic data suggests a 3-4 day doubling rate. If we look at the abundantly sequenced WA cases we see evidence for an introduction in late January that leads to the majority of cases in March. Figure from bedford.io/papers/bedford…. 3/9
With a 3-day doubling, we can go from a single infection at day 0 to ~1000 infections at day 30. This rapidity of epidemic spread is visible repeatedly across epidemics including New York, Italy and France. Figure from @hsalje et al. (hal-pasteur.archives-ouvertes.fr/pasteur-025481…). 4/9
Additionally, if we look at a transmission chain in the US, we see that it rapidly bounces between states owing to the level of within-US travel. 5/9 nextstrain.org/ncov/north-ame…
The report of a death in Santa Clara on Feb 6 does not effect my overall timeline of first introductions occurring in the US in Jan 2020 into locations with strong travel connections to China. This death is likely part of one of these early transmission chains. 6/9
The puzzling aspect is the observation that if there was community transmission in Santa Clara in late Jan / early Feb, why didn't we see a similarly early epidemic in Santa Clara as we saw in King County? 7/9
My best guess is that the epidemic in Santa Clara didn't take off for stochastic reasons, despite virus being around in Jan / Feb, but it's also possible the epidemic was less detected in Santa Clara than elsewhere. 8/9
Further viral sequencing of Santa Clara / California samples should help to further clarify timeline. Currently we have 33 genomes. Hopefully more will be sequenced and shared soon. nextstrain.org/ncov/north-ame… 9/9
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Trevor Bedford
@trvrb
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: nextstrain.org/ncov/north-ame… 3/14
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Trevor Bedford
@trvrb
I'm seeing a bunch of talk about how the code behind the simulations for the March 16 @MRC_Outbreak report (imperial.ac.uk/mrc-global-inf…) was never previously released and is not well written. This is then taken to somehow mean that the "lockdown" policy was ill-founded. 1/11
However, the code and simulation mean little in terms of mortality expectations. As is usually the case, everything is about the assumptions of the model. Here, it was assumed that the fundamental reproductive number (R0) is 2.4 and infection fatality rate (IFR) is 0.9%. 2/11
In 1927(!), Kermack and McKendrick derived the total proportion of the population expected to be infected in the course of an epidemic in a simple SIR model as the attached equation. Solving this for R0 of 2.4, we get a total proportion infected (or attack rate) of 88%. 3/11
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Trevor Bedford
@trvrb
I wanted to address the hypothesis put forward in Korber et al (biorxiv.org/content/10.110…) that the mutation in spike protein D614G causes an increase in transmissibility of SARS-CoV-2 virus. I find this hypothesis to be plausible, but far from proven. 1/16
I've been watching D614G closely as mutations in spike protein deserve added attention due to spike's role in binding to the human ACE2 receptor. 2/16
This D614G mutation occurred in the transmission chain that initially seeded the European outbreak in ~Jan 2020. Almost all viruses possessing this mutation descend from this initial introduction into Europe. 3/16
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