By: Eric Gundersen
Nextstrain is tracking the SARS-CoV-2 genome evolution sampling 3170 genomes between Dec 2019 and Apr 2020 and open sourcing the data to aid epidemiological understanding and improve outbreak response. This platform is used by the World Health Organization Global Influenza Surveillance and Response System (GISRS) to aid in vaccine strain selection for seasonal influenza virus.
The app helps us understand today’s discovery that the first U.S. coronavirus death occurred in early February, weeks earlier than previously thought, signaling the virus may have spread — and been fatal — in the United States weeks earlier than previously thought.
[As reported in the Washington Post]
“The fact that there were deaths related to covid back in early February is very significant, because it means the virus was around for a lot longer than was initially realized,” Jeff Smith, a physician and the county executive in Santa Clara, told The Washington Post. “It’s been around for a while, and it’s probably been spreading in the community for quite some time.”
Trevor Bedford, who focuses on phylodynamic analysis of pathogen sequence data at the Fred Hutch in the Vaccine and Infectious Disease Division and the Computational Biology Program, co-developed Nextstrain. Trevor steps though his analysis of today’s news:
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
— @trvrb
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
— @trvrb
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 https://t.co/ryQawSDXVi. 3/9
— @trvrb
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. (https://t.co/RbCx697sMs). 4/9
— @trvrb
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 https://t.co/MlgjZwtfG9
— @trvrb
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
— @trvrb
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
— @trvrb
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
— @trvrb
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. https://t.co/omw5fi6sAB 9/9
— @trvrb
eric gundersen (@ericg) | Twitter
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NextStrain, and tracking the community spread in the absence of social distancing was originally published in maps for developers on Medium, where people are continuing the conversation by highlighting and responding to this story.