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Trevor Bedford Profile picture
@trvrb
Apr 22, 2020 • 9 tweets • 4 min read • Read on X
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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More from @trvrb

Trevor Bedford Profile picture
Dec 4, 2020
The US is reporting over 2000 deaths per day from Dec 1 and I believe will do so consistently throughout December based on daily case loads above 120k starting early November. 1/4
A drop in reporting over Thanksgiving weekend has made for some difficulty in directly comparing 7-day averaged deaths, but the trend is clear. Red bars are daily reported deaths from @COVID19Tracking and black line is 7-day sliding average. 2/4
The simple projection of 1.7% of reported cases into deaths 22 days later has remained largely accurate, although drop of reporting during Thanksgiving weekend is quite clear. We'll know soon whether 7-day average returns back to projection. 3/4
Read 4 tweets
Trevor Bedford Profile picture
Nov 11, 2020
After posting about sharply rising #COVID19 cases Friday, there were multiple replies to the effect of "but deaths aren't going up". As should be obvious to most at this point, (reported) deaths lag (reported) cases. This thread investigates. 1/8
There is a lag between when a case is diagnosed and when the individual may succumb to their disease and there is a further lag between date of death and when the death is reported. 2/8
Here, I compare state-level data from @COVID19Tracking for cases and deaths and find that a 22-day lag maximizes state-level correlations. 3/8
Read 8 tweets
Trevor Bedford Profile picture
Nov 7, 2020
I know that everyone has been (justifiably) distracted by other things, but the #COVID19 epidemic in the US is looking pretty dire with 125,552 confirmed cases reported Friday by @COVID19Tracking. 1/10
Please consider this somewhat of a follow up to the thread two weeks ago on circulation patterns across states. 2/10
Confirmed cases have continued to tick up across the US, though with the Midwest and Mountain West contributing to most of the recent increase. Data from @COVID19Tracking. 3/10 Image
Read 10 tweets

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