Scientist @fredhutch, studying viruses, evolution and immunity. Collection of #COVID19 threads here: bedford.io/misc/twitter/

Seattle, WA
Joined December 2010
Case counts for the US appear to have peaked at a 7-day average of 806k on Jan 14. Omicron grew from approximately 35k daily cases on Dec 14 to ~800k daily cases in ~4 weeks. 1/9
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Looking at cases per 100k population per day across states, downturns are clear in NY, NJ, MA, FL, etc..., but many states are not yet at peak case loads. 2/9
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If we partition @CDCgov cases between Delta and Omicron using @GISAID sequence data following approach by @marlinfiggins (bedford.io/papers/figgins-rt…) we can see clear Omicron epidemics. 3/9
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These epidemics have proceeded in a similar fashion across states with initial rapid exponential growth that slowed as epidemics grew in size. It appears that states are largely on the same curve, just some are farther ahead on this curve compared to others. 4/9
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We estimate that as of Jan 17 the US as whole has had a cumulative ~15M confirmed cases of Omicron, or approximately 4.5% of the population recorded as confirmed cases. The large majority (>90%) of these accumulated since Dec 14. 5/9
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Assuming between a 1 in 4 and 1 in 5 case reporting rate suggests that between 18% and 23% of the country was infected by Omicron by Jan 17, with the large majority infected in a span of just ~4 weeks. 6/9
Replying to @trvrb
I don't have a good sense of how well testing infrastructure held up in London and how this compares to the US, but in general, this would suggest to me to be using something closer to 1 in 4 or 1 in 5 for reporting rate in the US rather than the 1 in 10 I've seen floated. 14/15
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There may be a longer tail of circulation after the peak (as seen in South Africa), but a rough expectation would have an equivalent number of cases in the next 4 weeks on the other side of the peak. This would suggest 36-46% of the US infected by Omicron by mid-Feb. 7/9
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Having ~40% of the population infected by a single pathogen in the span of 8 weeks is remarkable and I can't think of an obvious modern precedent. Flu seasons generally have perhaps 10% infected in the span of 16 weeks. 8/9
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My big question now is to what extent will Omicron-like emergence events characterize "endemic" circulation of SARS-CoV-2? Given it occurred once, having it occur again would not be at all surprising, but I don't know whether to expect this every year or every ten. 9/9
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Here, I'll be comparing @ONS survey data to @UKHSA case counts in a dataset compiled by @seedragons and available at github.com/seedragons/london… (and supplemented with data through Dec 31 via ons.gov.uk/peoplepopulationa…). 5/15
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Recent data from late Dec from London had ~9% of individuals positive by PCR for SARS-CoV-2. So roughly 1 in 11 people with infections with detectable virus in London. 6/15
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In late December, London had ~26k daily confirmed cases, or 0.3% of the population being recorded as confirmed cases every day. 7/15
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We can compare timeseries of prevalence to cases since Oct 2020. Here we observe a 0-day compatible lag between specimen collection date for cases and prevalence. 8/15
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We can plot the ratio of prevalence to cases with this 0-day lag to arrive at the following picture through time, where there's some variation, but a ~35X ratio of daily prevalence to daily cases is decently consistent. 9/15
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If we assume the average infection tests positive for ~10-days (based on @stephenkissler et al nejm.org/doi/full/10.1056/NE…), we get an estimated reporting rate of 10/35 = ~29% or very roughly detecting 1 in 3.5 infections as a case. 10/15
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Importantly if we look at this ratio in Dec during which time Omicron became predominant and case loads increased dramatically, we see that both prevalence and cases increased in tandem and the ~35X ratio was largely maintained. 11/15
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This suggests to me that despite severe outcomes being more rare with Omicron and despite a huge surge in cases that reporting rate for Omicron in London remained fairly stable and did not differ hugely from Delta. 12/15
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This fits with case reports suggesting a large fraction of symptomatic infections for Omicron (eurosurveillance.org/content…, medrxiv.org/content/10.1101/…). 13/15
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I don't have a good sense of how well testing infrastructure held up in London and how this compares to the US, but in general, this would suggest to me to be using something closer to 1 in 4 or 1 in 5 for reporting rate in the US rather than the 1 in 10 I've seen floated. 14/15
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Given ~680k cases per day, this would in turn suggest 0.8% or 1% of the US being infected with SARS-CoV-2 every day. This would translate to perhaps 5% or 10% of individuals currently infected with SARS-CoV-2 in the US. 15/15
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