Trevor Bedford Profile picture
Mar 2, 2020 11 tweets 4 min read Read on X
A follow up to Saturday's analysis of undetected #COVID19 transmission in Washington State. 1/11
As before, the genomic data support a linkage between the case WA1 from Jan 19 and the case WA2 from Feb 24, both from Snohomish County. 2/11
This suggests that the case WA1 infected someone who was missed by surveillance due to mild symptoms and a transmission chain was initiated at this point in mid-Jan. 3/11
Because the case definition from mid-Jan until Feb 27 required direct travel from China, any of these subsequent cases in the transmission chain would not have been tested for #SARSCoV2. 4/11
Assuming an introduction into Snohomish County on Jan 15, Mike Famulare @IDMOD_ORG simulated onward transmission using consensus epidemiological parameters curated by the @MIDAS_Network (github.com/midas-network/…). 5/11
Running these simulations forward with a mean doubling time of 6.1 days, we estimate the number of current infections in this transmission chain on March 1 to be 570 with an 90% uncertainty interval of between 80 and 1500. 6/11 Image
In addition to this "bottom-up" approach, Mike used a "top-down" approach in which we accounted for the single positive screening result out of the number of samples screened to date along with census information. 7/11
This approach leads to a similar estimate of the number of current infections at 330 with a 90% uncertainty interval of between 20 and 1500 infections. 8/11
We believe this particular transmission chain will have a foci in Snohomish County. We're working as fast as possible to understand extent of spread in the greater Seattle area. 9/11
Please consider this to be a preliminary analysis. We are actively working on this and will continue to update our numbers. 10/11
We are hugely thankful to @SnoHD, @KCPubHealth and @WADeptHealth for their support and clear thinking for state and local public health. They are doing a fantastic job. 11/11

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More from @trvrb

Dec 5, 2022
Currently, the US is reporting about 54k daily cases of COVID-19 (16 per 100k per capita) and the UK is reporting about 4k (6 per 100k). This seems comfortingly low compared to even this summer's BA.5 wave and let alone last winter's BA.1 wave. Figure from @OurWorldInData. 1/16
However, at this point, nearly all infections will be in individuals with prior immunity from vaccination or infection and this combined with a roll back in testing makes it unclear how to interpret current case counts compared to previous time periods. 2/16
We're interested in the case detection rate or the ratio of underlying new infections compared to reported cases. Throughout much of 2020 and 2021, I had a working estimate of 1 infection in ~3.5 getting reported as a case. 3/16
Read 16 tweets
Aug 16, 2022
Largely through partial immune escape, lineage BA.5 viruses resulted in sizable epidemics throughout much of the world. However, in most countries these epidemics are now beginning to wind down. What do we expect after BA.5? 1/10
Lineage BA.2.75 (aka 'Centaurus') has been high on watch lists due to sustained increase in frequency in India combined with the presence of multiple mutations to spike protein. We now have enough sampled BA.2.75 viruses from outside India to make some initial conclusions. 2/10
If we look at frequency data we see sustained logistic growth of BA.2.75 in India, Japan, Singapore and the US. Critically, in India it is clearly displacing BA.5. 3/10
Read 10 tweets
Aug 3, 2022
Based on the experience in winter 2020/2021, seasonal influence on SARS-CoV-2 transmission is quite clear, but much of the Northern Hemisphere is currently experiencing large summer epidemics driven the spread of evolved BA.5 viruses. 1/11
It's necessarily fraught to try to make predictions of seasonal circulation patterns going forwards, but we can gain some intuition from simple epidemiological models. 2/11
In particular, we can use an SIRS system in which individuals go from Susceptible to Infected to Recovered, and then return to the Susceptible class due to immune waning / antigenic drift of the virus. 3/11
Read 12 tweets
Jul 20, 2022
There seems to be a worry that telling people we've exited the "pandemic phase" will lead to further reduced precautions. As always however, I think it's best not to conduct messaging for intended behavioral effect and just try to make scientifically accurate statements. 1/5
Given vaccination and infection, the US and global population now has widespread immunity to SARS-CoV-2 and deaths per-infection are about 10 times lower than they were pre-immunity in 2020 with a ballpark IFR of 0.05% (though this will vary by immunity and age demographics). 2/5
You can see this reduction in mortality rate in looking at projections of deaths from lagged-cases keyed to early case fatality rate. 3/5
Read 5 tweets
Jun 27, 2022
The @US_FDA VRBPAC committee will be meeting tomorrow to discuss variant-specific COVID-19 vaccines (fda.gov/advisory-commi…). Based on present observations, I would argue that the most important metric to optimize are titers against BA.4/BA.5 viruses. 1/10
We've seen repeated replacement of SARS-CoV-2 variants during 2022, first of Delta by Omicron BA.1 and then by sub-lineages of Omicron, with BA.2 replacing BA.1 and now with BA.4/BA.5 replacing BA.2. 2/10
Viruses have been evolving to be higher fitness through both increases in intrinsic transmissibility (seen in BA.2 vs BA.1) as well as escape from existing population immunity (seen in Omicron vs Delta as well as BA.4/BA.5 vs BA.2). 3/10
Read 10 tweets
Jun 3, 2022
Global monkeypox confirmed and suspected cases compiled by @globaldothealth show initial rapid increase as case-based surveillance comes online, followed by slower continued growth. 1/10
This is data from github.com/globaldothealt… and has had a 7-day smoothing applied and all y-axes are shown on a log scale. 2/10
If we focus on the last 11 days, we can see steady exponential growth in global cases with a ~7.7 day doubling. 3/10
Read 11 tweets

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