Trevor BedfordVerifizierter Account

@trvrb

Scientist , studying viruses, evolution and immunity. Collection of threads here:

Seattle, WA
bedford.io
Beigetreten Dezember 2010
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  1. 12. Juli

    We're recruiting a bioinformatician and a full-stack developer to the Bedford Lab to work on and . Details here: .

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  2. 1. Juli

    Follow up #2: This supports the expectation that we'll see Delta circulation influenced by degree of regional vaccine coverage.

    We know from that B.1.617.2 is primarily transmitting through the unvaccinated (or partially vaccinated) population. It's difficult to predict the size of a B.1.617.2 epidemic we'll see, but I would expect at least some correlation with regional vaccine coverage. 12/12
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  3. 1. Juli

    Follow up #1: Prompted by question on Twitter () I just did a simple correlation of total population fully vaccinated against Delta-specific Rt across 20 states with good data. We get a decently strong negative correlation with R^2 of 0.32.

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  4. 30. Juni

    Although I don't have a huge amount of faith in this specific 11% estimate, at the moment, just based on what's happening in the UK, I would expect there to be a US wave driven by Delta (figure showing Rt in UK from ). 16/16

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  5. 30. Juni

    Another 11% of the population infected is of course substantial, though we expect lower rates of mortality on a per case basis due to vaccination coverage differing substantially across age groups (). 15/16

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  6. 30. Juni

    I'd hope for these two effects to largely come out in the wash. 14/16

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  7. 30. Juni

    Second, vaccination is not perfect and vaccine efficacy against symptomatic disease drops from ~89% against Alpha to ~79% against Delta per report (). Breakthrough infections imply a smaller fraction of the population immune than the 62%. 13/16

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  8. 30. Juni

    A couple obvious places where this calculation is wrong. First, vaccination and infection are not independent and instead probably anti-correlated. This would imply a larger fraction of the population immune than the 62% used above. 12/16

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  9. 30. Juni

    This would imply that Delta has a susceptible pool of 38% of the US population and given final size of 29% would suggest 11% of the total US population infected with Delta or 36M people. 11/16

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  10. 30. Juni

    CDC lists 46% of the US population as fully vaccinated. Following , we take ~30% of the US population as having been infected. Assuming that vaccination and infection are independent yields 46% + 54% x 30% = 62% of the population with immunity. 10/16

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  11. 30. Juni

    Inputting R0 of 1.18 in the final epidemic size equation yields 29% of the susceptible population infected in the Delta wave. 9/16

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  12. 30. Juni

    Variant-specific estimates of Rt from using case counts and sequence data suggests Rt of Delta variant of 1.18 averaged across 20 states analyzed. 8/16

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  13. 30. Juni

    We've recently seen rapid growth of Delta, where it's displacing other circulating viruses in many states. Here, predominance of Delta in Arkansas, Colorado, Missouri and Utah occurred in only ~4 weeks. 7/16

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  14. 30. Juni

    Notably, the (super rough) math seems to work here. Initial Rt of ~1.1 translated to ~20% of the population infected, which is close to the 18% mathematical expectation. 6/16

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  15. 30. Juni

    From Sep through Mar, the US reported 24M cases of COVID-19. If we assume 2.7 infections per reported case (via ) we arrive at 65M infections in a population of 328M for ~20% of the US infected in the fall/winter wave. 5/16

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  16. 30. Juni

    Before we get to Delta, we can see how this logic works with the fall/winter wave in the US. Here, state-level estimates of Rt were ~1.1 in Sep and Oct 2020 and declined to ~0.9 in Mar 2021 as the epidemic ran its course and left a wake of population immunity. 4/16

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  17. 30. Juni

    Given a specified R0, we can calculate final epidemic size in a simple SIR model with the following equation where Z is final epidemic size. For initial R0 of 1.1, an epidemic is expected to infect 18% of the susceptible population. 3/16

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  18. 30. Juni

    First off, epidemic size is determined by two primary factors: 1. Efficiency of onward transmission from an index case, commonly quantified as R0 2. Size of susceptible pool 2/16

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  19. 30. Juni

    How big of a wave of do we expect in the US from the Delta variant? Here I describe a simple approach to this question and attempt a rough back-of-the-envelop estimate. 1/16

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  20. 24. Juni

    As I've said before, I believe both zoonosis and lab leak to be plausible hypotheses for COVID origins. I'm not pushing any narrative, just trying to figure out what's going on with this particular datapoint. 15/15

    I am in the both are plausible camp. The data (as it exists) is consistent with zoonosis, but it's also consistent with lab leak. Parsing the relative probabilities of the two depends on multiple lines of evidence and is necessarily assumption ridden. 2/8
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