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trvrb's profile
Trevor Bedford
Trevor Bedford
Trevor Bedford
Verified account
@trvrb

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Trevor BedfordVerified account

@trvrb

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

Seattle, WA
bedford.io
Joined December 2010

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    1. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      Trevor Bedford Retweeted Trevor Bedford

      I've revised my own phylodynamic estimates of rate of spread with a couple improvements. First off, I'm now using 206 Omicron genomes generously shared by researchers through @GISAID. 8/18https://twitter.com/trvrb/status/1464353254267965440 …

      Trevor Bedford added,

      Trevor BedfordVerified account @trvrb
      However, rather than looking at raw frequency of genomic lineage or clade assignments, we can take a phylodynamic approach to estimate clade growth. This approach uses a molecular clock along with branching patterns in the phylogeny to infer viral population dynamics. 11/16
      Show this thread
      1 reply 31 retweets 293 likes
      Show this thread
    2. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      Secondly, I'm now masking spike which has issues of spurious within-Omicron diversity due to amplicon dropout during sequencing. I've adjusted molecular clock rate from 8×10^-4 to 5.5×10^-4 to compensate (determined from sequences taken over the course of the pandemic). 9/18

      3 replies 24 retweets 248 likes
      Show this thread
    3. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      This updated analysis gives a median estimate of the common ancestor to Omicron viruses of Sep 30 with a 95% credible interval of between Sep 9 and Oct 13. 10/18pic.twitter.com/PRqdBbqDNI

      4 replies 86 retweets 417 likes
      Show this thread
    4. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      This also gives a median estimate of doubling time of 4.9 days, which we can convert to an estimate of Rt assuming a generation interval of 5.1 days (https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.17.2000257 …). Doing so gives a median estimate of Rt of 2.0 with a 95% credible interval of 1.6 to 2.6. 11/18pic.twitter.com/WMpVqtg5jx

      3 replies 62 retweets 351 likes
      Show this thread
    5. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      Having two very different methods give Rt estimates of between 2.0 and 2.5 gives me some (small) degree of confidence. We can triangulate relative fitness with Rt so that Delta in South Africa is at Rt of ~0.8 and Omicron is at about three times this with Rt of ~2.5. 12/18

      6 replies 82 retweets 434 likes
      Show this thread
    6. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      Trevor Bedford Retweeted Trevor Bedford

      We can then use the approach here to factor possible scenarios of intrinsic transmission vs immune escape that would give Omicron Rt of 2.5. 13/18https://twitter.com/trvrb/status/1465364313980354560 …

      Trevor Bedford added,

      Trevor BedfordVerified account @trvrb
      Person-to-person transmission potential can be quantified with Rt as the number of secondary infections caused by an index case by a particular variant in a particular context and depends on both intrinsic transmissibility and immune escape. 7/15
      Show this thread
      2 replies 26 retweets 270 likes
      Show this thread
    7. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      Under a scenario of 90% population immunity against previous variants, we get the following picture where Omicron could lie anywhere along the dashed line ranging from an intrinsic R0 of 3 and 83% immune escape to an intrinsic R0 of 9 and 20% immune escape. 14/18pic.twitter.com/nh2CzoL0L4

      29 replies 300 retweets 994 likes
      Show this thread
    8. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      Note the these estimates are sensitive to assumed population immunity. Under a scenario of 85% population immunity, we get the following picture instead that shifts the required level of immune escape upwards for a particular R0 value. 15/18pic.twitter.com/UJUZdqBTmW

      23 replies 78 retweets 473 likes
      Show this thread
    9. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      Again, based on wildly divergent spike protein, I'm guessing that immune escape will be substantial and so I still suspect that it's quite possible that Omicron will show lower intrinsic transmissibility than Delta. My updated diagram. 16/18pic.twitter.com/T4vuiEN75I

      35 replies 318 retweets 1,051 likes
      Show this thread
    10. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      Note also that high immune escape, lower intrinsic transmissibility is not necessarily a good thing. Higher immune escape places previously infected and vaccinated individuals more at risk. 17/18

      29 replies 139 retweets 750 likes
      Show this thread
      Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      We'll know much more about this level of risk in ~2 weeks when we get neutralization results. I'm particularly interested in neutralization titers of individuals with two doses of vaccine vs individuals with three doses of vaccine. 18/18

      8:08 AM - 1 Dec 2021
      • 158 Retweets
      • 1,311 Likes
      • Uwe Klages MsGabriel Tax Billionaires Into Millionaires Bodil Håheim Velvet Meow Anna Wójtowicz Robert Scheiber Adrian E. Jason Tan
      61 replies 158 retweets 1,311 likes
        1. New conversation
        2. Pirate Captain‏ @Pirate__Captain 1 Dec 2021
          Replying to @trvrb

          For the for several tweets, you're focusing on the data from South Africa, which has a low vaccination rate, their population immunity is very likely less than 50%, which would put it much closer to delta in terms of immunity escape and more of a transmission advantage, right?

          2 replies 0 retweets 4 likes
        3. loafingcactus‏ @loafingcactus 1 Dec 2021
          Replying to @Pirate__Captain

          SA population prior exposure is estimated to be in the 95% range, higher than the US 80 to 85% range, due to higher infection.

          1 reply 0 retweets 3 likes
        4. End of conversation
        1. New conversation
        2. MrKittens‏ @Shaunblahblah 1 Dec 2021
          Replying to @trvrb

          At the risk of outing myself as an idiot, can you give a TL,DR with an ELI5 theme? (Not kidding, I relay info like this to my 80 something parents)

          3 replies 0 retweets 4 likes
        3. loafingcactus‏ @loafingcactus 1 Dec 2021
          Replying to @Shaunblahblah

          Vaccination and a booster is very likely to help you avoid getting very sick. It is very likely to help even if you get Omicron. Probably a higher number of people will get sick (if we don’t increase protections). There will probably be more group impacts like more full hospitals

          1 reply 0 retweets 10 likes
        4. Show replies
        1. Jason Parsons‏ @jpsaffron 1 Dec 2021
          Replying to @trvrb

          Any thoughts on immune escape in a vaccinated vs previously infected population? Is the spike in infection in S. Africa in a population with relatively low vax / high previous infection? How does this impact comparisons to US? Thanks!

          0 replies 0 retweets 11 likes
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        1. epsilon‏ @epsilon3141 1 Dec 2021
          Replying to @trvrb

          "individuals with three doses of vaccine" Israel reports 2 doctors (each 3x vaccinated) to test positive for #omicron (one even infected the other). (Anecdotal evidence, nevertheless interesting)https://www.jpost.com/health-and-wellness/coronavirus/two-israeli-doctors-test-positive-for-omicron-covid-variant-687412 …

          1 reply 8 retweets 14 likes
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        1. tony grimes‏ @toegrimes 1 Dec 2021
          Replying to @trvrb

          Given that increased transmissibility has correlated with increased virulence for alpha and delta then this *could* support idea of milder infection (but sure wider infected pop > deaths)? Bad news for high vax countries tho

          0 replies 0 retweets 5 likes
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        1. New conversation
        2. des‏ @desgren 1 Dec 2021
          Replying to @trvrb

          Do we have enough data yet to rule out Antigen Dependent Enhancement (ADE) which would put previously infected and/or vaccinated folk more at risk.

          3 replies 0 retweets 1 like
        3. Dr Kevin Purcell  🇬🇧 🇮🇪 🇺🇸  😷 💉 💉 💉‏ @kevinpurcell 1 Dec 2021
          Replying to @desgren @trvrb

          Derek Lowe has written about ADE repeatedly. There is zero evidence for ADE in infections after Covid vaccination. https://www.science.org/content/blog-post/antibody-dependent-enhancement-and-coronavirus-vaccines … https://www.science.org/content/blog-post/new-antibody-dependent-enhancement-hypothesis …

          1 reply 0 retweets 0 likes
        4. Show replies
        1. New conversation
        2. Peggy Blair‏ @peggy_blair 1 Dec 2021
          Replying to @trvrb

          What percentage of the population in Gauteng and South Africa are vaccinated?

          3 replies 0 retweets 1 like
        3. Show replies

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