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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

      But as stated previously, I believe this estimate is likely to drop somewhat as more data comes in. But I wouldn't be surprised if this drops to something still significant, say 3X or 4X the transmission rate of Delta in South Africa. 4/18https://twitter.com/trvrb/status/1465364321303597061 …

      Trevor Bedford added,

      Trevor BedfordVerified account @trvrb
      Note that these estimates of current fitness advantage of Omicron are very likely to get lower in the coming days as bias from preferential sequencing eases as more surveillance samples are sequenced. 11/15 https://twitter.com/trvrb/status/1464353251147481089 …
      Show this thread
      4 replies 68 retweets 435 likes
      Show this thread
    2. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      In addition to changes in relative frequency, we can look at what's happening with case counts, which have been rising rapidly in Gauteng and South Africa. We can measure the exponential growth in cases via Rt (the number of secondary cases caused by an index case). 5/18

      1 reply 24 retweets 278 likes
      Show this thread
    3. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      In work from @lrossouw we get a rapid rise in Rt in Gauteng from ~0.8 to ~2.5 over the course of Nov corresponding to the take off of Omicron (https://unsupervised.online/static/covid-19/estimating_r_za.html#54_Gauteng …). 6/18pic.twitter.com/PkKHB5VdoJ

      7 replies 67 retweets 373 likes
      Show this thread
    4. Trevor Bedford‏Verified account @trvrb 1 Dec 2021

      Work from @seabbs and colleagues gives a similar result of Rt increasing from ~0.8 to above 2 over the course of November in Gauteng (https://epiforecasts.io/covid/posts/subnational/south-africa/gauteng/ …). 7/18pic.twitter.com/n1JZ885zbb

      2 replies 33 retweets 286 likes
      Show this thread
    5. 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 294 likes
      Show this thread
    6. 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 249 likes
      Show this thread
    7. 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 418 likes
      Show this thread
    8. 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 352 likes
      Show this thread
    9. 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 435 likes
      Show this thread
    10. 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 271 likes
      Show this thread
      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

      8:08 AM - 1 Dec 2021
      • 300 Retweets
      • 994 Likes
      • Paul Roundy Steven Gussman Uwe Klages Elizabeth Gabay MW 🇪🇺🍷🌹 Dr.Ramneesh Trehan MBBS MD keyser soze Sebastian Schmidt Evan Z Kapp viba
      29 replies 300 retweets 994 likes
        1. New conversation
        2. 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 474 likes
          Show this thread
        3. 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 317 retweets 1,051 likes
          Show this thread
        4. 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 749 likes
          Show this thread
        5. 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

          61 replies 158 retweets 1,311 likes
          Show this thread
        6. End of conversation
        1. New conversation
        2. Nafnlaus‏ @enn_nafnlaus 1 Dec 2021
          Replying to @trvrb

          There's a report (not yet published) from Israel that breakthroughs and reinfections are twice as common - for example, boosted Pfizer v. infection drops 95%->90%. I assume that's "50%" on your graph, putting R0 at 4,5 if true?

          2 replies 3 retweets 6 likes
        3. Nafnlaus‏ @enn_nafnlaus 1 Dec 2021
          Replying to @enn_nafnlaus @trvrb

          If so, this might support Hotez's hypothesis of an upcoming dual-strain pandemic in countries that haven't been hit as hard by Delta - Delta attacking naive populations better and omicron doing more breakthroughs and reinfections among the under-protected.

          1 reply 6 retweets 14 likes
        4. Show replies
        1. This Tweet is unavailable.
        2. Rael Rutherford‏ @RaelRutherford 1 Dec 2021
          Replying to @DavidWe01239506 @trvrb

          It was much better in the 60s and 70s when there were good scientists and epidemiologists working on these things. Now everyone is in an existential crisis to make enough money to pay their outrageous mortgages.

          0 replies 1 retweet 8 likes
        3. End of conversation
        1. New conversation
        2. Steve Miller‏ @SteveMillerOC 1 Dec 2021
          Replying to @trvrb

          The few sources I have seen discussing contact tracing for omicron (the four Nov 11 cases from diplomats in Botswana, and subsequent EU cases) have all said that 100% of close contacts tested negative. Doesn’t that suggest lower intrinsic R0?

          3 replies 0 retweets 18 likes
        3. Neil H‏ @NeilHUSA 1 Dec 2021
          Replying to @SteveMillerOC @trvrb

          CNBC just reported the same with the first case identified in the US who came from South Africa. Interesting.

          1 reply 0 retweets 3 likes
        4. Show replies

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