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trvrb's profile
Trevor Bedford
Trevor Bedford
Trevor Bedford
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@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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    Trevor Bedford‏Verified account @trvrb 29 Feb 2020

    The team at the @seattleflustudy have sequenced the genome the #COVID19 community case reported yesterday from Snohomish County, WA, and have posted the sequence publicly to http://gisaid.org . There are some enormous implications here. 1/9

    8:20 PM - 29 Feb 2020
    • 6,685 Retweets
    • 11,572 Likes
    • Xavier David Doborjginidze Elin Svensson Ghoul Lazarus soda_troubles Stewart Lonky, MD JMC Jason Fagone Zbigniew Hałat
    358 replies 6,685 retweets 11,572 likes
      1. New conversation
      2. Trevor Bedford‏Verified account @trvrb 29 Feb 2020

        This case, WA2, is on a branch in the evolutionary tree that descends directly from WA1, the first reported case in the USA sampled Jan 19, also from Snohomish County, viewable here: https://nextstrain.org/ncov?f_division=Washington … 2/9pic.twitter.com/LBH26A0AFC

        51 replies 795 retweets 2,358 likes
        Show this thread
      3. Trevor Bedford‏Verified account @trvrb 29 Feb 2020

        This strongly suggests that there has been cryptic transmission in Washington State for the past 6 weeks. 3/9

        64 replies 1,314 retweets 3,533 likes
        Show this thread
      4. Trevor Bedford‏Verified account @trvrb 29 Feb 2020

        It's possible that this genetic similarity is a coincidence and these are separate introductions. However, I believe this is highly unlikely. The WA1 case had a variant at site 18060. This variant is only present in 2/59 viruses from China. 4/9pic.twitter.com/Rb9N5uvgwg

        14 replies 413 retweets 1,811 likes
        Show this thread
      5. Trevor Bedford‏Verified account @trvrb 29 Feb 2020

        I'd assess the p-value for this coincidence at 2/59=0.03 and so is statistically significant. Additionally, these two cases are geographically proximal, both residing in Snohomish County. 5/9

        21 replies 291 retweets 1,656 likes
        Show this thread
      6. Trevor Bedford‏Verified account @trvrb 29 Feb 2020

        I believe we're facing an already substantial outbreak in Washington State that was not detected until now due to narrow case definition requiring direct travel to China. 6/9

        101 replies 2,065 retweets 5,239 likes
        Show this thread
      7. Trevor Bedford‏Verified account @trvrb 29 Feb 2020

        We will be working closely with @KCPubHealth and @WADeptHealth to investigate the full extent of the outbreak. 7/9

        9 replies 288 retweets 1,765 likes
        Show this thread
      8. Trevor Bedford‏Verified account @trvrb 29 Feb 2020

        We're hoping to update soon with better estimates of the number of infections in Washington State using available data. 8/9

        8 replies 246 retweets 1,541 likes
        Show this thread
      9. Trevor Bedford‏Verified account @trvrb 29 Feb 2020

        Thank you to the @seattleflustudy team, and particularly to @lea_starita, for exceptionally fast turnaround from diagnostic assay at @WADeptHealth to sequenced genome. 9/9

        24 replies 297 retweets 2,267 likes
        Show this thread
      10. Trevor Bedford‏Verified account @trvrb 29 Feb 2020

        An update, because I see people overly speculating on total outbreak size. Our best current expectation is a few hundred current infections. Expect more analyses tomorrow.

        91 replies 716 retweets 2,959 likes
        Show this thread
      11. Trevor Bedford‏Verified account @trvrb 29 Feb 2020

        One more update: my best guess at a p-value here is 0.03 as above based on shared mutations (still possible this pattern was chance). If we get another sequence or two from additional WA community cases this should clinch the matter one way or another.

        74 replies 210 retweets 1,601 likes
        Show this thread
      12. End of conversation

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