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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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    1. Trevor Bedford‏Verified account @trvrb 30 Nov 2020

      I don't think that this study by Basavaraju et al from @CDCgov can be taken as evidence that #COVID19 was circulating in the US in December 2019. 1/10https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa1785/6012472 …

      58 replies 451 retweets 1,179 likes
      Show this thread
    2. Trevor Bedford‏Verified account @trvrb 30 Nov 2020

      The authors do a careful serological investigation, but it necessarily suffers from testing a large number of samples with an assay that is not perfectly specific. 2/10

      5 replies 16 retweets 198 likes
      Show this thread
    3. Trevor Bedford‏Verified account @trvrb 30 Nov 2020

      The ELISA used by the authors has a stated specificity of 99.3% and the authors tested 519 "true negative" blood samples collected from 2016 to 2019 from healthy adults and suspected hanta virus patients and observed 3 false positives (0.6%) matching this specificity. 3/10

      1 reply 13 retweets 169 likes
      Show this thread
    4. Trevor Bedford‏Verified account @trvrb 30 Nov 2020

      The authors tested 1912 blood samples collected between Dec 13 and Dec 16 2019 and observed 39 positives (2.0%). A Fisher's Exact Test comparing 3/519 to 39/1912 is narrowly significant with p = 0.02. 4/10

      1 reply 12 retweets 134 likes
      Show this thread
    5. Trevor Bedford‏Verified account @trvrb 30 Nov 2020

      However, there is ample reason to expect that individuals recently recovered from seasonal coronavirus infection will have more cross-reactivity to SARS-CoV-2 than random healthy adults. In fact this can be seen in this paper by Freeman et al (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239067/ …). 5/10

      7 replies 24 retweets 229 likes
      Show this thread
    6. Trevor Bedford‏Verified account @trvrb 30 Nov 2020

      Here, ELISA titers are higher in individuals who were recently infected with seasonal coronavirus compared to random healthy adults. This is particularly the case in related betacoronaviruses OC43 and HKU1. 6/10pic.twitter.com/ljh7UC8qPZ

      1 reply 13 retweets 137 likes
      Show this thread
    7. Trevor Bedford‏Verified account @trvrb 30 Nov 2020

      Additionally, we know that seasonal coronaviruses circulate at higher frequencies in the winter. We can see this in @seattleflustudy data where there is significant seasonal coronavirus circulation in Dec 2019. 7/10pic.twitter.com/VrvdtRKllp

      5 replies 17 retweets 144 likes
      Show this thread
    8. Trevor Bedford‏Verified account @trvrb 30 Nov 2020

      It seems highly likely to me that the 39 "positives" from Dec 13 to Dec 16 reported by Basavaraju et al are due to cross-reactivity from recent seasonal coronavirus infection. It would just take a slight decrease of assay specificity to ~98% to explain this outcome. 8/10

      8 replies 55 retweets 271 likes
      Show this thread
      Trevor Bedford‏Verified account @trvrb 30 Nov 2020

      The authors highlight the study's limitation due to "potential cross reactivity with human common coronavirus infection" in the paper's discussion, but it unfortunately didn't make it into the @WSJ story (https://www.wsj.com/articles/covid-19-likely-in-u-s-in-mid-december-2019-cdc-scientists-report-11606782449 …). 9/10

      9:41 PM - 30 Nov 2020
      • 55 Retweets
      • 329 Likes
      • RockPaperScissors Hon Prof CD Butler Christine blah Tak VangurpR Ed lili AstroturfJesus
      5 replies 55 retweets 329 likes
        1. New conversation
        2. Trevor Bedford‏Verified account @trvrb 30 Nov 2020

          The other angle to consider is that if we're supposed to believe that 2.0% of random blood donors in Dec 2019 are COVID+ this would translate to millions of infections in the population at large, in which case we would have noticed due to people dying in large numbers. 10/10

          36 replies 78 retweets 620 likes
          Show this thread
        3. Trevor Bedford‏Verified account @trvrb 1 Dec 2020

          Trevor Bedford Retweeted Trevor Bedford

          Follow up #1: Also, a reminder that we at the @seattleflustudy PCR tested 3600 samples from individuals with acute respiratory illness collected in January 2020 from Seattle and found zero positives for COVID-19. This is a much more specific assay.https://twitter.com/trvrb/status/1249414295042965504 …

          Trevor Bedford added,

          Trevor BedfordVerified account @trvrb
          We tested 3600 samples collected in Jan 2020 for COVID-19 status and found zero positives. We tested 3308 samples collected in Feb 2020 and found a first positive on Feb 21 with a total of 10 samples testing positive in Feb. 5/18 pic.twitter.com/Jcx0qzdfx8
          Show this thread
          8 replies 65 retweets 340 likes
          Show this thread
        4. Trevor Bedford‏Verified account @trvrb 1 Dec 2020

          Follow up #2: This doesn't mean that COVID-19 was completely absent from the US in January 2020, just that prevalence at that time was exceptionally low. Finding 0/3600 COVID+ acute respiratory specimens doesn't square with theoretical 2% ELISA positivity in Dec.

          22 replies 40 retweets 282 likes
          Show this thread
        5. End of conversation
        1. boopie‏ @sarajean323 1 Dec 2020
          Replying to @trvrb @WSJ

          Then its unreliable data. That should be the papers conclusion.

          2 replies 0 retweets 5 likes
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