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jbloom_lab's profile
Bloom Lab
Bloom Lab
Bloom Lab
@jbloom_lab

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Bloom Lab

@jbloom_lab

Lab studying molecular evolution of proteins and viruses. Affiliated with @fredhutch @HHMINEWS @uwgenome.

Seattle, WA
research.fhcrc.org/bloom/en.html
Joined June 2014

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    Bloom Lab‏ @jbloom_lab 22 Jun 2021

    In a new study, I identify and recover a deleted set of #SARSCoV2 sequences that provide additional information about viruses from the early Wuhan outbreak: https://www.biorxiv.org/content/10.1101/2021.06.18.449051v1 … (1/n)

    2:09 PM - 22 Jun 2021
    • 2,627 Retweets
    • 5,939 Likes
    • Cohn-Kahn DrRooting4Science Théorie Du Pangolin Fools Multiply 🏖️𝓛𝓪𝓲 𝓓𝓪𝓶𝓪⛱️ Huisman FataL mita Anderson Nascimento
    199 replies 2,627 retweets 5,939 likes
      1. New conversation
      2. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Specifically, NIH maintains the Sequence Read Archive, where scientists around world deposit deep sequencing data for others to analyze. I noted https://peerj.com/articles/9255  lists all #SARSCoV2 data in archive as of March-31-2020. Most from a project by Wuhan University. (2/n)pic.twitter.com/9V4dchZVUl

        9 replies 165 retweets 689 likes
        Show this thread
      3. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        But when I went to Sequence Read Archive, I found entire project was gone! (Note that as detailed below, this does *not* imply malfeasance by NIH. Sequence Read Archive policy allows submitters to delete by e-mail request.) (3/n)pic.twitter.com/fEzOaVYZLZ

        9 replies 147 retweets 625 likes
        Show this thread
      4. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        I was able to determine deleted data corresponded to a study that partially sequenced “45 nasopharyngeal samples from [Wuhan] outpatients with suspected COVID-19 early in the epidemic“ https://www.medrxiv.org/content/10.1101/2020.03.04.20029538v1.full … (4/n)

        3 replies 150 retweets 642 likes
        Show this thread
      5. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        I discovered that even though the files were deleted from archive itself, they could be recovered from the Google Cloud at links like https://storage.googleapis.com/nih-sequence-read-archive/run/SRR11313485/SRR11313485 … (5/n)

        11 replies 143 retweets 875 likes
        Show this thread
      6. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Using this approach, I recovered files for the 34 early samples that were virus positive. I was able to use the data in the files to reconstruct partial viral sequences (from start of spike to end of ORF10) for 13 of these samples. (6/n)

        5 replies 115 retweets 716 likes
        Show this thread
      7. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Now I need to give background to explain a confusing scientific mystery about other early #SARSCoV2 sequences. Although events that led to emergence of #SARSCoV2 in Wuhan are unclear (zoonosis vs lab accident), everyone agrees deep ancestors are coronaviruses from bats. (7/n)

        3 replies 105 retweets 654 likes
        Show this thread
      8. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Therefore, we’d expect the first #SARSCoV2 sequences would be more similar to bat coronaviruses, and as #SARSCoV2 continued to evolve it would become more divergent from these ancestors. But that is *not* the case! (8/n)

        6 replies 212 retweets 836 likes
        Show this thread
      9. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Instead, early Huanan Seafood Market #SARSCoV2 viruses are more different from bat coronaviruses than #SARSCoV2 viruses collected later in China and even other countries. @lpipes @ras_nielsen give nice technical analysis at https://academic.oup.com/mbe/article/38/4/1537/6028993 … (9/n)

        7 replies 196 retweets 791 likes
        Show this thread
      10. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        The conundrum is easily seen by plotting the relative differences from the bat coronavirus RaTG13 outgroup versus collection date for early #SARSCoV2. See how the first reported viruses from Wuhan (leftmost blue points) aren’t the closest to RaTG13. (10/n)pic.twitter.com/YuVp4efUNq

        11 replies 146 retweets 586 likes
        Show this thread
      11. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Same result if we use other bat coronaviruses like RpYN06 or RmYN02. To see this, go to https://jbloom.github.io/SARS-CoV-2_PRJNA612766/deltadist.html … for an interactive plot that allows you to select the bat coronavirus outgroup and mouse over points for strain details. (11/n)

        3 replies 65 retweets 414 likes
        Show this thread
      12. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        How do deleted sequences I recovered relate to this conundrum? If we include those sequences, and note 4 sequences from Guangdong are from two groups of people infected in Wuhan in late Dec / early Jan, we get plausible scenarios that resolve above problems. (12/n)

        1 reply 72 retweets 460 likes
        Show this thread
      13. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        These two scenarios are plotted below. Each has a different “progenitor”, which is the sequence that gave rise to all *currently* known #SARSCoV2 sequences (still may not be virus that infected patient zero if other early sequences remain unknown). (13/n)pic.twitter.com/3k7eHrgNgf

        9 replies 107 retweets 508 likes
        Show this thread
      14. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Both putative progenitors have 3 mutations relative to Seafood Market viruses that make them more similar to bat coronavirus. One is progenitor inferred by @kumar_lab @sergeilkp et al (https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab118/6257226 …), other has C8782T, T28144C, and C29095T relative to Wuhan-Hu-1. (14/n)

        4 replies 82 retweets 427 likes
        Show this thread
      15. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Both progenitors suggest #SARSCoV2 was circulating in Wuhan before December outbreak at Huanan Seafood Market, which is corroborated by lots of other evidence, including news articles from China in early 2020 (see intro to my paper linked in first Tweet in this thread). (15/n)

        11 replies 262 retweets 958 likes
        Show this thread
      16. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        There are also broader implications. First, fact this dataset was deleted should make us skeptical that all other relevant early Wuhan sequences have been shared. We already know many labs in China ordered to destroy early samples: https://www.scmp.com/news/china/society/article/3084635/china-confirms-unauthorised-labs-were-told-destroy-early … (16/n)pic.twitter.com/ajtm8SxfVu

        10 replies 283 retweets 1,136 likes
        Show this thread
      17. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Sequence sharing could be further limited by fact that scientists in China are under an order from the State Council requiring central approval of all publications: https://apnews.com/article/united-nations-coronavirus-pandemic-china-only-on-ap-bats-24fbadc58cee3a40bca2ddf7a14d2955 … (17/n)pic.twitter.com/rGwfFUONTn

        2 replies 111 retweets 608 likes
        Show this thread
      18. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Second major implication is that it may be possible to obtain additional information about early spread of #SARSCoV2 in Wuhan even if efforts for more on-the-ground investigations are stymied. (18/n)

        2 replies 89 retweets 535 likes
        Show this thread
      19. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Scientific communication and data sharing typically rely on trust. The NIH Sequence Read Archive has >13,000,000 runs, so they have to trust authors when they request deletions as not feasible to validate reasons for all requests, some of which are legitimate. (19/n)

        2 replies 60 retweets 457 likes
        Show this thread
      20. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        In case of data set I describe above, it seems possible that trust that the NIH Sequence Read Archive grants to scientific authors to delete data may have been used to obscure sequences informative for understanding early #SARSCoV2. (20/n)

        2 replies 88 retweets 517 likes
        Show this thread
      21. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Fortunately, Sequence Read Archive has rigorous data tracking enabling them to determine when data deleted & stated justification by authors. In fact, @NIHDirector @NCBI have already determined this & generously shared info w me, but will let them share more widely. (21/n)

        7 replies 73 retweets 540 likes
        Show this thread
      22. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        It is important to examine if other trust-based systems in science conceivably may have also been used to hide data relevant to origins / early spread of #SARSCoV2. This includes not only looking more at sequence databases, but also paper reviews, grant reporting, etc. (22/n)

        3 replies 101 retweets 587 likes
        Show this thread
      23. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Third major implication is that scientists need to stay focused on data-driven study of #SARSCoV2 origins / early spread. After spending the last 4 months studying this closely, I am cautiously optimistic that additional relevant data are still likely to come to light. (23/n)

        1 reply 93 retweets 662 likes
        Show this thread
      24. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        We should therefore avoid dogmatic arguments about #SARSCoV2 origins / early spread, and instead focus on following two questions: (1) How can we get more data? (2) How can we better analyze the data we have? (24/n)

        12 replies 162 retweets 1,052 likes
        Show this thread
      25. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Finally, my analysis is on GitHub at https://github.com/jbloom/SARS-CoV-2_PRJNA612766 … where you can access all code, data, & paper drafts. All updates are via time-stamped commits. This ensures transparency/reproducibility of this study are not in doubt, regardless of your views on interpretation. (25/n)

        39 replies 216 retweets 1,311 likes
        Show this thread
      26. Bloom Lab‏ @jbloom_lab 22 Jun 2021

        Bloom Lab Retweeted Bloom Lab

        https://twitter.com/jbloom_lab/status/1407542296497688580 …

        Bloom Lab added,

        Bloom Lab @jbloom_lab
        A short addendum to my pre-print on early Wuhan #SARSCoV2 sequences deleted from the Sequence Read Archive (https://twitter.com/jbloom_lab/status/1407445604029009923 …), courtesy of an anonymous Twitter user. (1/n)
        Show this thread
        22 replies 34 retweets 242 likes
        Show this thread
      27. End of conversation

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