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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 31 Aug 2021

    Bloom Lab Retweeted zeynep tufekci

    @zeynep, here are some more interesting early #SARSCov2 dates for you. Check out the description of the samples in the final published version of this paper (https://academic.oup.com/cid/article/71/15/713/5780800 …): "Eight COVID-19 pneumonia samples were collected from hospitals in Wuhan in January 2020." (1/3)https://twitter.com/zeynep/status/1432869196216651777 …

    Bloom Lab added,

    zeynep tufekciVerified account @zeynep
    New Spike Lee documentary about the pandemic opens with Ian Lipkin—Columbia virologist—saying he first heard about the outbreak on *December 15th*. Watched it three times to make sure I heard it right. Lee asks and Lipkin repeats the date. This is a big deal, no? December 15??? pic.twitter.com/nE355EALac
    Show this thread
    8:11 PM - 31 Aug 2021
    • 59 Retweets
    • 137 Likes
    • FataL Alexa El Demiurgo morgendorffer Fkssnc Lolo 🇺🇸 Khaled Talaat Zedd KlaasV
    9 replies 59 retweets 137 likes
      1. New conversation
      2. Bloom Lab‏ @jbloom_lab 31 Aug 2021

        See if you can spot difference in how same samples are described in PubMed Central version (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108196/pdf/ciaa203.pdf …), which would have been built from original peer-reviewed manuscript: "Eight COVID-19 were collected from hospitals in Wuhan from December 18 to 29, 2019." (2/3)

        1 reply 8 retweets 37 likes
        Show this thread
      3. Bloom Lab‏ @jbloom_lab 31 Aug 2021

        Journal early access version of manuscript, which would have been the peer-reviewed version, also says samples from December 18-29, 2019 (https://web.archive.org/web/20200308003758/https:/watermark.silverchair.com/ciaa203.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAmswggJnBgkqhkiG9w0BBwagggJYMIICVAIBADCCAk0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMUvB1YKwP2bcB5dTjAgEQgIICHhCVB_L3-QgfUyzQ5G-v68bJ1kHhDf8lLShRGqC9bK7DlebkU5yUv6DPXGfkYCHNhvUVkawokppu_0H1qyLMACdOSYBspS7NvV5gembGXwlwt9_Aci4waeoxJX96d777yav5KH7giT_Tx8xzQR26RlMHyFDq4oUhCej7jiTdl0H3JFPULiDU1FGeW9SA3EiSy4iKiLv4n2lyTBkTYF2LpQ59SKThu1vic0sPDTpTihihfPedjRnk3XoIHIWWRzO_SmC7gBYZs6i5kY-XfDUBRauvezNPPOcrwC7bcUCjJ4OEKa8ym9ssdhVlKHgB-UPbQLRaTZ285BTc5f1wWAjRRJX7Hkb7ik4A5qWkKnFePKsu_rRuJ_8cKRv9rfYJODY2VNeHGf3QyHrIC_xCSMjPRlTGpTD5aTdw2vIQuPzf9hLT44YBGKD0beExJUhqCMeq2i5yUn582z8MMW4LYKq-0qS49z0mjAGVjvpftdPVY-6MhhjL7KWz48RB69vFaMTqybNKmqKOg0NKxXLi4iq8C3orPY_sBKagy1GKGuvfz39pUkh6MyAwM1XPzKmzevfDKd8xHNyYGdRTK8F3ThZI4PTdvkMXSq0Tp8v3d3x6mpsUzQ0bd2ypmQ7KyUauEnH_AxfZ8nYIYq9KebygrgFHVqkHzUb2l53vE0rbYqQdy1twbFJCkIfGtRpIkQfl5izggBvLKWOw5yA7sLDrJJba …). There is no correction in journal, so presumably dates changed at post-peer review manuscript proofing stage. (3/3)

        2 replies 10 retweets 38 likes
        Show this thread
      4. Bloom Lab‏ @jbloom_lab 31 Aug 2021

        @acritschristoph, here is GitHub repo where I re-aligned the raw data from both the *.bam and *.sra files on Sequence Read archive: https://github.com/jbloom/SARS-CoV-2_Shen_et_al … I think I got pretty much the same mutations reported in the paper. I found these mutations puzzling, as I expected...

        1 reply 7 retweets 29 likes
        Show this thread
      5. Bloom Lab‏ @jbloom_lab 31 Aug 2021

        ... if they were early sequences, some of the mutations might be polarized towards bat coronavirus (RaTG13, RmYN02, etc). But although sequences have quite a few mutations relative to Wuhan-Hu-1, none are polarized towards bat coronaviruses.

        2 replies 9 retweets 33 likes
        Show this thread
      6. Bloom Lab‏ @jbloom_lab 31 Aug 2021

        They were also all lineage B, which would be surprising if you think (as I do) that lineage A is ancestral. But even if A not ancestral to B, still surprised that early lineage B seqs would not have some mutations polarized to bat coronaviruses as that must be where it came from.

        3 replies 10 retweets 38 likes
        Show this thread
      7. Bloom Lab‏ @jbloom_lab 31 Aug 2021

        I have *not* tried to connect these with early patients, but I think that's a good idea. Let me know if you succeed! Maybe @franciscodeasis tried this too?

        2 replies 4 retweets 39 likes
        Show this thread
      8. End of conversation
      1. New conversation
      2. Meme_Guru2020‏ @MGuru2020 31 Aug 2021
        Replying to @jbloom_lab @zeynep

        Are you referring to the following sequences: The family cluster - end of Dec. WIV02 - MN996527 WIV04 - MN996528 WIV05 - MN996529 WIV06 - MN996530 WIV07 - MN996531 HKU-SZ-002a - MN938384 HKU-SZ-005b - MN975262 The 3 versions of Wuhan-Hu-1: MN908947.1, MN908947.2, & MN908947.3

        2 replies 0 retweets 1 like
      3. Meme_Guru2020‏ @MGuru2020 31 Aug 2021
        Replying to @MGuru2020 @jbloom_lab @zeynep

        More on those 👇👇👇👇👇https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30154-9/fulltext …

        2 replies 0 retweets 2 likes
      4. Show replies
      1. Fkssnc‏ @FKssnc 4 Sep 2021
        Replying to @jbloom_lab @zeynep

        It can be earlier, if the project determined in 2018 is correctly estimatedIt can be earlier, if the project determined in 2018 is correctly estimated

        0 replies 0 retweets 0 likes
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      2. Thread Reader App‏ @threadreaderapp 11 Sep 2021
        Replying to @Dali_Yang

        Hello, you can read it here: @zeynep, here are some more interesting early #SARSCov2 dates for… https://threadreaderapp.com/thread/1432903935312818178.html … See you soon. 🤖

        0 replies 0 retweets 0 likes
      3. End of conversation

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