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Slack / Private Message Drop, pp.77-78 [SLACK_000291] · slack_pm:msg:00782

Page text: p.77, p.78 · original PDF

Date
2020-06-13 09:35
Type
chat message · slack
recipient
Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker
Andrew Rambaut
Topics
Furin cleavage site and molecular featuresNatural origin / zoonotic spillover

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Jotting down some of the new stuff: Bill's potential source of the furin site - perhaps could dig into that more. Looks like SARS-CoV-2 can infect and readily transmit in mink (in the Netherlands). https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.23.2001005#html_fulltext - some severe disease too. Infects cats. So broad host range. Look into that press-release about infecting fruit bats (and cats). Recombination of RBD variable loop out of RaTG13 rather than in to SARS-CoV-2 from pangolins. Large variety of pangolin viruses (these are illegally imported from SE Asia - so where are they getting them from). Seems to readily loose furin site in cell culture. Really odd mutation patterns with lots of C->T and A->T, much higher NSyn/Syn ratio than you would expect? RmYN02 being closer in ORF1ab but recombines out in the rest - tell us something but not sure what just yet. Deletions in the accessory genes - suggests ORF7 & 8 maybe don't have much function in humans - somebatty thing?

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StatementGradeAttributionStance
Jotting down some of the new stuff: Bill's potential source of the furin site - perhaps could dig into that more. needs context uncertain explicit hedge asserts
Large variety of pangolin viruses (these are illegally imported from SE Asia - so where are they getting them from). own voice, substantive speaker_own asserts

In context

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  1. 2020-06-13 08:48 Robert F. Garry open
    "time for an update review - there is lots of new stuff to think about.":beer:
  2. 2020-06-13 09:35 Andrew Rambaut
    Jotting down some of the new stuff: Bill's potential source of the furin site - perhaps could dig into that more. Looks like SARS-CoV-2 can infect and readily transmit in mink (in the Netherlands). https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.23.2001005#html_fulltext - some severe disease too. Infects cats. So broad host range. Look into that press-release about infecting fruit bats (and cats). Recombination of RBD variable loop out of RaTG13 rather than in to SARS-CoV-2 from pangolins. Large variety of pangolin viruses (these are illegally imported from SE Asia - so where are they getting them from). Seems to readily loose furin site in cell culture. Really odd mutation patterns with lots of C->T and A->T, much higher NSyn/Syn ratio than you would expect? RmYN02 being closer in ORF1ab but recombines out in the rest - tell us something but not sure what just yet. Deletions in the accessory genes - suggests ORF7 & 8 maybe don't have much function in humans - somebatty thing?
  3. 2020-06-13 10:08 Robert F. Garry open
    Well done Kristian [to BBC] and Andrew [above}! Andrew's list is great - I don't see anything that points to active[cloning] or passive [cell or animal passage] lab manipulation however for balance we could put in some of Kristian's points above. [shared file(s): 220px-Leafy_Seadragon_on_Kangaroo_Island.jpg]
  4. 2020-06-13 10:24 Andrew Rambaut open
    We just resubmitted our revised MS on the 'distal' origin. I added a new figure to supplementary on the variable loop recombination: [shared file(s): image.png]
  5. 2020-06-13 10:31 Andrew Rambaut open
    Shows better how the pangolin distance is exactly the same in the variable as the rest of the CTD whereas RaTG13jumps out.

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