COVID-19 Records

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Slack / Private Message Drop, p.468 [SLACK_000682] · slack_pm:msg:04860

Page text: p.468 · original PDF

Date
2021-01-31 15:12
Type
chat message · slack
recipient
Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut
speaker
Robert F. Garry

Recipients on this medium are inferred from channel membership, not per-message addressing.

Needs to be fixed on GSAID

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

  1. 2021-01-31 15:08 Robert F. Garry open
    irus name: hCoV-19/South Africa/KRISP-EC-K006856/2020 Accession ID: EPI_ISL_736936 Type: betacoronavirus GISAID Clade GH PANGO Lineage B.1.351 (version: 2021-01-22) AA Substitutions Spike A243T, Spike A701V, Spike D80A, Spike D215G, Spike D614G, Spike E484K, Spike K417N, Spike L18F, Spike L241del, Spike N501Y, Spike Q239del, Spike T240del, E P71L, N T205I, NS3 Q57H, NS3 S171L, NSP2 T85I, NSP3 K837N, NSP5 K90R, NSP6 F108del, NSP6 G107del, NSP6 S106del, NSP12 M124I, NSP12 P323L Passage details/history: Original
  2. 2021-01-31 15:09 Robert F. Garry open
    Here's one with LLA, but only three include LLA on GSAID.
  3. 2021-01-31 15:10 Kristian G. Andersen open
    Here's the full alignment from RSA - the deletion is out of frame, so that's probably why there's some confusion. LLAis definitely what's deleted, so that's 241-243. This fucking virus... [shared file(s): Nucleotide alignment.geneious]
  4. 2021-01-31 15:11 Robert F. Garry open
    Actually happy to hear all this !
  5. 2021-01-31 15:12 Robert F. Garry
    Needs to be fixed on GSAID
  6. 2021-01-31 15:15 Kristian G. Andersen open
    And NextStrain... And Covariats... I'll make sure we get it right on Outbreak.info :wink:
  7. 2021-01-31 15:16 Robert F. Garry open
    But now I need to unfix the Christmas Card.:rage4:
  8. 2021-01-31 15:16 Kristian G. Andersen open
    Sorry Bob...
  9. 2021-01-31 15:17 Robert F. Garry open
    It what I got when I did the alignment myself which is why it shows up in our virological post that way. Somehow Ithought I got it wrong.

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