COVID-19 Records

Chat message

Slack / Private Message Drop, p.467 [SLACK_000681] · slack_pm:msg:04854

Page text: p.467 · original PDF

Date
2021-01-31 15:07
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.

Somthings off Virus name: hCoV-19/Denmark/DCGC-32298/2021 Accession ID: EPI_ISL_869302 Type: betacoronavirus GISAID Clade GH PANGO Lineage B.1.351 (version: 2021-01-22) AA Substitutions Spike A243del, Spike A701V, Spike D80A, Spike D215G, Spike D614G, Spike E484K, Spike K417N, Spike L18F, Spike L242del, Spike L244del, Spike N501Y, E P71L, N P13S, N T205I, NS3 Q57H, NS3 S171L, NSP2 T85I, NSP3 K837N, NSP5 K90R, NSP6 F108del, NSP6 G107del, NSP6 S106del, NSP12 P323L, NSP14 F240V, NSP14 V14L

In context

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

  1. 2021-01-31 15:02 Robert F. Garry open
    Ok now I'm confused...
  2. 2021-01-31 15:04 Andrew Rambaut open
    They (Tulio & co) are using some hokey bioinformatics that initially was very poor at indels.
  3. 2021-01-31 15:04 Kristian G. Andersen open
    Yeah, they're tricky. Definitely LLA (241-243) though - just checked the Danish genomes.
  4. 2021-01-31 15:06 Kristian G. Andersen open
    Here's what I have - I think somewhat accurate, although I'm not convinced some of the other mutations are really there... [shared file(s): Screen Shot 2021-01-31 at 3.05.48 PM.png]
  5. 2021-01-31 15:07 Robert F. Garry
    Somthings off Virus name: hCoV-19/Denmark/DCGC-32298/2021 Accession ID: EPI_ISL_869302 Type: betacoronavirus GISAID Clade GH PANGO Lineage B.1.351 (version: 2021-01-22) AA Substitutions Spike A243del, Spike A701V, Spike D80A, Spike D215G, Spike D614G, Spike E484K, Spike K417N, Spike L18F, Spike L242del, Spike L244del, Spike N501Y, E P71L, N P13S, N T205I, NS3 Q57H, NS3 S171L, NSP2 T85I, NSP3 K837N, NSP5 K90R, NSP6 F108del, NSP6 G107del, NSP6 S106del, NSP12 P323L, NSP14 F240V, NSP14 V14L
  6. 2021-01-31 15:08 Kristian G. Andersen open
    Yeah, those DEL assignments are wrong...
  7. 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
  8. 2021-01-31 15:09 Robert F. Garry open
    Here's one with LLA, but only three include LLA on GSAID.
  9. 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]

Full conversation →