Slack / Private Message Drop — page 424

[2021-01-19 04:44:50] [Andrew Rambaut] [thread - ID: 2021-01-19 04:44:50] What is the nucleotide sequence? Is there a repeat? Could it be a slippage (forwards for deletion, backwards to insert). [2021-01-19 05:30:28] [Robert Garry] Have to be on a CEPI call at 7:30, but well get more info shortly.. [2021-01-19 06:37:52] [Robert Garry] Still sorting this out - these are the pango sequences on GenBank - clearly something going on with indel regions. [shared file(s): image.png] [2021-01-19 06:46:23] [Robert Garry] QHR63300 is of course RatG13 [2021-01-19 07:59:43] [Robert Garry] !channel This alignment boils it down: Cell culture passage of a GX virus backfills the B1.1.7 like delH69V70. PangoGD has a single aa deletion in indel region 2. GD pango has a deletion in IR3 close to de145Y in B1.1.7. GD pago also has an Indel region 5 deletion and one of the pango Gxs has a IR6 deletion. As Tommy notes the cell culture backfill in IR2 by the vero passed Gx virus is important. He should write this up or we should bring him on to the virological post. [2021-01-19 08:00:44] [Robert Garry] !channel This alignment boils it down: Cell culture passage of a GX virus backfills the B1.1.7 like delH69V70. PangoGD has a single aa deletion in indel region 2. GD pango has a deletion in IR3 close to de145Y in B1.1.7. GD pago also has an Indel region 5 deletion and one of the pango Gxs has a IR6 deletion. As Tommy notes the cell culture backfill in IR2 by the vero passed Gx virus is important. He should write this up or we should bring him on to the virological post. [shared file(s): image.png] [2021-01-19 09:45:06] [Robert Garry] >QIG55945.1 surface glycoprotein [Pangolin coronavirus GD2019]; ```>QIQ54048.1 spike protein [Pangolin coronavirus GX-P2Vcell culture] >QIA48623.1 spike protein [Pangolin coronavirus GX2017 GX-P1E] >QIA48614.1 spike protein [Pangolin coronavirus GX-P4L]``` GD2019 aka isolate MP789: QIG55945.1, MT121216.1; GX-P2Vcell culture: QIQ54048.1, MT072864.1; GX-P1E: QIA48623.1, MT040334.1; GX-P4L: QIA48614.1, MT040333.1 [2021-01-19 09:50:24] [Robert Garry] [thread - ID: 2021-01-19 04:44:50] @Andrew Rambaut Nucleotide sequences IDs below agree this could be slippage/copy choice error ... [2021-01-19 10:05:40] [Robert Garry] In the figure as drawn I used Pango GD QIG55945.1 and for Pango GX I used QIA48623.1, which happens to have the 2 aa del in IR6. If Tommy wants to write up his own post maybe we could just refer to this data and not modify the figure. If Tommy wants to come on to the Ruff post I'd add the Vero passed GX virus to the figure.