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mpxv-lineages / lineage-designation

Official place for proposals and details around monkeypox virus lineage designations
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Proposal for B.1 lineage with G175093A [35 seqs, 33x USA, 1x UK, 1x Germany] #24

Closed mbosm closed 2 years ago

mbosm commented 2 years ago

This is the largest branch on the tree, not counting already labeled lineages. https://nextstrain.org/groups/illinois-gagnon-private/monkeypox/0928

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This mutation carries the amino acid change OPG204: D188N

Earliest sample with firm date: 6/17/2022 Latest sample with firm date: 8/04/2022 (The german sample has only 08/2022 as a collection date)

All but one of the samples have secondary mutation C132520T. There are another two samples with G175093A but without C132520T, but they've been sorted elsewhere on the tree. They are hMPX/Human/USA/CA-LAC-PHL-MA00092 and MA00096.

mbosm commented 2 years ago

Oh, should probably put all the strain names, too, huh?

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strain | accession | date | country | division -- | -- | -- | -- | -- MPXV-USA-IL-IDPH-002 | OP536663 | 2022-08-04 | USA | Illinois MPXV-USA-IL-IDPH-016 | OP536677 | 2022-07-05 | USA | Illinois MPXV-USA-IL-IDPH-084 | OP536745 | 2022-07-06 | USA | Illinois MPXV-USA-IL-IDPH-071 | OP536732 | 2022-07-01 | USA | Illinois MPXV-USA-IL-IDPH-072 | OP536733 | 2022-06-30 | USA | Illinois MPXV-USA-IL-IDPH-011 | OP536672 | 2022-07-05 | USA | Illinois MPXV_USA_2022_IL0020 | OP225962 | 2022-06-02 (2022-06-01 - 2022-06-30) | USA | Illinois MPXV22/human/USA-OK-86 | OP351285 | 2022-07-27 | USA | Oklahoma MPXV22/human/USA-OK-66 | OP351281 | 2022-07-22 | USA | Oklahoma MPXV-USA-IL-IDPH-001 | OP536662 | 2022-07-23 | USA | Illinois MPXV-USA-IL-IDPH-008 | OP536669 | 2022-07-04 | USA | Illinois MPXV-USA-IL-IDPH-059 | OP536720 | 2022-07-06 | USA | Illinois MPXV-USA-IL-IDPH-035 | OP536696 | 2022-06-17 | USA | Illinois MPXV-USA-IL-IDPH-073 | OP536734 | 2022-06-30 | USA | Illinois MPXV/Germany/2022/RKI287 | OP270476 | 2022-08-31 (2022-08-04 - 2022-08-31) | Germany |   MPXV_USA_2022_IL0040 | OP303786 | 2022-06-02 (2022-06-01 - 2022-06-30) | USA | Illinois MpxV/human/USA/OH-UW-073812/2022 | OP257254 | 2022-08-01 (2022-08-01 - 2022-08-26) | USA | Ohio MPXV-USA-IL-IDPH-076 | OP536737 | 2022-07-01 | USA | Illinois MPXV-USA-IL-IDPH-070 | OP536731 | 2022-06-30 | USA | Illinois MpxV/human/USA/OH-UW-085701/2022 | OP310050 | 2022-08-01 (2022-08-01 - 2022-08-31) | USA | Ohio MpxV/human/USA/OH-UW-079847/2022 | OP169337 | 2022-07-10 (2022-07-01 - 2022-07-31) | USA | Ohio MpxV/human/USA/OH-UW-070426/2022 | OP123051 | 2022-07-10 (2022-07-01 - 2022-07-31) | USA | Ohio MPXV-USA-IL-IDPH-006 | OP536667 | 2022-07-06 | USA | Illinois MPXV_USA_2022_KY0001 | OP303788 | 2022-06-30 (2022-06-14 - 2022-06-30) | USA | Kentucky MPXV_USA_2022_IL0023 | OP225966 | 2022-06-30 (2022-06-01 - 2022-06-30) | USA | Illinois MPXV-USA-IL-IDPH-056 | OP536717 | 2022-07-09 | USA | Illinois MPXV-USA-IL-IDPH-077 | OP536738 | 2022-07-01 | USA | Illinois MPXV_USA_2022_MN0006 | OP451003 | 2022-07-01 (2022-07-01 - 2022-07-26) | USA | Minnesota MPXV_USA_2022_TN0004 | OP450988 | 2022-07-07 (2022-07-01 - 2022-07-31) | USA | Tennessee MPXV-USA-IL-IDPH-043 | OP536704 | 2022-06-22 | USA | Illinois MPXV_USA_2022_IL0028 | OP303783 | 2022-06-22 (2022-06-19 - 2022-06-30) | USA | Illinois hMpxV/UK/LMO-046a/2022 | OP390205 | 2022-07-26 | United Kingdom | Scotland MpxV/human/USA/WA-UW-082670/2022 | OP310053 | 2022-08-01 (2022-08-01 - 2022-08-26) | USA | Washington MPXV-USA-IL-IDPH-040 | OP536701 | 2022-06-22 | USA | Illinois MPXV-USA-IL-IDPH-005 | OP536666 | 2022-06-30 | USA | Illinois

emmahodcroft commented 2 years ago

Thank you so much for this @mbosm - and apologies it's taken us a while to get to it - it'll be going in very soon!