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Potential BA.2*/BA.1* Recombinant with Likely Breakpoint at ORF3a/M Protein (50 Seqs as of 2022-05-31 in Czech, Germany and UK) #607

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c19850727 opened this issue May 7, 2022 · 5 comments
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Potential BA.2*/BA.1* Recombinant with Likely Breakpoint at ORF3a/M Protein (50 Seqs as of 2022-05-31 in Czech, Germany and UK) #607

c19850727 opened this issue May 7, 2022 · 5 comments
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designated recombinant recombinant proposal
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XAD

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@c19850727
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c19850727 commented May 7, 2022 •
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Although this potential recombinant sublineage doesn't meet the minimum criteria of 50 sequences, I thought it's still worth proposing considering it is recently re-emerging in Germany, 2 months after the first sampling in Czech Republic.

Description

Recombinant between: BA.2* & BA.1*
Earliest sequence: 2022/2/7 (Czech)
Most recent sequence: 2022/4/23 (Germany-NW)
Countries circulating: Czech Republic, UK (England), Germany (NW, ST, BY, BB, BE, SN, SH)
Likely breakpoint: between 26063 and 26528 (ORF3a-M).
Mutations on branch: A1250G (ORF1a:T329A)

Conserved Nuc mutations (those in red frames are likely from the donor from the BA.1 side):
image
Cov-spectrum query: A1250G, C26060T, A26530G, 29510A
GISAID query: M_D3G, NS3_T223I, NSP1_S135R, NSP2_T149A

Evidence

Usher tree:
image
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6e05_5d0ab0.json?branchLabel=nuc%20mutations&c=gt-nuc_1250&label=nuc%20mutations:A28877T,G28878C
(btw, the sibling branch is another interesting potential recombinant cluster I've been watching)

Genomes:

EPI_ISL_10132609, EPI_ISL_10735086, EPI_ISL_10795404, EPI_ISL_11327010, EPI_ISL_11327042, EPI_ISL_11343555, EPI_ISL_11343558, EPI_ISL_11472699, EPI_ISL_11472708, EPI_ISL_11472716, EPI_ISL_11472718, EPI_ISL_11473842, EPI_ISL_11478141, EPI_ISL_11614122, EPI_ISL_11614143, EPI_ISL_11620507, EPI_ISL_11642864, EPI_ISL_11658829, EPI_ISL_11664909, EPI_ISL_11673455, EPI_ISL_11817720, EPI_ISL_11905953, EPI_ISL_12015556, EPI_ISL_12023459, EPI_ISL_12026868, EPI_ISL_12085810, EPI_ISL_12186938, EPI_ISL_12193107, EPI_ISL_12200175, EPI_ISL_12256760, EPI_ISL_12333989, EPI_ISL_12361039, EPI_ISL_12519103, EPI_ISL_12520176, EPI_ISL_12520201, EPI_ISL_12520318, EPI_ISL_12520382, EPI_ISL_12523233
@corneliusroemer corneliusroemer added the recombinant recombinant proposal label May 8, 2022
@c19850727 c19850727 changed the title Potential BA.2*/BA.1* Recombinant with Likely Breakpoint at ORF3a/M Protein (38 Seqs as of 2022-05-06 in Czech, Germany and UK) Potential BA.2*/BA.1* Recombinant with Likely Breakpoint at ORF3a/M Protein (39 Seqs as of 2022-05-11 in Czech, Germany and UK) May 12, 2022
@c19850727
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39 sequences as of 2022-05-11. The latest one was from Czech.

@c19850727
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42 sequences as of 2022-05-16, and now also found in Slovakia.

@c19850727 c19850727 changed the title Potential BA.2*/BA.1* Recombinant with Likely Breakpoint at ORF3a/M Protein (39 Seqs as of 2022-05-11 in Czech, Germany and UK) Potential BA.2*/BA.1* Recombinant with Likely Breakpoint at ORF3a/M Protein (48 Seqs as of 2022-05-27 in Czech, Germany and UK) May 28, 2022
@c19850727
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48 sequences as of 2022-05-27, and newly found in Peru.

@c19850727 c19850727 changed the title Potential BA.2*/BA.1* Recombinant with Likely Breakpoint at ORF3a/M Protein (48 Seqs as of 2022-05-27 in Czech, Germany and UK) Potential BA.2*/BA.1* Recombinant with Likely Breakpoint at ORF3a/M Protein (50 Seqs as of 2022-05-31 in Czech, Germany and UK) May 31, 2022
@chrisruis chrisruis added the accepted A proposal for a new lineage has been accepted and will be designated. label Jun 13, 2022
chrisruis added a commit that referenced this issue Jun 13, 2022
@chrisruis
Added new lineage XAD from #607 with 39 new sequence designations and…
6d151fe 
… 3 updated from BA.2
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Thanks @c19850727 We've added this as XAD

@chrisruis chrisruis added this to the XAD milestone Jun 13, 2022
@chrisruis chrisruis added designated and removed accepted A proposal for a new lineage has been accepted and will be designated. labels Jun 13, 2022
@JosetteSchoenma
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XAD

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@corneliusroemer @chrisruis @c19850727 @JosetteSchoenma