Potential BA.1*/BA.2* Recombinant with Likely Breakpoint at NSP6/NSP9 (62 Seqs as of 2022-05-19 in France, Israel, UK and US)

[c19850727]

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 multiple regions (especially in the US), 2 months after the first sampling (in France).

Description

Recombinant between: BA.1* & BA.2*
Earliest sequence: 2022/2/28 (France)
Most recent sequence: 2022/4/29 (US-NC)
Countries circulating: France, Israel, UK (Scotland), US (NJ, NC, DC, NY, PA, FL, MD)
Likely breakpoint: between 11540 and 12879 (NSP6-NSP9).
Mutations on branch: A1585G, T11049C (ORF1a:V3595A), C12085T (homoplasic), A22351G, C26058T (homoplasic)

Conserved Nuc mutations (those in red frames are likely from the donor from the BA.1 side):

Cov-spectrum query: T11049C, C12085T, A22351G, C26058T
GISAID query: N_S413R, NS3_T223I, NSP3_A1892T, NSP6_I189V, NSP6_V26A, NSP13_R392C

Evidence

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_59ac_5c90c0.json?branchLabel=nuc%20mutations&c=gt-nuc_12085&label=nuc%20mutations:C2470T

Genomes:###
EPI_ISL_11248486, EPI_ISL_11853906, EPI_ISL_11953320, EPI_ISL_11981157, EPI_ISL_12047966, EPI_ISL_12087269, EPI_ISL_12169920, EPI_ISL_12181532, EPI_ISL_12181916, EPI_ISL_12256119, EPI_ISL_12280646, EPI_ISL_12302275, EPI_ISL_12302321, EPI_ISL_12303240, EPI_ISL_12304717, EPI_ISL_12305005, EPI_ISL_12325537, EPI_ISL_12330186, EPI_ISL_12421170, EPI_ISL_12433854, EPI_ISL_12462094, EPI_ISL_12462213, EPI_ISL_12499373, EPI_ISL_12499906, EPI_ISL_12502489, EPI_ISL_12506477, EPI_ISL_12506641, EPI_ISL_12506834, EPI_ISL_12507171, EPI_ISL_12558951, EPI_ISL_12566224, EPI_ISL_12566254, EPI_ISL_12566304, EPI_ISL_12566309, EPI_ISL_12566311, EPI_ISL_12566330

[c19850727]

44 sequences as of 2022-05-09, with 8 new sequences uploaded from US-MD, PA, NJ, NC, RI, NH.

[c19850727]

48 sequences as of 2022-05-10. Latest batch were from US-DC and US-NC.

[c19850727]

50 sequences as of 2022-05-11.

[c19850727]

52 sequences as of 2022-05-12, and now found in one more US state (VA).

[c19850727]

56 sequences as of 2022-05-16, and now found in one more US state (MO).

[InfrPopGen]

Thanks for submitting. We've added recombinant lineage XY with 36 newly designated sequences, and 0 updated designations.

[JosetteSchoenma]

XY