Description
This is a relatively old recombinant cluster likely from India-MH that I used to be monitoring since August. I was surprised to see it's still growing after almost a month of hiatus in September/October, and this time in a geographically distant areas (mainly Canada and the US).
Interestingly this pattern of hiatus and reemergence is similar to #896 , which is another BA.2.76/BA.5.2* recombinant.
Description
Recombinant between: BA.2.76 and BF.3
Earliest sequence: 2022/07/25 (India-MH)
Most recent sequence: 2022/12/07 (Canada-ON)
Countries circulating: US (33 seqs), Canada (17 seqs), India (15 seqs), Denmark (5 seqs), Germany (1 seq), Maritius (1 seq), UK-Scotland (1 seq).
Likely breakpoint: between 22601 and 22915 (Spike S1)
Nuc mutations (those in red frames are likely from BA.2.76):
Likely donor from B.2.76 side: EPI_ISL_14988943 from India-MH (BA.2.76 with additional G19891A and A19812G)
Likely donor from BF.3 side: BF.3 with additional C27549T
GISAID and cov-spectrum query: C27549T, G24620T, C23202T, A19812G
Evidence
Usher tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_26d38_d09d20.json?branchLabel=Spike%20mutations&c=gt-nuc_19891&label=id:node_7264411
Genome:
EPI_ISL_14355946, EPI_ISL_14832149, EPI_ISL_14861661, EPI_ISL_14915762, EPI_ISL_14923215, EPI_ISL_14923226, EPI_ISL_14923237, EPI_ISL_14989096, EPI_ISL_15028332, EPI_ISL_15047992, EPI_ISL_15059096, EPI_ISL_15059167, EPI_ISL_15063868, EPI_ISL_15074003, EPI_ISL_15074108, EPI_ISL_15074115, EPI_ISL_15074192, EPI_ISL_15085366, EPI_ISL_15146825, EPI_ISL_15275372, EPI_ISL_15348746, EPI_ISL_15373833, EPI_ISL_15422688, EPI_ISL_15433369, EPI_ISL_15497617, EPI_ISL_15497635, EPI_ISL_15618796, EPI_ISL_15689056, EPI_ISL_15706030, EPI_ISL_15744932, EPI_ISL_15744934, EPI_ISL_15744936, EPI_ISL_15766235, EPI_ISL_15768444, EPI_ISL_15772791, EPI_ISL_15772992, EPI_ISL_15778901, EPI_ISL_15804951, EPI_ISL_15819065, EPI_ISL_15851020, EPI_ISL_15854670, EPI_ISL_15854679, EPI_ISL_15860299, EPI_ISL_15904857, EPI_ISL_15930330, EPI_ISL_15944329, EPI_ISL_15948596, EPI_ISL_15950139, EPI_ISL_15959665, EPI_ISL_15960138, EPI_ISL_15960173, EPI_ISL_15974648, EPI_ISL_15999557, EPI_ISL_16015652, EPI_ISL_16015736-16015737, EPI_ISL_16015987, EPI_ISL_16016029-16016030, EPI_ISL_16025058, EPI_ISL_16032429, EPI_ISL_16040373, EPI_ISL_16063881, EPI_ISL_16068527, EPI_ISL_16081997, EPI_ISL_16085765, EPI_ISL_16085836, EPI_ISL_16086636, EPI_ISL_16086640, EPI_ISL_16086767, EPI_ISL_16086779-16086780, EPI_ISL_16100942