Potential BA.2/BA.5 recombinant (53 sequences as of 2022-08-05)

[c19850727]

Description

Recombinant between: BA.2* and BA.5*
Earliest sequence: 2022/06/10 (Israel)
Most recent sequence: 2022/07/25 (Italy)
Countries circulating: Israel, Sweden, New Zealand, Indonesia, Metropolitan France, France-Reunion, UK (England, Scotland), Canada (ON), US (OH, NJ, NE, MA, CA)

Likely breakpoint: 15960-17278 (NSP12/NSP13)
Private mutations: C6606T (ORF1a:S2114F), C15960T, G17278T (ORF1b:V1271L), T27889C (reversion from BA.5)
GISAID query: NSP3_S1296F, NSP13_V348L, Spike_F486V, M_D3, NSP4_L438F
Cov-spectrum query: C6606T, C15960T, G17278T, T27438C, T27889C

Evidence

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_18445_dc64f0.json?branchLabel=aa%20mutations&c=gt-nuc_9866&label=nuc%20mutations:C6606T

Genomes:

EPI_ISL_13354671, EPI_ISL_13424883, EPI_ISL_13442003, EPI_ISL_13604020, EPI_ISL_13620086, EPI_ISL_13702250, EPI_ISL_13738377, EPI_ISL_13739835, EPI_ISL_13742694, EPI_ISL_13744106, EPI_ISL_13744179, EPI_ISL_13764258, EPI_ISL_13782164, EPI_ISL_13784137, EPI_ISL_13797890, EPI_ISL_13806199, EPI_ISL_13823541, EPI_ISL_13838880, EPI_ISL_13839521, EPI_ISL_13839674, EPI_ISL_13873644, EPI_ISL_13875529, EPI_ISL_13875951, EPI_ISL_13896299, EPI_ISL_13947961-13947962, EPI_ISL_14021587, EPI_ISL_14022635, EPI_ISL_14022637, EPI_ISL_14022643, EPI_ISL_14022646-14022647, EPI_ISL_14027978, EPI_ISL_14032339, EPI_ISL_14067379, EPI_ISL_14074893, EPI_ISL_14080844, EPI_ISL_14095959, EPI_ISL_14096734, EPI_ISL_14105005, EPI_ISL_14131009, EPI_ISL_14171333, EPI_ISL_14184111, EPI_ISL_14187834, EPI_ISL_14194749, EPI_ISL_14196908, EPI_ISL_14200666, EPI_ISL_14212070, EPI_ISL_14224516, EPI_ISL_14228679, EPI_ISL_14268855, EPI_ISL_14275040-14275041

[corneliusroemer]

59 sequences now, probably worth designating? It's above 50 sequences and has quite some international spread.

[InfrPopGen]

Thanks for submitting. We've added recombinant lineage XAV with 59 newly designated sequences, and 2 updated designations from BA.5.