Potential BA.1/BA.2 Recombinant with Likely Breakpoint at NSP10/NSP12 (28 Sequences in Denmark as of 2022-03-27)

[c19850727]

Description

Recombinant between: BA.1* & BA.2
Earliest sequence: 2022/1/31 (Denmark)
Most recent sequence: 2022/3/4 Denmark)
Countries circulating: Denmark
Likely breakpoint: between 13196 and 15713 (NSP10 to NSP12)
Conserved Nuc mutations and AA changes (those in red frames are likely from the donor from the BA.1 side):

Private mutations: C3583T
Cov-spectrum query: C3583T, T5386G, T13195C, C15714T, A20055G, C22792T

Evidence

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_15e47_b7b560.json?c=gt-nuc_3583&label=nuc%20mutations:A11537G,T12880C,T13195C

Genomes

EPI_ISL_9653629, 9653714, 9788858, 9859723, 10064888, 10094246, 10205420, 10210786, 10352947, 10633947, 10634868, 10677314, 10732655, 10807605, 10809722, 10810199, 10811843, 10859747

[c19850727]

28 sequences as of 2022-03-27, according to cov-spectrum.

[chrisruis]

Thanks @c19850727 We've just published some guidelines for recombinant lineages here. In most cases we expect new recombinant lineages to contain at least 50 sequences, however exceptions to this may arise if the recombinant has particular novelty or significance, with unusual breakpoints and/or parental lineages

From covSpectrum, it looks like there's 32 sequences in this lineage now, 31 of which are from Denmark. Given the large number of Denmark sequences, I'd suggest we don't designate this one for now. I'll close for now but can reopen if the clade grows in future

[c19850727]

Hi Chris, recently there were a few more sequences uploaded from Italy (EPI_ISL_12355295, EPI_ISL_12355398, EPI_ISL_12355448, EPI_ISL_12457594, EPI_ISL_12457595, EPI_ISL_12457597, EPI_ISL_12457598). The total count now is 41.

[corneliusroemer]

They look indeed to be the same recombinant. I'll reopen and have attached the monitor label. Appearance in Italy is very interesting because Italy sequences much less than Denmark and also it indicates spread.

[chrisruis]

Thanks @c19850727 I think the combination of several months circulation, a reasonable number of sequences and appearing in multiple countries supports a designation. We've added this as XV

[JosetteSchoenma]

XV