Potential BA.2*/BA.5.1 recombinant (67 sequences as of 2022-07-28, Ireland, Croatia, Germany, France, Portugal, Greece, Israel, Spain, Denmark, Canada, Switzerland, Canada and the US)

[c19850727]

I'm to propose this small cluster of BA.5.1 recombinants for monitoring purpose as it has been picked up in 3 countries now.

Description

Recombinant between: BA.2* & BA.5.1*
Earliest sequence: 2022/05/10 (Spain-AS)
Most recent sequence: 2022/05/27 (Denmark)
Countries circulating: Spain (IB, AS, PV), Denmark and Switzerland
Likely breakpoint: anywhere downstream of 12160 (or 17822?) and upstream of 21765.
Mutations on branch: C7973A (ORF1a:L2570M), C17822T (ORF1b:P1452L), T27696C

Conserved Nuc mutations:

Evidence of potential BA.2 donor: reversion A12160G and C9866T.
Evidence of potential BA.5.1 donor: C29666T (ORF10:L37F)
Cov-spectrum query: C7973A, C17822T, T27696C, A12160G, C9866T, C29666T
GISAID query: Spike_F486V, NSP3_L1752M, NSP13_P529L, NSP4_L438F

Evidence

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_147e2_d46cb0.json?branchLabel=nuc%20mutations&c=gt-nuc_7973&label=nuc%20mutations:T27808C

Genomes:

EPI_ISL_13067124, EPI_ISL_13107749, EPI_ISL_13107759, EPI_ISL_13114110, EPI_ISL_13251121, EPI_ISL_13342923, EPI_ISL_13343310

[liamxg]

by mutation sites or recombination regions?

[FedeGueli]

Hi @c19850727 great catch i found the putative parental BA.2 sublineage curculating in Demmark and it has also A18163G. so the breakpoint is after that nucleotide
https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=orf1b%3A1452L%2Corf1a%3A2570M%2CS%3A486F&pangoLineage=BA.2*&

Parental BA.2 ids:

gisaidEpiIsl

EPI_ISL_11807645
EPI_ISL_12345222
EPI_ISL_11806369
EPI_ISL_11833311
EPI_ISL_11990568
EPI_ISL_12286850
EPI_ISL_11990885

it was characterized by the two orf1ab mutarions described here plus N:T334I

Edited:
we were 'lucky' this putative parental BA.2 has
C19862T that is missing in the recombinant so we can identify with good confidence that thw breakpoint is between A18163G and C19862T

[c19850727]

One more sequence from Netherland: EPI_ISL_13369802. 8 in total.

[c19850727]

One more sequence from Canada-BC: hCoV-19/Canada/BC-BCCDC-451464/2022

[c19850727]

12 sequences as of 2022-06-26. Newly found in US-CA and Canada-QC.

[c19850727]

14 sequences as of 2022-06-27. Newly found in Spain-MD (the previous Spanish ones were from PV, AS and IB)

[c19850727]

24 sequences as of 2022-07-07. Newly found in Italy.

[c19850727]

27 sequences as of 2022-07-08. Newly found in Canada-un (surveillance of international border crossing)

[c19850727]

29 sequences as of 2022-07-09. Newly found in Israel.

[c19850727]

37 sequences as of 2022-07-14. Newly found in Greece.

[AngieHinrichs]

Great find @FedeGueli with those Denmark BA.2 > C22792T > C7973A > C19862T > C26681T > C29274T > C17822T sequences! (regarding A18163G, I think that is common to all BA.*, so I think the breakpoint uncertainty region starts at 17823)

[FedeGueli]

Thx @AngieHinrichs !

[c19850727]

43 sequences as of 2022-07-19. Newly found in Portugal and France.

[c19850727]

50 sequences as of 2022-07-19. Newly found in Germany and Canada-ON.

[c19850727]

62 sequences as of 2022-07-27. Newly found in Croatia.

[corneliusroemer]

Seems to be worth designating now? @chrisruis @InfrPopGen

Here's a query for the BA.2 donor part - seems to be vanilla BA.2, most common in Italy.

https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?nucMutations=7973A%2C9866T%2C6336.%2C1302.%2C2388.&pangoLineage=BA.2*&

[c19850727]

67 sequences as of 2022-07-28. Newly found in Ireland.

[InfrPopGen]

Thanks for submitting. We've added recombinant lineage XAN with 35 newly designated sequences, and 4 updated designations.