BF.31.1/BQ.1.10* Recombinant (>55 seq, Apr 13)

[ryhisner]

Description

Earliest sequence: 2022-12-28, Chile, Nuble — EPI_ISL_16743083
Most recent sequence: 2023-2-2, Chile, Nuble — EPI_ISL_16942046, EPI_ISL_16942049, EPI_ISL_16942050
Countries circulating: Chile (all 21)
Number of Sequences: 12
GISAID Query: NSP8_A74T, Spike_S247N, Spike_Y248del, Spike_N460K, Spike_K444T
GISAID Nucleotide Query: G12311A, T22348A
CovSpectrum Query: [4-of: A11126G, G12311A, T22348A, C27600T, T28282C]
Substitutions on top of BF.31.1/BQ.1.10:
ORF1a: M3621V, A4016T
Nucleotide: A11126G, G12311A, T22348A, T28282C
Breakpoint: Between 22304 and 22893 (S:248 and S:444)

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/BF.31.1%2CBQ.1_21seq_subtreeAuspice1_genome_43e16_1610.json

Evidence
Pretty clear breakpoint somewhere in 22304-22893. In addition to ORF1a:M3621V and ORF1a:A4016T, 14/21 sequences have S:A262S. Peculiarly, two of the three nucleotides at S:262 are mutated, including the synonymous mutation T22348A, which has only appeared in 41 other sequences in the last six months.

The presence of C26700T, along with the relatively high prevalence of BQ.1.10 in Chile is what makes me think the 3' end of this recombinant comes from BQ.1.10.

Genomes

Genomes

EPI_ISL_16654149, EPI_ISL_16660713, EPI_ISL_16740976, EPI_ISL_16741051, EPI_ISL_16741053, EPI_ISL_16743083, EPI_ISL_16761006, EPI_ISL_16833908, EPI_ISL_16833909, EPI_ISL_16833913-16833914, EPI_ISL_16847302, EPI_ISL_16847304-16847306, EPI_ISL_16935366, EPI_ISL_16935367, EPI_ISL_16935369, EPI_ISL_16942046, EPI_ISL_16942049, EPI_ISL_16942050

[ryhisner]

30 sequences now, but still confined to Chile.

[ryhisner]

This lineage has continued to show up in Chile with 12 sequences collected in March so far, but today the first sequence from outside of South America showed up in South Korea. EPI_ISL_17373830

The South Korean sequence is on the 2-nuc S:A262S branch and has a few additional mutations not found thus far in the Chilean sequences: ORF1a:N1042S, ORF1b:E1264D, and ORF1b:N1684H (NSP3_N224S, NSP13_E341D, and NSP14_N160H).

[ryhisner]

First sequence of this recombinant from Europe was uploaded today from France. EPI_ISL_17383910

[InfrPopGen]

Thanks for submitting. We've added recombinant lineage XCB with 46 newly designated sequences, and 0 updated. Defining mutations A11126G (ORF1a:M3621V), G12311A (ORF1a:A4016T), C14724T, G18651A, T22348A, C27600T, T28282C (following T22942A (S:N460K)).