Sublineage of BA.5.2 (ORF1b:T1050N) with S:K444T, S:L981I, ORF1a:A2249V, ORF1a:L3829F, & ORF1b:S1182L (54 seq, Nov 16)

[ryhisner]

Description

Sub-lineage of: BA.5.2
Earliest sequence: 2022-9-12, Australia, South Australia — EPI_ISL_15052933
Most recent sequence: 2022-10-19, Australia, Victoria — EPI_ISL_15532081
Countries circulating: Australia (19), New Zealand (1)
Number of Sequences: 20
GISAID Query: Spike_K444T, Spike_L981I, NSP6_L260F, NSP3_A1431V
CovSpectrum Query: Nextcladepangolineage:BA.5.2* & S:K444T & S:L981I & ORF1a:L3829F & ORF1b:T1050N
Substitutions on top of BA.5.2:
Spike: K444T, L981I
ORF1a: L3829F
ORF1b: S1182L
Nucleotide: C1426T, C7011T, C11750T, C17012T, A22893C, T24352C, C24503A, C26873T

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/BA.5.2%20%2B%20K444T%20%2B%20L981I%20%2B%20ORF1aL3829F%20%2B%20ORF1bS1182L%20-%20subtreeAuspice1_genome_3321c_efdb70.json

Evidence
This lineage appears to be growing quickly, with 9 of the current 20 sequences being uploaded last week. The advantage granted by S:K444T is beyond doubt at this point, as is that of ORF1b:T1050N. It’s less obvious that ORF1a:L3829F (NSP6_L260F) is advantageous, but it has evolved independently many times, including in quite a few chronic-infection cases, which is usually a sign that a mutation confers some sort of advantage.

There are eight nucleotide mutations leading up to this lineage—seven of which are interrupted by only two sequences—yet 13 of the 20 sequences are identical, with the other seven only differing from the rest by a single nucleotide. As @corneliusroemer has said many times, this is an indication of rapid growth.

S:L981F was in BA.1, and in their study “Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2,” Theo Sanderson and others found that S:L981F enhanced spike-mediated infection. I have no idea if the same would be true of S:L981I, but it seems possible given how little change there has been in S2 in BA.5.2 relative to BA.1. https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(22)00352-3

Genomes

Genomes

EPI_ISL_15185602, EPI_ISL_15300998, EPI_ISL_15300999, EPI_ISL_15323089, EPI_ISL_15357354, EPI_ISL_15357765, EPI_ISL_15357804, EPI_ISL_15357828, EPI_ISL_15416367, EPI_ISL_15416489, EPI_ISL_15429954, EPI_ISL_15472690, EPI_ISL_15476081, EPI_ISL_15476251, EPI_ISL_15531494, EPI_ISL_15531496, EPI_ISL_15531856, EPI_ISL_15532081, EPI_ISL_15532685, EPI_ISL_15532726

[FedeGueli]

Another seequence uploaded today from Australia EPI_ISL_15578279.
It is going. great catch and proposal Ryan

[ryhisner]

One more from Australia today that had the additional spike mutation A263S. EPI_ISL_15641084

[FedeGueli]

23 seqs as today right @ryhisner ?

[ryhisner]

14 sequences uploaded today from Australia, bringing the total to 45 sequences.

[FedeGueli]

I SEE 64 SEQS OF THIS ONE NOW

[InfrPopGen]

Thanks for submitting. We've added lineage BA.5.2.42 with 50 newly designated sequences, and 0 updated designations. Defining mutations C17012T (ORF1b:S1182L), C24503A (S:L981I) (following C26873T on current tree).