Sublineage of BA.5.2.20 (or less likely BA.5.2.36) with S:N148S, S:K150E, S:N334K, S:444T & ORF1a:E726K (34 seq)

[ryhisner]

Description

Sub-lineage of: BA.5.2.20
Earliest sequence: 2022-9-28, Sweden, Stockholm — EPI_ISL_15307037
Most recent sequence: 2022-10-13, Sweden, Skane — EPI_ISL_15479721, & Stockholm — EPI_ISL_15485325
Countries circulating: Sweden
Number of Sequences: 9
GISAID Query: Spike_N148S, Spike_K150E, Spike_N334K, NSP2_E546K
CovSpectrum Query: Nextcladepangolineage:BA.5.2.20* & S:N148S & S:K150E & S:N334K
Substitutions on top of BA.5.2.36:
Spike: N148S, K150E, N334K, K444T
ORF1a: E726K
Nucleotide: G2441A, T6067C, A22005G, A22010G, C22564A, A22893C

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/BA.5.2_%2B_N148S%2CK150E%2CN334K%2CK444T%2CORF1aE762K_v.2_subtreeAuspice1_genome_aa5b_700b80.json

Evidence
It looks like a mini-saltation from BA.5.2.20 led to this lineage, most likely from a long-term infection in one individual. One of the nine sequences is placed earlier in the tree, without K444T, but it has zero RBM coverage, so it almost certainly belongs with the other eight, meaning all nine sequences here are identical. This suggests rapid growth, though numbers are too small to be sure about anything yet.

Six of the sequences here are from Stockholm, but three of the most recent four have been from Skane. Skane appears to be a county in the extreme south of Sweden, over 300 miles away from Stockholm, so it seems there has already been some geographic spread here.

Genomes

Genomes

EPI_ISL_15307020, EPI_ISL_15307037, EPI_ISL_15393194, EPI_ISL_15393348, EPI_ISL_15393415, EPI_ISL_15479635, EPI_ISL_15479693, EPI_ISL_15479721, EPI_ISL_15485325

[ryhisner]

The first sequence in this lineage outside of Sweden showed up today—in Colorado, right in the middle of the US. It has also picked up S:R346I, a mutation not found in any of the previous sequences. EPI_ISL_15585173

Also, I just ran an Usher tree, and now Usher places this lineage within BA.5.2.36, not BA.5.2.20. There are no reversions, and the proximity of Sweden to England—the primary home of BA.5.2.36—suggests this is the right placement. I've changed the title of the proposal to reflect this. There's also now a sequence from Bahrain that shares a synonymous mutation with this lineage but none of the AA mutations.

[AngieHinrichs]

now Usher places this lineage within BA.5.2.36, not BA.5.2.20

Yes -- both BA.5.2.20 and BA.5.2.36 are one mutation after the undesignated BA.5.2 > 4-mutation big branch with ORF1b:T1050N. BA.5.2.20 is branch > C23707T and BA.5.2.36 is branch > A22893C (S:K444T). These sequences have both C23707T and A22893C, so they fit equally well on either branch by parsimony.

[corneliusroemer]

Homoplasic mutations should be given less weight. Counting mutations/parsimony is fine in most cases but for tie-breaking it makes sense to use likelihood approach. Hence this is more likely to be a BA.5.2.20 rather than BA.5.2.36 sublineage.

[ryhisner]

Seven more sequences of this lineage uploaded yesterday, all from Sweden, bringing the total to 17.

[ryhisner]

Four more sequences from Sweden uploaded yesterday, making 26 sequences in total now.

[FedeGueli]

33 sequences as today with Spike_N334K,Spike_K444T,Spike_n148S
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_293bb_cf0890.json?label=id:node_6892983

[ryhisner]

Nothing for 9 days, so I'm pretty sure this one is dead.

[ryhisner]

Not entirely dead, apparently, as four more sequences from Sweden showed up today. Still clearly on the decline, however.