BA.2 sublineage with S:W64L, S:N450D, S:Q607K, S:E1144Q (26 seq as of 2022-07-01, mainly Pakistan)

[silcn]

Proposal for a sublineage of BA.2
Earliest sequence: 2022-05-28 (Pakistan)
Countries detected: Pakistan (12 seq), UK-Scotland (2)

Defining mutations:
S:W64L, N450D, Q607K, E1144Q
ORF1a:S2030L
nuc:C11308T, C28657T

Another lineage with only a small number of genomes, but Pakistan sequences very little. The proportion of sequences from Pakistan belonging to this lineage by week is as follows:
05-23 to 05-29: 1/6
05-30 to 06-05: 0/7
06-06 to 06-12: 4/19
06-13 to 06-19: 7/23
So this lineage is at ~25% in the last couple of weeks. It should be noted that almost all recent Pakistani sequences come from Islamabad so this may not reflect prevalence across the country as a whole. Nevertheless, I think this is worth monitoring: prevalence in an undersampled region, multiple S mutations, recent appearance, not obviously declining in the face of BA.4/5...

https://nextstrain.org/fetch/github.com/silcn/subtreeAuspice1/raw/main/auspice/subtreeAuspice1_genome_20fa2_fc6050.json?c=gt-S_64&label=nuc%20mutations:C11308T,G21753T,A22910G,C23381A,G24992C
(the two apparent branches aren't real, that's caused by a dropout around ORF1a:2030 in a few seqs)

Genomes:
EPI_ISL_13302859
EPI_ISL_13302860
EPI_ISL_13302861
EPI_ISL_13302862
EPI_ISL_13324864
EPI_ISL_13352550
EPI_ISL_13354543
EPI_ISL_13354544
EPI_ISL_13354545
EPI_ISL_13354550
EPI_ISL_13355609
EPI_ISL_13355610
EPI_ISL_13355616
EPI_ISL_13355620

Cov-spectrum query:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AW64L%2CS%3AQ607K%2CS%3AE1144Q&pangoLineage=BA.2*&

Note that this is often misidentified as BA.2.14 by pangoLEARN because of the shared S:W64L.

[FedeGueli]

👍
@ryhisner pointed to us this one last night too! always very happy when there are more than two eyes on this kind of things thx @silcn

[silcn]

Now also found in France: EPI_ISL_13450052.

24 sequences with sample dates in June were uploaded from Pakistan yesterday, mostly from Karachi, and none were this lineage; looks like the 25% estimate is more reflective of Islamabad than Pakistan as a whole.

[silcn]

Now found in the US (Maryland): EPI_ISL_13549373. Also a few sequences from England.
Total is 26 sequences.

[FedeGueli]

33 sequences as today (on covspectrum)

[FedeGueli]

36 Sequences as today on covspectrum and newly sampled in Netherlands and Canada

42 sequences on Usher:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3ced_744960.json?c=country&label=nuc%20mutations:A22910G

[FedeGueli]

52 sequences as today on covspectrum
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AW64L%2CS%3AQ607K%2CS%3AE1144Q&pangoLineage=BA.2*&

[FedeGueli]

60 sequences as today. Significant international spread to 10 countries in 3 continents

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_d816_4596d0.json?c=country&label=nuc%20mutations:A22910G

These seqeunces clustering togrther in Germany could represent local transmission of this variant or maybe just a familiar cluster intercepted by airport surveillance

@silcn @corneliusroemer @chrisruis
i think this should be designated very significant 4 spike mutations and epidemiological relevant behaviour, being one of the few BA.2ers still spreading I would not be surprise to see this one competing with last emerging sublineages .

[ryhisner]

Interesting to see that one of these recently popped up in Nebraska, USA, with ORF1a:T2264I, ORF1a: A4357V, and S:S255F. It seems like S255F is popping up more and more recently, though BA.2.3.6 is the only designated Omicron lineage with it (that I know of). EPI_ISL_14057310

[c19850727]

One of sequences from Japan (with travel history from Pakistan) obtained an additional S:L455F.
EPI_ISL_14320247