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XBB.2.3.3 Sublineage with S:F456L, M:G6S, ORF1a:T891I, ORF1a:Y1814C (+ S:S494P branch) (16 seq, 10 countries, Oct 20) #675

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ryhisner opened this issue Aug 25, 2023 · 3 comments
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XBB.2.3.3 Sublineage with S:F456L, M:G6S, ORF1a:T891I, ORF1a:Y1814C (+ S:S494P branch) (16 seq, 10 countries, Oct 20) #675

ryhisner opened this issue Aug 25, 2023 · 3 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest Interesting diversity in the tree the tree shows multiple interesting branches S:456
Milestone
GJ.6

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@ryhisner
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ryhisner commented Aug 25, 2023 •
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Description

Sub-lineage of: XBB.2.3.3
Earliest sequence: 2023-7-31, India, Maharashtra — EPI_ISL_18120271, EPI_ISL_18120272
Most recent sequence: 2023-8-8, Singapore (local case) — EPI_ISL_18127408
Countries circulating: India (2), Singapore (1)
Number of Sequences: 3
GISAID Nucleotide Query: C2937T, A5706G, G6536A
CovSpectrum Query: Nextcladepangolineage:XBB.2.3* & [3-of: C2937T, A5706G, T22930A, G26538A]
Substitutions on top of XBB.2.3.3:
Spike: F456L
M: G6S
ORF1a: T891I, Y1814C
Nucleotide: C2937T, A5706G, T22930A, G26538A

Phylogenetic Order of Mutations: A5706G (ORF1a:Y1814C) → C2937T, T22930A, G26538A (ORF1a:T891I, S:F456L, M:G6S)
Further Mutations in S:S494P Branch: → T17863C, T23042C, G29711C (ORF1b:Y1466H/NSP13_Y543H, S:S494P, 5' UTR)

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.2.3.3_F456L_M-G6S_ORF1a-T891I_ORF1a-Y1814C.json?c=gt-nuc_26538&label=id:node_7360913

image

Evidence
There are only three sequences here, but the two in Maharashtra may represent a much larger number present in that region, which has a population of over 110 million. The sequence in Singapore indicates that it is likely at least somewhat widespread in Maharashtra and perhaps other regions of India. There have only been 97 legible sequences from all of India with collection dates of July 1 or later and just 38 since July 30, so these two Indian sequences make up a substantial proportion of recent Indian sequences.

M:G6S is present in a number of divergent sequences. I believe this region of spike projects outside of the virion, so mutations from M:2-20 or so are probably antigenic mutations.

The Indian branch also has S:S494P, ORF1b:Y1466H/NSP13_Y543H, and a 5' UTR mutation with G27911C.

You can see that below this branch, there is another fascinating branch with S:N87K, S:L452Q, and S:K478N with two sequences. One is from several months ago, but another was collected July 31 and has several additional mutations, including S:A397V and an apparent 10-nucleotide enlargement of the standard BA.2* s2m deletion—∆29725-29760 instead of the usual ∆29734-29759. With just one recent sequence, it's not deserving of even a pre-proposal, but it bears watching.

Genomes

Genomes EPI_ISL_18120271, EPI_ISL_18120272, EPI_ISL_18127408
@FedeGueli FedeGueli added S:456 Rapid review needed Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest Interesting diversity in the tree the tree shows multiple interesting branches labels Aug 25, 2023
@FedeGueli FedeGueli changed the title XBB.2.3.3 Sublineage with S:F456L, M:G6S, ORF1a:T891I, ORF1a:Y1814C (+ S:S494P branch) (3 seq, 2 countries, Aug 24) XBB.2.3.3 Sublineage with S:F456L, M:G6S, ORF1a:T891I, ORF1a:Y1814C (+ S:S494P branch) (5 seq, 2 countries, Aug 24) Sep 4, 2023
@FedeGueli
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2 more sequence uploaded from India.

@FedeGueli
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I just noticed this is sibling lineage of #739

@FedeGueli FedeGueli changed the title XBB.2.3.3 Sublineage with S:F456L, M:G6S, ORF1a:T891I, ORF1a:Y1814C (+ S:S494P branch) (5 seq, 2 countries, Aug 24) XBB.2.3.3 Sublineage with S:F456L, M:G6S, ORF1a:T891I, ORF1a:Y1814C (+ S:S494P branch) (7 seq, 4 countries, Sept.23) Sep 23, 2023
@FedeGueli
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FedeGueli commented Sep 23, 2023 •
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It doesnt seem fast but was sampled in two more countries Denmark (with S:K444N) and Netherlands

@FedeGueli FedeGueli added Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. and removed Rapid review needed labels Sep 23, 2023
Over-There-Is referenced this issue in cov-lineages/pango-designation Oct 15, 2023
@corneliusroemer
Designate GJ.6 (XBB.2.3.3.6, S:F456L (T22930A), M:G6S, India) with 15…
7804cb5 
… seqs
@FedeGueli FedeGueli added this to the GJ.6 milestone Oct 15, 2023
@FedeGueli FedeGueli changed the title XBB.2.3.3 Sublineage with S:F456L, M:G6S, ORF1a:T891I, ORF1a:Y1814C (+ S:S494P branch) (7 seq, 4 countries, Sept.23) XBB.2.3.3 Sublineage with S:F456L, M:G6S, ORF1a:T891I, ORF1a:Y1814C (+ S:S494P branch) (16 seq, 10 countries, Oct 20) Oct 20, 2023
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest Interesting diversity in the tree the tree shows multiple interesting branches S:456
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