XBB.1* Sublineage with S:L335S, S:R403K, S:S486P, ORF1a:T403I, ORF1b:S2212I (11 seq, 4 continents, May 16, 1 seq from Republic of Congo,Brazzaville)

[ryhisner]

Description

Sub-lineage of: XBB.1* (Possibly XBB.1.28, but I'm not certain) Earliest sequence: 2023-3-27, France — EPI_ISL_17480623 Most recent sequence: 2023-4-24, France Countries circulating: France (2), China (1), USA (1) Number of Sequences: 4 GISAID AA Query: Spike_L335S, Spike_F486P, Spike_R403K GISAID Nucleotide Query: G22770A, T22566C, T23018C CovSpectrum Query: Nextcladepangolineage: Substitutions on top of XBB.1: Spike: L335S, R403K, S486P ORF1a: T403I (NSP2_T223I) ORF1b: S2212I (NSP15_S161I) Nucleotide: C1473T, G20102T, G22770A, T22566C, T23018C

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1_L335S_R403K_S486P_4seq.json

Evidence There are only four sequences at this point, but they are spread across three continents, with sequences from China, USA, and France. Short description of additional mutations on each sub-branch:

• USA sequence—S:G476S, ORF1b:V1402I (NSP13_V479I) + synonymous nuc mutations G12331A, C17850T, C25276T, and C29416G

• France sequence 1 — synonymous nuc mutations G12331A, C17850T, C25276T, and C29416G

• France sequence 2—ORF6:L35H, ORF1a:R24C, ORF1a:A117T, ORF1a:E1293D, ORF1a:P1497T

• China sequence—S:K478R, ORF1a:L397F, ORF1b:I829V, ORF1b:Y1200H plus synonymous nuc mutations C17850T, C25276T, and C29416G

Genomes

Genomes

EPI_ISL_17480623, EPI_ISL_17593232, EPI_ISL_17615418, EPI_ISL_17618380

[krosa1910]

If the sequences each have very distinct mutations， could that simply be a layout of distinct branches instead of sharing a common ancestor？

[ryhisner]

@krosa1910, I think the likelihood of ORF1a:T403I, ORF1b:S2212S, S:L335S, and S:R403K all appearing together independently in different XBB.1* sequences is vanishingly small. ORF1b:S2212I has only been in 138 other sequences over the past 6 months, and S:L335S is even rarer, only occurring 29 times (outside this lineage) over the past 6 months.

[ryhisner]

After three sequences were uploaded today, this one is up to eight sequences. There has now been one sequence from England (poor coverage w/ artifactual reversions) and sequences from three US states (New York, Pennsylvania, New Jersey). All three US sequences also have S:G476S.

[FedeGueli]

I think this could be transferred to the main pango proposals github page due: 1) convergent mutations 2) diversity shown with a tendency to accumulate more rbd mutations some already known to confer some potential advantage 3) quite wide geographical spread.

@ryhisner please fix you the timing for transfer (do you want to wait it reaches 10,15,20 seqs? )

[ryhisner]

@FedeGueli, given how geographically widespread this one is, I'd say it's worth transferring to the main page when it reaches 10 sequences. I don't know exactly how to transfer it to the main page, however.

[FedeGueli]

@FedeGueli, given how geographically widespread this one is, I'd say it's worth transferring to the main page when it reaches 10 sequences. I don't know exactly how to transfer it to the main page, however.

@ryhisner just copy and paste redoing the tree (only time absorbing thing but necessary to give an up to date tree to the proposal. Thank you!

Now Usher clearly branches it under the XBB.1.28 tree so this is XBB.1.28

It has to be noticed that two seqs further acquired S:T478R

[FedeGueli]

This went to 10 with two new samples coming in from France and NYC @ryhisner i urge you to re propose it in the main Pango page.

[HynnSpylor]

One more seq from Congo. 4 continents now

[FedeGueli]

One more seq from Congo. 4 continents now

good catch did u fiond it with the alternative query: C1473T, G20102T , T22566C ?

[FedeGueli]

Proposed here: https://github.com/cov-lineages/pango-designation/issues/1997