XDB: XBB.1.16.19 Mystery 3’-end Recombinant with novel suboptimal TRS (T1834A, G1835A, G1836A = ORF1a:G524N) + ORF3a:H93Y, ORF1b:V1590I

[ryhisner]

Description

Sub-lineage of: XBB.1.16.19 Earliest sequence: 2023-8-7, France — EPI_ISL_18215129, EPI_ISL_18215132, EPI_ISL_18228734 Most recent sequence: 2023-9-25, France — EPI_ISL_18387785 Countries circulating: France (29), Luxembourg (1), New Zealand (1) Number of Sequences: 31 GISAID Nucleotide Query: (T1834A, G1835A, G1836A ) specific query for this : G1835A, G1836A, T2935C (EDITED) CovSpectrum Query: Nextcladepangolineage:XBB.1* & [3-of: T1834A, G1835A, G1836A] Substitutions on top of XBB.1.16.19: ORF3a: H93Y ORF1a: G524N ORF1b: V1590I Nucleotide: T1834A, G1835A, G1836A, T2935C, T6262C, G18235A, C25669T, C26885T

Phylogenetic Order of Mutations: C26885T → T2935C, T6262C, G18235A, C25669T (ORF3a:H93Y, ORF1b:V1590I) → T18975C, G22225T → T1834A, G1835A, G1836A (ORF1a:G524N)

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XCV_T1834A_G1835A_G1836A.json?c=gt-nuc_1834&gmax=2834&gmin=834&label=id:node_3313929

Evidence I’m not certain that this comes from a recombinant lineage, but there seem to be about 250 sequences of XBB.1.16.19 that lack A28447G and C29386T, both of which are in all other XBB.1.16* lineages. The country with the most is Indonesia, with 71 according to CovSpectrum. Perhaps it’s an artifact of some sort. If so, I’ll edit the title and the proposal.

I keep track of novel TRS motifs that I come across & have seen over a hundred, but this one was new to me. Turns out there have been 13 previous sequences with this multi-nuc mutation, but the most recent was in September 2022.

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Interestingly, one sequence has already picked up a 4th mutation—an A→C mutation no less—that adds to the extended homology.

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Genomes

Genomes

EPI_ISL_18215129, EPI_ISL_18215132, EPI_ISL_18228734, EPI_ISL_18228858, EPI_ISL_18228861, EPI_ISL_18229524-18229525, EPI_ISL_18231871, EPI_ISL_18258281, EPI_ISL_18258367, EPI_ISL_18258374, EPI_ISL_18258383, EPI_ISL_18258448, EPI_ISL_18258458, EPI_ISL_18258464, EPI_ISL_18258694, EPI_ISL_18280724, EPI_ISL_18280832, EPI_ISL_18281000, EPI_ISL_18287732, EPI_ISL_18287753, EPI_ISL_18313751, EPI_ISL_18314177, EPI_ISL_18326552, EPI_ISL_18326864, EPI_ISL_18326869, EPI_ISL_18357037, EPI_ISL_18357160, EPI_ISL_18387693, EPI_ISL_18387785, EPI_ISL_18391674,

[FedeGueli]

Thx @ryhisner i ve edited the query in G1835A, G1836A, T2935C cause your one catches also old unrelated samples!

[FedeGueli]

It doesnt seem too slower than HK.3: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=G1835A%2CG1836A%2CT2935C&analysisMode=CompareToBaseline& and clearly faster than parent XBB.1.16 :https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=XBB.1.16&nucMutations1=G1835A%2CG1836A%2CT2935C&analysisMode=CompareToBaseline&

Could this be a good catch for some recombinations??

[xz-keg]

I looked at branches of this XBB.1.16.19-recomb, and no seqs with C26885T, C2878T or T10150C(3 largest sub-branch) appears together with both G15982A and (28447 or 29386).

This means the recomb is likely real and these mutations are all gained after the recomb event. Variants for recomb is plain XBB.1.16.19 without additional mutation / anything.

G15982A,T28297C,-28447,-29386,A22101T this query finds 239.

[xz-keg]

@corneliusroemer The root of this one is also a 200-sized growing recombinant despite Fede doesn't put a label.

[corneliusroemer]

Thanks I've seen this too - I agree double reversion makes this a likely a real recombinant so will designate

[FedeGueli]

Designated XDB via https://github.com/cov-lineages/pango-designation/commit/f1e5c7261d5f0344c7b4e647cac12554b00b2c29