Spike P521S mutaatiosta Sars-Cov-2 rekombinanttivariantissa XBB.1.16.1 (VOI-variantti)

 https://github.com/cov-lineages/pango-designation/issues/1942

B.1.16.1 Sublineage with S:P521S, ORF1a:L681F #1942

ryhisner opened this issue Apr 22, 2023 · 2 comments

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monitor currently too small, watch for future developments Recommend if grows An interesting lineage that should be prioritised for designation if it continues to grow at all reviewed XBB proposed sublineage of XBB

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Description Sub-lineage of: XBB.1.16.1 Earliest sequence: 2023-3-16, France — EPI_ISL_17497793 2nd-Earliest Sequence: 2023-4-1, Belgium — EPI_ISL_17484410 Most recent sequence: 2023-4-3, France — EPI_ISL_17524580 Countries circulating: France (3), Australia (2), Belgium (1) Number of Sequences: 6 GISAID AA Query: Spike_T547I, Spike_P521S, NSP2_L401F GISAID Nucleotide Query: C2306T, C23123T, C23202T CovSpectrum Query: Nextcladepangolineage:XBB.1.16* & C2306T & C23123T & C23202T Substitutions on top of XBB.1.16.1: Spike: P521S ORF1a: L681F Nucleotide: C2306T, C23123T Evidence According to CovSpectrum Collection 42, created & run by Andrew Urquhart, after XBB.1.16 and XBB.1.16.1, the fastest-growing variants (as measured by low CI growth advantage) with ≥250 sequences are XBB.2.3.2, EU.1 (XBB.1.5.26.1), EU.1.1 (XBB.1.5.26.1.1), and XBB.2.3. All of these lineages possess S:P521S. This mutation has not been noticeably advantageous previously, but the same could be said for S:K478R/Q/N. Whether due to epistasis with other XBB* + S:S486P mutations or due to some change in population immunity, S:P521S seems now to confer some degree of benefit. Furthermore, other mutations at the same site have appeared in other XBB* lineages, mainly S:P521Q and S:P521S. Notably, the four sequences from France and Belgium all have the 2-nucleotide extended homology (A28877T, G28878C) for the TRS-B of N*, the novel sgRNA created by the 3-nucleotide N:203-204 mutations that has been in every B.1 lineage since it first emerged in 2020, and which one early study found to mess with host-cell interferon expression and increase viral loads. https://www.nature.com/articles/s41467-022-28287-8   ,,,,,,,,,,,,,,,,,         Tällä VOI variantilla XBB,1,16,1,  on muitakin  alalinjaehdokkaita.  on alalinja XBB.1.16.1 1 merkitään FU.1. Se taas  omaa alalinjoja, joka on suuri ryhmä ja parhaillaan sen fylogeneetistä puuta  ollaan selvittämässä. FU.1.1 ja FU.2 ovat jo saaneet designaationsa.  Esim seuraava  FU.1 alalinja odottaa selvitystään: https://github.com/cov-lineages/pango-designation/issues/2037

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