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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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Mini saltation XDV.1.8 appeared in Taiwan with 4 spike mutations S:A67G (C>G), S:N148T , S:T240I, S:R683W (2) #2038

Closed FedeGueli closed 1 month ago

FedeGueli commented 1 month ago

Just two sequences but featuring four spike mutations worth proposing it here.

Defining mutations: XDV.1.8 >> T9892G > A23971G, A9715T, Orf1a:A3615V (C11109T), S:A67G (C21762G), S:N148T (A22005C), S:T240I (C22281T), S:R683W (C23609T) Query: C21762G,A22005C Samples: 2 Country: 1 (Taiwan) Tree:

Screenshot 2024-09-16 alle 10 43 09

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_326b9_7ed040.json?c=gt-S_67&label=id:node_7188833

Highlights: A67G is a C>G nuc mutation rare in the course of the pandemic (less than 100seqs) S:N148T has been successful especially in GE.1.2.1 and XBB.1.28 S:T240I was in BQ.1.24 and previously in an undesignated branch of AY.122 S:R683W should disrupt the FCS

xz-keg commented 1 month ago

G6183A (rev, real?) , T9142C (rev, real?), C13339T(rev, real?) do not really appear in any XDV.1, they are a known usher bug. Usher fix those mutations to JN.1 sub-branches to avoid artefacts, but it cause recombinants having additional non-existing mutations then.

Hope @AngieHinrichs can specify out XDV.1 from JN.1.1 so that this bug won't affect the tree.

Over-There-Is commented 1 month ago

G6183A and C13339T are reverted while recombining, and XDV never got C9142T but Usher places it under a JN.1.1+C9142T branch, so 9142 reverts later.

FedeGueli commented 1 month ago

G6183A and C13339T are reverted while recombining, and XDV never got C9142T but Usher places it under a JN.1.1+C9142T branch, so 9142 reverts later.

thx u and @aviczhl2

FedeGueli commented 1 month ago

closing for now