FedeGueli
commented
2 weeks ago Very interesting one : Orf7a:P34L/S has been in 50K sequences and mutliple lineages especially in the vocs era. 435S is the only convergent&successful mutation in the rbd recently (beyond 493E,FLiRT, 445X and 478X) S:A1174V (here is T) is convergent (and going) in #1843 and #1997 despite not being widespread it was already in B.1.1.7 and other lineages. Plus double Orf9b/N mutation are always something to watch although this one has not been widesporead
ryhisner
Description Sub-lineage of: XDY Earliest sequence: 2024-7-31, USA, Massachusetts — EPI_ISL_19347338 Most recent sequence: 2024-8-28, USA, South Carolina — EPI_ISL_19394879 Continents circulating: Europe (4), North America (2) Countries circulating: France (2), USA (2), Scotland (1), Sweden (1) Number of Sequences: 6 GISAID Nucleotide Query: C27494T, G28380A, G22865T CovSpectrum Query: [3-of: C27494T, G28380A, G22865T] Substitutions on top of XDY: Spike: A435S, A1174T (+ T572I in further, 3-seq branch) N: R36Q ORF7a: P34L ORF9b: D33N ORF1a: ∆82-84, M85V (only in further, 3-seq branch) Nucleotide: G22865T, G25082A, C27494T, G28380A (+ ∆510-518, C23277T in further branch)
Phylogenetic Order of Mutations: C27494T (ORF7a:P34L) → G25082A, G28380A (S:A1174T, N:R36Q, ORF9b:D33N) → G22865T (S:A435S) → ∆510-518, C23277T (ORF1a:∆82-84, ORF1a:M85V, S:T572I)
USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons3/main/XDY_A435S_A1174T.json
Evidence Seems to be a lot of positive selection in this branch. All mutations here are non-synonymous, and one sequence here has, on top of baseline XDY, eight AA mutations—four in spike—on just seven nuc substitutions (5/6 non-synonymous with one double N/ORF9b mutation + an out-of-frame ORF1a deletion causing ORF1a:M85V). Wide geographic spread and recent collection dates make it worth watching.
Genomes
Genomes
EPI_ISL_19344396, EPI_ISL_19347338, EPI_ISL_19357169, EPI_ISL_19372202, EPI_ISL_19389996, EPI_ISL_19394879