XBB.1.17.1 Sublineage with S:N148T, S:∆177-181, S:Q218R, S:S494P, S:P521S, E:S68F, ORF1a:E622G, ORF1a:T1429I, ORF1b:G1568C (17 seq, France, Uk, NY , Quebec Oct 15)

ryhisner commented 1 year ago

Description

Sub-lineage of: XBB.1.17.1 Earliest sequence: 2023-8-21, France, Ile-de-France, Bobigny, — EPI_ISL_18221906, EPI_ISL_18221907 Most recent sequence: 2023-8-21, France, Ile-de-France, Bobigny — EPI_ISL_18221906, EPI_ISL_18221907 Countries circulating: France (2) Number of Sequences: 2 GISAID AA Query: NSP14_G44C, E_S68F, Spike_Q218R Alternative Query : A22215G, T25902A,T23042C (4/4) or C8140T, C9298T, C26447T (3/4)(EDITED) GISAID Nucleotide Query: T12655C, A22215G, T25902A (2/4) CovSpectrum Query: Nextcladepangolineage:XBB.1.17.1* & [2-of: T12655C, A22215G, T25902A] Substitutions/Deletions on top of XBB.1.17.1: Spike: N148T, ∆177-181, Q218R, S494P, P521S N: ORF1a:E622G, T1422I (NSP2_E442G, NSP3_T611I) ORF1b: G1568C (NSP14_G44C) Nucleotide: A2130G, C4511T, C8140T, C9298T, T12655C, G18169T, ∆22091-22105, A22005C, A22215G, T23042C, C23123T, T25902A, C26447T

Phylogenetic Order of Mutations: A2130G, C4511T (ORF1a:E622G, ORF1a: T1429I) → C23123T (S:P521S) → A22005C, T23042C (S:N148T, S:S494P) → C8140T, C9298T, T12655C, G18169T, ∆22091-22105, A22215G, T25902A, C26447T

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.17.1__N148T_177-181del_Q218R_S494P_P521S.json?c=gt-S_218&gmax=25384&gmin=21563&label=id:node_7051983

Evidence This lineage consists, so far, of only two sequences from separate hospitalized patients in France, both collected on August 21. I'm posting it here because XBB.1.17.1 seems likely to have originated in western Africa and is presumably still most common there. We get so few sequences from that region that it's impossible to know what is circulating in recent weeks. These two identical sequences have a large number of mutations, particularly in spike, so I think it's conceivable it evolved in a stepwise manner through fairly wide circulation in some part of Africa. Most likely it will disappear soon, but it seems worth tracking to me, particularly with its very unusual (perhaps unique) deletion in the N4 NTD loop (S:∆177-181).