XBB.1.5 Saltation: S:∆138-144, N149K, ∆242-243, R403K, L452R, E583D, L611F, P621S, D1153Y; ORF9b:I5T; ORF1a: S1372A, L2234S, S4119A; ORF1b:D2179Y (4 seq, Italy, Germany Nov 21))

[ryhisner]

Description Sub-lineage of: XBB.1.5 Earliest sequence: 2023-8-23, Italy, Apulia — EPI_ISL_18209924 Most recent sequence: 2023-9-22, Italy, Abruzzo — EPI_ISL_18326806, EPI_ISL_18326807 Countries circulating: Italy (3) Number of Sequences: 3 GISAID AA Query: NSP3_S554A, NSP8_S177A GISAID Nucleotide Query: T4379G, T12620G CovSpectrum Query: Nextcladepangolineage:XBB.1.5* & [5-of: T4379G, T6966C, T12620G, A13938G, G16377A, G20002T, C22009A, G22770A, T22917G, G23311C, C23393T, C23423T, G25019T, T28297C] Substitutions/Deletions on top of XBB.1.5: Spike: ∆138-144, N149K, ∆242-243, R403K, L452R, E583D, L611F, P621S, D1153Y ORF9b: I5T ORF1a: S1372A, L2234S, S4119A (NSP3_S554A, NSP3_L1416S, NSP8_S177A) ORF1b: D2179Y Nucleotide: T4379G, T6966C, T12620G, A13938G, G16377A, G20002T, ∆21974-21994, C22009A, ∆22289-22294, G22770A, T22917G, G23311C, C23393T, C23423T, G25019T, T27504C, T28297C, A29694G

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.5_Saltation_Italy_3_seq.json?c=gt-nuc_4379&gmax=5379&gmin=3379&label=id:node_4039693

Evidence These sequences come from different patients according to metadata. The first, collected August 23, is from Apulia, Italy, while the two most recent (collected Sept 22) are from Abruzzo, Italy. These regions are not far from each other but do not share a border. The Apulia sequence has no coverage from S:255-421, so I have assumed it has S:R403K like the other two sequences.

It’s rare to see lineages with large deletions in spike, like ∆138-144, transmit. I could be wrong, but I don’t think there’s ever been a designated lineage with ∆138-144 or ∆138-145, despite these being not uncommon in chronic-infection singlets. My guess is that such large deletions efficiently evade antibodies but are destabilizing, making them advantageous within a host but deleterious between hosts.

ORF1a:S1372A is convergent in chronics but otherwise very rare. ORF1a:S4119A is extremely rare, with just 159 sequences all time and 12 in 2023.

Genomes

Genomes

EPI_ISL_18209924, EPI_ISL_18326806, EPI_ISL_18326807

[FedeGueli]

apparently dying off, lets track it for a bit more

[ryhisner]

New sequence just showed up from Germany, collected October 24. EPI_ISL_18525840

Nucleotide mutations on the German branch: A3069G, C3619T, C3587T, A25998G AA mutations: ORF1a:D935G, ORF1a:H1108Y

[FedeGueli]

Still 4 and no new sequence i m closing it