XBB.1.5 Sublineage with S:∆180-184, S:N185D, S:F456L, ORF1a:T1437I (43 seq, Aug 19)

[ryhisner]

Description — transferred from sars-cov-2-variants/lineage-proposals#592

Sub-lineage of: XBB.1.5
Earliest sequence: 2023-4-18, Argentina — EPI_ISL_17886076
Most recent sequence: 2023-7-31 – USA, New York & Georgia — EPI_ISL_18095032, EPI_ISL_18090265
Countries circulating: Argentina (19), USA (5), France (1), Paraguay (1)
Number of Sequences: 26
GISAID Nucleotide Query: C4575T, T22928C
CovSpectrum Query: Nextcladepangolineage:XBB.1.5* & [2-of: C4575T, T22928C] & 22105- & 22110-
Substitutions/Deletions on top of XBB.1.5:
Spike: ∆180-184, N185D, F456L
ORF1a: T1437I
Nucleotide: C4575T, T10204C, ∆22101-22114, T22928C

Phylogenetic Order of Mutations: T10204C → ∆22101-22114 (S:180-184del, S:N185D) → C4575T, T22928C (ORF1a:T1437I, S:F456L)

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.5_180-184del_F456L.json?c=gt-nuc_4575&label=id:node_3037968

Evidence
Deletions in four of the five NTD loops (located at spike AA sites 14-26, 67-81, 140-158, and 241-263) have been very common throughout the pandemic. These deletions have been associated with both antibody evasion and higher infectivity in cultured cells, though such advantages appear to come at a cost in spike stability. SARS-CoV-2's NTD loops are larger than those in other closely related viruses, including SARS-CoV-1.

NTD loop 4 (spike AA 172-190) has rarely seen deletions, and it's not entirely clear why. We've certainly seen a lot of substitutions there.

Since June 26, there have only been 34 sequences submitted from Argentina, and 10 of those have come from this lineage. It makes up 4 of the 13 sequences from Argentina with collection dates in July.

One of the five USA sequences is a travel sequence from Argentina. This likely isn't a very fast lineage as it was detected back in April, but it does seem to make up a substantial proportion of sequences in Argentina. 22 of the 26 sequences also possess T21357C (synonymous) and T27878G (ORF7b:C41W).

See the three excellent studies below for more on NTD deletions.

"Dynamics of SARS-CoV-2 Spike Proteins in Cell Entry: Control Elements in the Amino-Terminal Domains"
Enya Qing, Tom Kicmal, Binod Kumar, Grant M. Hawkins, Emily Timm, Stanley Perlman, Tom Gallagher https://journals.asm.org/doi/10.1128/mbio.01590-21

"Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike"
Diego Cantoni, (…) Connor GG Bamford, & Joe Grove
https://www.embopress.org/doi/full/10.15252/embr.202154322

"Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7"
https://www.sciencedirect.com/science/article/pii/S221112472100663X
Bo Meng, Ravi Gupta

Genomes

Genomes

EPI_ISL_17822145, EPI_ISL_17886076, EPI_ISL_17886164-17886165, EPI_ISL_17966266, EPI_ISL_17978708, EPI_ISL_18031853, EPI_ISL_18049313, EPI_ISL_18050275, EPI_ISL_18057918, EPI_ISL_18090265, EPI_ISL_18095032, EPI_ISL_18095188-18095190, EPI_ISL_18095290, EPI_ISL_18095335, EPI_ISL_18095342-18095347, EPI_ISL_18095352-18095354

[ryhisner]

Though most of the sequences are from Argentina, this one's begun to spread internationally a bit. Yesterday, five sequences from Houston, Texas, USA, were uploaded with collection dates from July 27 to August 4. And today a US travel sequence from Germany was uploaded, collection date August 4. Since Germany has basically stopped all sequencing, it's hard to know whether or not this lineage is spreading there.

[FedeGueli]

cc @corneliusroemer look at this please it is going vertical in Argentina.

[HynnSpylor]

42 seqs now (+5 in US)

---the S:Del180-184+S:N185D also emerged in XBB.2.3.1 sublienage in Finland (5 seqs) and FY.3 sublineage in China (2 seqs)

[FedeGueli]

This is literally flying. 42 virus the last four from today from US (TX and Connecticut) yesterday a couple of GBW sample with travel history from Germany.

[FedeGueli]

Designated XBB.1.5.103 milestone added in the original issue to save Cornelius time.

via 168e64b

[FedeGueli]

@aviczhl2 should i remove the milestone in the other issue or your code overwriite it?

[aviczhl2]

@aviczhl2 should i remove the milestone in the other issue or your code overwriite it?

Yes thanks.

[FedeGueli]

@aviczhl2 should i remove the milestone in the other issue or your code overwriite it?

Yes thanks.

Thank you. So @corneliusroemer i wont add anymore milestones on the other site if proposed here ? ok?