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Repository for suggesting new lineages that should be added to the current scheme
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XBB.1.5 Sublineage with S:∆180-184, S:N185D, S:F456L, ORF1a:T1437I (43 seq, Aug 19) #2192

Closed ryhisner closed 1 year ago

ryhisner commented 1 year ago

Description — transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/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

image

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.

image

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 commented 1 year ago

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 commented 1 year ago

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

HynnSpylor commented 1 year ago

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)

屏幕截图 2023-08-17 112411
FedeGueli commented 1 year ago

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 commented 1 year ago

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

via https://github.com/cov-lineages/pango-designation/commit/168e64b0edf5ffb3f8ed32b8f33759c799312139

FedeGueli commented 1 year ago

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

xz-keg commented 1 year ago

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

Yes thanks.

FedeGueli commented 1 year ago

@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?