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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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LB.1 with S:∆S31, R190T (5 seq, 4 countries including Qatar) + Recombinant with KP.2 (1 seq, Canada) + Recombinant with KP.3.2 (4 seq, Sweden,Spain) [May 27] #1559

Closed ryhisner closed 3 months ago

ryhisner commented 4 months ago

Description of LB.1 + S:∆S31, R190T, ORF1b:G2068R Sub-lineage of: LB.1 (JN.1 + S:Q183H, S:R346T, S:F456L) Earliest sequence: 2024-4-21, Qatar (sample from traveler to New York, USA) Most recent sequence: 2024-4-21, Qatar (sample from traveler to New York, USA) Continents circulating: Asia (1) Countries circulating: Qatar (1) Number of Sequences: 1 GISAID Nucleotide Query: [Edited by mod: i suggest to use G22111T, G22131C, G22599C, T22928C] vs Original query: G22111T, G22131C,T3565C CovSpectrum Query: Nextcladepangolineage:JN.1* & [3-of: G19669A, G22111T, G22131C] Substitutions/Deletions on top of LB.1: Spike: ∆S31, R190T ORF1b: G2068R (NSP15_G17R) Nucleotide: C8692T, ∆21653-21655, G19669A, G22131C Usher Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/LB.1_S31del_R190T.json?c=gt-S_190&gmax=25384&gmin=21563&label=id:node_2409627 Genomes

Genomes EPI_ISL_19108797
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Description of LB.1 + S:∆S31, R190T/KP.2 Recombinant Recombinant of: LB.1 (JN.1 + S:Q183H, S:R346T, S:F456L) + ∆S31, R190T and KP.2 Breakpoint: 22131-24871 Earliest sequence: 2024-4-22, Canada, Quebec — EPI_ISL_19118127 Most recent sequence: 2024-4-22, Canada, Quebec — EPI_ISL_19118127 Continents circulating: North America (1) Countries circulating: Canada (1) Number of Sequences: 1 GISAID Nucleotide Query: G17334T, G22111T, G22131C CovSpectrum Query: Nextcladepangolineage:JN.1* & [3-of: G17334T, G22111T, G22131C] Substitutions/Deletions on top of LB.1 + S:∆S31, R190T/KP.2: ORF3a: P104T Nucleotide: C4891T, C25702A USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/LB.1_S31del_R190T_KP.2%20Recomb.json?c=gt-S_190&gmax=25384&gmin=21563 Genomes

Genomes EPI_ISL_19118127
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Description of LB.1 + S:∆S31, R190T/KP.3 Recombinant Recombinant of: LB.1 (JN.1 + S:Q183H, S:R346T, S:F456L) + ∆S31, R190T and KP.3 Breakpoint: 22131-22599 Earliest sequence: 2024-5-2, Sweden, Varmland Most recent sequence: 2024-5-2, Sweden, Varmland Continents circulating: Europe (1) Countries circulating: Sweden (1) Number of Sequences: 1 GISAID Nucleotide Query: G22111T, G22131C, C23039G CovSpectrum Query: Nextcladepangolineage:JN.1* & [3-of: G22111T, G22131C, C23039G] Substitutions/Deletions on top of LB.1 + S:∆S31, R190T/KP.3: Nucleotide: C22858T USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/LB.1_S31del_R190T.json?c=gt-S_190&gmax=25384&gmin=21563&label=id:node_2409627 Genomes

Genomes EPI_ISL_19136338

Normally I would ignore singlet recombinants, but these seem quite unusual. The original lineage has only been detected in a traveler to the USA (New York) from Qatar. Yet there are already two recombinants of this lineage on two different continents, meaning that this lineage has spread to three continents and already undergone two recombinations with fast-growing, recent lineages. It seems very likely to me that this lineage is widespread and growing rapidly in some unsampled part of the world.

FedeGueli commented 4 months ago

Great catch Ryan! i ve modified the query of the non recombinant( DONOR ) to exclude its recombinant : new query: G22111T, G22131C,T3565C . It is enough to remove T3565C to catch all the four samples.

FedeGueli commented 3 months ago

Second sequence for the KP.3 recomb, this time from... Spain! (it seems everything fast is there right now)

corneliusroemer commented 3 months ago

Hah, I independently found this LB.1 + 190T / KP.3.2 recombinant:

hCoV-19/Sweden/S-1260950467R4/2024|EPI_ISL_19136338|2024-05-02
hCoV-19/Spain/CT-HUVH-E46508/2024|EPI_ISL_19165017|2024-05-20

Breakpoint between 22132 (S:190T) and 22599 (S:346T) - fascinating that it chose to get rid of 346T, as if that wasn't useful in KP.3

The donor is KP.3.2 by the way, as it contains C22858T

Brave Browser 2024-05-28 18 45 24

Query is: G22111T,G22131C,C22858T

FedeGueli commented 3 months ago

Same thought on 346T .

ryhisner commented 3 months ago

Yeah, I've thought from the beginning that KP.3 probably would not get R346T. It's always been bad on an N450D background, and Q493E is in the same region as both residues, making me suspect KP.3 has found a way to evade antibodies without suffering the ill effects of the R346T-N450D combo.

Two more sequences from the non-recombinant branch (with the Qatar travel sequence) showed up today: one in Wales and one in California. Both with collection dates in May. EPI_ISL_19177079, EPI_ISL_19177989

EDIT: Usher makes it look as if the new California sequence sits between the KP.3.2 and KP.2 recombinant, but that can't be right. It has G19669A (ORF1b:G2068R)—which comes from the parent LB.1 lineage from which the KP.3.2 recombinant springs—but NOT C22858T, S:Q493E, or S:V1104L which Usher seems to think both it and the Canadian sequence have, though neither have any of those.

Can someone tag Angie Hinrichs on this? I'm not sure why, in this case, Usher is ignoring so many mutations/non-mutations, and I can't seem to tag her here for some reason.

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FedeGueli commented 3 months ago

5 with G22111T, G22131C, G22599C, T22928C,

Updated tree:

Screenshot 2024-06-04 alle 00 17 00

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5af81_e3fa60.json?label=id:node_7131110

HynnSpylor commented 3 months ago

2 more LB.1 x KP.3.2 recombinant in Spain. Interesting

corneliusroemer commented 3 months ago

This designation will help untangle/monitor stuff here:

commit 03122159898f6456c28d8bc616d08ba503c57e49 (HEAD -> master, origin/master, origin/HEAD)

  3 Date:   Tue Jun 4 13:22:27 2024 +0200
  4 
  5     Designate LB.1.2 (ORF1b:G2068R) and LB.1.2.1 (S:R190T)
  6     
  7     See https://github.com/sars-cov-2-variants/lineage-proposals/issues/1559
  8     for discussion of this branch and potential recombinants
  9
corneliusroemer commented 3 months ago

@HynnSpylor - hah I just saw this as well - I hadn't read your comment before.

Can someone do a proper recombinant analysis, with breakpoints? Then we can designate it!

Speaking of this one:

Description of LB.1 + S:∆S31, R190T/KP.3 Recombinant
Recombinant of: LB.1 (JN.1 + S:Q183H, S:R346T, S:F456L) + ∆S31, R190T and KP.3
Breakpoint: 22131-22599
Earliest sequence: 2024-5-2, Sweden, Varmland
Most recent sequence: 2024-5-2, Sweden, Varmland
Continents circulating: Europe (1)
Countries circulating: Sweden (1)
Number of Sequences: 1
GISAID Nucleotide Query: G22111T, G22131C, C23039G
CovSpectrum Query: Nextcladepangolineage:JN.1* & [3-of: G22111T, G22131C, C23039G]
Substitutions/Deletions on top of LB.1 + S:∆S31, R190T/KP.3:
Nucleotide: C22858T
USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/LB.1_S31del_R190T.json?c=gt-S_190&gmax=25384&gmin=21563&label=id:node_2409627
Genomes

Very interesting Spike, combination of the 2 fittest lineages around, and spotted in 2 countries, and in sentinel surveillance over time, so unlikely this is unreal.

corneliusroemer commented 3 months ago

Ok I'll do it:

It's a KP.3.2 recombinant because it has C22858T

On the other side it's an LB.1.2.1.

Breakpoint between G22131C (S:190) and G22599C (S:346)

corneliusroemer commented 3 months ago

Designated as XDY in https://github.com/cov-lineages/pango-designation/commit/e14d5bfd8745f3da579dd5c8a48cfe254e75589b

FedeGueli commented 3 months ago

Designated as XDY in cov-lineages/pango-designation@e14d5bf

Sorry @corneliusroemer for some reasons i didnt receive the notifications of your comments