XBB.2.3/XBB.1.16 Recombinant (51 seq, Sept 21)

[ryhisner]

Description

Recombinant of: XBB.2.3/XBB.1.16
Breakpoint: Between S:521 and ORF7a:13 (23123-27430)
Earliest sequence: 2023-7-6, USA, Iowa — EPI_ISL_18012194
Most recent sequence: 2023-8-21, USA, Maryland — EPI_ISL_18163068
Countries circulating: USA (28), India (1)
Number of Sequences: 29
GISAID AA Query: Spike_I210del, Spike_P521S
GISAID Nucleotide Query: T6394C, G8863T, T14305C
CovSpectrum Query: [5-of: T6394C, G8863T, T14305C, G18636A, T18882C, C27684T, C27513T, T28034C]
Substitutions/Deletions on top of XBB.2.3/XBB.1.16:
Spike: I210del
**ORF1b:**Y280H
Nucleotide: T6394C, G8863T, T14305C, G18636A, T18882C, ∆22190-22192, C27684T, C27513T, T28034C

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.2.3_XBB.1.16_Recombinant.json?c=gt-nuc_8863&gmax=9863&gmin=7863&label=id:node_7391224

Evidence
XBB.2.3 has never picked up ORF9b:I5T, which has proven advantageous for XBB.1* lineages. It has also never picked up an ORF8 stop codon. It's not clear if there's a connection between those two things, but this recombinant lineage has picked up both, along with ORF9b:N55S. It seemed slow for a while, but in the past week its numbers have doubled from ~15 to ~30.

Just one sequence has been from India, but given the extremely low level of sequencing in that country of over 1.4 billion, it's possible this lineage is more common there than anywhere else.

Genomes

Genomes

EPI_ISL_18012194, EPI_ISL_18012785, EPI_ISL_18061007, EPI_ISL_18098772, EPI_ISL_18099225, EPI_ISL_18107710, EPI_ISL_18113783, EPI_ISL_18115190, EPI_ISL_18119727, EPI_ISL_18119760, EPI_ISL_18120279, EPI_ISL_18120962, EPI_ISL_18121722, EPI_ISL_18126531, EPI_ISL_18131591, EPI_ISL_18160398, EPI_ISL_18162514, EPI_ISL_18162532, EPI_ISL_18162559, EPI_ISL_18162596, EPI_ISL_18162936, EPI_ISL_18163068, EPI_ISL_18165514, EPI_ISL_18165596, EPI_ISL_18168409, EPI_ISL_18212749, EPI_ISL_18212766, EPI_ISL_18212811, EPI_ISL_18216934

[ryhisner]

The longest branch in this lineage is a sequence from Illinois, USA, that has what is either an unusual artifact or an unusual combination of mutations in NSP3. This is a CDC sequence, and they are invariably of high quality, so I'm inclined to think it's real. EPI_ISL_18212749
ORF1a:T1055L, V1056L, V1057I
A3428T, C3429T, G3431C, G3433A, G3434A

If it is real, it's possible it is an import from ORF6, specifically 27243-27252. However, it's easy to fool yourself with coincidental similarities, and this could be a coincidence.
.

[FedeGueli]

Original issue : sars-cov-2-variants/lineage-proposals#535

[xz-keg]

The XBB.2.3-side donor is from a subbranch used to have 15% prevalence in Bangladesh. sars-cov-2-variants/lineage-proposals#328

[FedeGueli]

The XBB.2.3-side donor is from a subbranch used to have 15% prevalence in Bangladesh. sars-cov-2-variants/lineage-proposals#328

yes the one evaporated suddenly!

[ryhisner]

The first European sequences came in yesterday and today: one from Germany and one from France. Both collected August 21. EPI_ISL_18229297, EPI_ISL_18234598

EPI_ISL_18222172 is a US sequence from a traveler from Argentina.

[ryhisner]

First sequence from Canada, collected August 22: EPI_ISL_18256685

Only four sequences in the past week, however, so it seems slow.

[FedeGueli]

47 as today

[FedeGueli]

now 58. it slowed a lot in my chart. https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=T6394C%2CG8863T%2CT14305C&analysisMode=CompareToBaseline&

[FedeGueli]

Designated XCW via f44449c

[FedeGueli]

@corneliusroemer you should add the milestone here casue Ryan proposed this one directly here without preproposal in the secondary report.

[FedeGueli]

@corneliusroemer you should add the milestone here casue Ryan proposed this one directly here without preproposal in the secondary report.

Scratch that it's already in lineage notes .