Potential XBB.1.9.1/(1.9.2 or XBB.1.22.2) recombinant (103 samples) with a branch with S:Y200C and S:K478R (16 samples)

[JosetteSchoenma]

Description: XBB.1.9.1/XBB.1.9.2 recombinant, with a big (mostly South Korean) branch with ORF8:I74V and a smaller branch which first gained S:Y200C and an ORF3a frameshift and after that a small saltation with S:478R (Australia, USA, the Netherlands, China) Private mutations: C6285T, G12907A, C28770T Breakpoint: between nucleotide 16878 and 27507 Earliest sequence: 2023-03-10 from England (with S:Y200C and ORF3a frameshift) 2023-03-22 from South Korea (with ORF8:I74V) 2023-03-29 from NSW/Australia (with extra small saltation with S:478R) Most recent sequence: 2023-05-15 from Fujian/China Countries circulating: South Korea 31, Australia/USA 7, China 3, Japan/England 2, the Netherlands/Indonesia/Ireland/Taiwan 1 GISAID query: C6285T, C11956T, A27507C CovSpectrum query: https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?nucMutations=C6285T%2CC11956T%2CA27507C&nextcladePangoLineage1=xbb.1.9.1*& to which S:T478R or A28113G could be added to find the various sublineages. Usher tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_8b73_effb30.json?branchLabel=nuc%20mutations&label=id:node_6674447

Please note that because the XBB.1.9.2. part only differs one mutation from XBB.1.9.1 (A27507C), convergent evolution cannot be ruled out. But because of the extra private mutations, I think recombination is more likely.

Please see this issue from Fede for more background info and discussion: https://github.com/sars-cov-2-variants/lineage-proposals/issues/73.

[JosetteSchoenma]

EPI_ISL_17257300 EPI_ISL_17408992 EPI_ISL_17408993 EPI_ISL_17474493 EPI_ISL_17486324 EPI_ISL_17538740 EPI_ISL_17538786 EPI_ISL_17538789 EPI_ISL_17538825 EPI_ISL_17551409 EPI_ISL_17601614 EPI_ISL_17603875 EPI_ISL_17604506 EPI_ISL_17604507 EPI_ISL_17604650 EPI_ISL_17604753 EPI_ISL_17604791 EPI_ISL_17604836 EPI_ISL_17604967 EPI_ISL_17605107 EPI_ISL_17605182 EPI_ISL_17606011 EPI_ISL_17614765 EPI_ISL_17614857 EPI_ISL_17616209 EPI_ISL_17619092 EPI_ISL_17630732 EPI_ISL_17631979 EPI_ISL_17637630 EPI_ISL_17637843 EPI_ISL_17646850 EPI_ISL_17647343 EPI_ISL_17647413 EPI_ISL_17647543 EPI_ISL_17647788 EPI_ISL_17648589 EPI_ISL_17657166 EPI_ISL_17661231 EPI_ISL_17677572 EPI_ISL_17677617 EPI_ISL_17677934 EPI_ISL_17678411 EPI_ISL_17680081 EPI_ISL_17682885 EPI_ISL_17683629 EPI_ISL_17689132 EPI_ISL_17690576 EPI_ISL_17690748 EPI_ISL_17690983 EPI_ISL_17691002 EPI_ISL_17691273 EPI_ISL_17691484 EPI_ISL_17691653 EPI_ISL_17696738 EPI_ISL_17698828 EPI_ISL_17703980

[FedeGueli]

Thx @JosetteSchoenma !

To track the smaller sublineage of this one with S:K478R i suggest this query :A22161G,C15390A, T26457C, G12907A.

cc @corneliusroemer @InfrPopGen @AngieHinrichs @thomaspeacock My personal suggestion is a rapid review followed eventually by a designation of ( 'XC?' and .1 and .2 )

[aviczhl2]

A27507C is also in AY.25 and XBB.1.22.2.

[JosetteSchoenma]

Indeed, @aviczhl2 . I checked and it might have recombined with XBB.1.22.2 as well.

It is the same from G15451A (ORF:G662S) and forward. XBB.1.22.2 does have C15237T, which this recombinant and XBB.1.9.1/2 do not have. So, the breakpoint would be after that in case it recombined with XBB.1.22.2.

I do see 5 XBB.1.9.2 with C28770T, while I see no XBB.1.22.2 with it, which might make it sightly more likely that it recombined with XBB.1.9.2.

The Delta's with A27507C look very different, of course.

Thank you! I will adjust title.

[aviczhl2]

Sorry, what I actually want to express is that A27507C, despite being a synonym mutation, is moderately convergent, so it is more likely convergent mutation.

But, yes, recombination is also very common in SARS-2 too, with so many variants and infection rate being so high.

[JosetteSchoenma]

18 new samples. Mostly from South Korea, but also 3 from Shanghai and 2 from Australia.

74 in total now.

[JosetteSchoenma]

96 samples now. New samples mostly from South Korea but one from Austria from the A28113G branch.

[FedeGueli]

@corneliusroemer ping

[JosetteSchoenma]

103 samples now. New ones from South Korea, Indonesia and China (Anhui). The one from Indonesia comes from the branch with S:Y200C and S:478R.

[ryhisner]

The S:Y200C, S:K478R, ORF1a:G519S, ORF1b:H641Q branch here has something super interesting going on that I don't think I've seen before. There are two deletions in ORF3a, both of which cause frameshifts. The first is ∆25474-25477 and the second ∆25520-25521, and they cancel each other out so that everything before and after them remains the same. But in between, there's a stretch of 14 frameshifted AA.

I've tried to put together the resulting new AA residues in the diagram below. On the top, I've lined up the old and new AA sequences. The red are polar/charged residues. Residues 1 and 14 are the same in both, so I put both deletions at the end, even though the actual deletions aren't arranged that way.

[FedeGueli]

After this analysis by @ryhisner showing this lineage has a heavy mutated orf3a, i suggest to designate this one to track it in the next weeks beyond any growth advantage talk

cc @corneliusroemer , @InfrPopGen

[FedeGueli]

135 samples as today . one new sample comes from Taiwan too.

[corneliusroemer]

I designated the 200C/478R sublineage as FL.18.1.1 - yes it could potentially be an FY.5 recombinant, but too little evidence to sacrifice the benefit of hierarchical lineage names.