Sibling lineage of XBB.1.5.59 with F456L and Orf1a:T654A spreading in South Korea and South America (52)

[FedeGueli]

In the same tree of XBB.1.5.59 and XCF now is clearly visible a new XBB.1.5 sublineage with S:F456L

Gisaid query: A2225G,C5512T, C17439T, A29700G finds : 22 samples from 7 countries mainly South Korea

Samples:

EPI_ISL_17768046, EPI_ISL_17779305, EPI_ISL_17780614, EPI_ISL_17816933, EPI_ISL_17853017, EPI_ISL_17853114, EPI_ISL_17954142, EPI_ISL_17960522, EPI_ISL_17969427, EPI_ISL_17969448, EPI_ISL_17979152, EPI_ISL_18010883, EPI_ISL_18011000, EPI_ISL_18031207-18031210, EPI_ISL_18031547-18031551,

Defining mutations: XBB.1.5 >> S:F456L (T22928C) > Orf1a:T654A (A2225G), C5512T, C17439T, A29700G

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1484c_fe4450.json?c=gt-ORF1ab_654&label=id:node_7003423

Note that Usher misclassify it as XBB.1.5.59 while it is missing the defining mutation of XBB.1.5.59

Growth comparison: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=A2225G%2CC5512T%2CC17439T%2CA29700G&analysisMode=CompareToBaseline&

[FedeGueli]

Interestingly there was a sublineage of XBB.1.5.86 circulating n SOuth korea with Orf1a:T654A we cant exclude the lineage proposed here comes from a recombination between XBB.1.5.59 and XBB.1.5.86

But unlikely looking at this:

https://cov-spectrum.org/explore/South%20Korea/AllSamples/Past6M/variants?aaMutations=Orf1a%3AT654A%2CS%3Af456L&aaMutations1=orf1a%3AT654A&nextcladePangoLineage1=XBB.1.5.86*&nextcladePangoLineage2=XBB.1.5.59*&analysisMode=CompareEquals&

[FedeGueli]

Although slow last samples came from Costarica and from Germany via GBW US Surveillance)

[FedeGueli]

New samples from Colombia, Ecuador and Utah

[FedeGueli]

Last samples came from Spain, Canada, Trinidad and US

[FedeGueli]

52 now many samples coming from Scotland Switzerland Netherlands

[FedeGueli]

It doest seem slow now: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=A2225G%2CC5512T%2CC17439T%2CA29700G&analysisMode=CompareToBaseline&

cc @ryhisner @hynnspylor @aviczhl2 @Nkrmnzr @over-there-is should i propose this?

[ryhisner]

It seems geographically widespread enough to justify a proposal to me. I say go for it.

A29700G has always intrigued me. It seems to show up a lot in interesting sequences, but it's not in a particularly interesting position and doesn't seem like it should have any real function. According to this depiction of the secondary RNA structure of the 3' UTR, it switches one pair from an A-T bond to a G-T bond, which shouldn't make much difference. However, maybe it allows a slight shift into a more favorable conformation?

[FedeGueli]

Thx @ryhisner proposed

[aviczhl2]

Designated XBB.1.5.109 via https://github.com/cov-lineages/pango-designation/commit/67d6881fe1502f20371ea5411d66bfdc7265325c