XCJ: GM.2 and FP.1 recombinant (28 seqs, 4 countries) further gained S:S494P (17 seqs, 4 countries) with a singlet got extra S:K444T

[NkRMnZr]

Defining Mutations: GM.2 > T7105C_rev > T4234C_rev, C6312T(ORF1a:T2016I), A6536G_rev(ORF1a:S2091G_rev), A6616G
Query: C6312T, A6616G, G22103C

Query for further S:S494P sub-branch: C6312T, G22103C, T23042C
Query for further S:S494P + S:K444T sub-branch: C6312T, G22103C, A22893C

Recombinant Profile:

• Donor A: GM.2 (XBB.2.3.6.1), from 5' End to 1st breakpoint, from 2nd breakpoint to 3' End
• Donor B: FP.1 (XBB.1.11.1.1), betewen 2 breakpoints
• Breakpoint 1: from nuc 1063 to nuc 4234
• Breakpoint 2: from nuc 7105 to nuc 16342/ORF1ab_5360

Earliest seq: 2023-04-17 (EPI_ISL_17596226, Singapore)
Latest seq: 2023-07-26 (EPI_ISL_18097192, Hongkong, China)
Sampled Countries: Singapore (15), China (1, HK), USA (1, CA)

Genomes:

EPI_ISL_17596117, EPI_ISL_17596163, EPI_ISL_17596226, EPI_ISL_17670383, EPI_ISL_17670456, EPI_ISL_17670533, EPI_ISL_17670567, EPI_ISL_17694782, EPI_ISL_17724538, EPI_ISL_17724540, EPI_ISL_17724543, EPI_ISL_17724558, EPI_ISL_17724566, EPI_ISL_17790782, EPI_ISL_17790799, EPI_ISL_17866083, EPI_ISL_18097192

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1a781_a3b060.json?f_userOrOld=uploaded%20sample

Trivia:

• The recombinant itself is nothing spectacular, except for being placed on UShER tree as the largest sub-branch of GM.2 right now.
• It soon gained S:S494P then the latest sequence Hong_Kong/VB23126930/2023|EPI_ISL_18097192|2023-07-26 gained another RBD Level S:K444T that are missing from XBB* backbone, so I'll leave it here to monitor for a while.

[FedeGueli]

Thx great catch. HK one could be very interesting: it has also S:G181R>P ans S:S254F

[NkRMnZr]

Tracking updates:

08-22, 11 seqs from Canada (S:S494P branch)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_16e20_4c1510.json?f_userOrOld=uploaded%20sample&label=id:node_7348836

EPI_ISL_18124503, EPI_ISL_18124532, EPI_ISL_18124534-18124538, EPI_ISL_18124544, EPI_ISL_18124562, EPI_ISL_18124599, EPI_ISL_18124601

[FedeGueli]

Please propose it.

[corneliusroemer]

Great work - just independently came to the same conclusion that this is a GM.2 with a little bit of FP.1 (sandwich) when seeing all the CAN-ON-PHL sequences.

Will designate straight away

[FedeGueli]

@NkRMnZr the sublineage with S:F494P has reached 36
showing this advzantage versus dominant lineages: https://cov-spectrum.org/explore/World/AllSamples/from%3D2023-05-29%26to%3D2023-08-31/variants?aaMutations=Orf1b%3AD54N&nucMutations1=C6312T%2CG22103C%2CT23042C&analysisMode=CompareToBaseline&

I urge you to propose it separately. )obviously it could be just canadain effect but better to track)

[NkRMnZr]

Follow-up #752

[FedeGueli]

XCJ