FY.4.2 sublineage with S:L212S recently spreading in Japan and found multiple times in travellers to US (114 as 19/09)

[FedeGueli]

Originally discussed here: https://github.com/sars-cov-2-variants/lineage-proposals/issues/487#issuecomment-1667139571 with @HynnSpylor

I noticed an international spread branch of FY.4 defined by Orf1b:V2287I that has further acquired S:L212S. S:L212S has been quite homoplasic at the end of original BA.2 era conferring some slight advantage. As noticed by @hynnspylor XBB.1.22.1 has an apparent propension to acquire further S1 mutations so it is not surprising to see S:L212S appearing here.

Defining mutations: FY.4 >> C7417T, ORF1b:V2287I (G20326A) > ORF1a:Y2171F (A6777T) > ORF3a:S177I (G25922T) > S:L212S (T22197C) > N:A218T (G28925A)

NSPs mutations: NSP15_V236I > Orf1b:V2287I NSP3_Y1353F > ORF1a:Y2171F

Gisaid query : G20326A,T22197C, G28925A

Samples: 18 all very recent mostly from Japan, Japanese travellers to US (3 from different airports) with one, the first, from Kenya not on Gisaid

First: KEN/SS11824/2023|OR045009.1|2023-05-08 Last: hCoV-19/Japan/PG-553168/2023 | Original | EPI_ISL_18071663 | 2023-07-21

EPI_ISLs

EPI_ISL_17986666, EPI_ISL_18010943, EPI_ISL_18011708, EPI_ISL_18013336, EPI_ISL_18036876, EPI_ISL_18036887, EPI_ISL_18036950, EPI_ISL_18036959, EPI_ISL_18047108, EPI_ISL_18049184, EPI_ISL_18049331, EPI_ISL_18051828, EPI_ISL_18051964, EPI_ISL_18054419, EPI_ISL_18054456, EPI_ISL_18071589, EPI_ISL_18071663

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2d2e6_a19a0.json?label=id:node_6841786

Growth advantage: It shows a faster growth rate of EG.5.1 , but lets keep in ind that GBW samples are usually duplicated and that could be a confounder. For sure it is a recent lineage showing fitness while spreading in competition with fast variants. Alternatively it could be related to a superspreading event as swimming world championship in Fukuoka , but i would have expected a more random distribution in international cases , or finally it could be related to a region/population with specific links to US (excluding Okinawa after the recent upload that showed Arcturus being the dominant variant in that prefecture) https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?nextcladePangoLineage=EG.5.1*&nucMutations1=G20326A%2CT22197C%2CG28925A&analysisMode=CompareToBaseline&

[FedeGueli]

cc @corneliusroemer @InfrPopGen @thomaspeacock @AngieHinrichs i suggest rapid review of this one.

[HynnSpylor]

Its parent lineage (with ORF1a:Y2171F, ORF1b:V2287I) has been designated as FY.4.2

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One more seq from Shanghai, China

[FedeGueli]

Its parent lineage (with ORF1a:Y2171F, ORF1b:V2287I) has been designated as FY.4.2

One more seq from Shanghai, China

thx i ve changed the title and added the milestone in the other repo.

[FedeGueli]

One more from US - Michigan

[HynnSpylor]

29 seqs now 2 samples from Mississippi, US show S:K528R and S:M1237V

[FedeGueli]

33 seqs now also in Australia. this should be designated. Growth rate in the high range: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=G20326A%2CT22197C%2CG28925A&analysisMode=CompareToBaseline&

[FedeGueli]

55 now doubling around 15-16 days in line with the fast lineages giving birth to a wave now.
Note that is present in 12 american states.

[FedeGueli]

while COvspectrum shows it as fast as current dominant lineages i am seeing it slowing down . another week and i'll close it : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=G20326A%2CT22197C%2CG28925A&analysisMode=CompareToBaseline&

[FedeGueli]

70 now mostly spreading in the US : in Delaware it reached a significant 3% of samples in August

[FedeGueli]

while COvspectrum shows it as fast as current dominant lineages i am seeing it slowing down . another week and i'll close it : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=G20326A%2CT22197C%2CG28925A&analysisMode=CompareToBaseline&

i was wrong.

[FedeGueli]

@corneliusroemer not sure this can compete vs HK.3 : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=G20326A%2CT22197C%2CG28925A&analysisMode=CompareToBaseline&

Still seems faster thatn the rest of the family :https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=FY.4*&nucMutations1=G20326A%2CT22197C%2CG28925A&analysisMode=CompareToBaseline&

Is this still relavant? let me know your thoughts so i can choose selecting thighter or looser the criteria to be proposed. If we put HK.3 (that is already 1000seq worlwide as baseline very few proposal could be supported) . Let me know please so we can be coordinated.

[FedeGueli]

114, closing it cause no chance to compete