XBB.1.9.1 + Orf1a:L3588F (NSP6_L19F) spreading in China and multiple countries (118 seqs) Full credit to @Over-There-is and @Memorablea for exploring the chinese tree

[FedeGueli]

I have identified in a tree maintained of chinese sequences maintained by @Over-There-Is and @Memorablea ( Thank you great work) a fast sublineage of XBB.1.9.1 defined by NSP6_L19F (Orf1a:L3588F)

Defining mutations:
XBB.1.9.1 >> C4586T, C6541T, Orf1a:L3855F (G11029T)

Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_48e38_b05b30.json?label=id:node_6639348

Gisaid query:
C4586T, C6541T, G11029T (edited)

Samples:
EPI_ISL_17398101, EPI_ISL_17440394, EPI_ISL_17689385,
EPI_ISL_17689397, EPI_ISL_17689441-17689444, EPI_ISL_17704004,
EPI_ISL_17704008, EPI_ISL_17704024, EPI_ISL_17704037-17704038,
EPI_ISL_17704047, EPI_ISL_17724966-17724968, EPI_ISL_17729797-17729798,
EPI_ISL_17729845, EPI_ISL_17729848, EPI_ISL_17729850,
EPI_ISL_17729856-17729860, EPI_ISL_17729862-17729864, EPI_ISL_17729866-17729867,
EPI_ISL_17729869, EPI_ISL_17729871, EPI_ISL_17729876,
EPI_ISL_17729878, EPI_ISL_17768465, EPI_ISL_17782260,
EPI_ISL_17790390, EPI_ISL_17793408, EPI_ISL_17794432,
EPI_ISL_17794878, EPI_ISL_17794926, EPI_ISL_17795239,
EPI_ISL_17801810-17801811, EPI_ISL_17801935, EPI_ISL_17801954,
EPI_ISL_17801962, EPI_ISL_17801975, EPI_ISL_17801977-17801979,
EPI_ISL_17801982-17801984, EPI_ISL_17801986, EPI_ISL_17801991-17801994,
EPI_ISL_17801996, EPI_ISL_17802010

Growth advantage in China:
Apparently this has a growth advantage versus the apparently fastest lineage in the world that is EG.5.1 + Orf1b:D54N
(Although not all the CIs are showing that)

https://cov-spectrum.org/explore/China/AllSamples/from%3D2023-04-01%26to%3D2023-06-15/variants?aaMutations=Orf1b%3AD54N&nucMutations1=T22072C%2CC4586T%2CC6541T%2CG11029T&analysisMode=CompareToBaseline&

[FedeGueli]

With the new update on Covspectrum it seems to have broaden its growth advantage CIs from -10% to +40% over Orf1b:D54N this points likely to have little or no advantage

[Memorablea]

this

[Memorablea]

There are currently 72 sequences from 6 countries.

[Over-There-Is]

T22072C in query seems not necessary.

[Over-There-Is]

There are currently 72 sequences from 6 countries.

one of them is Korean cases imported from Japan, so it should be 7countries.

[Over-There-Is]

I did not notice that the T22072C is the largest branch under L3855F.
usher
But it seems the sequences without T22072C is also related to the others.
These 2 seems to be recombined with XBB.1.16 or #187, one has Orf1a:S1819Grev and L3829F, another has Orf1a:V1019F and C22987T.

And this one recombined with XBB.1.16:

And this one have too much reversion.

[Memorablea]

There are currently 72 sequences from 6 countries.

one of them is Korean cases imported from Japan, so it should be 7countries.

Yes.You are right.

[Over-There-Is]

Korea+2 (Local), Brunei +1, China +1(from Thailand), Singapore +1(Local). 77 seq in 9 countries.

[Over-There-Is]

Japan+2

[Over-There-Is]

Japan+2, China+4(Amoy and Shanghai), 87 now.

[Over-There-Is]

Japan +1, 88 now.

[FedeGueli]

It has calmed down a lot. better closing for now.

[Over-There-Is]

Japan 07-08

[Over-There-Is]

104 seqs now. 11 sequences from 5 Guangdong cities, and 4 sequences from 3 Japanese prefectures.
But their collection dates are all earlier than the latest sequences.

[FedeGueli]

@Over-There-Is would you like to propose it? you have tracked it far better than me and i discovered it in your tree!!

[FedeGueli]

107, very recent samples from Scotland

[Over-There-Is]

118, and the latest sequence is collected on 07-28 in Fukushima, Japan.

[FedeGueli]

no samples from August i m closing it.

[Over-There-Is]

131, latest sequence collected 08-16 in Saitama, Japan
But seems still uncompetable

[Over-There-Is]

134, also found in Norway and Greece
But not later than the latest sequence