FL.2.3 (XBB.1.9.1.2.3) with ORF1ab: K5784R and S: Q146K（198 seqs multiple countries）

[Memorablea]

Sub-lineage of:FL.2
Earliest sequence:2023-04-07,Guangdong
Most recent sequence:2023-05-11,USA
Countries circulating:China 70, Ireland 1, England 1, United States 1
GISAID search：T4579A,A17615G,C21998A

sequence

Genomes:

EPI_ISL_17545640, EPI_ISL_17584630, EPI_ISL_17615002,EPI_ISL_17625276, EPI_ISL_17625305, EPI_ISL_17625315，EPI_ISL_17625360, EPI_ISL_17625389,EPI_ISL_17625431, EPI_ISL_17625499, EPI_ISL_17625567,EPI_ISL_17625585, EPI_ISL_17632975 ，EPI_ISL_17632976, EPI_ISL_17645472,EPI_ISL_17645513, EPI_ISL_17664527, EPI_ISL_17671914,EPI_ISL_17671919, EPI_ISL_17671944 ，EPI_ISL_17671945,EPI_ISL_17671949,EPI_ISL_17671951, EPI_ISL_17671956，EPI_ISL_17671957,EPI_ISL_17672024,EPI_ISL_17678284,EPI_ISL_17678372,EPI_ISL_17678427,EPI_ISL_17678450, EPI_ISL_17680003, EPI_ISL_17684000,EPI_ISL_17684191, EPI_ISL_17684329, EPI_ISL_17696835,EPI_ISL_17697630, EPI_ISL_17697636, EPI_ISL_17697691,EPI_ISL_17697695, EPI_ISL_17697698, EPI_ISL_17697760,EPI_ISL_17697763, EPI_ISL_17697767, EPI_ISL_17697786, EPI_ISL_17697803, EPI_ISL_17697836, EPI_ISL_17697849-17697850, EPI_ISL_17697880, EPI_ISL_17697883, EPI_ISL_17697914, EPI_ISL_17698013, EPI_ISL_17698015, EPI_ISL_17698032, EPI_ISL_17698034, EPI_ISL_17698046, EPI_ISL_17698073, EPI_ISL_17698078, EPI_ISL_17698087, EPI_ISL_17698104, EPI_ISL_17698123, EPI_ISL_17698226, EPI_ISL_17698233-17698234, EPI_ISL_17698248, EPI_ISL_17698260, EPI_ISL_17698267, EPI_ISL_17698275, EPI_ISL_17698284, EPI_ISL_17698292, EPI_ISL_17700760, EPI_ISL_17703623, EPI_ISL_17703996

UShER Tree：
I directly referenced the UShER tree of @Over-There-Is because it seems to better reflect. I'm sorry for the error, but the UShER tree seems to be dirty.
https://nextstrain.org/fetch/github.com/Over-There-Is/subtreeAuspice/raw/main/subtreeAuspice_genome_39469_cdac30.json

[JosetteSchoenma]

Thank you for making this issue. I was keeping an eye on this one as well, but I got a different and confusing Usher tree with a H146K reversion branch. Would you like to tell me how you made this your tree?

I used this query on GISAID. C11956T, C12789T, -T17124C, A17615G, Spike_H146K plus -G27225a (78 samples) to exclude a branch of mostly samples from the USA, of which I am not sure whether Usher misplaced them.

USA branch (XBB.1.9.1)

And I checked Guandong. It seems to have jumped to around 7% of the samples in week 16, but did not seem to grow after that. 6% in week 18.

[FedeGueli]

It has been already pre proposed here in #78 and theb transferred to Pango : cov-lineages/pango-designation#2016

[FedeGueli]

Once the parental lineage got assigned then we can open #78
or this one.

[Memorablea]

Thank you for making this issue. I was keeping an eye on this one as well, but I got a different and confusing Usher tree with a H146K reversion branch. Would you like to tell me how you made this your tree?

I apologize. It's like this, I noticed an error while filtering, and the correct UShER tree has been updated.

[Memorablea]

Once the parental lineage got assigned then we can open #78 or this one.

I understand, as I just said, there was an error in my screening, and I'm sorry. Next, let's wait for #2016

[Over-There-Is]

It seems unreasonable that the earlier detected sequences are placed on the further place, so I downloaded the json file and edit it manually.

[Over-There-Is]

Hubei+2, Yunnan+1. Totally 77 seq now.

[Over-There-Is]

Ohio, US+1

[Memorablea]

Ohio, US+1

Thanks for your contribution, I'll change the title as the sequence grows.

[Over-There-Is]

South Korea 1, Singapore 1, Shanghai 4(1 from S. Korea, 1 from Vietnam, 1 from Thailand), Hubei 3, Shanxi 1. 88 seq now.
Not only China, US, UK, Ireland, Singapore, S. Korea, but also Vietnam, Thailand, and there was a sequence in Shanghai imported from UAE, totally 9 countries.

[Over-There-Is]

+1, Sichuan

[Over-There-Is]

Totally 89 now, but two of them also have N:R189L mutation. S:Q146K is more homoplastic than N:R189L, therefore I believe their gain N:R189L before S:Q146K.

[Over-There-Is]

California+1

[Over-There-Is]

Spain +1

[Over-There-Is]

HK+2, and additionally 1 without 11956

[Over-There-Is]

Anhui +1

[Over-There-Is]

California +1, Shanghai +2(1 from Malaysia)

[Over-There-Is]

Xinjiang +1, 98 now

[Over-There-Is]

South Korea +1, from China

[Memorablea]

Open this.@FedeGueli

[FedeGueli]

Reopened this one. Be aware that in my opinion 146 is very tricky always. i dont see this one clearly faster than other sub-branches.

[FedeGueli]

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=Orf1b%3A1383R%2CN%3AG236V&aaMutations1=S%3A146K%2Corf1b%3A1383R&analysisMode=CompareToBaseline&

[Over-There-Is]

S:Q146K was the largest subbranch, but N:R189L seems growing faster and became the largest subbranch later.

[Over-There-Is]

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=Orf1b%3A1383R%2CN%3AG236V&aaMutations1=S%3A146K%2Corf1b%3A1383R&analysisMode=CompareToBaseline&

#127 is also Orf1b:K1383R+S:H146K.

[Memorablea]

I think we should continue to pay attention to it

[Over-There-Is]

France +1

[Over-There-Is]

61 seqs from several provinces in China, 1 also have N:R189L (maybe convergent)

[FedeGueli]

175 as today

[FedeGueli]

Could you compare this one with the other branches of FL.2.3 please? if it shows advantage over N:189 an N:236 and the other ones i think it should be proposed being close to 200 seqs and multiples countries.

[Memorablea]

198 now

[NkRMnZr]

There's a branch got S:F456L, follows:
FL.2.3 > G28839T(N:R189L) > T16977C > T22928C(S:F456L)

There's S:Q146K(C21998A)/S:K146Q(A21998C) flip-flop on UShER tree, and is neglected here due to potential artifact. The issue exists when FL.2.3 gets designated.

Query: G28839T, T22928C finds 4, all from Shanghai

Genomes:

EPI_ISL_17625561, EPI_ISL_17811306, EPI_ISL_17811318, EPI_ISL_17836662

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_30417_bf7650.json?f_userOrOld=uploaded%20sample

There's also another one got S:F490P (on top of XBB's T23019C/S:F490S), follows:
FL.2.3 > ORF1a:S2900L(C8964T), S:F490P(T23030C)
query: T23030C, C8964T, A17615G finds 3 from different provinces.

Genomes:

EPI_ISL_17795684, EPI_ISL_17819898, EPI_ISL_17830389

[FedeGueli]

@Memorablea please propose this one in the main page.

@NkRMnZr please propose the two branches you found with 456 and 490 in two separated issues. thank you

[Memorablea]

@Memorablea please propose this one in the main page.

Home page? Do you mean sars-cov-2-variants or cov-lineages?

@NkRMnZr please propose the two branches you found with 456 and 490 in two separated issues. thank you

And do you mean what NkRMnZr pointed out?

[FedeGueli]

@Memorablea please propose this one in the main page.

Home page? Do you mean sars-cov-2-variants or cov-lineages?

The main page is the official pango page.

@NkRMnZr please propose the two branches you found with 456 and 490 in two separated issues. thank you

And do you mean what NkRMnZr pointed out?

Yes i mean he/she should propose them both , separately

[Memorablea]

OK

[Memorablea]

转移至cov-lineages/pango-designation#2078