FL.2.3+S:146K, S:P521S(40 seqs, 7 countries)

[xz-keg]

FL.2.3+S:146K, S:P521S(C21998A,C23123T)

More precise query found by @Over-There-Is : C23123T, A17615G, T4579A, -G28980T, -A22320G

No. of seqs: 6 (Germany 1 Ireland 1 Hong Kong 1 Fujian 1 Shanghai 1(from Japan) Jiangxi 1) First seq: EPI_ISL_17794369, Jiangxi, 2023-5-4 Latest seq: EPI_ISL_17811046, Shanghai, 2023-6-2

All 6 seqs for FL.2.3+S:P521S have C21998A (S:146K), so here S:146K is likely to be real not artefact.

usher

[Over-There-Is]

                 /organism="Severe acute respiratory syndrome coronavirus 2"
                 /mol_type="genomic RNA"
                 /isolate="SARS-CoV-2/human/CHN/SH-HG20230605-1651/2023"
                 /isolation_source="Pharyngeal swab"
                 /host="Homo sapiens; Host_age: 32; Host_sex: Male"
                 /country="China:Shanghai"
                 /collection_date="2023-06-02"
                 /note="Passage_details/history: Original;
                 Additional_host_information: Patient infected while
                 traveling in Japan"

[Over-There-Is]

Fujian +2

[Over-There-Is]

Shanghai +2, 1 from Russia, 1 from Germany

[xz-keg]

also in UK.

[FedeGueli]

one more sequence not more recent than the last one.

[Over-There-Is]

GDCDC_SZHG_1719/2023|EPI_ISL_18036297|2023-06-03 XBB.2.3* / FL.2.3 recombinant? only this one does not have C21998A.

[Over-There-Is]

C21998A is masked by usher now.

[FedeGueli]

The new tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_179a1_c4490.json?c=userOrOld&label=id:node_6770643

[FedeGueli]

It is not that far from EG.5.1 : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=EG.5.1*&nucMutations1=C23123T%2CA17615G%2CT4579A&analysisMode=CompareToBaseline&

[Over-There-Is]

+3

[xz-keg]

+1 USA

[FedeGueli]

Apparently it camt compete: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=C23123T%2CA17615G%2CT4579A&analysisMode=CompareToBaseline&

[xz-keg]

+1 South Korea

[Over-There-Is]

USA/TX-HMH-M-131884/2023|EPI_ISL_18164304|2023-08-16 Recombined with XBB.1.5.49?

[Over-There-Is]

C23123T, A17615G, T4579A, -G28980T, -A22320G gives 37 sequences.

1 sequence is on N:G236V branch and got S:P521S convergently, so use -G28980T to exclude it. 3 sequences are FL.2.3 / XBB.2.3 recombinants, one is FL.2.3/XBB.2.3.7 recombinant with 1 sequence (from Guangdong, probably originated in Fujian), and the other one is FL.2.3/GJ.1 recombinant with 2 sequences (from South Korea), so exclude them with -A22320G. Both recombinants are related to N:G236V branch.

Guangdong/GDCDC_GZ_0518/2023 has T4579A and C21998A dropout, you may also include it with the query C23123T, A17615G, G5720A, -A16878T, -G28980T, -A22320G.

Or you could also use query C23123T, A17615G, T4579A, C21998A, but there are 2 Japanese sequences with dropout on 21998, they also have Y144- dropout.

And there are two US sequences under T931A branch with dropout on 23123: T931A, -C23123T, A17615G, T4579A.

Totally, there are 40 sequences now. Since those Korean sequences all belong to the recombinant proposed in #708, this sublineage is not in South Korea yet, It's only in 7 countries right now: China (Including Mainland and Hong Kong), US, UK, Japan, Germany, Russia and Ireland.

https://nextstrain.org/fetch/github.com/Over-There-Is/subtreeAuspice/raw/main/subtreeAuspice_genome_39469_cdac30.json?c=country&label=id:node_6723890

[FedeGueli]

C23123T, A17615G, T4579A, -G28980T, -A22320G gives 37 sequences.

1 sequence is on N:G236V branch and got S:P521S convergently, so use -G28980T to exclude it. 3 sequences are FL.2.3 / XBB.2.3 recombinants, one is FL.2.3/XBB.2.3.7 recombinant with 1 sequence (from Guangdong, probably originated in Fujian), and the other one is FL.2.3/GJ.1 recombinant with 2 sequences (from South Korea), so exclude them with -A22320G. Both recombinants are related to N:G236V branch.

Guangdong/GDCDC_GZ_0518/2023 has T4579A and C21998A dropout, you may also include it with the query C23123T, A17615G, G5720A, -A16878T, -G28980T, -A22320G.

Or you could also use query C23123T, A17615G, T4579A, C21998A, but there are 2 Japanese sequences with dropout on 21998, they also have Y144- dropout.

And there are two US sequences under T931A branch with dropout on 23123: T931A, -C23123T, A17615G, T4579A.

Totally, there are 40 sequences now. Since those Korean sequences all belong to the recombinant proposed in #708, this sublineage is not in South Korea yet, It's only in 7 countries right now: China (Including Mainland and Hong Kong), US, UK, Japan, Germany, Russia and Ireland.

https://nextstrain.org/fetch/github.com/Over-There-Is/subtreeAuspice/raw/main/subtreeAuspice_genome_39469_cdac30.json?c=country&label=id:node_6723890

thank you great analysis i ve edited the query and the title subsequently.

[FedeGueli]

It is really far from HK.3 : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=C23123T%2CA17615G%2CT4579A%2C22320A%2C28980G&analysisMode=CompareToBaseline&