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There seems to be a lot of S:478 mutation branches on XDV.1.
This one is only in Hubei, but appears in 7 different regions, mostly of rural areas. Consider neighboring provinces aren't uploading any …
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1509
Other than KP.1.1.1(S:K182N), other seqs on the Orf1b:L2213F branch of KP.1.1 have another NTD mutation set that usher does…
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Dear all
I just realized that the Cumulative Prevalence for different lineages in your superb web resource seems to be calculate by #GISAID_sample_with_lineage_X/#GISAID_sample. Generally this seem…
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LZ.2.1+A22994G(S:K478E)
GISAID query: A22994G,C29642T,T21738C
No. of seqs: 8(China 5(Hubei-Jingzhou) USA 2(GBW from Hong Kong) Singapore 1)
First: EPI_ISL_19299466, Hubei-Jingzhou, 2024-7-23
L…
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XDY+C29466T(N:A398V)+G25166C(S:E1202Q)
GISAID query: C29466T,G25166C,G19669A
No. of seqs: 15(USA 14(NJ,ND,CT,IA,RI,TX,MN,AZ,NY,NE) Canada 1)
First: EPI_ISL_19285227, USA-NY, 2024-7-8
Latest: E…
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KP.3.1.1+C7093T+C25349A(S:P1263T)
GISAID query: C7093T, C25349A, C12616T
No. of seqs: 22(USA 3(MD, GBW from Spain) Spain 4 France 15)
First: EPI_ISL_19375059, Spain, 2024-7-6
Latest: EPI_ISL_1…
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KP.1.1.3+A4364C(Orf1a:I1367L)+C7162A(Orf1a:D2299E)+C3096T,C9803T, C13019T, C22212A(Or(f1a:S944L, S:P217H)+C22097A, T28729C(S:L179I)
GISAID query: C22097A, C22212A
No. of seqs:9(USA 8(TX,DE,NY,NJ),…
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KP.2+T25039C(Same branch as KP.2.8)+C21627A(S:T22N)+G4105A, C19170T, A23416T, C27434T,T21653C,A22995C(S:S31P,K478T rev, Orf7a: T14I)
GISAID query: T25039C, C21627A, T21653C
No. of seqs: 4( Denmark…
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These workflows:
- https://github.com/nextstrain/ncov-ingest/blob/master/.github/workflows/fetch-and-ingest-gisaid-master.yml
- https://github.com/nextstrain/ncov-ingest/blob/master/.github/workflo…
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We at Colorado are testing different primers and are interested in knowing what references were picked for RSV-A and RSV-B. If you have it, could you provide us with a GISAID, GenBank, or other ID?