Multiple JN.1* branches with S:F456L #1253 - GitHub

[Mary Wilson]

aviczhl2 commented Jan 4, 2024​

It seems that S:F456L is very convergent in JN.1 now.

General query: T3565C,C18894T,T22926C, Spike_F456L (27 seqs)

• Branch 1: JN.1.1+S:G181E+S:F456L, Issue JN.1.1 plus S:G181E (35) with a sub-lineage with S:F456L (7) France, Switzerland, Belgium #1147
• Branch 2: JN.1.1+S:F456L, Issue Another JN.1.1+S:F456L(3 seqs, 2 countries) #1249
• Branch 3: JN.1+S:F456L, Query: T22928C, T3565C, T22926C, -C1762A, -18453, -18093, -2782, -3589,-7113, 10 seqs, UK, Canada
• Branch 4: JN.1 with S:V1104L parental of SLip Branch 4 of #1253 emerged in India ( 10-11 seqs) #1262+Orf1a:T2283I,S:F456L Query: C7113T,T22928C,T3565C, 3 seqs, India

Doublets:

Singlets

1. JN.1 sublineage with ORF1a:T170I, ORF1b:G662S, and T18453C first detected in Denmark (73 GISAID seqs as of 2024-01-05; Denmark, Belgium, Finland, Sweden, USA) #1155+Orf1a:T4087I+S:F456L Query: T18453C, C12525T,T22928C, USA
2. JN.1+T18453C with C28201T（ORF8:S103L）（1272seqs） #1171+S:F456L Query: C28201T, T22928C, T22926C, Sweden
3. JN.1.1+Orf1a:E4388K+S:F456L Query: G13427A, T22928C, C9142T, Brazil
4. JN.1+A18093G+S:F456L Query: A18093G, T22928C,T3565C, Singapore
5. JN.1+G2782T+S:F456L Query: G2782T, T22928C, T3565C, USA
6. JN.1+C3589T+S:F456L Query: C3589T,T22928C,T3565C,France

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https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
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