Xu Zou

JN.1+2-nuc Orf1b:I2273S(48 seqs, 13 countries, 20 with S:R346T, 13 with additional S:F456L)

8

There seems to be a 2-nuc mutation under JN.1. JN.1+T20285C,A20284T(Orf1b:I2273S) GISAID query: T20285C, A20284T, C18894T,-13584,-1762,-C774T,-29684,-12781,-17334 No. of seqs: 41(Brazil 2 Canada 1 Costa Rica 6 UK 6 France 2 Germany...

JN.1.30+Orf1a:T4302I,S2030L,S:T29N (20 seqs, 2 countries)

1

JN.1.30+C29137T+C13170T(Orf1a:T4302I)+C6354T,C21648A(Orf1a:S2030L,S:T29N) GISAID query: C29137T,C13170T,C21648A No. of seqs: 20(China 5 Australia 15) First: EPI_ISL_18997658, China, 2024-3-1 Latest: EPI_ISL_19140650,Australia, 2024-5-6 [usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice36_genome_test_41b73_8834a0.json?label=id:node_7071077) 

Unsure about the function of this new Orf9b mutation, but it is suddenly detected in a lot of countries. KP.2.2+A28468G(Orf9b:N62S) GISAID query: A28468G,T21737C,A25359G No. of seqs: 9(USA 2(from France), France...

XBB.1.16--JN.1.11--XBB.1.16 Breakpoint 1 between 1459 and 3430 Breakpoint 2 between 27916 and 28296 Additional mutations: C1458T, A1777G C1458T from XBB.1.16 branch, A1777G is private mutation. GISAID query: C29386T, A405G, G17334T,...

KW.1.1.1+Orf9b:T72I(36 seqs, 5 countries)

1

Orf9b:T72I seems to be another very convergent site inside JN.1, which appears in JN.1.4, KP, JN.1.30 and this KW.1.1.1 branches. KW.1.1.1+C10456T+C28498T(Orf9b:T72I) GISAID query:C10456T,C28498T,C21846G No. of seqs: 7(USA 1(from Japan),Australia 5...

JN.1.4/JG.3 recombinant(10 seqs, USA)

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There is a new JN.1.4/JG.3 recombinant. JN.1.4--JG.3 Breakpoint between 23424 and 23602  Additional mutations: T11247C, C17502T, C24919T, T25303C (new) Orf1a: M3661T C17502T from a JN.1.4 branch, T11247C is private...

Issue to Register Singlet Recombinants that shall be not be removed by usher

392

I'd like to post this issue to help everyone propose any recombinant sequence that may be added to usher. Anything with >5 reversion(refer to the last checkpoint ,usually a designation)...

KP.3.2+S:A263V(10 seqs, 3 countries) with a singlet carrying S:30-31del + S:F32I

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KP.3.2 (A2611C) +C26858T+C22350T(S:A263V) GISAID query: C23039G,C26858T,C22350T No. of seqs: 7(Australia 4 Singapore 2 Spain 1) First: EPI_ISL_19095773, Singapore, 2024-4-11 Latest: EPI_ISL_19131027, Spain, 2024-5-3 [usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_36de4_e26520.json?label=id:node_6984012)  Edited: There is S:S31del branch...

Multiple branches of BA.2.86* with S:S31del 7 Branches as of 8/16

97

It seems that there's many S:S31del lineages emerge now. This deletion was in previous variants but rather rare, however under BA.2.86* it seems much frequent. A very interesting fact is...

LF.1.1 (JN.1.16.1+Orf1a:A1268T,S2103F+S:P1263L) with a sub branch with S:S31del (6)

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LF.1.1 = [JN.1.16.1+G4067A,C6573T(Orf1a:A1268T,S2103F)+C18912T+C16551T,C25350T(S:P1263L)] GISAID query: C18912T,C16551T,C25350T GISAID query for S:31del branch: C18912T,C16551T,C25350T,del21653 (@FedeGueli ) No. of seqs: 6(USA 5(4 from Qatar, 1 from Turkey) Sweden 1) First: EPI_ISL_18882963, 2024-1-28, Sweden...