Multiple branches of BA.2.86* with S:S31del 11 Branches as of 5/09

[aviczhl2]

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 that this deletion seems tied extensively to S:R346T.

GISAID query: del21653_21655,del22193_22195

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1. DeFLiRT Branch 1, parent of KP.2.3.1, KP.2.3+S:S31del(148 seqs, 21 countries, 5 with S:A475V) cov-lineages/pango-designation#2575
2. DelRT Branch 2, JN.1.1+C9442T+S:S31del,R346T,S455A, Orf7a:T28I, JN.1.1+S:R346T mini saltation branch with S:L455S->A, S:31del and ORF7a:T28I (3 seqs in Singapore and Malaysia) #1499
3. DelRT Branch 3, JN.1.1+S:R346T+S:S31del, Query: del21653_21655,C11747T, G22599C,-9442 19 seqs, Canada, South Korea, Singapore, USA, India,Mexico, Japan, Canary Islands
4. Branch 4, JN.1+Orf1a:G993D,A656V+C26013T+S:S31del, Query: del21653_21655,C26013T, C2232T,G3243A, 19 seqs, South Korea, China
5. DeFLiRT Branch 5, Designated KP.1.1.3, KP.1.1+C4999T+S:S31del, KP.1.1+S:S31del(46 seqs, 11 countries) cov-lineages/pango-designation#2580
6. DeFLiRT Branch 6, JN.1.9+S:R346T+S:F456L+S:S31del, LB.1 (JN.1.9 + FLiRT) with S:S31del (339) with a singlet with S:A475V (this subbranch spotted by @hynnspylor) cov-lineages/pango-designation#2546
7. DelRT Branch 7, JN.1.48.2+Orf1a:A427V, S:R346T, S:S31del, Query: C1545T, A3829G, del21653_21655, 23 seqs, India,Spain,California,Hawaii, Australia
8. DelRT Branch 8, JN.1+Orf1b:I2273S+S:R346T+N:A134V, S:S31del, Query: del21653_21655,C7573T,C28674T, 5 seqs, Sweden
9. Branch 9, JN.1.4+S:S31del, Query: C774T,T18453C, -28201, del21653_21655, 18 seqs, Brazil, USA, UK, Italy, Norway, Denmark
10. DelRT Branch 10, JN.1.30.1+Orf1a:I1128F,S:S31del, Query: A3647T,del21653_21655, 3 seqs, India,Singapore
11. DelRT Branch 11, JN.1.4.5+S:R346T+Orf1b:P2404S,S:S31del, Query: C28201T, del21653_21655,G22599C, 9 seqs, USA, Portugal, Canada
12. DeFLiRT Branch 12, KP.2 > C9286T > :C4921T, Orf1a:T4087I (C12525T), C14919T, G21204A, T27089C Query:del21653, C9286T 12 seqs. USA (Ohio), Singapore
13. DeFLiRT Branch 13, LF.1.1 (JN.1.16.1+Orf1a:A1268T,S2103F+S:P1263L) with a sub branch with S:S31del (16) #1448
14. DeFLiRT Branch 14, Designated LF.2, By @FedeGueli, JN.1.16.1 > Orf1a:K247R (A1005G) ,ORF3a:Y184H (T25942C ) Query: 1005G, T25942C Samples :15, Canada, USA, Germany, Ethiopia
15. Branch 15, JN.1.52 plus S:S31del S:R346I S:S704L (5 sequences, 5 countries ) #1575
16. Branch 16, KP.3.2.1 (S:A263V) with S:30-31del + S:F32I (2) #1556
17. Branch 17, Designated KP.3.1.1, KP.3.1 with S:31del [18 seq, Basque, Extremadura,Madrid, Catalunya- Spain, Italy, USA, Wales] #1563

Also various singlets, they may be actually gathered under JN.1+S:S31del, however usher doesn't show that branch so hard to tell.

[FedeGueli]

@ryhisner thinks it could create a new Glycan at S:N30.
Maybe he wants to comment here too

[aviczhl2]

https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?nextcladePangoLineage=JN.1*&aaMutations1=S%3AS31-&nextcladePangoLineage1=JN.1*&analysisMode=CompareToBaseline&

It's growth is 25%.

https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?aaMutations=S%3AR346T&nextcladePangoLineage=JN.1*&aaMutations1=S%3AS31-%2CS%3AR346T&nextcladePangoLineage1=JN.1*&analysisMode=CompareToBaseline&

And it adds 60%(total 101%) to S:R346T variants, super fast combo, as fast as S:F456L does.

@AngieHinrichs, may be the first time usher facing a real problem, that a super-fast convergent deletion appears.

[FedeGueli]

Very good job @aviczhl2 thank you.

[FedeGueli]

Br 5 and 7 look fast.
br 5 now has 7

[FedeGueli]

Br 5 7 9 new sequences count updated.

[FedeGueli]

Updated the existing branches. (Tracking comment) CLOSED

There should be more:

1. Dead

JN.1.45 > C26606T > Orf1a:P971S (C3176T),Orf1a:T2137I (C6675T), A21018G
G18756T,del21653,T3565C 3 samples Taiwan, Shanghai,USa

2. LF.1.1

Branch 13 now (05/07)
a sub branch DeFliRT of #1448
Query: C18912T,C16551T,C25350T,del21653 Samples 4 (all gbw from Egypt and Germany)

3. Slow

Branch 12 (05/07)
Another KP.2 sublineage KP.2 > C9286T > :C4921T, Orf1a:T4087I (C12525T), C14919T, G21204A, T27089C
Query:,del21653, C9286T Samples: 5

4. SLow

Another KP.2> C11020T > T9499G, G14118T, C24358A, Orf3a:A110S (G25720T), Orf8:G77S(G28122A)
Query: del21653,T9499G, G14118T
Samples: 2 (1 on gisaid)
5)SLow
DEFviRT Jn.1.18>S:f456V > C13620T > 11749G, T21610C, S:R190S (G22132T),S:E780A (A23901C), C27649T, ORF10:N36S(A29664G) Query: del21653, C13620T

6. Dead

DELRT : JN.1.30.1 > Orf1a:I1128F (A3647T) ,S:S31Del Query: del21653,A3647T,T3565C Samples 3

7. Dead

KP.1.1 + S:S31del + S:G184D , S:Q836L Query:T15330C, A24069T sample: 1

8. LF.2

JN.1.16.1 > Orf1a:K247R (A1005G) ,ORF3a:Y184H (T25942C ) Query: 1005G, T25942C Samples :5

9. JN.1.4> > S:346T, Orf8:E106Q Query: G22599C, G28209C,del21653,T3565C samples: 5 Brazil
10. JN.1.25.1 > > C7318T > G26648A > C28948T > S:F456L (T22928C) > G991A, Orf1a::A656V (C2232T),ORF1b:T794I (C15848T), ORF1b:I2166S (T19964G), S:S31del (del21653_2165) ,A22666G Query: G26648A,del21653_21655, T22928C samples: 1
11. JN.1.4.5 > A29700G > orf1a:G519S (G1820A), S:S31del (del21653_2165) ,S:R346T (G22599C), C29386T
    Query: G1820A, G22599C, C28201T,del21653 Samples: 3 (Singapore, Myanmar,Taiwan)

[FedeGueli]

Updated the existing branches.

There should be more:

1. JN.1.45 > C26606T > Orf1a:P971S (C3176T),Orf1a:T2137I (C6675T), A21018G
   G18756T,del21653,T3565C 3 samples Taiwan, Shanghai,USa
2. a sub branch DeFliRT of JN.1.16.1+Orf1a:A1268T,S2103F+S:P1263L(18 seqs, 12 countries) with a sub branch with S:S31del (4) #1448
   Query: C18912T,C16551T,C25350T,del21653 Samples 4 (all gbw from Egypt and Germany)
3. Another KP.2 sublineage KP.2 > C9286T > :C4921T, Orf1a:T4087I (C12525T), C14919T, G21204A, T27089C
   Query:,del21653, C9286T Samples: 5

updated. this one and main proposal count i would propose Branch 5 KP.1.1 it seems growing quite fast.

[FedeGueli]

there is an interesting DeFViRT singlet from #2538:
Jn.1.18>S:f456V > C13620T > 11749G, T21610C, S:R190S (G22132T),S:E780A (A23901C), C27649T, ORF10:N36S(A29664G)
Query: del21653, C13620T

[FedeGueli]

Br.7 is JN.1.48

[FedeGueli]

Br.12 now goes to 8

[FedeGueli]

6. DELRT : JN.1.30.1 > Orf1a:I1128F (A3647T) ,S:S31Del Query: del21653,A3647T,T3565C
   new branch added to my tracking comment

[FedeGueli]

From #1089: FIrst ever DelTRIO

70. DelTRIO (First ever) LB.1+S:S31Del > S:T572I (C23277T)
    Query:C23277T,G22111T , G22599C , T22928C,del21653 (Israel)

[FedeGueli]

@Sinickle found yesterday the first DelKP.3 :
KP.3 > G15372T, A19722G >C12616T >Orf1a:S4286C (A13121T), T25686A
Query:C12616T , A13121T
Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_23942_9f1cc0.json?c=userOrOld&label=id:node_11435290

[FedeGueli]

sequence count updated for unproposed lineages , also countries added . Branch 9 seems expanding in Brazil ( i didnt check tough if it the same lineage or query needs to be updated) @aviczhl2

Update: Br. 9 seems not monophyletic: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_d0f1_cb1a30.json?f_userOrOld=uploaded%20sample&label=id:node_7063835

The Brazilian branch seems an independent having JN.1.4> > S:346T, Orf8:E106Q but it is splitted on Usher.
A query that finds all 5 brazilian samples is : G22599C, G28209C,del21653,T3565C

So i suggest C774T,T18453C, -28201, del21653_21655,-G28209C as new query for Br.9

[FedeGueli]

sequence count updated for unproposed lineages , also countries added . Branch 9 seems expanding in Brazil ( i didnt check tough if it the same lineage or query needs to be updated) @aviczhl2

Update: Br. 9 seems not monophyletic: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_d0f1_cb1a30.json?f_userOrOld=uploaded%20sample&label=id:node_7063835

The Brazilian branch seems an independent having JN.1.4> > S:346T, Orf8:E106Q but it is splitted on Usher. A query that finds all 5 brazilian samples is : G22599C, G28209C,del21653,T3565C

So i suggest C774T,T18453C, -28201, del21653_21655,-G28209C as new query for Br.9

@aviczhl2 analysis done

[aviczhl2]

The Brazilian branch seems an independent having JN.1.4> > S:346T, Orf8:E106Q but it is splitted on Usher. A query that finds all 5 brazilian samples is : G22599C, G28209C,del21653,T3565C

So i suggest C774T,T18453C, -28201, del21653_21655,-G28209C as new query for Br.9

There seems no non-31del seqs on that Orf8:E106Q branch, suggesting the path being JN.1.4+(R346T,S31del)+Orf8:E106Q, it can be the 31del sub-branch getting R346T, or JN.1.4+R346T getting 31del.

[FedeGueli]

The Brazilian branch seems an independent having JN.1.4> > S:346T, Orf8:E106Q but it is splitted on Usher. A query that finds all 5 brazilian samples is : G22599C, G28209C,del21653,T3565C
So i suggest C774T,T18453C, -28201, del21653_21655,-G28209C as new query for Br.9

There seems no non-31del seqs on that Orf8:E106Q branch, suggesting the path being JN.1.4+(R346T,S31del)+Orf8:E106Q, it can be the 31del sub-branch getting R346T, or JN.1.4+R346T getting 31del.

true

[FedeGueli]

Interesting singlet KP.1.1 from Canada (query:T15330C, A24069T) with S:S31del S:G184D S:Q836L
tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_27e09_ce3320.json?c=userOrOld

[FedeGueli]

One more DeFLirt branch: JN.1.16.1 > Orf1a:K247R (A1005G) ,ORF3a:Y184H (T25942C ) Query: 1005G, T25942C Samples :3 see tracking comment

[FedeGueli]

KP.2 DeFLiRT Branch 12 + 4 today all from Ohio

[FedeGueli]

There is new DelRI branch with S:S704L

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_4333a_3cdb10.json?c=userOrOld&label=id:node_11449834

JN.1 > > Orf1a:K3353R (A10323G) > S:R346I (G22599T), S:S704L (C23673T), T25207C > S:S31del (del21653-55)
Query: G22599T,del21653,C23673T
Samples: 3
Countries: Germany, Denmark,

[FedeGueli]

@Sinickle found yesterday the first DelKP.3 : KP.3 > G15372T, A19722G >C12616T >Orf1a:S4286C (A13121T), T25686A Query:C12616T , A13121T

now 2 both from Basque Country Spain, @Sinickle please propose it

[FedeGueli]

Jn.1.25.1 FLirt last sample from Canada has S:S31del proposed in Branch 139 of #1089

JN.1.25.1 > > C7318T > G26648A > C28948T > S:F456L (T22928C)
Query: C7318T , G26648A ,T22928C
Samples: 4 Canada , UAE (GBW), Uk (Climb only)
the sample from Canada has also S:S31del DeFLiRT (Query: G26648A,del21653_21655, T22928C)

[FedeGueli]

JN.1.16.1 > Orf1a:K247R (A1005G) ,ORF3a:Y184H (T25942C ) Query: 1005G, T25942C Samples :5
tracked in my tracking comment above is now 5 i suggest to add it as branch cc @aviczhl2

[FedeGueli]

Branch 7 is now under Jn.1.48.2 topping now 23 from Australia Hawaii and California i would propose it

Jn.1.48.2 is 30 samples so 23/30 have the deletion

[FedeGueli]

My tracking comment now updated: #1502 (comment)
There is a new DelRT branch oin JN.1.4.5 in Singpaore and MYanmar too

[FedeGueli]

There is new DelRI branch with S:S704L https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_4333a_3cdb10.json?c=userOrOld&label=id:node_11449834

JN.1 > > Orf1a:K3353R (A10323G) > S:R346I (G22599T), S:S704L (C23673T), T25207C > S:S31del (del21653-55) Query: G22599T,del21653,C23673T Samples: 3 Countries: Germany, Denmark,

4 , +1 Australia

[FedeGueli]

G22599T,del21653,C23673T

5 now GBW from Qatar i m going to propose it separately

#1575

[FedeGueli]

Branch 14 jumped to 15, looking at metadata last Canadian samples are not an elderly people cluster

[FedeGueli]

Branch 14 jumped to 15, looking at metadata last Canadian samples are not an elderly people cluster

Branch 14 designated LF.2 ( broader cause trhe s:s31del is not accompanied by a nuc) via cov-lineages/pango-designation@544be2a

[FedeGueli]

Branch 5 designated KP.1.1.3 (broader for the usual reasons) via cov-lineages/pango-designation@3a035bd

[FedeGueli]

A2512G, T7049C, T15047C for a spanish singlet belonging to BA.2.86.3 that got 346T 31del and 455S in a row:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice10_genome_test_4871_707ae0.json?c=userOrOld&label=id:node_6920044

[FedeGueli]

T15555C, T16242A, C29364T
for a doublet 346T +31del from Canada:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice9_genome_test_4871_707ae0.json?label=id:node_6966083

[FedeGueli]

New JN.1.4 branch from Guatemala
Query: A27675C,G22599C,T3565C,del21653
Jn.1.4>> T18453C > A29799G > S:R346T G22599C > Orf7a:Q94H (A27675C ),S:S31del (del21653-21655)
Samples:4

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice6_genome_test_4871_707ad0.json?label=id:node_7097863

[FedeGueli]

XDK.3 (572I-456L) got S:S30-31del and S:F32I
Query: T6253C, A7201G, del21650_21655
Samples: 3 (UK,Sweden)

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice8_genome_test_4871_707ae0.json?label=id:node_7037916

[FedeGueli]

10. JN.1.25.1 > > C7318T > G26648A > C28948T > S:F456L (T22928C) > G991A, Orf1a::A656V (C2232T),ORF1b:T794I (C15848T), ORF1b:I2166S (T19964G), S:S31del (del21653_2165) ,A22666G Query: G26648A,del21653_21655, T22928C

This is now designated LM.1 and the branch with S:S31del went to 4
new defining mutations:
LM.1 > G991A, Orf1a:A656V (C2232T), ORF1b:T794I (C15848T), S:S31del (del21653_2165)
NEW Query: del21653,G991A, C15848T , C2232T
Samples: 4
IDs:EPI_ISL_19140331, EPI_ISL_19173644, EPI_ISL_19173747,
EPI_ISL_19173754
Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_42270_8313a0.json?label=id:node_11473483

[FedeGueli]

It is likely that Branch 10 JN.1.30.1 + 31del is broader : i suggest to use G21255T , G22599C,T3565C,G11727A,Del21653 to track it : it returns 7 samples in three branches

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_416b0_9831b0.json?f_userOrOld=uploaded%20sample&label=id:node_7145645

[FedeGueli]

I ve just proposed another JN.1.16.1 DeFLiRT : #1590