Multiple branches of BA.2.86* with S:S31del 2 Unproposed branches as of 8/23

[xz-keg]

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

Tasks

Preview Give feedback

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, Dead, JN.1.1+S:R346T+S:S31del, Query (obsolete - not monophyletic): del21653_21655,C11747T, G22599C,-9442 19 seqs, Canada, South Korea, Singapore, USA, India,Mexico, Japan, Canary Islands
4. Branch 4, Dead, JN.1+Orf1a:G993D,A656V+C26013T+S:S31del, Query: del21653_21655,C26013T, C2232T,G3243A, 23 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, Designated LB.1, 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, Dead JN.1.48.2+Orf1a:A427V, S:R346T, S:S31del, Query: C1545T, A3829G, del21653_21655, 29 seqs, India,Spain,California,Hawaii, Australia
8. DelRT Branch 8, dead 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,S:R346T,Orf7a:Q94H,Proposed in JN.1.4+S:S31del, S:R346T, Orf7a:Q94H (54 seqs, 3 countries) cov-lineages/pango-designation#2739
10. DelRT Branch 10, DEAD JN.1.30.1+Orf1a:I1128F,S:S31del, Query: A3647T,del21653_21655, 4 seqs, India,Singapore
11. DelRT Branch 11, dead (one mid july sample now) JN.1.4.5+C11020T+S:R346T,S:S31del, Query: C28201T, del21653_21655,C11020T, 11 seqs, USA, UK, Russia, South Korea
12. DeFLiRT Branch 12,Designated KP.2.24, proposed in KP.2+S:S31del with C9286T branch (67 seqs) #1693 , KP.2 > C9286T,C14919T, S:S31del Query:del21653, C9286T,C14919T 41 seqs. USA,Germany, Canada, Portugal, China
13. DeFLiRT Branch 13,Designated LF.1.1.1, 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 (17 sequences, 5 countries, likely from Qatar ) #1575
16. Branch 16, KP.3.2.1 (S:A263V) with S:30-31del + S:F32I (3) #1556
17. DeFLuQE Branch 17, Designated KP.3.1.1, KP.3.1 with S:31del [18 seq, Basque, Extremadura,Madrid, Catalunya- Spain, Italy, USA, Wales] #1563
18. DeFLiRT Branch 18,Designated KP.2.23, proposed in KP.2+S:S31del+Orf3a:A110S,Orf8:G77S( 105 seqs, 9 countries) cov-lineages/pango-designation#2702
19. DeFLiRT Branch 19, Designated KP.2.19, KP.2+C832T+Orf1a:V28I,S:S31del, KP.2+Orf1a:V28I+S:S31del with C832T branch (65 seqs, 8 countries) #1814
20. DeFLiRT Branch 20, Dead, KP.1.1+Orf1a:L2778I,S:S31del, most with additional S:A376S, Query: del21653,C8597A,C12473T, 11 seqs, UK, USA
21. DeFLiRT Branch 21, Designated KP.4.2.4, KP.4.2+Orf1a:Q575R+S:S256L,S:S31del, most with additional S:R190S, Query:del21653,A1989G,C6070T, 19 seqs, UK, Sweden,France, Moldova, USA, UAE
22. Branch 22, Designated MA.1 JN.1.18.3 + S:∆S31, S:R190S, C27259A (rev) (20 seqs, 5 continents, Jun 21) #1635
23. DeFLiRT Branch 23, Designated LF.4.1, New JN.1.16.1 with S:S31del and Orf8:Q29* emerged recently in France (21 seqs, 8 countries) #1590
24. FULL QUAD Branch 24, JN.1.16.1+S:T572I(52 seqs=31+9+12(additional S:S31del)) #1687
25. DeFLiRT Branch 25, Dead, By @FedeGueli LR.1 (FLirt) >> C1648T, T11890G, C19269T, S:S31del (del21653-55), S:R190S (G22132T), Orf3a:L111F (A25725T), C27453T, N:A152T (G28727A) Query: C1648T, T11890G, Samples: 3
26. Branch 26, Designated KP.6, JN.1.11.1+S:R346I+S:S31del (11 seqs, 5 countries) #1682
27. DeFLuQE branch 27, KP.3.1 got again S:S31del and Orf1a:N4256S (NSP10_N3S) ( 43 seqs, >10 places) #1770
28. Branch 28, Tracked as branch 8 of Multiple JN.1* sub-lineages with S:S31- and S:R190S, 2 ongoing unproposed branches as of 12/30 #1771
29. DeFLiRT Branch 29,Designated KP.2.22, By @FedeGueli KP.2> T22795G >C4780T, Orf1a:V3718F (G11417T),S:S31del (Del21653-55) Query:C4780T,G11417T,del21653,T3565C Samples: 14 Taiwan, Japan, Australia, USA
30. DeFLuQE Branch 30, Designated MR.1, Recent KP.3.3 + Orf1a:I1367L branch got S:S31del expanding fast (12 seqs, 6 countries ) cov-lineages/pango-designation#2704
31. DeFLuQE Branch 31, KP.3.3.1+S:A163V+S:S31del, previous singlet in Other KP.3 sublineages with S:S31del #1700, query for S:A163V: C22050T, C23202A,C25803T, 21 seqs, Laos, USA, China, Japan, South Korea, France, Query for S:S31del: C22050T, C23202A,C25803T,del21653, 2 seqs
32. DeFLuQE Branch 32, KP.3.2+Orf1b:K2557R, Orf1a:T568I+C7267T,S:S31del, Query: T16723C,A3064G,C7267T, 11 seqs, France, USA, Denmark, Sweden, Spain
33. DeFLiRT Branch 33, KP.2.5+C592T+Orf1a:N704K,S:S31del, have S:A688V and V83F further sub-branches, Proposed in KP.2.5+Orf1a:N704K, S:S31del (82 seqs, 13 countries, 22 with S:A688V, 6 with S:T22N) cov-lineages/pango-designation#2740
34. DeFLiRT Branch 34, KP.1.1+S:S71Y,S:S31del (or KP*/LP.2 recombinant) proposed in KP.1.1+S:S71Y,S31del or JN.1.11.1/LP.2 recombinant(62 seqs, 14 countries) cov-lineages/pango-designation#2747
35. Branch 35, JN.1.4+S:R346T,S:S31del,Orf8:E106Q, Proposed in JN.1.4+S:S31del,Orf8:E106Q+S:R346T(95 seqs, 6 countries, 12 with S:F456V) cov-lineages/pango-designation#2738

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

[xz-keg]

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. Designated KP.2.24

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

4. Designated KP.2.23

Another KP.2> C11020T > T9499G, G14118T, C24358A, Orf3a:A110S (G25720T), Orf8:G77S(G28122A)
Query: del21653,T9499G, G14118T
Samples: 2 (1 on gisaid)

5. Designated MA.1

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: 61 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: 5 it revives in Scotland recently
    12)Dead

JN.1.4.5 > A29700G > orf1a:G519S (G1820A), S:S31del (del21653_2165) ,S:R346T (G22599C), C29386T
Query: G1820A, G22599C, C28201T,del21653 Samples: 6 (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

Now July 4 is MA.1 (edited)

[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

[FedeGueli]

It seems that the Orf8:E106Q is a separate branch. I'll propose.

thank you

[xz-keg]

@FedeGueli Branch 34 isn't fully LP.2.
Half of the seqs doesn't have the KP.1.1.3-defining C4999T. They are not dropouts, but real 4999C.

So actually shall be two separate branches.

1: KP.1.1+S:S71Y,S31del
2: KP.1.1.3(KP.1.1+C4999T,S:S31del)+S:S71Y （This is LP.2）

@corneliusroemer what do you think of the possibility of branch 1 being a recombinant of LP.2 and KP*?

I've altered the query for branch 34 to exclude LP.2.

[FedeGueli]

Branch 31 is now 5, last one from France, still no sample from August if one more from August will come please propose it.

[FedeGueli]

@FedeGueli Branch 34 isn't fully LP.2. Half of the seqs doesn't have the KP.1.1.3-defining C4999T. They are not dropouts, but real 4999C.

So actually shall be two separate branches.

1: KP.1.1+S:S71Y,S31del 2: KP.1.1.3(KP.1.1+C4999T,S:S31del)+S:S71Y （This is LP.2）

@corneliusroemer what do you think of the possibility of branch 1 being a recombinant of LP.2 and KP*?

I've altered the query for branch 34 to exclude LP.2.

Good catch! so i tend to think it is a recombinant losing Orf1b:T2376I and 4999T

[xz-keg]

Branch 31 becomes 10, +5 from South Korea.

No, only the GBW one of the branch has S:S31del, others seem separated prior to that with only S:A163V

Branch 34 Now 32 seqs. Continue being detected in South Korea and Malaysia in August,

[FedeGueli]

No, only the GBW one of the branch has S:S31del, others seem separated prior to that with only S:A163V

i didnt get what you mean

[FedeGueli]

Ah got it so add Dead label to it, i was monitoring it in the other issue and it has been 2 from a long time, no neeed to track 163V here no?

[FedeGueli]

Please propose Br.34 please

[xz-keg]

Ah got it so add Dead label to it, i was monitoring it in the other issue and it has been 2 from a long time, no neeed to track 163V here no?

Yeah pls make a separate issue if you want.

[FedeGueli]

Ah got it so add Dead label to it, i was monitoring it in the other issue and it has been 2 from a long time, no neeed to track 163V here no?

Yeah pls make a separate issue if you want.

Pls do it , if it is going!

[xz-keg]

Branch 21 detected in France and Moldova.

[xz-keg]

Branch 21 detected in USA local and imported case from UAE.

[xz-keg]

I'll propose branch 21 and close this multi-lineage issue. For future S:S31- branches please make separate issues.

[FedeGueli]

Br.31 reached 16 with a sample from Laos maybe worth extracting it?

[FedeGueli]

Br.31 reached 16 with a sample from Laos maybe worth extracting it?

nevermind it is the infiltrated here withoiut 31del sorry.

[FedeGueli]

There is a KP.4.1 branch + S:S31del that i am going to propose, it is quite an old one but got 5/63 samples after Sept 1 from three different continents.
I have the feeling we tracked or discussed it somewhere but i cannot find who and where. If anyone recognizes it then i will credit him

cc @xz-keg

[xz-keg]

There is a KP.4.1 branch + S:S31del that i am going to propose, it is quite an old one but got 5/63 samples after Sept 1 from three different continents. I have the feeling we tracked or discussed it somewhere but i cannot find who and where. If anyone recognizes it then i will credit him

cc @xz-keg

I think that branch is just separated by usher recently, previously likely hidden in some artifact flip-flop branches.

[FedeGueli]

There is a KP.4.1 branch + S:S31del that i am going to propose, it is quite an old one but got 5/63 samples after Sept 1 from three different continents. I have the feeling we tracked or discussed it somewhere but i cannot find who and where. If anyone recognizes it then i will credit him
cc @xz-keg

I think that branch is just separated by usher recently, previously likely hidden in some artifact flip-flop branches.

Yeah likely

[FedeGueli]

KP.3.2 defluqe branch 32 went to 11 with 4 samples from September 2 Sweden, 2 Spain GBW (1 pooled)

[FedeGueli]

There is an untracked KP.1.1 s:s31del branch still circulating in a mini saltation branch with S:175L and S:K478I in Sweden

KP.1.1 > C3457T > C3695T, Orf1a: E2089D (G6532T), A14457G, C18981T > S:S31del (del21653-55) >
ORF1a:C2180F (G6804T) > C11758T,A12595 S:F175L (T22085C), S:T478I (A22995T), C25728T, N:S37P (T28382C)
Query : C3457T ,C3695T,G6532T,del21653 finds 11
Query for the circulating mini saltation branch: A12595G ,C11758T, T22085C, finds 4
Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4062c_d6cc0.json?c=userOrOld&label=id:node_2536457

if it will grow further i will make a separate issue for the mini saltation branch