Multiple JN.1* sub-lineages with S:S31- and S:R190S, 16 ongoing unproposed branches as of 8/29

aviczhl2 commented 1 month ago

It seems that there is a new convergent mutation of S:R190S. It usually couples with S:S31del.

Cov-spectrum shows its growth is negative with S:S31S, but large growth advantage with S:S31-. It seems that like S:Q493E must be gained after S:F456L, this S:R190S must present under S:S31- variants.

### Tasks
- [x] Branch 1, Designated MA.1
- [x] Branch 2, Designated LP.1.2 https://github.com/sars-cov-2-variants/lineage-proposals/issues/1664 count 35
- [ ] Branch 3, https://github.com/cov-lineages/pango-designation/issues/2755
- [ ] Branch 4, (KP.4.2) Proposed in https://github.com/cov-lineages/pango-designation/issues/2759
- [x] Branch 5, Designated LB.1.4.1
- [ ] Branch 6, LB.1.7+S:R190S, Proposed in https://github.com/cov-lineages/pango-designation/issues/2713
- [ ] Branch 7, LB.1.7+C22096T+S:R190S, Query: G22132T, C4784T,del21653,C22096T, 13 seqs, USA,Italy
- [x] Branch 8, **Designated JN.1.59.1** JN.1.59+Orf1a:I841V+S:R190S,R346T,S31del, Proposed in https://github.com/cov-lineages/pango-designation/issues/2714
- [ ] Branch 9, KP.2.3+C28714T+S:R190S, Query: C28714T, G22132T, del21653, -28344,-14115, -16293, -24418, -29095, -6184, -22986, -7438,-6312,-7165,-9019 14 seqs, USA, Peru, Singapore, Canada, France, India, New Zealand
- [x] Branch 10, (LR.1) Tracked as branch 25 of  #1502 count:3
- [x] Branch 11, (JN.1.4.5)By @FedeGueli, Branch 11 of #1502+ S:K147E (A22001G), S:R190S (G22132T), A28058G, N:G236D (G28980A), Query A22001G,G22132T, A28058G Samples: 3 Russia
- [ ] Branch 12, LB.1+S:R190S, Proposed in https://github.com/cov-lineages/pango-designation/issues/2746
- [x] Branch 13,Dead LB.1+Orf1a:G227S+S:R190S, Query: G22132T, G22111T, G944A, C29095T, 5 seqs, Australia, USA, UK
- [x] Branch 14,Dead JN.1 > C25566T +Orf3a:A110S,S:S31del, A67V, R190S, R346T with C29119G, Query: G22132T,del21653, C29119G, 3 seqs, Brazil, UK
- [ ] Branch 15, KP.2.3+C28714T,C29095T+S:R190S, Query: C28714T, G22132T, C29095T, 7 seqs, Canada, USA, Israel, India
- [ ] Branch 16, KP.2.3+C28714T,C16293T+S:R190S, Query: C28714T, G22132T, C16293T, 16 seqs, Canada, USA,Spain,Sweden
- [ ] Branch 17, JN.1.16.1+S:S31del, R190S, Query: del21653, G22132T, -22111, G22599C, T22928C,-17334,-28714,-13620, 14 seqs, Denmark, USA, Canada, France,Egpyt, Israel, Italy, Spain, South Africa, Thailand
- [ ] Branch 18, KP.2.3+C28714T+Orf1a:R1973S+S:K478T(rev)+S:R190S, Query: C28714T, A6184C, G22132T, 9 seqs, USA, India, UAE, China
- [ ] Branch 19, KP.2.3.1+S:R190S, Query: C28714T, G22132T, C22986T, 3 seqs, USA, Mexico, India
- [ ] Branch 20, MC.6+C29503T+Orf1a:P2055S, Orf1b:P218L, S:R190S, Query: G22132T, C29503T, G6536A 4 seqs, USA, Finland, Germany,Canada
- [ ] Branch 21, LB.1+Orf1b:L186T+S:R190S, Query: G14023A, G22132T, G22111T , 7 seqs, USA
- [ ] Branch 22, KP.2.3+A17755C,C346T,C28603T+S:R190S, Query: A17755C,C346T,G22132T, 12 seqs, USA
- [ ] Branch 23, By @FedeGueli, LB.1.3.1 >> S:R190S (G22132T), C24382T, S:C1243F (G25290T), Query: G22132T, C24382T, G25290T, 6 seqs, France, Spain,Denmark,New Zealand
- [ ] Branch 24, KP.2.3+S:K478T(rev)+Orf8:S67F,S:R190S, Query: G22132T, C28093T,-22995,G25593T, 9 seqs, USA, Botswana,Qatar, UAE, Dominician Republic,India
- [ ] Branch 25, LB.1.3+Orf1a:H13Y, F617L, S:R190S, Query: C302T, T2116A, G22132T, 3 seqs, USA, France, Denmark
- [ ] Branch 26, KP.4.2+Orf1b:T132I,S:S31-,R190S, Query: G22132T, C6070T, C13862T, 4 seqs, UK, Japan, USA, Pakistan
- [ ] Branch 27, KP.1.1.3+C1909T,C24904T+S:R190S,Query: G22132T, C1909T,C24904T, 4 seqs, USA, Italy
- [ ] Branch 28, KP.2.3+C28714T+N:T24N,Orf10:A8V+Orf1a:L1762F, Orf1b:M1573T, Orf3a:G100D, S:R190S, Query:G22132T,C28344A,C29580T, 3 seqs, USA, Netherlands
- [ ] Branch 29, MC.8+Orf9b:G38D+S:R190S, Query: G22132T, G28396A, C6751T, 3 seqs, Germany

https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?variantQuery=S%3A31S&aaMutations1=S%3AR190S%2CS%3A31S&analysisMode=CompareToBaseline& https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?variantQuery=S%3A31-&aaMutations1=S%3AR190S%2CS%3AS31-&analysisMode=CompareToBaseline&

FedeGueli commented 1 month ago

@aviczhl2 LP.1.1 is not LP.1 + S:R190S , designation of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1664 is still pending. Please correct that!

FedeGueli commented 1 month ago

@aviczhl2 please add branch 25 of #1502 and also this one ah i see it is already branch 8, it has been tracked in #1502 in the comments some weeks ago.

FedeGueli commented 1 month ago

Also branch 21 of #1502 should be added here ()

FedeGueli commented 1 month ago

Also branch 21 of #1502 should be added here ()

already branch 4 of this sorry.

FedeGueli commented 1 month ago

i ve added (lineage) for branches of other issues to make easier to identify them

it should be all ok now. thanks for this important tracking issue.

cc @dailycovidcases please wait a bit before proposing them separately: at least wait them to reach 30 seqs

FedeGueli commented 1 month ago

br 6 edited to exclude the Bat viruses

FedeGueli commented 1 month ago

Br 8 jumped to 11 Br.6 to 8 Br.7 to 6 Br.9 to 5

aviczhl2 commented 1 month ago

Br 8 jumped to 11 Br.6 to 8 Br.7 to 6 Br.9 to 5

As said all branches are fastly growing.

FedeGueli commented 1 month ago

New 31del+190S branch this time from Russia and on JN.1.4 backbone: JN.1.4.5>> T18453C > Orf8:S103L (C28201T) > C11020T > S:R346T (G22599C) >> S:S31del (Del21653-55) S:K147E (A22001G), S:R190S (G22132T), A28058G, N:G236D (G28980A) Query:A22001G,G22132T, A28058G Samples: 3 Russia Saint Petersburg tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_45e73_97bd30.json?label=id:node_7141875

cc @aviczhl2

aviczhl2 commented 1 month ago

New 31del+190S branch this time from Russia and on JN.1.4 backbone: JN.1.4.5>> T18453C > Orf8:S103L (C28201T) > C11020T > S:R346T (G22599C) >> S:S31del (Del21653-55) S:K147E (A22001G), S:R190S (G22132T), A28058G, N:G236D (G28980A) Query:A22001G,G22132T, A28058G Samples: 3 Russia Saint Petersburg tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_45e73_97bd30.json?label=id:node_7141875

cc @aviczhl2

Shall be recombinant of JN.1.4.5 and branch 18 of #1502 ? Is C11020T convergent?

No it has T18453C isn't it? That blocks chances of simple recombs with 1 or 2 BPs.

aviczhl2 commented 1 month ago

I checked and C11020T is very convergent. So the Russian one is a new branch.

FedeGueli commented 1 month ago

I checked and C11020T is very convergent. So the Russian one is a new branch.

Yeah i was thinking the same

FedeGueli commented 1 month ago

Br.6 to 13 Br.7 to 7 Br.8 to 13 Br.9 to 7 all growing

FedeGueli commented 1 month ago

@aviczhl2 i suggest to track all of them here not in #1502, i mean the count and the query here not there

aviczhl2 commented 1 month ago

Add branch 12, LB.1+S:R190S direct branch

aviczhl2 commented 1 month ago

Add branch 13 and 14.

FedeGueli commented 1 month ago

Branch 14 is very interesting it stems out of the Jn.1+C25566T branch that is the branch leading then to JN.1.7 so i suspect it is either old one or some sort of recombinant, it is also misplaced in a 28603T branch that got FLipFLopped then

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_17ccc_e3eea0.json?c=gt-nuc_28603&gmax=29603&gmin=27603&label=id:node_7211805

ah and it is 4 on Usher with a Uk Climb sample too

FedeGueli commented 1 month ago

@aviczhl2 please propose branch 6 and branch 8

aviczhl2 commented 1 month ago

Add branch 15-17. Branch 17 is interesting, JN.1 with raw add-ons DeFLiRT+S:R190S without any other things, 5 seqs detected in 4 countries.

aviczhl2 commented 1 month ago

Branch 12 becomes 15.

aviczhl2 commented 4 weeks ago

Branch 8 designated JN.1.59.1 via https://github.com/cov-lineages/pango-designation/commit/699fb71616e45ddde4f74e0af21644fda0c4ef24

aviczhl2 commented 3 weeks ago

Add branch 18, KP.2.3 with S:478T reversion, S:R190S and 2-nuc Orf1a:1973S. detected in India local and GBW from India and UAE.

FedeGueli commented 3 weeks ago

New old branch from Brazil:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice24_genome_test_4b277_5129e0.json?label=id:node_7230994 i have excluded the flip flop C28603T from the defining. JN.1 >> C25566T >S:A67V (C21762T),S:R190S (G22132T), G25494T, ORF3a:A110S (G25720T), C29119G > S:R346T (G22599C) , S:S31del (del21653-55) My query is : G22132T, G25494T,del21653 Samples : 3 (5 on Usher) most recent sampled on 6/21 so it is not recent.

aviczhl2 commented 3 weeks ago

New old branch from Brazil: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice24_genome_test_4b277_5129e0.json?label=id:node_7230994 i have excluded the flip flop C28603T from the defining. JN.1 >> C25566T >S:A67V (C21762T),S:R190S (G22132T), G25494T, ORF3a:A110S (G25720T), C29119G > S:R346T (G22599C) , S:S31del (del21653-55) My query is : G22132T, G25494T,del21653 Samples : 3 (5 on Usher) most recent sampled on 6/21 so it is not recent.

That's Branch 14.

aviczhl2 commented 3 weeks ago

Branch 17 seems having a lot of seqs and merged with LF.7 on usher(due to usher unable handling deletions) now.

Top: LF.7 Bottom: Branch 17.

@AngieHinrichs, this is another example of a branch without deletion merged with a deletion branch. (the others include KP.1.1.1 and https://github.com/cov-lineages/pango-designation/issues/2649, LB.1 and LB.1.8, KP.2.3 and https://github.com/cov-lineages/pango-designation/issues/2722)

aviczhl2 commented 3 weeks ago

Add branch 19 and branch 20

Branch 16 becomes 12 Branch 7 becomes 11

FedeGueli commented 3 weeks ago

Branch 17 seems having a lot of seqs and merged with LF.7 on usher(due to usher unable handling deletions) now.

Top: LF.7 Bottom: Branch 17.

@AngieHinrichs, this is another example of a branch without deletion merged with a deletion branch. (the other is KP.1.1.1 and cov-lineages/pango-designation#2649)

To me it is ok enough tp broaden LF to 190S and then differentiate in the lineages with 31P and 31del

Ping @corneliusroemer

aviczhl2 commented 3 weeks ago

Branch 17 seems having a lot of seqs and merged with LF.7 on usher(due to usher unable handling deletions) now. Top: LF.7 Bottom: Branch 17. @AngieHinrichs, this is another example of a branch without deletion merged with a deletion branch. (the other is KP.1.1.1 and cov-lineages/pango-designation#2649)

To me it is ok enough tp broaden LF to 190S and then differentiate in the lineages with 31P and 31del

Ping @corneliusroemer

The trajectory is clearly different. It is not likely for R190S to appear before S31del or T22N. They have to be separate lineages.

FedeGueli commented 3 weeks ago

Branch 17 seems having a lot of seqs and merged with LF.7 on usher(due to usher unable handling deletions) now. Top: LF.7 Bottom: Branch 17. @AngieHinrichs, this is another example of a branch without deletion merged with a deletion branch. (the other is KP.1.1.1 and cov-lineages/pango-designation#2649)

To me it is ok enough tp broaden LF to 190S and then differentiate in the lineages with 31P and 31del Ping @corneliusroemer

The trajectory is clearly different. It is not likely for R190S to appear before S31del or T22N. They have to be separate lineages.

yeah but if usher keeps them together wee can also decide to follow it without making things harder, at the end every decision is conventional reinforced by likelyhood or parsimony.

FedeGueli commented 3 weeks ago

Br.9 now 14 and BR.12 now 24, please propose it if all of the new samples belong to it, i suspect may be some new -s should be needed for both these branches

aviczhl2 commented 3 weeks ago

yeah but if usher keeps them together wee can also decide to follow it without making things harder, at the end every decision is conventional reinforced by likelyhood or parsimony.

It uses a false likelihood not considering deletions, resulting in bad assignment.

FedeGueli commented 3 weeks ago

yeah but if usher keeps them together wee can also decide to follow it without making things harder, at the end every decision is conventional reinforced by likelyhood or parsimony.

It uses a false likelihood not considering deletions, resulting in bad assignment.

i mean if there is not a nuc mutation that makes a lineage needed to be moved elsewhere , how does it matter if placed here or there? likely LF.7 is not Jn.1.16 but unrleated but as @corneliusroemer explained some lineages have been designated as JN.1.16 derivatives, and for sure JN.1.16 itself collects some independent acquisition of T22928C, but if this doesn't impact our work i dont see any issue with that. Consider that time of the few people involved in variant tracking and more importantly in designations, nextclading etc is limited, i think if there is no clear difference the easiest thing is the best one.

aviczhl2 commented 3 weeks ago

Br.9 is 9 after adding more -s , Br.12 is still at 21 from various countries after excluding those. Propose Br.12.

aviczhl2 commented 3 weeks ago

Also add branch 21.

FedeGueli commented 3 weeks ago

Also add branch 21.

The query doesnt work apparently

aviczhl2 commented 3 weeks ago

Also add branch 21.

The query doesnt work apparently

Sorry, shall be G14023A, query edited

aviczhl2 commented 2 weeks ago

Add branch 22.

FedeGueli commented 2 weeks ago

There should be a branch with 190S under Lb.1.3.1 , two samples collected on July 22 from two countries Denmark, France Query:G22132T, C24382T, G25290T LB.1.3.1 >> S:R190S (G22132T), C24382T, S:C1243F (G25290T) the French sample has gained also S:D111N and S:T1116N suggesting circulation in some undersampled zone. tree:

aviczhl2 commented 2 weeks ago

There should be a branch with 190S under Lb.1.3.1 , two samples collected on July 22 from two countries Denmark, France Query:G22132T, C24382T, G25290T LB.1.3.1 >> S:R190S (G22132T), C24382T, S:C1243F (G25290T) the French sample has gained also S:D111N and S:T1116N suggesting circulation in some undersampled zone. tree:

Added as branch 23.

aviczhl2 commented 2 weeks ago

Branch 18 becomes 7 with new samples from India and GBW from China.

aviczhl2 commented 2 weeks ago

Add branch 24, another KP.2.3+S:S31-, S:K478T rev,S:R190S, 5 GBW seqs from Botswana, UAE, Qatar and Dominician Republic

aviczhl2 commented 2 weeks ago

Add branch 25.

FedeGueli commented 2 weeks ago

@aviczhl2 the 478T parent of BR.24 has been proposed?

aviczhl2 commented 2 weeks ago

Branch 23 becomes 4 ,with 2 more from NZL

aviczhl2 commented 2 weeks ago

Add branch 26, another KP.4.2+S31-+R190S, detected in Japan and UK, as well as GBW from Pakistan

aviczhl2 commented 2 weeks ago

Add branch 27.

aviczhl2 commented 2 weeks ago

Branch 9 becomes 14. Add branch 28.

FedeGueli commented 2 weeks ago

Updated query for Branch 3 : -C3885A,-C1909T,-T24079C,-T14508C,-T13123C,A24819G,G22132T,4999,T3565C finds 54 Now proposed in https://github.com/cov-lineages/pango-designation/issues/2755

aviczhl2 commented 1 week ago

Usher tree changes for Branch 24 and now it becomes 9 and includes an Indian seq.

FedeGueli commented 4 days ago

BR.18 to 9 both new samples from New Jersey

sars-cov-2-variants / lineage-proposals

Multiple JN.1* sub-lineages with S:S31- and S:R190S, 16 ongoing unproposed branches as of 8/29 #1771