Multiple JN.1* sub-lineages with S:S31- and S:R190S, 2 ongoing unproposed branches as of 2/5

[xz-keg]

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.

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1. Branch 1, Designated MA.1
2. Branch 2, Designated LP.1.2 LP.1 + S:R190S emerged inDominican Rep./ Puertorico ( 35 seqs, 6 countries including Dom.Rep, PR, Salvador) #1664 count 35
3. Branch 3,Designated LP.7 LP.7 [KP.1.1.3 + S:R190S ] with a S:G75S+S:A475V branch (24) cov-lineages/pango-designation#2755
4. Branch 4, (KP.4.2.4) Proposed in KP.4.2.4(S:S256L,S:S31del)+S:R190S(84 seqs,>10 places) cov-lineages/pango-designation#2759
5. Branch 5, Designated LB.1.4.1
6. Branch 6, LB.1.7+S:R190S, Proposed in LB.1.7+S:R190S(109 seqs, 8 countries) cov-lineages/pango-designation#2713
7. Branch 7, LB.1.7+C22096T+S:R190S,Dead Query: G22132T, C4784T,del21653,C22096T, 23 seqs, USA,Italy, France
8. Branch 8, Designated JN.1.59.1 JN.1.59+Orf1a:I841V+S:R190S,R346T,S31del, Proposed in JN.1.59+Orf1a:I841V+S:R190S,R346T,S31del (19 seqs, 6 countries) cov-lineages/pango-designation#2714
9. Branch 9, KP.2.3+C28714T+S:R190S, Dead Query: C28714T, G25593T, G22132T, del21653, -28344,-14115, -16293, -24418, -29095, -6184, -22986, -7438,-6312,-7165,-9019,-18555,-12085,-22896C,-C1267T 27 seqs, USA, Peru, Singapore, Canada, France, India, New Zealand,Poland, Denmark,Italy,Russia
10. Branch 10, (LR.1) Tracked as branch 25 of Multiple branches of BA.2.86* with S:S31del 2 Unproposed branches as of 8/23 #1502 count:3
11. Branch 11, (JN.1.4.5)By @FedeGueli, Branch 11 of Multiple branches of BA.2.86* with S:S31del 2 Unproposed branches as of 8/23 #1502+ S:K147E (A22001G), S:R190S (G22132T), A28058G, N:G236D (G28980A), Query A22001G,G22132T, A28058G Samples: 3 Russia
12. Branch 12, LB.1+S:R190S, Proposed in LB.1+S:R190S (88 seqs, 25 countries) cov-lineages/pango-designation#2746
13. Branch 13,Dead LB.1+Orf1a:G227S+S:R190S, Query: G22132T, G22111T, G944A, C29095T, 5 seqs, Australia, USA, UK
14. Branch 14,Dead JN.1 > C25566T +Orf3a:A110S,S:S31del, A67V, R190S, R346T with C29119G, Query: G22132T,del21653, C29119G, 4 seqs, Brazil, UK, USA
15. Branch 15, KP.2.3+C28714T,C29095T+S:R190S, Dead,Query: C28714T, G22132T, C29095T, 11 seqs, Canada, USA, Israel, India,Austria, Ireland,Poland
16. Branch 16,Dead, KP.2.3+C28714T,C16293T+S:R190S, Query: C28714T, G22132T, C16293T, 20 seqs, Canada, USA,Spain,Sweden,UK
17. Branch 17,Dead, JN.1.16.1+S:S31del, R190S, Query: del21653, G22132T, -22111, G22599C, T22928C,-17334,-28714,-13620,-16551,-24872,-16791 17 seqs, Denmark, USA, Canada, France,Egpyt, Israel, Italy, Spain, South Africa, Netherlands,
18. Branch 18, KP.2.3.11+S:K478T(rev)+S:R190S, Proposed in KP.2.3.11+S:R190S,K478T(rev)(38 seqs, >10 places ) cov-lineages/pango-designation#2787
19. Branch 19,Dead KP.2.3.1+S:R190S, Query: C28714T, G22132T, C22986T, 3 seqs, USA, Mexico, India
20. Branch 20, Dead Now proposed in MC.6 subbranch with S:R190S, Orf1a:P2055S and Orf1b:P218L(12 sequences, 6 countries) #2061 MC.6+C29503T+Orf1a:P2055S, Orf1b:P218L, S:R190S, Query: G22132T, C29503T, G6536A 9 seqs, USA, Finland, Germany,Canada,Italy, Spain
21. Branch 21,Dead, LB.1+Orf1b:L186T+S:R190S, Query: G14023A, G22132T, G22111T , 8 seqs, USA
22. Branch 22, Dead, KP.2.3+A17755C,C346T,C28603T+S:R190S, Query: A17755C,C346T,G22132T, 16 seqs, USA
23. Branch 23, Designated NL.1, By @FedeGueli, LB.1.3.1 >> S:C1243F (G25290T)>C24382T, S:R190S (G22132T),Query: G22132T, C24382T, G25290, Now proposed in LB.1.3.1 (S:H445P) acquired S:C1243F and S:R190S (34 seqs, 9 Places, 5% in NZL after Oct.1) with a S:D111N subbranch (5 seqs, 4 places) cov-lineages/pango-designation#2806
24. Branch 24,Designated NK.1 KP.2.3+S:K478T(rev)+Orf8:S67F,S:R190S, Proposed in KP.2.3+S:S31del+S:K478T(rev)+Orf8:S67F,S:R190S (17 seqs, 11 countries) cov-lineages/pango-designation#2779
25. Branch 25, Dead,LB.1.3+Orf1a:H13Y, F617L, S:R190S, Query: C302T, T2116A, G22132T, 4 seqs, Canada, USA, France, Denmark
26. Branch 26, Designated KP.4.2.6 KP.4.2+Orf1b:T132I,S:S31-,R190S, proposed in KP.4.2+Orf1b:T132I+S:S31-,R190S widespread in Central/South Asia(39 seqs, >10 places, 4 with S:A435S+A475V) cov-lineages/pango-designation#2852
27. Branch 27,Dead, KP.1.1.3+C1909T,C24904T+S:R190S,Query: G22132T, C1909T,C24904T, 4 seqs, USA, Italy
28. Branch 28,Dead, KP.2.3+C28714T+N:T24N,Orf10:A8V+Orf1a:L1762F, Orf1b:M1573T, Orf3a:G100D, S:R190S, Query:G22132T,C28344A,C29580T, 3 seqs, USA, Netherlands
29. Branch 29,Dead, MC.8+Orf9b:G38D+S:R190S, Query: G22132T, G28396A, C6751T, 4 seqs, Germany,Canada
30. Branch 30, Designated LP.8.1, LP.8+S:R190S, KP.1.1.3 with S:F186L,S:V445R and S:Q493E (22 seqs - 6 countries including Philippines) with two branches: one with S:R190S (20) and the other with S:L176F+S:M153I (2) #2126
31. Branch 31, KP.3.1.1+S:R190S, KP.3.1.1+S:R190S(98 seqs, >10 places) cov-lineages/pango-designation#2815
32. Branch 32 Dead LB.1.2.2> S:D253G (A22320G), T24202C > T11713C, G21901A,S:R190S (G22132T), Orf3a:S166L (C25889T) Query: A22320G, T24202C,T11713C 3 Seqs UAE, US, Sweden
33. Branch 33, Dead, LB.1.4+Orf1a:P4233L+Orf1b:D260G+S:R190S, Query: G22132T,C12933T,A14246G, 3 seqs,USA, Brazil
34. Branch 34,Designated XEJ.2 XEJ+S:R190S, Query: C16551T,T19209C, G22132T, 28 seqs, Russia, Netherlands
35. Branch 35,Dead KP.3.1.1+Orf1a:T1678A+S:R190S, Query: C12616T, A5297G,G22132T and C12616T, A5297G,C21034T,-22132 18 seqs, USA, Japan,Italy,Poland,France
36. Branch 36, NL.5+S:R190S, Designated NL.5.2, Query:C28714T,C14599T,G22132T, 23 seqs,UK,Israel,USA
37. Branch 37, MC.24+C20823T,S:R190S, Query: C20823T, G22132T,G25595T, 12 seqs, USA, France

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]

@aviczhl2 LP.1.1 is not LP.1 + S:R190S , designation of #1664 is still pending. Please correct that!

[FedeGueli]

@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]

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]

br 6 edited to exclude the Bat viruses

[FedeGueli]

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

[xz-keg]

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]

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

[xz-keg]

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.

[xz-keg]

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

[FedeGueli]

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

Yeah i was thinking the same

[FedeGueli]

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

[FedeGueli]

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

[xz-keg]

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

[xz-keg]

Add branch 13 and 14.

[FedeGueli]

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]

@aviczhl2 please propose branch 6 and branch 8

[xz-keg]

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.

[FedeGueli]

Not fast LB.1.9 (478T) branch got 335F and 190S:
LB.1.9 > C15654T > T25893A > Orf1a:P3359T (C10340A) S:R190S (G22132T), S:L335F (G22567T)
Query: C15654T,G22567T,T3565C finds 3 Us, Germany

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice2_genome_test_4e068_56690.json?label=id:node_7195584

[xz-keg]

add branch 35, another KP.3.1.1+S:R190S from Poland

[FedeGueli]

Branch 26 dying off, please update it

3 recent in Ontario

[xz-keg]

Add branch 36, NL.5+S:R190S

[FedeGueli]

KP.2.3.12 got S:R190S in two separate singlets in Brazil
one found with T8883C, G14428T, G27806T
the other found with C28205A ,G22132T, C26388T

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_58429_8a9a20.json?c=gt-S_190&f_userOrOld=uploaded%20sample&label=id:node_7390560

[Over-There-Is]

Branch 35 is 16 now

[FedeGueli]

Branch 35 is 16 now

thx spreading in Colorado while Br.36 is now 7 with NJ

[Over-There-Is]

There is a novel JN.1 + 190T + DEFLIRT with just two samples in Austria and Spain the only nucs that could be on its path are C11455T or C3373T or C28214T, i think we can place safely it as JN.1.16.1 +31del+ C11455T, C3373T, C28214T, S:R190T Query:C3373T, C28214T,T3565C Samples: 2 Austria and Spain Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_1356e_320fc0.json?label=id:node_11749152

Oman+2, without C3373T.

[xz-keg]

There is a novel JN.1 + 190T + DEFLIRT with just two samples in Austria and Spain the only nucs that could be on its path are C11455T or C3373T or C28214T, i think we can place safely it as JN.1.16.1 +31del+ C11455T, C3373T, C28214T, S:R190T Query:C3373T, C28214T,T3565C Samples: 2 Austria and Spain Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_1356e_320fc0.json?label=id:node_11749152

Oman+2, without C3373T.

make a separate issue

[FedeGueli]

maybe better to extrapolate br.36

[xz-keg]

branch 34 designated XEJ.2 via cov-lineages/pango-designation@5872a5a#diff-ead4244ff49c81bc758e9f068f5ef42156bd985b9c86de8fa4d6fcd7f2829090R1436

[FedeGueli]

There could be a big LB.1.2.2 branch in Peru with 190S checking it
Scrathc that just one from Gbw the remaining are the LF.7s with 572I

[xz-keg]

branch 26 is 18 now also in Malaysia and New Zealand

[xz-keg]

branch 26 +2 Canada. I'll propose it.

[FedeGueli]

a third apparently unrelated S:R190S branch of KP.2.3.12 apparently

[xz-keg]

a third apparently unrelated S:R190S branch of K.2.3.12 apparently

add it if it has some seqs

[FedeGueli]

Br.36 +1 England

[FedeGueli]

Kp.3.1.1 got 190S with 67V in Denmark Query: A2526G, C4276T, C21762T, Samples :3
Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_592af_7fb780.json?label=id:node_11829898

[xz-keg]

add branch 37, MC.24+S:R190S.

[FedeGueli]

add branch 37, MC.24+S:R190S.

Unfortunately mostly Ohio without collection date so growth advantage not reliable for this one

[FedeGueli]

Br.36 +2

[FedeGueli]

Br.36 designated NL.5.2 via cov-lineages/pango-designation@7ac925e

[xz-keg]

The only one remaining seems not advancing. Finally close this down. @FedeGueli pls make separate issues for future R190S branches.