Multiple JN.1* sub-lineages with S:S31- and S:R190S, 4 ongoing unproposed branches as of 10/24 #1771

xz-keg · 2024-07-24T08:56:51Z

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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Branch 1, Designated MA.1
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
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
Branch 4, (KP.4.2.4) Proposed in KP.4.2.4(S:S256L,S:S31del)+S:R190S(45 seqs,>10 places) cov-lineages/pango-designation#2759
Branch 5, Designated LB.1.4.1
Branch 6, LB.1.7+S:R190S, Proposed in LB.1.7+S:R190S(90 seqs, 7 countries) cov-lineages/pango-designation#2713
Branch 7, LB.1.7+C22096T+S:R190S,Dead Query: G22132T, C4784T,del21653,C22096T, 23 seqs, USA,Italy, France
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
Branch 9, KP.2.3+C28714T+S:R190S, Query: C28714T, G25593T, G22132T, del21653, -28344,-14115, -16293, -24418, -29095, -6184, -22986, -7438,-6312,-7165,-9019,-18555,-12085,-22896C,-C1267T 26 seqs, USA, Peru, Singapore, Canada, France, India, New Zealand,Poland, Denmark,Italy,Russia
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
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
Branch 12, LB.1+S:R190S, Proposed in LB.1+S:R190S (68 seqs, 19 countries) cov-lineages/pango-designation#2746
Branch 13,Dead LB.1+Orf1a:G227S+S:R190S, Query: G22132T, G22111T, G944A, C29095T, 5 seqs, Australia, USA, UK
Branch 14,Dead JN.1 > C25566T +Orf3a:A110S,S:S31del, A67V, R190S, R346T with C29119G, Query: G22132T,del21653, C29119G, 4 seqs, Brazil, UK, USA
Branch 15, KP.2.3+C28714T,C29095T+S:R190S, Dead,Query: C28714T, G22132T, C29095T, 11 seqs, Canada, USA, Israel, India,Austria, Ireland,Poland
Branch 16,Dead, KP.2.3+C28714T,C16293T+S:R190S, Query: C28714T, G22132T, C16293T, 20 seqs, Canada, USA,Spain,Sweden,UK
Branch 17, JN.1.16.1+S:S31del, R190S, Query: del21653, G22132T, -22111, G22599C, T22928C,-17334,-28714,-13620, 35 seqs, Denmark, USA, Canada, France,Egpyt, Israel, Italy, Spain, South Africa, Thailand,Russia,Netherlands
Branch 18, KP.2.3.11+S:K478T(rev)+S:R190S, Proposed in KP.2.3.11+S:R190S,K478T(rev)(23 seqs, >10 places ) cov-lineages/pango-designation#2787
Branch 19,Dead KP.2.3.1+S:R190S, Query: C28714T, G22132T, C22986T, 3 seqs, USA, Mexico, India
Branch 20, Now proposed in MC.6 subbranch with S:R190S, Orf1a:P2055S and Orf1b:P218L(9 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
Branch 21,Dead, LB.1+Orf1b:L186T+S:R190S, Query: G14023A, G22132T, G22111T , 8 seqs, USA
Branch 22, Dead, KP.2.3+A17755C,C346T,C28603T+S:R190S, Query: A17755C,C346T,G22132T, 16 seqs, USA
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
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
Branch 25, Dead,LB.1.3+Orf1a:H13Y, F617L, S:R190S, Query: C302T, T2116A, G22132T, 4 seqs, Canada, USA, France, Denmark
Branch 26, KP.4.2+Orf1b:T132I,S:S31-,R190S, Query: -A1989G,G22132T, C6070T, C13862T 11 seqs, UK, Japan, USA, Pakistan, Afghanistan, Qatar, Canada,Italy,Saudi Arabia
Branch 27,Dead, KP.1.1.3+C1909T,C24904T+S:R190S,Query: G22132T, C1909T,C24904T, 4 seqs, USA, Italy
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
Branch 29,Dead, MC.8+Orf9b:G38D+S:R190S, Query: G22132T, G28396A, C6751T, 4 seqs, Germany,Canada
Branch 30, 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
Branch 31, KP.3.1.1+S:R190S, KP.3.1.1+S:R190S(30 seqs, >10 places) cov-lineages/pango-designation#2815
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
Options

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 · 2024-07-24T14:41:31Z

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

FedeGueli · 2024-07-24T17:37:49Z

@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 · 2024-07-25T07:57:00Z

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 · 2024-07-25T08:40:56Z

br 6 edited to exclude the Bat viruses

FedeGueli · 2024-07-28T11:34:56Z

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

xz-keg · 2024-07-29T04:25:57Z

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 · 2024-07-31T00:07:43Z

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 · 2024-07-31T01:54:49Z

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 · 2024-07-31T03:20:36Z

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

FedeGueli · 2024-07-31T09:12:24Z

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

Yeah i was thinking the same

FedeGueli · 2024-07-31T13:31:19Z

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

FedeGueli · 2024-07-31T13:31:53Z

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

xz-keg · 2024-08-03T09:28:47Z

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

xz-keg · 2024-08-03T09:33:47Z

Add branch 13 and 14.

FedeGueli · 2024-08-03T14:41:15Z

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 · 2024-08-03T15:02:34Z

@aviczhl2 please propose branch 6 and branch 8

xz-keg · 2024-08-09T07:26:25Z

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 · 2024-10-07T05:37:17Z

@aviczhl2 important! Branch 30 tre has changed it appears to be a real lineage with two branches: one proposed here as Br.30 and the other with 176F and 153I i suggest to extrapolate it from here with both branch highlighted in a separate issue.
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3d8d6_3159c0.json?c=userOrOld&label=id:node_7286077
Query for the whole branch: C22120A, 22896G, C23039G Sasmples: 4 Places: Israel, Germany, US, Philippines

Yeah you can make a separate issue.

Ok! Proposed in #2126

FedeGueli · 2024-10-07T12:47:27Z

Br.23 went to 19 with Sweden new country
Br.20 went to 9 new country Spain
Br.31 went to 15

FedeGueli · 2024-10-07T17:16:21Z

cc @xz-keg Branch 26 got a new recent GBW sequence from...Afghanistan!

Branch 26, KP.4.2+Orf1b:T132I,S:S31-,R190S, Query: G22132T, C6070T, C13862T, 5 seqs, UK, Japan, USA, Pakistan, Afghanistan

the one on the bottom

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_151f1_4167e0.json?f_userOrOld=uploaded%20sample&label=id:node_7301312

FedeGueli · 2024-10-15T07:47:25Z

cc @xz-keg Branch 26 got a new recent GBW sequence from...Afghanistan!

Branch 26, KP.4.2+Orf1b:T132I,S:S31-,R190S, Query: G22132T, C6070T, C13862T, 5 seqs, UK, Japan, USA, Pakistan, Afghanistan

now Qatar and Canada

FedeGueli · 2024-10-15T07:48:39Z

Br.31 > 15 , Italy

FedeGueli · 2024-10-15T07:50:25Z

Not to be added yet. but there is a LB.1.2.2 branch with 190S , 253G and 222S in the last sample: query: A22320G, T24202C,T3565C

One more of this from NJ

One more from Canada maybe worth i will add to the branches
Now it is Branch 32

FedeGueli · 2024-10-15T08:05:20Z

Not to be added yet. but there is a LB.1.2.2 branch with 190S , 253G and 222S in the last sample: query: A22320G, T24202C,T3565C

One more of this from NJ

One more from Canada maybe worth i will add to the branches Now it is Branch 32

the tree has changed (or better sayinfd i mistook the query) all of them have 253G but only two have 190S i adjusted the query and the branch (sorry if i had known that i would have not added it as branch)

xz-keg · 2024-10-15T08:41:13Z

Not to be added yet. but there is a LB.1.2.2 branch with 190S , 253G and 222S in the last sample: query: A22320G, T24202C,T3565C

One more of this from NJ

One more from Canada maybe worth i will add to the branches Now it is Branch 32

the tree has changed (or better sayinfd i mistook the query) all of them have 253G but only two have 190S i adjusted the query and the branch (sorry if i had known that i would have not added it as branch)

make a separate issue?

FedeGueli · 2024-10-15T09:18:45Z

Not to be added yet. but there is a LB.1.2.2 branch with 190S , 253G and 222S in the last sample: query: A22320G, T24202C,T3565C

One more of this from NJ

One more from Canada maybe worth i will add to the branches Now it is Branch 32

the tree has changed (or better sayinfd i mistook the query) all of them have 253G but only two have 190S i adjusted the query and the branch (sorry if i had known that i would have not added it as branch)

make a separate issue?

i will wait a bit it is in my list and checked here in the 190S branch

xz-keg · 2024-10-16T02:24:07Z

branch 26 gets 3 more seqs from Italy, now 10.

FedeGueli · 2024-10-16T08:01:46Z

branch 26 gets 3 more seqs from Italy, now 10.

worth extrapolating it maybe ?

xz-keg · 2024-10-18T10:32:35Z

Branch 23 becomes 28 with new samples from Argentina and New Zealand. @FedeGueli you can propose it?
It also has a S:D111N sub-branch now.

FedeGueli · 2024-10-19T09:55:33Z

Branch 23 becomes 28 with new samples from Argentina and New Zealand. @FedeGueli you can propose it? It also has a S:D111N sub-branch now.

wow quite crazy in NZL. i will do now

Done: cov-lineages/pango-designation#2806

thx !

xz-keg · 2024-10-24T01:43:35Z

branch 31 is 25 now I'm proposing it.

xz-keg · 2024-10-24T01:58:34Z

B7,B15->DEad
B9->25
B17->27
B26->13

FedeGueli · 2024-10-24T07:28:41Z

B7,B15->DEad B9->25 B17->27 B26->13

Thx the most interesting seems BR.26 the others are slow apparently

FedeGueli · 2024-10-24T07:38:38Z

B7,B15->DEad B9->25 B17->27 B26->13

Thx the most interesting seems BR.26 the others are slow apparently

Wait B.26 query seems to catch some seqs belonging to cov-lineages/pango-designation#2759:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4d97b_9f7510.json?c=userOrOld&label=id:node_7382232

So i suggest to adjust the query to -A1989G,G22132T, C6070T, C13862T that gives 10

xz-keg · 2024-10-25T18:36:48Z

B3->LP.7 via cov-lineages/pango-designation@9db833c
B23->NL.1 via cov-lineages/pango-designation@d393047
B24->NK.1 via cov-lineages/pango-designation@b2f9b67

FedeGueli · 2024-10-26T01:06:24Z

Br.32 +1 from Sweden

xz-keg · 2024-10-27T01:26:51Z

branch 17 becomes 35 after a Russian upload.

FedeGueli · 2024-10-27T11:13:41Z

branch 17 becomes 35 after a Russian upload.

Please propose it if any sample from october comes up

FedeGueli · 2024-10-27T13:35:38Z

Br.26>> 13

xz-keg · 2024-11-01T14:31:42Z

branch 26 +1 GBW from Saudi Arabia, additional A435S+A475V.

xz-keg mentioned this issue Jul 24, 2024

Multiple branches of BA.2.86* with S:S31del 2 Unproposed branches as of 8/23 #1502

Closed

FedeGueli added Multiple lineages S:190 S:31del N Glycan labels Jul 24, 2024

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xz-keg changed the title ~~Multiple JN.1* sub-lineages with S:S31- and S:R190S~~ Multiple JN.1* sub-lineages with S:S31- and S:R190S, 5 ongoing unproposed branches as of 7/31 Jul 31, 2024

FedeGueli changed the title ~~Multiple JN.1* sub-lineages with S:S31- and S:R190S, 5 ongoing unproposed branches as of 7/31~~ Multiple JN.1* sub-lineages with S:S31- and S:R190S, 8 ongoing unproposed branches as of 8/03 Aug 3, 2024

FedeGueli added the To be proposed Green light for proposal label Aug 3, 2024

This was referenced Aug 6, 2024

LB.1.7+S:R190S(90 seqs, 7 countries) cov-lineages/pango-designation#2713

Open

JN.1.59+Orf1a:I841V+S:R190S,R346T,S31del (19 seqs, 6 countries) cov-lineages/pango-designation#2714

Closed

xz-keg changed the title ~~Multiple JN.1* sub-lineages with S:S31- and S:R190S, 8 ongoing unproposed branches as of 8/03~~ Multiple JN.1* sub-lineages with S:S31- and S:R190S, 14 ongoing unproposed branches as of 8/09 Aug 9, 2024

FedeGueli mentioned this issue Oct 7, 2024

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

Closed

xz-keg changed the title ~~Multiple JN.1* sub-lineages with S:S31- and S:R190S, 10 ongoing unproposed branches as of 9/26~~ Multiple JN.1* sub-lineages with S:S31- and S:R190S, 5 ongoing unproposed branches as of 10/12 Oct 12, 2024

xz-keg mentioned this issue Oct 24, 2024

KP.3.1.1+S:R190S(30 seqs, >10 places) cov-lineages/pango-designation#2815

Open

xz-keg changed the title ~~Multiple JN.1* sub-lineages with S:S31- and S:R190S, 5 ongoing unproposed branches as of 10/12~~ Multiple JN.1* sub-lineages with S:S31- and S:R190S, 3 ongoing unproposed branches as of 10/24 Oct 24, 2024

xz-keg changed the title ~~Multiple JN.1* sub-lineages with S:S31- and S:R190S, 3 ongoing unproposed branches as of 10/24~~ Multiple JN.1* sub-lineages with S:S31- and S:R190S, 4 ongoing unproposed branches as of 10/24 Oct 24, 2024

Multiple JN.1* sub-lineages with S:S31- and S:R190S, 4 ongoing unproposed branches as of 10/24 #1771

Multiple JN.1* sub-lineages with S:S31- and S:R190S, 4 ongoing unproposed branches as of 10/24 #1771

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