Multiple JN.1* sub-lineages with S:S31- and S:R190S, 10 ongoing unproposed branches as of 9/26

[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.

### 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, 17 seqs, USA,Italy, France
- [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, G25593T, G22132T, del21653, -28344,-14115, -16293, -24418, -29095, -6184, -22986, -7438,-6312,-7165,-9019,-18555,-12085,-22896C,-C1267T 17 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, 4 seqs, Brazil, UK, USA
- [ ] Branch 15, KP.2.3+C28714T,C29095T+S:R190S, Query: C28714T, G22132T, C29095T, 10 seqs, Canada, USA, Israel, India,Austria, Ireland
- [ ] Branch 16, 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, 19 seqs, Denmark, USA, Canada, France,Egpyt, Israel, Italy, Spain, South Africa, Thailand,Russia
- [ ] Branch 18, KP.2.3+C28714T+Orf1a:R1973S+S:K478T(rev)+S:R190S, Proposed in https://github.com/cov-lineages/pango-designation/issues/2787
- [x] Branch 19,Dead KP.2.3.1+S:R190S, Query: C28714T, G22132T, C22986T, 3 seqs, USA, Mexico, India
- [ ] Branch 20, Now proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/2061 MC.6+C29503T+Orf1a:P2055S, Orf1b:P218L, S:R190S, Query: G22132T, C29503T, G6536A 9 seqs, USA, Finland, Germany,Canada,Italy, Spain
- [x] Branch 21,Dead, LB.1+Orf1b:L186T+S:R190S, Query: G14023A, G22132T, G22111T , 8 seqs, USA
- [x] Branch 22, Dead, KP.2.3+A17755C,C346T,C28603T+S:R190S,  Query: A17755C,C346T,G22132T, 16 seqs, USA
- [ ] Branch 23, By @FedeGueli, LB.1.3.1 >> C24382T, S:C1243F (G25290T)> S:R190S (G22132T),Query: G22132T, C24382T, G25290T, 19 seqs, France, Spain,Denmark,New Zealand,Ireland,Australia, Sweden
- [ ] Branch 24, KP.2.3+S:K478T(rev)+Orf8:S67F,S:R190S, Proposed in https://github.com/cov-lineages/pango-designation/issues/2779
- [x] 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: G22132T, C6070T, C13862T, 5 seqs, UK, Japan, USA, Pakistan, Afghanistan
- [x] Branch 27,Dead, KP.1.1.3+C1909T,C24904T+S:R190S,Query: G22132T, C1909T,C24904T, 4 seqs, USA, Italy
- [x] 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
- [x] Branch 29,Dead, MC.8+Orf9b:G38D+S:R190S, Query: G22132T, G28396A, C6751T, 4 seqs, Germany,Canada
- [ ] Branch 30, KP.1.1.3+Orf3a:P178L+S:F186L,H445R,Q493E+S:R190S https://github.com/sars-cov-2-variants/lineage-proposals/issues/2126
- [ ] Branch 31, KP.3.1.1+S:R190S, Query: C12616T,A13121T,G22132T,-29503,-9803,-5297,-6312,-9748,-10681,-6536,-C25163A,-T7380C 15 seqs, USA, Canada, Spain, Greece, Sweden

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&