JN.1.18+S:F456V misplaced as JN.1.16.1+S:L456V(109 seqs, 19 countries)

[xz-keg]

From branch 37 of sars-cov-2-variants/lineage-proposals#1253 and sars-cov-2-variants/lineage-proposals#1437

JN.1.18+S:F456V(T22928G)

GISAID query: G22599C, T22928G,C18894T, -6705,-C774T,-25658,-7789
No. of seqs: 5(USA 3 Singapore 1(from Saudi Arabia) Bangladesh 1)

First: EPI_ISL_18851598, Singapore from Saudi Arabia, 2024-1-12
Latest: EPI_ISL_19011021, USA, 2024-3-16

Usher places it in JN.1.16.1(R346T+F456L)+S:L456V (C22928G) . However that means position 22928 has to mutate from T->C->G in a short time, which is highly unlikely.
@AngieHinrichs @corneliusroemer

A better explanation shall be JN.1.18(R346T)+S:F456V(T22928G).

usher

[FedeGueli]

Thank you i noticed you havve excluded a couple more of convergent lineages are they among the ones already tracked?

[xz-keg]

Thank you i noticed you havve excluded a couple more of convergent lineages are they among the ones already tracked?

No. They are singlets, one under JN.1.30.1 and another under an undesignated JN,1 branch

[FedeGueli]

Thank you i noticed you havve excluded a couple more of convergent lineages are they among the ones already tracked?

No. They are singlets, one under JN.1.30.1 and another under an undesignated JN,1 branch

thx just checked one is Singlet 6 of # 1089 while the other is unknown till you spotted i will add with credits to the tracking issue

[FedeGueli]

7 now two more GBW one from NZL

[xz-keg]

+1 Canada

[xz-keg]

14, India

[xz-keg]

20, Australia

[FedeGueli]

21

[FedeGueli]

24 now (+4 with 2 from Qatar ) ping @corneliusroemer

[FedeGueli]

31 now @corneliusroemer i suggest to designate this one.

[FedeGueli]

35 now with 4 new sequences coming from New Zealand, i suggest designating it.

[FedeGueli]

36 now last from England

[xz-keg]

37, Japan, UK,

[FedeGueli]

the fastest FViRT: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?%2FAllSamples%2FPast3M%2Fvariants%3FnextcladePangoLineage=JN.1*&nextcladePangoLineage=JN.1*&nucMutations1=G22599C%2CT22928G%2CC18894T%2CC774C%2C6705A%2C25658C%2C7789T&analysisMode=CompareToBaseline&

[FedeGueli]

43 (+6 California,Illinois, NJ, Queensland, England )

[FedeGueli]

53 +6 South Australia +3 Canada +1 Sweden

[FedeGueli]

59 (5 England +1 Japan)

[FedeGueli]

One of the UK sequences got S:S31Del and two additional spike mutations
Jn.1.18>S:f456V > C13620T > 11749G, T21610C, S:R190S (G22132T),S:E780A (A23901C), C27649T, ORF10:N36S(A29664G)
Query: del21653, C13620T

[xz-keg]

65, South Korea, UAE,

[FedeGueli]

83

[FedeGueli]

88, designation needed

[FedeGueli]

106 in 17 countries + airports samples that i didnt count in countries ,now
ping @corneliusroemer now also Australia and New Zealand

[xz-keg]

109, Thailand, Peru, Germany, Norway, Brazil

[FedeGueli]

+1 Jap

[xz-keg]

Designated JN.1.18.3

[FedeGueli]

Jn.1.18.3 via 978a25a