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

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Repository for suggesting new lineages that should be added to the current scheme

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JN.1.18+S:F456V misplaced as JN.1.16.1+S:L456V(109 seqs, 19 countries) #2538

Closed aviczhl2 closed 1 month ago

aviczhl2 commented 3 months ago

From branch 37 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253 and https://github.com/sars-cov-2-variants/lineage-proposals/issues/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 commented 3 months ago

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

aviczhl2 commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

7 now two more GBW one from NZL

aviczhl2 commented 3 months ago

+1 Canada

aviczhl2 commented 2 months ago

14, India

aviczhl2 commented 2 months ago

20, Australia