search

sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
43 stars 2 forks source link

JN.1.4+ S:R346T & S:S31del & Orf7a:Q94H emerged in Guatemala (39 samples, 8% local prevalence after July 1) #1714

Closed DailyCovidCases closed 1 month ago

DailyCovidCases commented 3 months ago

Edited Proposal: hence the original proposal found not one lineage but multiple unrelated DelRT lineages i have checked them : most of them are already dead but one is worth to be proposed also because it emerged (or it is circulating) in an undersampled area Guatemala. Defining mutations: JN.1.4>T18453C > S:S31del (del21653) S:R346T (G22599C) ,Orf7a:Q94H (A27675C), A29799G Query: del21653,G22599C,A27675C,C774T Samples: 11 Countries: Guatemala (also via GBW)

Screenshot 2024-07-08 alle 10 22 41

IDs: EPI_ISL_19168189-19168191, EPI_ISL_19168194, EPI_ISL_19196279, EPI_ISL_19196281-19196284, EPI_ISL_19221367, EPI_ISL_19229727,

###############################

Original Proposal: From branch 9 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1502 JN.1.4+S:S31del Query: C774T,T18453C, -28201, del21653_21655 No. of seqs: 60 (Brazil 19 Canada 4 Denmark 1 France 1 Guatemala 9 Ireland 1 Italy 4 Norway 1 UK 7 USA 13) First: EPI_ISL_18710550, 2023-12-18 Latest: EPI_ISL_19224449, 2024-6-24 usher Screenshot (137)

FedeGueli commented 3 months ago

There are multiple JN.1.4 + DelRT branches on this JN.1.4 branch, one with 1263L is a recombinant already proposed , the three with Orf8:E106Q are likely dead , on the bottom of the tree sparse singlets already dead ,

the only one worth proposing is the branch from Guatemala on the top, i will edit the proposal consequently.

FedeGueli commented 2 months ago

New upload yesterday i would propose it @DailyCovidCases

DailyCovidCases commented 2 months ago

Tracked in branch9

DailyCovidCases commented 2 months ago

This branch is dead now, I will close it

FedeGueli commented 2 months ago

You have to wait the next upload from Guatemala before closing this.

FedeGueli commented 2 months ago

When the Emerged in an undersampled area label is applied it means it will be kept open for a longer time due the fact we can't track properly local circulation

FedeGueli commented 1 month ago

This is now 39, many recent samples and 7-8% prevalence in Guatemala @aviczhl2 would you propose it has been tracked originally in your #1502 please?