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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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JN.1.16.1 (Usher places it under LR.1) plus S:T22N, S31P, K182R, R190S, K444R + ORF9b:I5T + ORF1a:S2535L (7 seq, 6 countries; Aug 13) #2733

Closed ryhisner closed 2 months ago

ryhisner commented 2 months ago

Description Sub-lineage of: JN.1.16.1 Earliest sequence: 2024-6-24, Senegal Most recent sequence: 2024-7-27, Australia, Western Australia — EPI_ISL_19333883 Continents circulating: Africa (2), Europe (2), North America (1), Oceania (1) Countries circulating: Senegal (2), Australia (1), Canada (1), England (1), France (1), Unknown Travel sequence (1) Number of Sequences: 6-7 GISAID Nucleotide Query: C5239T, C7869T, C8818T, G12892A, T16600C CovSpectrum Query: Nextcladepangolineage:JN.1* & [4-of: C5239T, C7869T, C8818T, G12892A, T16600C] Substitutions on top of JN.1.16.1: Spike: T22N, S31P, K182R, R190S, K444R ORF1a: S2535L ORF9b: I5T Nucleotide: C5239T, C7869T, C8818T, G12892A, T16600C, C21627A, T21653C, A22107G, G22132T, C22792T, A22893G, C22993T, T28297C

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/JN.1.16.1_T22N_S31P_K182R_R190S_K444R.json?c=gt-S_444&gmax=25384&gmin=21563&label=id:node_6967258

image

Evidence Okay, so this has spread internationally. Putting together a permanent Usher tree link shortly, to be posted above.

Hoping that the GBW pooled sequence is soon matched with an individual sequence so that we know what country that travel sequence originated from.

Genomes

Genomes EPI_ISL_19273031, EPI_ISL_19273041, EPI_ISL_19293986, EPI_ISL_19305721, EPI_ISL_19324095, EPI_ISL_19331105, EPI_ISL_19333883
corneliusroemer commented 2 months ago

Possibly recombinant or maybe just convergent (chronic?) evolution? Given there are no reversions it does look liked

It shares with FL.1.5.1 (an XBB.1.9):

Given there are no reversions and the recombination would have to be super complex I'll not designate as recombinant for now unless someone finds better evidence.

corneliusroemer commented 2 months ago

Ah, the A21137G (ORF1b:K2557R) is not actually present at all - pretty clear Usher tree building error it seems @AngieHinrichs

Brave Browser 2024-08-15 14 43 00
corneliusroemer commented 2 months ago

Didn't find any other reasonable ancestor, so will designate as JN.1.16.1 sublineage (it's most likely homoplasy but in absence of evidence let's keep the naming simpler)

corneliusroemer commented 2 months ago

Also in Egypt now: hCoV-19/Egypt/CPHL-EGY24173/2024|EPI_ISL_19334646|2024-06-26 missing from Usher due to low quality I think.

FedeGueli commented 2 months ago

Designated LF.7 via https://github.com/cov-lineages/pango-designation/commit/43d7733254e29c91714acb4ed0ea2003b2873551

corneliusroemer commented 2 months ago

I just plugged the private mutations into SMDP and it has a little bit of a molnupiravir signature, on the lower end.

https://eringill.shinyapps.io/covid_mutation_distributions/

Google Chrome 2024-08-15 18 35 53 Google Chrome 2024-08-15 18 35 46

Not sure how to interpret movbranch results:

Google Chrome 2024-08-15 18 39 23

https://movbranchapp.streamlit.app/

ryhisner commented 2 months ago

Not impossible there was MOV involvement, but the relative lack of G->A mutations makes it doubtful I think. This may have been circulating in some part of Africa for a bit, though the five spike AA mutations suggest a probable (relatively short) chronic-infection origin.

FedeGueli commented 2 months ago

please close it is LF.7

HynnSpylor commented 2 months ago

Notice that the two seqs from Egypt get S:D614G->S. Another attempt to change the basic S:D614G