JN.1.4.7 (Orf3a:G18D) with S:R346T, 144 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024, 5% in South Africa in March) with S:F456V (21)

[FedeGueli]

Former branch 23 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089

I spotted this lineage less than ten days ago and it seems expanding in multiple countries. Notably one of the first sequences of this was sampled in December in Kenya, while earlier in january a sample was found from a traveller from Ghana, this makes me think it could be more widespread in that under-sampled continent and it is expanding from there, so i dont expect this to be espeacially fast but likely more widespread than what the count tells

Defining mutations: JN.1.4.7 [Orf3a:G18D (G25445A)]> S:R346T (G22599C) Query: G25445A,G22599C,C774T Samples: 27 Countries: 11 Continents: 3 Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4acfa_4911e0.json?c=gt-S_346&label=id:node_6926334

Samples: EPI_ISL_18767924, EPI_ISL_18777238, EPI_ISL_18788197, EPI_ISL_18790326, EPI_ISL_18796520, EPI_ISL_18796587, EPI_ISL_18799767, EPI_ISL_18811276, EPI_ISL_18816260, EPI_ISL_18816821, EPI_ISL_18832177, EPI_ISL_18833705, EPI_ISL_18861801, EPI_ISL_18872195, EPI_ISL_18877504, EPI_ISL_18878135, EPI_ISL_18878447, EPI_ISL_18878493, EPI_ISL_18878536, EPI_ISL_18882480, EPI_ISL_18882698, EPI_ISL_18902202, EPI_ISL_18903148, EPI_ISL_18903396, EPI_ISL_18907670, EPI_ISL_18913374, EPI_ISL_18913492

There is a branch with S:F456V (FViRT) JN.1.4 > Orf3a:G18D (G25445A)> S:R346T (G22599C) > S:F456V (T22928G) Query: G25445A,G22599C,T22928G,-C25350T Samples 2: EPI_ISL_18974137, EPI_ISL_18978808 (one Us, one GBW from unknown country)

Edited on April 16: There is a saltation singlet with S:F456L (FLiRT): JN.1.4.7 [Orf3a:G18D (G25445A)]> S:R346T (G22599C) > C1471T, A8882T, C15222T,, A15864G, Orf1b:L2218V = Nsp15_L167V (T20119G) , C20719T, S:A435T (G22865A), S:F456L (T22928C), S:V1264L (G25352C), C26625T Query: A8882T, A15864G

Edited on May 07: There is another FViRT singlet in the S:P1263L branch Query:C25350T, T5680C, T22928G

[FedeGueli]

cc @ryhisner there is a little scottish 3 seqs cluster of this showing a multiple nuc pattern between S:263-264:

i Don' t see it immediately as artifact but maybe i am wrong.

IDs:EPI_ISL_18913374, EPI_ISL_18913377, EPI_ISL_18913492 Query: Spike_A264N,Spike_A263T finds also an old BA.1.17 from England maybe useful to compare.

[FedeGueli]

28, +1 Nigeria confirming my hypothesis it is widespread in Africa ( it has been sampled in or from Kenya, Ghana and Nigeria) cc @corneliusroemer

[FedeGueli]

+1 Kenya this confirms further some sort of circulation on bopt eastern and western Africa ping @corneliusroemer

[FedeGueli]

+2 NY, ENG

[FedeGueli]

There is a S:K304N sublineage of this just two samples from UK query: A22474C ,C15656T,G25445A

[FedeGueli]

51 now and the 456V grew to 4 with 2 GBW samples from Kenya and Emirates. ping @corneliusroemer i suggest to designate both

[FedeGueli]

52 5 with S:F456V

[FedeGueli]

+1 on the FViRT branch

[FedeGueli]

parental lineage designated JN.1.4.7

[FedeGueli]

65 from 14 countries and 8 with 456V

[FedeGueli]

72 now, new country DRC (Congo where it represents 5/23 samples collected in 2024)

[FedeGueli]

ping @corneliusroemer

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_45293_ee8440.json?c=gt-S_456&f_userOrOld=uploaded%20sample&label=id:node_7044755

[FedeGueli]

82 for the 346T branch now with new samples coming from South Africa (3 new) Kenya (3) Canada (1) England (1) Italy(1 via GBW) and NZL this last one with S:F456V ( 9 FViRT in total now). @corneliusroemer i suggest designation of this : 1% of samples coming from Africa in 2024.

[FedeGueli]

86, and 11 with FViRT last two from Netherlands

[FedeGueli]

94 now 12 with FViRT

[DailyCovidCases]

101 now: https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?nucMutations=G25445A%2CG22599C%2CC774T&nextcladePangoLineage=JN.1.4.7*&

[FedeGueli]

118 / 13 FViRt (likely more due to dropouts)

[FedeGueli]

Designated LE.1 with 346T via https://github.com/cov-lineages/pango-designation/commit/622c0a2642a879a077fbea7ff0e382f84bdc1599 and LE.1.1 with 456V FVIRT via https://github.com/cov-lineages/pango-designation/commit/47360ae6992c24c01e6073fbf05781549a03f304

[FedeGueli]

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3e753_af7e90.json?label=id:node_7091851

cc @corneliusroemer LE.1 got FLiRT plus S:L84V and S:Q173K and looking at recency it is or fast or prevalent somewhere, proposing it but maybe worth designating it.