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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) #2493

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FedeGueli opened this issue Feb 20, 2024 · 19 comments
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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) #2493

FedeGueli opened this issue Feb 20, 2024 · 19 comments

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@FedeGueli
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FedeGueli commented Feb 20, 2024 •
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Former branch 23 of sars-cov-2-variants/lineage-proposals#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:
Screenshot 2024-02-20 alle 13 16 49
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
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cc @ryhisner there is a little scottish 3 seqs cluster of this showing a multiple nuc pattern between S:263-264:
Screenshot 2024-02-20 alle 13 57 18
i Don' t see it immediately as artifact but maybe i am wrong.
Screenshot 2024-02-20 alle 13 57 31
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 FedeGueli mentioned this issue Feb 21, 2024
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@FedeGueli FedeGueli changed the title New JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D (former Branch 23 of #1089 preproposals repo) New JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D (former Branch 23 of #1089 preproposals repo) 28 Sequences Feb 21, 2024
@FedeGueli
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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 FedeGueli changed the title New JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D (former Branch 23 of #1089 preproposals repo) 28 Sequences New JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D (former Branch 23 of #1089 preproposals repo) 29 Sequences Feb 22, 2024
@FedeGueli
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+1 Kenya this confirms further some sort of circulation on bopt eastern and western Africa ping @corneliusroemer

@FedeGueli FedeGueli changed the title New JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D (former Branch 23 of #1089 preproposals repo) 29 Sequences New JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D (former Branch 23 of #1089 preproposals repo) 32 Sequences Feb 26, 2024
@FedeGueli FedeGueli changed the title New JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D (former Branch 23 of #1089 preproposals repo) 32 Sequences New JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D (former Branch 23 of #1089 preproposals repo) 34 Sequences Feb 29, 2024
@FedeGueli
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+2 NY, ENG

@FedeGueli FedeGueli changed the title New JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D (former Branch 23 of #1089 preproposals repo) 34 Sequences JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 39 Sequences, 11 countries including 3 different african countries Mar 7, 2024
@FedeGueli FedeGueli changed the title JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 39 Sequences, 11 countries including 3 different african countries JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 39 Sequences, 11 countries including 3 different African countries Mar 7, 2024
@FedeGueli
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There is a S:K304N sublineage of this just two samples from UK query: A22474C ,C15656T,G25445A

@FedeGueli FedeGueli changed the title JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 39 Sequences, 11 countries including 3 different African countries JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 39 Sequences, 11 countries including 3 different African countries with a branch with S:F456V Mar 14, 2024
@FedeGueli FedeGueli changed the title JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 39 Sequences, 11 countries including 3 different African countries with a branch with S:F456V JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 39 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (2) Mar 14, 2024
@FedeGueli FedeGueli changed the title JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 39 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (2) JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 51 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (4) Mar 16, 2024
@FedeGueli
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51 now and the 456V grew to 4 with 2 GBW samples from Kenya and Emirates. ping @corneliusroemer i suggest to designate both

@xz-keg xz-keg mentioned this issue Mar 17, 2024
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@FedeGueli FedeGueli changed the title JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 51 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (4) JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 52 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (5) Mar 18, 2024
@FedeGueli
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52 5 with S:F456V

@FedeGueli FedeGueli changed the title JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 52 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (5) JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 57 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (5) Mar 28, 2024
@FedeGueli FedeGueli changed the title JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 57 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (5) JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 58 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (6) Apr 2, 2024
@FedeGueli
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+1 on the FViRT branch

@FedeGueli FedeGueli changed the title JN.1.4 with S:R346T likely emerged in Africa on the branch with Orf3a:G18D 58 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (6) JN.1.4.7 (Orf3a:G18D) with S:R346T likely emerged in Africa 58 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (6) Apr 2, 2024
@FedeGueli
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parental lineage designated JN.1.4.7

@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T likely emerged in Africa 58 Sequences, 11 countries including 3 different African countries with a branch with S:F456V (6) JN.1.4.7 (Orf3a:G18D) with S:R346T likely emerged in Africa 65 Sequences, 14 countries including 3 different African countries with a branch with S:F456V (8) Apr 12, 2024
@FedeGueli
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65 from 14 countries and 8 with 456V

@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T likely emerged in Africa 65 Sequences, 14 countries including 3 different African countries with a branch with S:F456V (8) JN.1.4.7 (Orf3a:G18D) with S:R346T likely emerged in Africa 72 Sequences, 15 countries including 4 different African countries with a branch with S:F456V (8) Apr 16, 2024
@FedeGueli
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72 now, new country DRC (Congo where it represents 5/23 samples collected in 2024)

@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T likely emerged in Africa 72 Sequences, 15 countries including 4 different African countries with a branch with S:F456V (8) JN.1.4.7 (Orf3a:G18D) with S:R346T, 72 Sequences, 15 countries including 4 different African countries(20% in DRC-Congo in 2024) with a branch with S:F456V (8) Apr 16, 2024
@FedeGueli
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FedeGueli commented Apr 16, 2024 •
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ping @corneliusroemer
Screenshot 2024-04-16 alle 23 08 58
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 FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T, 72 Sequences, 15 countries including 4 different African countries(20% in DRC-Congo in 2024) with a branch with S:F456V (8) JN.1.4.7 (Orf3a:G18D) with S:R346T, 72 Sequences, 15 countries including 4 different African countries(20% in DRC-Congo in 2024) with S:F456V (8) and S:F456L (1) branches Apr 16, 2024
@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T, 72 Sequences, 15 countries including 4 different African countries(20% in DRC-Congo in 2024) with S:F456V (8) and S:F456L (1) branches JN.1.4.7 (Orf3a:G18D) with S:R346T, 82 Sequences, 15 countries including 4 different African countries(20% in DRC-Congo in 2024) with S:F456V (9) and S:F456L (1) branches Apr 22, 2024
@FedeGueli
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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 FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T, 82 Sequences, 15 countries including 4 different African countries(20% in DRC-Congo in 2024) with S:F456V (9) and S:F456L (1) branches JN.1.4.7 (Orf3a:G18D) with S:R346T, 82 Sequences, 15 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (9) and S:F456L (1) branches Apr 22, 2024
@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T, 82 Sequences, 15 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (9) and S:F456L (1) branches JN.1.4.7 (Orf3a:G18D) with S:R346T, 82 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (9) and S:F456L (1) branches Apr 22, 2024
@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T, 82 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (9) and S:F456L (1) branches JN.1.4.7 (Orf3a:G18D) with S:R346T, 86 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (11) and S:F456L (1) branches Apr 23, 2024
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86, and 11 with FViRT last two from Netherlands

@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T, 86 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (11) and S:F456L (1) branches JN.1.4.7 (Orf3a:G18D) with S:R346T, 94 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (12) and S:F456L (1) branches Apr 30, 2024
@FedeGueli
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94 now 12 with FViRT

@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T, 94 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (12) and S:F456L (1) branches JN.1.4.7 (Orf3a:G18D) with S:R346T, 102 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (12) May 7, 2024
@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T, 102 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (12) JN.1.4.7 (Orf3a:G18D) with S:R346T, 103 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (12) May 8, 2024
@DailyCovidCases
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101 now:
https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?nucMutations=G25445A%2CG22599C%2CC774T&nextcladePangoLineage=JN.1.4.7*&

@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T, 103 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (12) JN.1.4.7 (Orf3a:G18D) with S:R346T, 118 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (13) May 11, 2024
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118 / 13 FViRt (likely more due to dropouts)

@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T, 118 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024) with S:F456V (13) JN.1.4.7 (Orf3a:G18D) with S:R346T, 118 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024, 5% in South Africa in March) with S:F456V (13) May 11, 2024
@FedeGueli
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Designated LE.1 with 346T via 622c0a2
and LE.1.1 with 456V FVIRT via 47360ae

FedeGueli referenced this issue May 15, 2024
@corneliusroemer
Designate LE.1.1 (S:F456V), LE.1.2 (S:K304N)
47360ae
@FedeGueli FedeGueli changed the title JN.1.4.7 (Orf3a:G18D) with S:R346T, 118 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024, 5% in South Africa in March) with S:F456V (13) 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) May 22, 2024
@FedeGueli
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Screenshot 2024-06-13 alle 15 47 49 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.

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