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JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (95, >8 places ) with very high recent prevalence in Pernambuco, Brazil ( after July 1 = 65%) #1678

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FedeGueli opened this issue Jul 3, 2024 · 14 comments
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JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (95, >8 places ) with very high recent prevalence in Pernambuco, Brazil ( after July 1 = 65%) #1678

FedeGueli opened this issue Jul 3, 2024 · 14 comments
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Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest FLiRT FLiRT is an Acronym for S:R346T + S:F456L High local prevalence Lineage that apparently gained high prevalence in one country or region PLPro s:677
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NU.1

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@FedeGueli
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FedeGueli commented Jul 3, 2024 •
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A JN.1.55.2 (456L) branch likely emerged in Brazil and now became FLiRT in a mini saltation.
Yesterday one GBW sample from Colombia have been uploaded pointing at a continued circulation in an undersampled area
[ Formerly tracked as Singlet 61 on #1089 ]

Defining
JN.1.55.2 >> T13246C > C19269T, S:R346T (G22599C), S:Q677H (G23593T), Orf3a:L52F (C25546T)
Query: C19269T,C25546T,T3565C + 8 with A1461G,T3565C,C25546T
Samples: 10
Countries: Brazil, Colombia, Spain, France, UK
IDs:EPI_ISL_19093670, EPI_ISL_19193046, EPI_ISL_19194956-19194957,
EPI_ISL_19194963, EPI_ISL_19199706, EPI_ISL_19205911,
EPI_ISL_19211192, EPI_ISL_19216643, EPI_ISL_19229734,

Tree: (updated on July 26)
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4062_3573b0.json?f_userOrOld=uploaded%20sample&label=id:node_7071428
Screenshot 2024-07-26 alle 11 51 50

Addendum July 26: the Brazilian branch is defined by Orf1a:P1640S (Jn.1.18/KW* sub-lineages have 1640L) corresponding to PLPro_P77S and it is showing a lot of interesting diversity as S:T572I or S:H445R or S:L84I
@FedeGueli FedeGueli added s:677 FLiRT FLiRT is an Acronym for S:R346T + S:F456L Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest labels Jul 3, 2024
@FedeGueli FedeGueli mentioned this issue Jul 3, 2024
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@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (10) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (13, 6 countries) Jul 6, 2024
@FedeGueli
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+3 of this from Spain Italy and pooled GBW

@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (13, 6 countries) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (15, 7 countries) Jul 14, 2024
@FedeGueli
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15 now new countries Italy and Japan

Ping @corneliusroemer this should have some prevalence in South America. 15 samples with 4 by GBW

@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (15, 7 countries) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (17, 7 countries) Jul 23, 2024
@FedeGueli
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17 +2 GBW from France

@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (17, 7 countries) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (36, 7 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) Jul 26, 2024
@FedeGueli
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36 with a skyhigh 80% prevalence since June 1 in Pernambuco Brazil

cc @corneliusroemer @AngieHinrichs i suggest to designate this.

@FedeGueli FedeGueli added High local prevalence Lineage that apparently gained high prevalence in one country or region PLPro labels Jul 26, 2024
@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (36, 7 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (38, 7 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) Aug 3, 2024
@Over-There-Is
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Netherlands

@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (38, 7 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (38, 9 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) Aug 4, 2024
@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (38, 9 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (39, 10 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) Aug 10, 2024
@FedeGueli
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39, Denmark

@FedeGueli
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Again a big batch of this from Brazil today not caught by the query , i m trying to update it

@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (39, 10 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (42, 10 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) Aug 20, 2024
@FedeGueli
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New query : A1461G,T3565C,C25546T but it catches only 42.

@Over-There-Is
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Over-There-Is commented Aug 26, 2024 •
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3 new sequences are uploaded. Two queries don't coincide, so the amount should be 47 now.

@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (42, 10 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (45, 10 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) Aug 26, 2024
@xz-keg xz-keg changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (45, 10 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (49, 10 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) Sep 14, 2024
@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (49, 10 countries) with very high recent prevalence in Pernambuco, Brazil (80%!) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (57, 10 countries) with very high recent prevalence in Pernambuco, Brazil ( after July 1 = 65%) Sep 19, 2024
@FedeGueli
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no recent samples.

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Sep 26, 2024
@Over-There-Is
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77, with 2 sequences collected on 09-17 in Veneto, Italy

@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (57, 10 countries) with very high recent prevalence in Pernambuco, Brazil ( after July 1 = 65%) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (66, >10 places ) with very high recent prevalence in Pernambuco, Brazil ( after July 1 = 65%) Oct 14, 2024
@Over-There-Is
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95

@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (66, >10 places ) with very high recent prevalence in Pernambuco, Brazil ( after July 1 = 65%) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (83, >8 places ) with very high recent prevalence in Pernambuco, Brazil ( after July 1 = 65%) Nov 24, 2024
@FedeGueli FedeGueli changed the title JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (83, >8 places ) with very high recent prevalence in Pernambuco, Brazil ( after July 1 = 65%) JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (95, >8 places ) with very high recent prevalence in Pernambuco, Brazil ( after July 1 = 65%) Nov 24, 2024
@FedeGueli
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95

thx but weirdly died off after spreading internationally

@xz-keg
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xz-keg commented Dec 19, 2024 •
edited by FedeGueli
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designated NU.1 via cov-lineages/pango-designation@4256d9b#diff-ead4244ff49c81bc758e9f068f5ef42156bd985b9c86de8fa4d6fcd7f2829090R1577

@xz-keg xz-keg added this to the NU.1 milestone Dec 19, 2024
FedeGueli referenced this issue in cov-lineages/pango-designation Dec 19, 2024
@corneliusroemer
Designate NU.1 (JN.1.55.2 + S:R346T, S:Q677H, ORF3a:L52F, Brazil) and…
4256d9b 
… XEC.16 (S:T678I)
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Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest FLiRT FLiRT is an Acronym for S:R346T + S:F456L High local prevalence Lineage that apparently gained high prevalence in one country or region PLPro s:677
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