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%)

[FedeGueli]

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 or NEW: 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

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]

+3 of this from Spain Italy and pooled GBW

[FedeGueli]

15 now new countries Italy and Japan

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

[FedeGueli]

17 +2 GBW from France

[FedeGueli]

36 with a skyhigh 80% prevalence since June 1 in Pernambuco Brazil

cc @corneliusroemer @angiehinrichs i suggest to designate this.

[Over-There-Is]

Netherlands

[FedeGueli]

39, Denmark

[FedeGueli]

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

[FedeGueli]

New query : A1461G,T3565C,C25546T but it catches only 42.

[Over-There-Is]

3 new sequences are uploaded. Two queries don't coincide, so the amount should be 47 now.

[FedeGueli]

no recent samples.