search

cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
Other
1.04k stars 98 forks source link

Fast XBB.1.11.1 saltation sublineage with S:T478R, ORF1a:I693T, Orf1a:T951A and ORF3a:W149C emerged in Indonesia (40 seqs) #2012

Closed FedeGueli closed 1 year ago

FedeGueli commented 1 year ago

This sublineage emerged in a part of tree first spotted and proposed by @agamedilab in #1807. in the same issue @HynnSpylor noticed a branch defined by S:T478R counting just an handful of sequences at that time.

Successively i independently discovered the whole branch and pre-prosed it in https://github.com/sars-cov-2-variants/lineage-proposals/issues/31

Since it started to grow rapidly i now propose it here officially:

Defining mutations: XBB.1.11.1>> > Orf1a:V3078I (G9497A) >S:F186S (T22119C) > G2281A, ORF1a:I693T (T2343C),orf1a:T951A (A3116G), ORF3a:W149C (G25839T), S:T478R (A22995G)

@corneliusroemer @InfrPopGen i suggest a double designation : first the bigger branch with S:F186S then its sublineage starting with S:T478R

Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_c6b1_ca5bc0.json?c=country&label=id:node_6902293 Schermata 2023-05-23 alle 13 42 16 Schermata 2023-05-23 alle 13 43 32 b1_ca5bc0.json?label=id:node_6902254 with Netherlands sample: Schermata 2023-05-23 alle 13 53 16 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_12ef3_ca87b0.json?label=id:node_6902293

Gisaid query: G2281A, T2343C, A3116G

Countries : Indonesia 30 , Malaysia 1, South Korea 1 ( related with travel from Thailand), 1 Netherlands (in an Elderly 85y old!)

Samples: 33 EPI_ISL_17324410, EPI_ISL_17469966, EPI_ISL_17470009, EPI_ISL_17470016-17470017, EPI_ISL_17546410, EPI_ISL_17551332, EPI_ISL_17551494, EPI_ISL_17612374, EPI_ISL_17622348, EPI_ISL_17630635, EPI_ISL_17654978, EPI_ISL_17655098, EPI_ISL_17655949, EPI_ISL_17681162, EPI_ISL_17681244, EPI_ISL_17681289, EPI_ISL_17681312, EPI_ISL_17686545, EPI_ISL_17689208, EPI_ISL_17696420, EPI_ISL_17696446-17696447, EPI_ISL_17696467, EPI_ISL_17696482, EPI_ISL_17696492, EPI_ISL_17696498, EPI_ISL_17696512, EPI_ISL_17696540, EPI_ISL_17696555, EPI_ISL_17696580, EPI_ISL_17696583,

Prevalence: in Indonesia it represents 21 out of 1220 samples collected in Indonesia after April 1 (1-2%)

FedeGueli commented 1 year ago

35 seqs as today last sequences from Malaysia , Indonesia.

FedeGueli commented 1 year ago

4 more seqs from Indonesia

Memorablea commented 1 year ago

It can be turned off and specified as FP. 2.1.@FedeGueli

ciscorucinski commented 1 year ago

@InfrPopGen @AngieHinrichs @FedeGueli Can you fix the milestone title not to include a space? It currently is FP. 2.1 but it should be FP.2.1

https://github.com/cov-lineages/pango-designation/milestone/762

InfrPopGen commented 1 year ago

@InfrPopGen @AngieHinrichs @FedeGueli Can you fix the milestone title not to include a space? It currently is FP. 2.1 but it should be FP.2.1

https://github.com/cov-lineages/pango-designation/milestone/762

I was just passing, and have removed that space.

FedeGueli commented 1 year ago

@InfrPopGen @AngieHinrichs @FedeGueli Can you fix the milestone title not to include a space? It currently is FP. 2.1 but it should be FP.2.1

https://github.com/cov-lineages/pango-designation/milestone/762

keep in mind i m not editor in this repo.thx