New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Fast XBB.1.11.1 saltation sublineage with S:T478R, ORF1a:I693T, Orf1a:T951A and ORF3a:W149C emerged in Indonesia (40 seqs) #2012
Comments
35 seqs as today last sequences from Malaysia , Indonesia. |
4 more seqs from Indonesia |
It can be turned off and specified as FP. 2.1.@FedeGueli |
@InfrPopGen @AngieHinrichs @FedeGueli Can you fix the milestone title not to include a space? https://github.com/cov-lineages/pango-designation/milestone/762 |
I was just passing, and have removed that space. |
keep in mind i m not editor in this repo.thx |
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 sars-cov-2-variants/lineage-proposals#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
b1_ca5bc0.json?label=id:node_6902254
with Netherlands sample:
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%)
The text was updated successfully, but these errors were encountered: