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While routinely screening lineages carrying S:R403K i found this one belonging to XBB.1.9 that emerged first in Indonesia but then was sampled in Poland and Israel too.
While i am not sure about its growth rate it is a mini saltation lineage with two spike mutations (the other one is S:570>T same residue that is defining in DY.1 S:570>S) arising from an undersampled area, so it is worth monitoring it for a while.
FedeGueli
changed the title
XBB.1.9 with S:R403K, S:A570T, orf1a:A967V, Orf1b:T577A,Orf7b:H42Q emerged in Indonesia 7 sequences
XBB.1.9 with S:R403K, S:A570T, orf1a:A967V, Orf1b:T577A,Orf7b:H42Q emerged in Indonesia 8 sequences
Apr 16, 2023
FedeGueli
changed the title
XBB.1.9 with S:R403K, S:A570T, orf1a:A967V, Orf1b:T577A,Orf7b:H42Q emerged in Indonesia 8 sequences
XBB.1.9 with S:R403K, S:A570T, orf1a:A967V, Orf1b:T577A,Orf7b:H42Q emerged in Indonesia 9 sequences
Apr 16, 2023
FedeGueli
changed the title
XBB.1.9 with S:R403K, S:A570T, orf1a:A967V, Orf1b:T577A,Orf7b:H42Q emerged in Indonesia 9 sequences
XBB.1.9 with S:R403K, S:A570T, orf1a:A967V, Orf1b:T577A,Orf7b:H42Q emerged in Indonesia 11 sequences
Apr 22, 2023
FedeGueli
changed the title
XBB.1.9 with S:R403K, S:A570T, orf1a:A967V, Orf1b:T577A,Orf7b:H42Q emerged in Indonesia 11 sequences
XBB.1.9 with S:R403K, S:A570T, orf1a:A967V, Orf1b:T577A,Orf7b:H42Q emerged in Indonesia 15sequences
May 23, 2023
While routinely screening lineages carrying S:R403K i found this one belonging to XBB.1.9 that emerged first in Indonesia but then was sampled in Poland and Israel too.
While i am not sure about its growth rate it is a mini saltation lineage with two spike mutations (the other one is S:570>T same residue that is defining in DY.1 S:570>S) arising from an undersampled area, so it is worth monitoring it for a while.
Defining mutations:
XBB.1.9 > > T446C > C26936T > T1147C, Orf1a:A967V (C3165T) , Orf1b:T577A (A15196G) , S:R403K (G22770A) , S:A570T (G23270A), Orf7b:H42Q (C27881A)
Tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice9_genome_2af10_de6b30.json?c=userOrOld&label=id:node_7718092
Gisaid&CovSpectrum query : T1147C, C3165T, A15196G, G22770A, G23270A, C27881A
Sequences:
EPI_ISL_17012183, EPI_ISL_17012196, EPI_ISL_17012229,
EPI_ISL_17189162, EPI_ISL_17241535, EPI_ISL_17325617,
EPI_ISL_17389293
Countries: Indonesia, Israel and Poland
Prevalence: between 0,5% - 1% in Indonesia for samples collected after 1st of February.
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