Triple spike mutations S:K182E,S:V551I,S:E554K for a saltation XBB.1.16 sublineage emerging in MH, India (20 seqs , 4 countries - Prevalence 15% in MH,India after July 1)) update Sept 1

[FedeGueli]

Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/672

Defining mutations: XBB.1.16 >> > C29386T > A25410G > Orf1a:P748L (T2242C),Orf1a:E972K (C2508T), G3179A, S:K182E (A22106G), S:V551I (G23213A), S:E554K (G23222A)

Gisaid query: G3179A, C2508T (NEW)

Samples: 12 from India (11= 9,MH + 2 GJ)) , Pennsylvania.,Us (1) First from MH collected on 2023-04-28 (There is a sample from 01/08 bit is for sure a date input error) Last from MH collected on 2023-08-12 IDs: EPI_ISL_17686342, EPI_ISL_17978171, EPI_ISL_18094379, EPI_ISL_18094384-18094385, EPI_ISL_18120269, EPI_ISL_18120320, EPI_ISL_18121354, EPI_ISL_18128324-18128325, EPI_ISL_18136389, EPI_ISL_18136391

Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5cf3f_bdb180.json?label=id:node_6841457

Prevalence: It represents 6 out of 46 samples collected in MH after July 1 so if this could represent a fair enough amount of infections in the real world.

[HynnSpylor]

1 more seq in Singapore (the 3rd detected country) EPI_ISL_18141171

[FedeGueli]

One more very recent sample from Australia: 2 exportations (collection date) in the last ten days make me thinking this is quite growing or already prevalent in India). cc @HynnSpylor i modified the query to catch them all. https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3efd9_a4b60.json?label=id:node_6843588

Ping @corneliusroemer something under the radar in India.

[FedeGueli]

Another big jump for this one all sequences from MH India . 15% its prevalence there in August.

ping @corneliusroemer