GE.1 + S:F456L (33 seqs emerged in India-MH , 10 countries)

[FedeGueli]

Note that also GE.1 acquired S:F456L recently in India and likely it is way bigger than the XBB.2.3.8 one proposed in #651

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3a9e5_d1d640.json?c=gt-S_456,478&gmax=25384&gmin=21563&label=id:node_7375363 Defining mutations: GE.1 > Orf1a:G661S (G2246A) > Orf1b:I847V (NSP12_I856V) > Orf1a:G519S (G1820A) > T508C, S:F456L (T22928C) Query T508C, G1820A, T22928C Samples : 3 IDs:EPI_ISL_18094383, EPI_ISL_18094388, EPI_ISL_18120275,

Originally posted by @FedeGueli in https://github.com/sars-cov-2-variants/lineage-proposals/issues/651#issuecomment-1685129616

[FedeGueli]

i just noticed that the entire branch with Orf1a:G519S has interesting samples pointing to a sustained undersampled circulation of the parental of the lineage proposal here. For example the query: G5156T, G11555A, C16173T, A22976C finds one sample with S:I472L and S:D215G. Residue 473 was recently highlighted by J.Bloom as one of the hotspot to evade recent XBB immunity on a xbb background.

[FedeGueli]

First exportation to France collected on 21-08.

[FedeGueli]

+1 EPI_ISL_18239122 was a traveller from India caught by surveillance in US airports. This makes me think this has gained some prevalence there.

[FedeGueli]

it represents around 10% of samples in MH in September. 4 samples from MH,India 1 sample intercepted from Us Airport surveillance in a traveller from India.

[FedeGueli]

ping @corneliusroemer local (India) but interesting XBB.2.3+ 456-478.

[FedeGueli]

+3 Denmark, Canada , Gujarat

[FedeGueli]

21 , 8 countries

[FedeGueli]

+3 Canada

[FedeGueli]

Now 33 ,6 from November, but interesting coming from 5 different countries, one intercercepted by GBW airport surveillance in a traveller coming from UAE, i m proposing it. it represents around 5% of sequences from or related to India after September 1.

[FedeGueli]

Proposed in https://github.com/cov-lineages/pango-designation/issues/2388