CH.1.1.17 + S:D215G, S:Q613H(228 sequences)

cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme

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CH.1.1.17 + S:D215G, S:Q613H(228 sequences) #1718

Closed DoropFan closed 1 year ago

DoropFan commented 1 year ago

Description Sub-lineage of:CH.1.1(BA.2.75.3.4.1.1.1.1) Earliest sequence:2022-12-30(New Zealand) Countries circulating:New Zealand10, United Kingdom6, Austria4, Germany4, Australia3, Netherlands2, Switzerland1, Denmark1, France1 Sequences:32

Nucleotide mutations:C11750T,C18657T,C21811T,A22206G,G23401T,A27156G,C29555T Amino acid changes:ORF1a:L3829F, S:D215G, S:Q613H, M:S212G CovSpectrum

Genomes ch11s215gs613h ch11s215gs613h2

aviczhl2 commented 1 year ago

oh, this one also have the orf1a:L3829F

And it is quite fast even among the fastest XBB sublineages, much faster than other CH.1.1s (baseline: S:F486P)

DoropFan commented 1 year ago

Correct M:S212G>ORF1a:L3829F, S:Q613H>S:D215G UShER Tree ch11s215gs613h3

hsnguyen commented 1 year ago

More sequences from Australia. GISAID query (Spike_Q613H, Spike_D215G, M_S212G) returned 66 seq. now

hsnguyen commented 1 year ago

I found that M_S212G is gone missing from a number of sequences within this clade due to ambiguous bases, so changed the GISAID query to (NSP6_L260F, NSP8_N118S, Spike_D215G,Spike_Q613H). This one returned 100 viruses as of 21 March. where NSP6_L260F = ORF1a_L3829F = C11750T NSP8_N118S = ORF1a_N4060S = A12444G

If only searching by spike mutations of CH.1.1+ Spike_Q613H, Spike_D215G, it'll return even more seqs as about 40 Austrian partial sequences (>2Kbp spike sequencing?) would add up to the result. I think this one deserves a name for itself, just not sure if it'd be a direct sub-lineage from CH.1.1 or something further down. Cheers,

corneliusroemer commented 1 year ago

I designated the parent lineage as CH.1.1.17 so this should become easier to track https://github.com/cov-lineages/pango-designation/commit/3812bd7e26a4d6cf5433766139348cba7ea75588

DoropFan commented 1 year ago

New Zealand

FedeGueli commented 1 year ago

it is 300 and its prent is already the fastest non - XBB lineage. @corneliusroemer @InfrPopGen i think it deserves a designation .:

And more it has already split in two: One branch with C27804T and the other with Orf1a:L384F

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_988e_609d80.json?c=userOrOld&label=id:node_8110628

InfrPopGen commented 1 year ago

Thanks for submitting. We've added lineage FK.1 with 70 newly designated sequences, and 89 updated from CH.1.1 (30) and CH.1.1.17 (59). Defining mutation A22206G (S:D215G) (following C11750T (ORF1a:L3829F), G23401T (S:Q613H)).