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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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GL.1+S:Y144del sublineage with ORF1a:KSF141-143del and ORF3a:D155H (58 seq. Mainly Tasmania, Australia ~40% prevalence in August 2023) #2222

Closed oobb45729 closed 11 months ago

oobb45729 commented 1 year ago

Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/701. 1 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_39b95_ae74a0.json?c=gt-ORF3a_155&label=id:node_6402106 https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGL.1*%26ORF3a%3AD155H& ORF1a:KSF141-143del (the same deletion as BA.4) has already occurred on GL.1 three times independently. It first appeared on the Austrian branch (without S:Y144-). https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGL.1%26ORF6%3AE46G& Then it appeared on this one. Then it appeared on the Canary Islands branch nuc:C8293T > ORF1a:E2089D(G6532T) > ORF1a:G7S(G284A)+ORF1a:KSF141-143del. https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AGL.1*%26ORF1a%3AG7S& 2

oobb45729 commented 1 year ago

51 now and it's gaining new spike mutations. 13 with S:E748Q and 6 further gained S:NG481-482S.

FedeGueli commented 1 year ago

It is 38/91 sequences collected in Tasmania after August 1, and 30/61 of sequences collected after August 15!

cc @corneliusroemer being this lineage now dominant in one region i think it should be prioritized

corneliusroemer commented 1 year ago

Tasmania has just 500k inhabitants and is an island, so founder effect likely

FedeGueli commented 1 year ago

Tasmania has just 500k inhabitants and is an island, so founder effect likely

Island effect ;) still gaining S:144del interesting!