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Repository for suggesting new lineages that should be added to the current scheme
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CM.8.1 sublineage with Orf1b:N1790D and Orf10:A28V circulating in philippines and exported globally (84 seqs) #1554

Closed FedeGueli closed 1 year ago

FedeGueli commented 1 year ago

Here i want to propose a CM.8.1 sublineage that appeared first in phillipines and has been exported fastly in several countries. I was digging a bit samples from Philippines or travel realted with Philippines after i have read that some regions of Philippines after reaching all time lows are now uptrending in positivity rates (Source: https://twitter.com/iamguidodavid/status/1613351017030246400) : in general BA.2.3.20 appears to be dominant there after a short XBC.1 interlude over 50%. More precisely CM.8* was over 30% of samples collected or related to Philippines after December 1st

Lineage here proposed is defined by : CM.8.1 +G14622A + Orf1b:N1790D (A18835G) + Orf10:A28V (C29640T)

Usher:

Schermata 2023-01-15 alle 08 30 37 Schermata 2023-01-15 alle 08 31 03

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_27976_393470.json?c=userOrOld&label=id:node_7929816

Gisaid query: A18835G, C29640T, G14622A

Sequences: 35 EPI_ISL_16017319, EPI_ISL_16073388, EPI_ISL_16091604, EPI_ISL_16091943, EPI_ISL_16161787, EPI_ISL_16203607, EPI_ISL_16265200, EPI_ISL_16271324, EPI_ISL_16279780, EPI_ISL_16306066, EPI_ISL_16323385, EPI_ISL_16329548, EPI_ISL_16329630, EPI_ISL_16331435, EPI_ISL_16332795, EPI_ISL_16340625, EPI_ISL_16369901, EPI_ISL_16370565, EPI_ISL_16386727, EPI_ISL_16397765, EPI_ISL_16404582, EPI_ISL_16422676, EPI_ISL_16425313, EPI_ISL_16425625, EPI_ISL_16442124, EPI_ISL_16456075, EPI_ISL_16473511, EPI_ISL_16485748, EPI_ISL_16501599, EPI_ISL_16503355, EPI_ISL_16503686, EPI_ISL_16505443, EPI_ISL_16510709, EPI_ISL_16514139, EPI_ISL_16515443

Countries with ongoing transmission: Philippines, Denmark , Japan, Germany, Canada

FedeGueli commented 1 year ago

3 out of 4 most recent samples have travel history from Philippines suggesting some degree of prevalence of this lineage there in this moment. @thomasppeacock @InfrPopGen @corneliusroemer

(5 out of 73 viruses with Philippines on Gisaid Metadata samples after 1st of december 229

FedeGueli commented 1 year ago

As expected looking at high prevalence in Philippines international spread was sustained during the past week: Usa : Texas and Hawaii Germany Netherlands plus two travellers from Philippines testing + in South Korea.

It represents 5 out of 17 samples collected in Singapore/ South Korea/ Japan airports in 2023 from Philippinos travellers suggesting a very high prevalence there.

reason why i ask @InfrPopGen @thomasppeacock @corneliusroemer to designate this one even if it doesnt have any spike mutation.

FedeGueli commented 1 year ago

2 new sequences from Canada and Japan

FedeGueli commented 1 year ago

61 sequences as today

8 out of 34 sequences sampled in 2023 found by Gisaid querying for "Philippines" belong to this lineage suggesting high prevalence there.

FedeGueli commented 1 year ago

not growing . closing it for the moment

FedeGueli commented 1 year ago

79 seqs as today, reopening it since it seems spreading globally (Canada, France, Austria, Japan)

FedeGueli commented 1 year ago

83 sequences as today last 4 from France, California, Singapore and Northern Mariana islands

FedeGueli commented 1 year ago

84 as today. last one came from Ukraine.

FedeGueli commented 1 year ago

I m reclosing this one. waiting for new uploads from philippines preannounced by local media.

FedeGueli commented 1 year ago

Designated as CM.8.1.4 in https://github.com/cov-lineages/pango-designation/commit/19d424643ee51b7e4eea27fc1c2ad21e15e3aaba