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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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Peruvian AY.39 sublineage with S:K1073N, ORF1a:E743D, ORF1a:K1817N [~20% in Peru, ~.5% US, 1k seq] #295

Closed corneliusroemer closed 3 years ago

corneliusroemer commented 3 years ago

New lineage proposal by @CorneliusRoemer

Description Sub-lineage of: AY.39 Earliest sequence: 2021-30 in US, 2021-31 in Peru Most recent sequence: Current Countries circulating: ~30% in Peru,

Lineage deriving from Delta AY.39 with extra substitutions S:K1073N, ORF1a:E743D, ORF1a:K1817N

First observed in US, but has high share in Lima, Peru (>30%). Seems to be growing fast in Peru and US (~3%-4%/day).

In the US, found >900 times with significant spread in Tennessee, New York, Massachusetts

Also found in Switzerland a few times.

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Country Total Variant Sequences First seq. found at Last seq. found at
United States 905 2021-30 2021-41
Peru 125 2021-31 2021-38
Switzerland 15 2021-34 2021-41
New Zealand 5 2021-34 2021-35
Australia 2 2021-34 2021-41
United Kingdom 1 2021-35 2021-35
Canada 1 2021-37 2021-37
France 1 2021-39 2021-39
Chile 2 2021-39 2021-39

https://cov-spectrum.ethz.ch/explore/World/AllSamples/Past3M/variants?aaMutations=S%3AK1073N%2CORF1b%3AQ2635H%2CORF7a%3AV71I

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https://nextstrain.org/groups/neherlab/ncov/sa-peru?c=gt-S_1073&m=div

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chrisruis commented 3 years ago

Thanks @corneliusroemer We've added this as AY.39.2 in v1.2.91 to start on a branch with G5716T (Orf1ab:K1817N) which appears to coincide with the introduction(s) into Peru

FedeGueli commented 3 years ago

Thx! already landed in Europe, it is 0,5/1% in Switzerland likely from chile probably undersampled in SA.