South African lineage defined by new variant 501Y.V2 - A more detailed description of the lineage is here and a preprint describing the variant is here
This report is recent as of 2021-01-18 19:03 GMT. All SARS-CoV-2 sequences were downloaded from GISAID and genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.
The sequences were then assigned lineages with pangolin v2.1.7, pangoLEARN version 2021-01-11.
Pangolin assigns B.1.351 to any sequences with more than 5 of the 9 defining B.1.351 SNPs, defined in the preprint here.
|Lineage||Country count||Country||Sequence count||Earliest sequence||Travel history|
|B.1.351||13||South_Africa 447, UK 54, Botswana 6, Australia 5, Germany 5, Ireland 3, France 2, Switzerland 2, Finland 2, Norway 1, South_Korea 1, Sweden 1, Netherlands 1||530||2020-10-08||1 Maldives/South;|
Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.
|Likely origin||South Africa|