Description

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

Data source and processing

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.

Table 1 | Summary of sequence data

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;

Lineage B.1.351

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.

Table B.1.351 | Lineage B.1.351

Statistic	Information
Count	530
Likely origin	South Africa
SNPs	aa:E:P71L aa:N:T205I aa:orf1a:K1655N aa:S:D80A aa:S:D215G aa:S:K417N aa:S:A701V aa:S:N501Y aa:S:E484K

Figure 1 | Cumulative sequence count over time B.1.351

Figure 2 | Date of earliest B.1.351 detected