grinch | global report investigating novel coronavirus haplotypes

B.1.351 report 2021-01-18



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

2021-01-18T20:32:23.784248 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Figure 2 | Date of earliest B.1.351 detected

2021-01-18T20:32:22.782873 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/