Thread by @AineToole

Updated SARS-CoV-2 lineage of concern report for 2021-01-30 now available at cov-lineages.org/global_report.…
@viralverity @arambaut @EvolveDotZoo @MOUGK @edwardcholmes

We report 72 countries with cases of B.1.1.7 (53 of which have sequences on GISAID). Georgia and Slovenia both report cases of B.1.1.7, however the report from Slovenia is informed by SGTF which will be further tested by sequencing. businessworld.in/article/Georgi… gov.si/en/news/2021-0…

In total, B.1.1.7 was assigned to 37,162 sequences on GISAID from 53 countries. 34,303 of those sequences are from the UK.

31 countries have reported cases of lineage B.1.351 (23 represented by sequences on GISAID).

B.1.351 was assigned by pangolin to 728 sequences. A clarification from yesterday, that the earliest sample from Mozambique with more than 5 of the defining mutations of B.1.351, and no reference alleles, is from 2020-12-14. @houzhou

This change comes with an updated release of pangolin. We're now checking for the absence of reference alleles in pangolin v2.1.10, in addition to the presence of 5 or more of the defining mutations for B.1.351 (501Y.V2). @houzhou

As of today, there are confirmed reports of lineage P.1 from a total of 9 countries. Newly reporting cases are the RIVM in the Netherlands (rivm.nl/en/news/brazil…) and the Instituto Nacional de Salud, Colombia (

https://twitter.com/INSColombia/status/1355531730422263809?s=20

)
@CaddeProject

38 sequences in total on GISAID for lineage P.1 from Brazil 28, Japan 4, Italy 3, Faroe_Islands 1, USA 1, South_Korea 1.

Please alert us of any reports of lineages of concern that we may not have covered either via Twitter or GitHub pull request here: github.com/cov-lineages/g…

Find the full lineage of concern report for 2021-01-30 here: cov-lineages.org/global_report.…