Tuesday, December 22, 2020

PrePrint: Emergence & Rapid Spread of a New SARS-CoV-2 Lineage with Multiple Spike Mutations in South Africa


 

#15,646

Last week's announced emergence of a new, potentially more transmissible SARS-CoV-2 variant in the UK has captured most of the world's attention, but at the same time researchers in South Africa have reported a similar variant that may prove equally challenging (see AP story New strain of COVID-19 is driving South Africa's resurgence).

Most of what we've heard from South Africa to his point has been anecdotal, but this morning we have a pre-print research article that describes what is currently known about this emerging variant, and discusses how it may have evolved. 

I've posted the link and abstract below, but you'll want to download the 19-page PDF file for a more complete report.


Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

Authors: Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenço J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T.
Journal: Pre-Print,: (2020)

Abstract
Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. 

Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance.
This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. 

Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.

Posted by at