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

By H. Tegally, Eduan Wilkinson, M. Giovanetti, A. Iranzadeh, V. Fonseca, J. Giandhari, D. Doolabh, S. Pillay, E. J. San, N. Msomi and 33 more. medRxiv, 2020

1,117 citations recorded by the source corpus.

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.

Subfields: Animal Science and Zoology, Infectious Diseases

View Paper: https://www.semanticscholar.org/paper/a08dd488e6d16658916351ac1f7b9dfd0444f019

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In Infectious Diseases

Citations in the corpus

Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 spike protein (2021, neutral): “Since the start of the outbreak, circulating SARS-CoV-2 field strains have acquired genetic changes that facilitate transmission (Avanzato et al., 2020; Choi et al., 2020; Hou et al., 2020; Kemp et al., 2020; McCarthy et al., 2020; Plante et al., 2020; Rambaut et al., 2020; Tegally et al., 2020).”
Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England (2021, background): “068) 23 (18-28) 37 (29-46) UK sequence separate-slopes binomial GLMM (1|LTLA/OBS) + REGION * DATE London B.”
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Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies (2021, background): “The site where mutations tend to have the largest effect on binding and neutralization is E484, which unfortunately is a site where mutations are present in several emerging SARS-CoV-2 lineages (Tegally et al., 2020; Voloch et al., 2020) .”
Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice (2021, neutral): “N501Y mutations (17, 18).”
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma (2021, positive): “N501Y has been shown to increase affinity for the human ACE2 receptor, which together with the repeated and independent evolution of 501Y containing lineages 25,26,31 , strongly argues for enhanced transmissibility of these new variants.”
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Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape (2021, background): “351 (28), first reported in the United Kingdom 159 and South Africa, have deletions in RDRs 1/2 and 4, respectively.”