Sixteen novel lineages of SARS-CoV-2 in South Africa

Tegally, H; Wilkinson, E; Lessells, RJ; Giandhari, J; Pillay, S; Msomi, N; Mlisana, K; Bhiman, JN; von Gottberg, A; Walaza, S; Fonseca, V; Allam, M; Ismail, A; Glass, AJ; Engelbrecht, S; Van Zyl, G; Preiser, W; Williamson, C; Petruccione, F; Sigal, A; Gazy, I; Hardie, D; Hsiao, N-Y; Martin, D; York, D; Goedhals, D; San, EJ; Giovanetti, M; Lourenço, JM; Alcantara, LCJ; de Oliveira, T

COVID-19 Collection

Journal article

Sixteen novel lineages of SARS-CoV-2 in South Africa

Abstract:: The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. Despite the early response, by November 2020, over 785,000 people in South Africa were infected, which accounted for approximately 50% of all known African infections2. In this study, we analyzed 1,365 near whole genomes and report the identification of 16 new lineages of SARS-CoV-2 isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere. We also show that three lineages (B.1.1.54, B.1.1.56 and C.1) spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. 3), was the most geographically widespread lineage in South Africa by the end of August 2020. An early South African-specific lineage, B.1.106, which was identified in April 2020 (ref. 4), became extinct after nosocomial outbreaks were controlled in KwaZulu-Natal Province. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2. Such genomic surveillance presented in this study has been shown to be crucial in the identification of the 501Y.V2 variant in South Africa in December 2020 (ref. 5).

Publication status:: Published

Peer review status:: Peer reviewed

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APA Style

Tegally, H., Wilkinson, E., Lessells, R. J., Giandhari, J., Pillay, S., Msomi, N., Mlisana, K., Bhiman, J. N., von Gottberg, A., Walaza, S., Fonseca, V., Allam, M., Ismail, A., Glass, A. J., Engelbrecht, S., Van Zyl, G., Preiser, W., Williamson, C., Petruccione, F., … de Oliveira, T. (2021). Sixteen novel lineages of SARS-CoV-2 in South Africa. Nature Medicine, 27(3), 440–446.

MLA Style

Tegally, H, et al. “Sixteen Novel Lineages of SARS-CoV-2 in South Africa.” Nature Medicine, vol. 27, no. 3, 2021, pp. 440–46.

Chicago Style

Tegally, H, E Wilkinson, RJ Lessells, et al. 2021. “Sixteen Novel Lineages of SARS-CoV-2 in South Africa.” Nature Medicine 27 (3): 440–46.
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