Sixteen novel lineages of SARS-CoV-2 in South Africa
Open accessPublished version of a preprint
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 infections 2. 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).
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Emerging variants of concern have spike mutations, including B.1.1.7 with eight spike mutations, B.1.351, and P.1 with multiple spike mutations.
“Several emerging viral variants of concern have been identified that have mutations in the spike protein, including the B.1.1.7 variant (originating from the UK and which has eight spike mutations92), the B.1.351 variant (originating from South Africa) and the P.1 variant (originating from Brazil and which also contains multiple mutations in the spike protein and is spreading widely)57,93.”
From Prospects for durable immune control of SARS-CoV-2 and prevention of reinfection (2021) · cites this paper as [93]
The B.1.1.7 variant is associated with increased transmissibility, and similar epidemiological observations have been reported for the SA and BR variants.
“The B.1.1.7 variant is associated with increased transmissibility,9,10 and similar epidemiological observations have been reported for the SA and BR variants.4,5”
From Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals (2021) · cites this paper as [4]
B.1.351 has key mutations K417N, E484K, and N501Y in the RBD.
“A number of isolates of B.1.351 have been described, all of which have the key mutations K417N, E484K, and N501Y in the RBD.”
From Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera (2021) · cites this paper as Tegally et al. (2021)
The B.1.351 strain used in this report has 8 changes relative to the Wuhan sequence and lacks L18F and R246I compared with the Tegally et al. (2021) isolate.
“Sequencing of the strain used in this report, from a case in the UK, shows only 8 changes and lacks L18F and R246I compared with the Tegally et al. (2021) isolate.”
From Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera (2021) · cites this paper as Tegally et al. (2021)
Progressive mutational change in SARS-CoV-2 is inevitable as it undergoes massive numbers of replicative cycles worldwide.
“Progressive mutational change in the virus is therefore inevitable as it undergoes massive numbers of replicative cycles worldwide (Tegally et al., 2021).”
From Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum (2021) · cites this paper as Tegally et al., 2021
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References 43 · Cited by 349
Research works printed but not linked: 1
- KRISP severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus sequencing in South-Africa. https://www.ncbi.nlm.nih.gov/sra/SRX8454220 (2020).
- Authors
- 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., Sigal, A., Gazy, I., Hardie, D., Hsiao, N.-Y., Martin, D., York, D., Goedhals, D., San, E. J., Giovanetti, M., Lourenço, J., Alcantara, L. C. J., & de Oliveira, T.
- Affiliations
- University of KwaZulu-Natal (ZA)
- National Health Laboratory Service (ZA)
- University of the Witwatersrand (ZA)
- Stellenbosch University (ZA)
- University of Cape Town (ZA)
- National Institute for Theoretical Physics (ZA)
- Max Planck Institute for Infection Biology (DE)
- Molecular Diagnostics Services (ZA)
- University of the Free State (ZA)
- Fundação Oswaldo Cruz (BR)
- University of Oxford (GB)
- ORCID
- Tegally, Houriiyah
- Wilkinson, Eduan
- Lessells, Richard J.
- Giandhari, Jennifer
- Pillay, Sureshnee
- Msomi, Nokukhanya
- Mlisana, Koleka
- Bhiman, Jinal N.
- Walaza, Sibongile
- Fonseca, Vagner
- Allam, Mushal
- Ismail, Arshad
- Glass, Allison J.
- Engelbrecht, Susan
- Preiser, Wolfgang
- Williamson, Carolyn
- Petruccione, Francesco
- Sigal, Alex
- Gazy, Inbal
- Hardie, Diana
- Martin, Darren
- Goedhals, Dominique
- Giovanetti, Marta
- Lourenço, José
- Alcantara, Luiz Carlos Junior
- de Oliveira, Tulio
- Venue
- Nature Medicine
- Published
- 2021-02-02
- Volume
- 27
- Issue
- 3
- Pages
- 440-446
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- OpenAlex
- W3128186941
- Cited by
- 349
- References
- 43
- Citations by year
- 2026: 3 · 2025: 9 · 2024: 16 · 2023: 40 · 2022: 109 · 2021: 170 · 2020: 1
- FWCI
- 26.50
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature Medicine (publishedVersion)
- medRxiv (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Arca - Repositório Institucional da Fiocruz (submittedVersion, other-oa)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, other-oa)
- Funders
- South African Medical Research Council
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Inyuvesi Yakwazulu-Natali
- Medical Research Council
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, COVID-19 pandemic, novel viral lineages, spike protein mutations, D614G, genomic surveillance, South Africa, first wave, hospital outbreak, KwaZulu-Natal, pandemic response
- MeSH terms
- Whole Genome Sequencing, COVID-19, SARS-CoV-2, Humans, Mutation, Phylogeny, South Africa, Genome, Viral, Sequence Analysis, RNA, Pandemics, Molecular Typing, Phylogeography, Real-Time Polymerase Chain Reaction, Datasets as Topic
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