Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages

Author:

Subramoney Kathleen123ORCID,Mtileni Nkhensani2,Giandhari Jennifer4ORCID,Naidoo Yeshnee5,Ramphal Yajna4,Pillay Sureshnee4ORCID,Ramphal Upasana4ORCID,Maharaj Akhil4,Tshiabuila Derek5ORCID,Tegally Houriiyah4ORCID,Wilkinson Eduan5ORCID,de Oliveira Tulio45,Fielding Burtram C.6ORCID,Treurnicht Florette K.12ORCID

Affiliation:

1. School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa

2. Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg 2193, South Africa

3. Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg 2131, South Africa

4. KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa

5. Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa

6. Molecular Biology and Virology Research Laboratory, Department of Medical BioSciences, University of the Western Cape, Cape Town 7535, South Africa

Abstract

SARS-CoV-2 lineages and variants of concern (VOC) have gained more efficient transmission and immune evasion properties with time. We describe the circulation of VOCs in South Africa and the potential role of low-frequency lineages on the emergence of future lineages. Whole genome sequencing was performed on SARS-CoV-2 samples from South Africa. Sequences were analysed with Nextstrain pangolin tools and Stanford University Coronavirus Antiviral & Resistance Database. In 2020, 24 lineages were detected, with B.1 (3%; 8/278), B.1.1 (16%; 45/278), B.1.1.348 (3%; 8/278), B.1.1.52 (5%; 13/278), C.1 (13%; 37/278) and C.2 (2%; 6/278) circulating during the first wave. Beta emerged late in 2020, dominating the second wave of infection. B.1 and B.1.1 continued to circulate at low frequencies in 2021 and B.1.1 re-emerged in 2022. Beta was outcompeted by Delta in 2021, which was thereafter outcompeted by Omicron sub-lineages during the 4th and 5th waves in 2022. Several significant mutations identified in VOCs were also detected in low-frequency lineages, including S68F (E protein); I82T (M protein); P13L, R203K and G204R/K (N protein); R126S (ORF3a); P323L (RdRp); and N501Y, E484K, D614G, H655Y and N679K (S protein). Low-frequency variants, together with VOCs circulating, may lead to convergence and the emergence of future lineages that may increase transmissibility, infectivity and escape vaccine-induced or natural host immunity.

Funder

National Research Foundation

National Health Laboratory Service

National Research Foundation Thuthuka

South African Medical Research Council

Department of Science and Innovation

Publisher

MDPI AG

Subject

Virology,Infectious Diseases

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