Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa

Graeme Dor, Eduan Wilkinson, Darren P. Martin, Monika Moir, Derek Tshiabuila, Dikeledi Kekana, Buhle Ntozini, Rageema Joseph, Arash Iranzadeh, Martin M. Nyaga, Dominique Goedhals, Tongai Maponga, Jean Maritz, Oluwakemi Laguda-Akingba, Yajna Ramphal, Caitlin MacIntyre, Lucious Chabuka, Sureshnee Pillay, Jennifer Giandhari, Cheryl Baxter, Nei-yuan Hsiao, Wolfgang Preiser, Jinal N. Bhiman, Mary-Anne Davies, Marietjie Venter, Florette K. Treurnicht, Nicole Wolter, Carolyn Williamson, Anne Gottberg, Richard Lessells, Houriiyah Tegally () and Tulio Oliveira ()
Additional contact information
Graeme Dor: Stellenbosch University
Eduan Wilkinson: Stellenbosch University
Darren P. Martin: University of Cape Town
Monika Moir: Stellenbosch University
Derek Tshiabuila: Stellenbosch University
Dikeledi Kekana: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Buhle Ntozini: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Rageema Joseph: University of Cape Town
Arash Iranzadeh: University of Cape Town
Martin M. Nyaga: University of the Free State
Dominique Goedhals: University of the Free State
Tongai Maponga: Tygerberg
Jean Maritz: Stellenbosch University
Oluwakemi Laguda-Akingba: National Health Laboratory Service
Yajna Ramphal: Stellenbosch University
Caitlin MacIntyre: University of the Witwatersrand
Lucious Chabuka: Stellenbosch University
Sureshnee Pillay: University of KwaZulu-Natal
Jennifer Giandhari: University of KwaZulu-Natal
Cheryl Baxter: Stellenbosch University
Nei-yuan Hsiao: University of Cape Town
Wolfgang Preiser: Tygerberg
Jinal N. Bhiman: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Mary-Anne Davies: University of Cape Town
Marietjie Venter: University of the Witwatersrand
Florette K. Treurnicht: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Nicole Wolter: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Carolyn Williamson: National Health Laboratory Service
Anne Gottberg: National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)
Richard Lessells: University of KwaZulu-Natal
Houriiyah Tegally: Stellenbosch University
Tulio Oliveira: Stellenbosch University

Nature Communications, 2025, vol. 16, issue 1, 1-10

Abstract: Abstract Since November 2021, five genetically distinct SARS-CoV-2 Omicron lineages (BA.1–BA.5) are believed to have emerged in southern Africa, with four (BA.1, BA.2, BA.4, and BA.5) spreading globally and collectively dominating SARS-CoV-2 diversity. In 2023, BA.2.86, a highly divergent BA.2 lineage that rose to prominence worldwide, was first detected in Israel and Denmark, but the subsequent diversity of South African sequences suggests it too emerged in the region. Using Bayesian phylogeographic inference, we reconstruct the origins and dispersal patterns of BA.1–BA.5 and BA.2.86. Our findings suggest that Gauteng province in South Africa likely played a key role in the emergence and/or amplification of multiple Omicron lineages, though regions with limited sampling may have also contributed. The challenge of precisely tracing these origins highlights the need for broader genomic surveillance across the region to strengthen early detection, track viral evolution, and improve preparedness for future threats.

Date: 2025
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DOI: 10.1038/s41467-025-60081-0

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