Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa
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 linea...
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Nature Portfolio
2025-05-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-60081-0 |
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| author | 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 von Gottberg Richard Lessells Houriiyah Tegally Tulio de Oliveira |
| author_facet | 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 von Gottberg Richard Lessells Houriiyah Tegally Tulio de Oliveira |
| author_sort | Graeme Dor |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-8d4c2e77c80d4098a462172df86df268 |
| institution | DOAJ |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-8d4c2e77c80d4098a462172df86df2682025-08-20T03:16:32ZengNature PortfolioNature Communications2041-17232025-05-0116111010.1038/s41467-025-60081-0Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South AfricaGraeme Dor0Eduan Wilkinson1Darren P. Martin2Monika Moir3Derek Tshiabuila4Dikeledi Kekana5Buhle Ntozini6Rageema Joseph7Arash Iranzadeh8Martin M. Nyaga9Dominique Goedhals10Tongai Maponga11Jean Maritz12Oluwakemi Laguda-Akingba13Yajna Ramphal14Caitlin MacIntyre15Lucious Chabuka16Sureshnee Pillay17Jennifer Giandhari18Cheryl Baxter19Nei-yuan Hsiao20Wolfgang Preiser21Jinal N. Bhiman22Mary-Anne Davies23Marietjie Venter24Florette K. Treurnicht25Nicole Wolter26Carolyn Williamson27Anne von Gottberg28Richard Lessells29Houriiyah Tegally30Tulio de Oliveira31Centre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch UniversityCentre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch UniversityDivision of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape TownCentre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch UniversityCentre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch UniversityNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)Division of Medical Virology, Department of Pathology, University of Cape TownComputational Biology Division, University of Cape TownNext Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free StateDivision of Virology, University of the Free StateNational Health Laboratory Service, TygerbergDivision of Medical Virology, Faculty of Medicine & Health Sciences, Stellenbosch UniversityNational Health Laboratory ServiceCentre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch UniversityEmerging Viral Threats, One Health surveillance and vaccines (EViTOH) Division, Infectious Disease and Oncology Research Institute (IDORI), School of Pathology, Faculty of Health Sciences, University of the WitwatersrandCentre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch UniversityKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-NatalKwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-NatalCentre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch UniversityDivision of Medical Virology, Department of Pathology, University of Cape TownNational Health Laboratory Service, TygerbergNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)Centre for Infectious Disease Epidemiology and Research, School of Public Health, University of Cape TownEmerging Viral Threats, One Health surveillance and vaccines (EViTOH) Division, Infectious Disease and Oncology Research Institute (IDORI), School of Pathology, Faculty of Health Sciences, University of the WitwatersrandNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)National Health Laboratory ServiceNational Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS)KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-NatalCentre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch UniversityCentre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch UniversityAbstract 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.https://doi.org/10.1038/s41467-025-60081-0 |
| spellingShingle | 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 von Gottberg Richard Lessells Houriiyah Tegally Tulio de Oliveira Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa Nature Communications |
| title | Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa |
| title_full | Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa |
| title_fullStr | Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa |
| title_full_unstemmed | Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa |
| title_short | Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa |
| title_sort | tracing the spatial origins and spread of sars cov 2 omicron lineages in south africa |
| url | https://doi.org/10.1038/s41467-025-60081-0 |
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