Dor Graeme, Wilkinson Eduan, Martin Darren P, Moir Monika, Tshiabuila Derek, Kekana Dikeledi, Ntozini Buhle, Joseph Rageema, Iranzadeh Arash, Nyaga Martin M, Goedhals Dominique, Maponga Tongai, Maritz Jean, Laguda-Akingba Oluwakemi, Ramphal Yajna, MacIntyre Caitlin, Chabuka Lucious, Pillay Sureshnee, Giandhari Jennifer, Baxter Cheryl, Hsiao Nei-Yuan, Preiser Wolfgang, Bhiman Jinal N, Davies Mary-Anne, Venter Marietjie, Treurnicht Florette K, Wolter Nicole, Williamson Carolyn, von Gottberg Anne, Lessells Richard, Tegally Houriiyah, de Oliveira Tulio
Centre for Epidemic Response and Innovation (CERI), School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Nat Commun. 2025 May 28;16(1):4937. doi: 10.1038/s41467-025-60081-0.
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.
自2021年11月以来，据信在南部非洲出现了五种基因不同的新冠病毒奥密克戎谱系（BA.1-BA.5），其中四种（BA.1、BA.2、BA.4和BA.5）在全球传播，并共同主导了新冠病毒的多样性。2023年，BA.2.86这一在全球崭露头角的高度分化的BA.2谱系首次在以色列和丹麦被检测到，但南非序列随后的多样性表明它也是在该地区出现的。利用贝叶斯系统发育地理推断，我们重建了BA.1-BA.5和BA.2.86的起源和传播模式。我们的研究结果表明，南非豪登省可能在多个奥密克戎谱系的出现和/或扩增中发挥了关键作用，尽管采样有限的地区也可能有贡献。精确追踪这些起源的挑战凸显了在该地区进行更广泛基因组监测的必要性，以加强早期检测、追踪病毒进化并提高对未来威胁的防范能力。
