KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
Discipline of Virology, University of KwaZulu-Natal, Durban, South Africa.
Nat Med. 2021 Mar;27(3):440-446. doi: 10.1038/s41591-021-01255-3. Epub 2021 Feb 2.
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). 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. 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. ), 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. ), 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. ).
南非首例严重急性呼吸系统综合征冠状病毒 2（SARS-CoV-2）感染于 2020 年 3 月 5 日确诊，到 3 月 26 日该国已全面封锁（牛津严格指数为 90）。尽管采取了早期应对措施，但到 2020 年 11 月，南非已有超过 78.5 万人感染，占非洲所有已知感染人数的约 50%。在这项研究中，我们分析了 1365 个近全基因组序列，并报告了在 2020 年 3 月 6 日至 8 月 26 日期间分离出的 16 种新的 SARS-CoV-2 谱系。这些谱系大多具有独特的突变，在其他地方尚未发现。我们还表明，在第一波疫情中，三种谱系（B.1.1.54、B.1.1.56 和 C.1）在南非广泛传播，占当时该国所有感染的约 42%。新发现的 SARS-CoV-2 谱系 C.1 与原始武汉序列相比有 16 个核苷酸突变，包括刺突蛋白上的一个氨基酸变化，D614G（参考文献），到 2020 年 8 月底，它是在南非分布最广的谱系。2020 年 4 月发现的早期南非特异性谱系 B.1.106 在夸祖鲁-纳塔尔省的医院暴发得到控制后灭绝。我们的研究结果表明，在非洲可以大规模实施基因组监测，以识别新的谱系并为控制 SARS-CoV-2 传播提供信息。本研究中提出的这种基因组监测对于 2020 年 12 月在南非发现 501Y.V2 变体至关重要（参考文献）。
