Sixteen novel lineages of SARS-CoV-2 in South Africa
Sixteen novel lineages of SARS-CoV-2 in South Africa
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DOI：
10.1038/s41591-021-01255-3
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发表时间：
2021-02-02
期刊：
影响因子：
82.9
通讯作者：
de Oliveira, Tulio
中科院分区：
文献类型：
--
作者：
Tegally, Houriiyah;Wilkinson, Eduan;de Oliveira, Tulio
南非于2020年3月5日发现首例严重急性呼吸系统综合征冠状病毒2型（SARS-CoV-2）感染，截至3月26日，该国已全面封锁（牛津严格指数为90）（1）。尽管有早期的反应，到2020年11月，南非有超过785，000人感染，约占所有已知非洲感染的50%。在这项研究中，我们分析了1，365个几乎全基因组，并报告了2020年3月6日至8月26日期间分离的16个新的SARS-CoV-2谱系。这些谱系中的大多数具有在其他地方未被鉴定的独特突变。我们还发现，在第一波疫情期间，三个谱系（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病例的42%。新发现的SARS-CoV-2的C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D 614 G上的一个氨基酸变化（参考文献（3）），是截至2020年8月底在南非地理分布最广的谱系。2020年4月发现的一个早期南非特有谱系B.1.106（参考文献（4）），在夸祖鲁-纳塔尔省医院内暴发得到控制后灭绝。我们的研究结果表明，基因组监测可以在非洲大规模实施，以确定新的谱系，并为控制SARS-CoV-2传播的措施提供信息。这项研究中提出的这种基因组监测已被证明对2020年12月在南非鉴定501Y.V2变异株至关重要（参考文献（5））。
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)(1). 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(2). 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 similar to 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. (3)), 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. (4)), 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. (5)).