科学家在南非发现16种SARS-CoV-2的新谱系
2021-02-06   阅读:659   来源:自然

南非夸祖鲁-纳塔尔大学Tulio de Oliveira团队在南非发现16种SARS-CoV-2的新谱系。相关论文于2021年2月2日在线发表在《自然—医学》杂志上。

研究人员分析了1,365个近乎完整的SARS-CoV-2基因组,并报告了在2020年3月6日至2020年8月26日期间分离出的16个新SARS-CoV-2谱系。这些谱系中的大多数具有独特的突变,在其他地方未发现。研究人员还发现,在第一波期间,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的约42%。

新发现的SARS-CoV-2 C.1谱系与原始序列相比具有16个核苷酸突变,其中包括突刺蛋白D614G的一个氨基酸变化,该突变株南非广泛的谱系。在控制夸祖鲁-纳塔尔省的医院爆发后,于2020年4月确定的南非早期谱系B.1.106已消失。这些研究结果表明,基因组监测可以在非洲大规模实施,从而发现新的谱系并提供控制SARS-CoV-2传播的措施。研究表明,这种基因组监测对2020年12月在南非鉴定到501Y.V2变体至关重要。 

附:英文原文

Title: Sixteen novel lineages of SARS-CoV-2 in South Africa

Author: Houriiyah Tegally, Eduan Wilkinson, Richard J. Lessells, Jennifer Giandhari, Sureshnee Pillay, Nokukhanya Msomi, Koleka Mlisana, Jinal N. Bhiman, Anne von Gottberg, Sibongile Walaza, Vagner Fonseca, Mushal Allam, Arshad Ismail, Allison J. Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Carolyn Williamson, Francesco Petruccione, Alex Sigal, Inbal Gazy, Diana Hardie, Nei-yuan Hsiao, Darren Martin, Denis York, Dominique Goedhals, Emmanuel James San, Marta Giovanetti, Jos Loureno, Luiz Carlos Junior Alcantara, Tulio de Oliveira

Issue&Volume: 2021-02-02

Abstract: 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 infections2. 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. 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). Interrogation of 1,365 near whole-genome sequences of SARS-CoV-2 variants isolated in South Africa during the first 6 months of the global pandemic reveals three major monophyletic lineages responsible for more than half of the infections in the country and underscores the value of integrating genomic surveillance methods to inform the national pandemic response.

DOI: 10.1038/s41591-021-01255-3

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