After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47% and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analysing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from mink farms. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly-introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.

中文翻译：

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对 24,181 名患者的 SARS-CoV-2 变异体的分析证明了全球化和人畜共患病在大流行中的作用

在 SARS-CoV-2 感染的第一次流行结束后，随着 2020 年夏季病例再次开始上升，我们在法国马赛的 IHU Méditerranée Infection 加强了对 SARS-CoV-2 的基因组监测，并描述了第一个病毒变体。在这项研究中，我们比较了不同国家 SARS-CoV-2 相关死亡的发生率曲线，并报告了我们研究所检测到的 SARS-CoV-2 变异的分类，以及感染的动力学和来源。我们使用了从 221 个国家的 COVID-19 数据库收集的死亡率。病毒变异是根据≥30个基因组共有的≥5个标志性突变来定义的。使用下一代基因组和基因测序确定了 24,181 名患者的 SARS-CoV-2 基因型（在 47% 和 11% 的病例中，分别）或变异特异性 qPCR（在 42% 的情况下）。通过分析 9,788 名 SARS-CoV-2 诊断患者的病毒基因组，确定了 16 种变异。我们的数据显示，自马赛第一次 SARS-CoV-2 流行以来，记录了七个新变种通过国外旅行输入。此外，对于穿山甲分类的 B.1.160 变体（又名 Marseille-4），我们怀疑是从水貂养殖场传播的。总之，我们观察到 SARS-CoV-2 感染的连续流行高峰与已经存在的病毒基因型的反弹无关，而是与新引入的变种有关。因此，我们建议边境管制是对抗此类引入的最佳手段，