IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.
IHU Méditerranée Infection, Marseille, France.
Clin Microbiol Infect. 2021 Sep;27(9):1352.e1-1352.e5. doi: 10.1016/j.cmi.2021.05.006. Epub 2021 May 12.
Surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic epidemiology led us to detect several variants since summer 2020. We report the recent spread of a new SARS-CoV-2 spike 501Y variant.
SARS-CoV-2 sequences obtained from human nasopharyngeal samples by Illumina next-generation sequencing were analysed using Nextclade and an in-house Python script and were compared using BLASTn to the GISAID database. Phylogeny was investigated using the IQ-TREE software.
We identified that SARS-CoV-2 genomes from four patients diagnosed in our institute harboured a new set of amino acid substitutions including L18F, L452R, N501Y, A653V, H655Y, D796Y, G1219V ± Q677H. These spike N501Y genomes are the first of Nextstrain clade 19B. We obtained partial spike gene sequences of this genotype for an additional 43 patients. All patients infected with this genotype were diagnosed since mid-January 2021. We detected 42 other genomes of this genotype in GISAID, which were obtained from samples collected in December 2020 in four individuals and in 2021 in 38 individuals. The 89 sequences obtained in our institute or other laboratories originated from the Comoros archipelago, western European countries (mostly metropolitan France), Turkey and Nigeria.
These findings warrant further studies to investigate the spread, epidemiological and clinical features, and sensitivity to immune responses of this variant.
对严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 基因组流行病学的监测导致我们自 2020 年夏天以来发现了几种变体。我们报告了一种新的 SARS-CoV-2 刺突 501Y 变体的近期传播情况。
使用 Illumina 下一代测序从人类鼻咽样本中获得的 SARS-CoV-2 序列使用 Nextclade 和内部 Python 脚本进行分析，并使用 BLASTn 与 GISAID 数据库进行比较。使用 IQ-TREE 软件进行系统发育分析。
我们发现，在我们研究所诊断的四名患者的 SARS-CoV-2 基因组中存在一组新的氨基酸替换，包括 L18F、L452R、N501Y、A653V、H655Y、D796Y、G1219V±Q677H。这些刺突 N501Y 基因组是 Nextstrain 分支 19B 的首例。我们为另外 43 名患者获得了该基因型的部分刺突基因序列。所有感染这种基因型的患者均于 2021 年 1 月中旬确诊。我们在 GISAID 中检测到了 42 个其他这种基因型的基因组，这些基因组来自 2020 年 12 月在 4 个人以及 2021 年在 38 个人的样本中获得。在我们研究所或其他实验室获得的 89 个序列来自科摩罗群岛、西欧国家（主要是法国本土）、土耳其和尼日利亚。
这些发现值得进一步研究，以调查该变体的传播、流行病学和临床特征以及对免疫反应的敏感性。
