Cassidy Hayley, Lizarazo-Forero Erley, Schuele Leonard, Van Leer-Buter Coretta, Niesters Hubert G M
The University of Groningen, University Medical Centre Groningen, Department of Medical Microbiology and Infection Prevention, Division of Clinical Virology, Groningen, Netherlands.
Front Microbiol. 2023 Feb 9;13:1088770. doi: 10.3389/fmicb.2022.1088770. eCollection 2022.
To explore an off-season enterovirus D68 (EV-D68) upsurge in the winter season of 2019/2020, we adapted a whole-genome sequencing approach for Nanopore Sequencing for 20 hospitalized patients with accompanying respiratory or neurological presentation. Applying phylodynamic and evolutionary analysis on Nextstrain and Datamonkey respectively, we report a highly diverse virus with an evolutionary rate of 3.05 × 10 substitutions per year (entire EV-D68 genome) and a positive episodic/diversifying selection with persistent yet undetected circulation likely driving evolution. While the predominant B3 subclade was identified in 19 patients, one A2 subclade was identified in an infant presenting with meningitis. Exploring single nucleotide variations using CLC Genomics Server showed high levels of non-synonymous mutations, particularly in the surface proteins, possibly highlighting growing problems with routine Sanger sequencing for typing enteroviruses. Surveillance and molecular approaches to enhance current knowledge of infectious pathogens capable of pandemic potential are paramount to early warning in health care facilities.
为探究2019/2020年冬季肠道病毒D68（EV-D68）的非季节性激增情况，我们采用全基因组测序方法对20例伴有呼吸道或神经系统症状的住院患者进行纳米孔测序。分别在Nextstrain和Datamonkey上进行系统发育动力学和进化分析，我们报告了一种高度多样化的病毒，其进化速率为每年3.05×10个替换（整个EV-D68基因组），且存在正向偶发性/多样化选择，持续但未被检测到的传播可能推动了进化。虽然在19例患者中鉴定出主要的B3亚分支，但在一名患有脑膜炎的婴儿中鉴定出一个A2亚分支。使用CLC基因组学服务器探索单核苷酸变异显示出高水平的非同义突变，特别是在表面蛋白中，这可能凸显了常规桑格测序用于肠道病毒分型时日益严重的问题。加强对具有大流行潜力的传染病原体当前认识的监测和分子方法对于医疗机构的早期预警至关重要。
