van Ackeren Vanessa, Schmutz Stefan, Pichler Ian, Ziltener Gabriela, Zaheri Maryam, Kufner Verena, Huber Michael
Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland.
Pathogens. 2024 May 8;13(5):390. doi: 10.3390/pathogens13050390.
Enteroviruses are among the most common viruses pathogenic to humans. They are associated with various forms of disease, ranging from mild respiratory illness to severe neurological diseases. In recent years, an increasing number of isolated cases of children developing meningitis or encephalitis as a result of enterovirus infection have been reported, as well as discrete enterovirus D68 outbreaks in North America in 2014 and 2016. We developed an assay to rapidly genotype enteroviruses by sequencing a region within the VP1 gene using nanopore Flongles. We retrospectively analyzed enterovirus-/rhinovirus-positive clinical samples from the Zurich, Switzerland area mainly collected during two seasons in 2019/2020 and 2021/2022. Respiratory, cerebrospinal fluid, and stool samples were analyzed. Whole-genome sequencing was performed on samples with ambiguous genotyping results and enterovirus D68-positive samples. Out of 255 isolates, a total of 95 different genotypes were found. A difference in the prevalence of enterovirus and rhinovirus infections was observed for both sample type and age group. In particular, children aged 0-4 years showed a higher frequency of enterovirus infections. Comparing the respiratory seasons, a higher prevalence was found, especially for enterovirus A and rhinovirus A after the SARS-CoV-2 pandemic. The enterovirus genotyping workflow provides a rapid diagnostic tool for individual analysis and continuous enterovirus surveillance.
肠道病毒是对人类致病的最常见病毒之一。它们与各种疾病形式相关，从轻度呼吸道疾病到严重的神经系统疾病。近年来，有越来越多关于儿童因肠道病毒感染而患脑膜炎或脑炎的孤立病例报告，以及2014年和2016年在北美发生的离散的肠道病毒D68疫情。我们开发了一种检测方法，通过使用纳米孔Flongles对VP1基因内的一个区域进行测序来快速对肠道病毒进行基因分型。我们回顾性分析了主要在2019/2020年和2021/2022年两个季节从瑞士苏黎世地区收集的肠道病毒/鼻病毒阳性临床样本。对呼吸道、脑脊液和粪便样本进行了分析。对基因分型结果不明确的样本和肠道病毒D68阳性样本进行了全基因组测序。在255株分离株中，共发现95种不同的基因型。在样本类型和年龄组方面均观察到肠道病毒和鼻病毒感染患病率的差异。特别是，0至4岁的儿童肠道病毒感染频率较高。比较呼吸道疾病季节，发现患病率较高，尤其是在新冠疫情之后的肠道病毒A和鼻病毒A。肠道病毒基因分型工作流程为个体分析和持续的肠道病毒监测提供了一种快速诊断工具。
