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通过直接下一代测序分析在一份来自苏格兰的环境样本中检测新出现的肠道病毒D68和C109毒株

Detection by Direct Next Generation Sequencing Analysis of Emerging Enterovirus D68 and C109 Strains in an Environmental Sample From Scotland.

作者信息

Majumdar Manasi, Martin Javier

机构信息

Division of Virology, National Institute for Biological Standards and Control, Hertfordshire, United Kingdom.

出版信息

Front Microbiol. 2018 Aug 21;9:1956. doi: 10.3389/fmicb.2018.01956. eCollection 2018.

Abstract

Human enteroviruses (EVs) have been linked with severe disease and syndromes as varied as acute respiratory illness, myocarditis, and flaccid paralysis. With global polio eradication on sight the focus of clinical investigations has expanded to the identification of other EV serotypes associated with severe neurological conditions such as EV-D68, responsible for large outbreaks in 2014 and 2016 that spread worldwide and were related with severe respiratory disease leading to acute myelitis in some cases. New EV serotypes with epidemic potential continue to emerge such as EV-C104, EV-C105, EV-C109, and EV-C117 identified in respiratory samples in recent years. We used a next generation sequencing (NGS) approach to detect multiple EV serotypes directly in a sewage concentrate from Glasgow (Scotland, United Kingdom) generating whole-capsid nucleotide sequences that were compared to sequences of cell culture isolates from this sewage sample and clinical EV isolates from GenBank. Thirteen different serotypes belonging to all four A, B, C, and D EV species were identified in the sewage concentrate. EV strains closely related to EV-D68 epidemic isolates of B3 lineage reported in the United States and Europe in 2016 and to EV-C109 respiratory isolates found in Denmark and Netherlands in 2015 were identified. Environmental surveillance (ES) can effectively detect EV circulation in human populations. The use of NGS for ES can help overcoming the limitations of traditional cell culture and sequencing methods, which are selective and biased, and can contribute to the early detection and assessment of spread of emerging EV pathogens.

摘要

人类肠道病毒(EVs)与多种严重疾病和综合征有关,如急性呼吸道疾病、心肌炎和弛缓性麻痹。随着全球消灭脊髓灰质炎在望,临床研究的重点已扩大到识别与严重神经系统疾病相关的其他肠道病毒血清型,如肠道病毒D68型(EV-D68),它在2014年和2016年引发了大规模全球疫情,与严重呼吸道疾病有关,在某些情况下还导致急性脊髓炎。具有流行潜力的新型肠道病毒血清型不断出现,例如近年来在呼吸道样本中发现的肠道病毒C104型(EV-C104)、肠道病毒C105型(EV-C105)、肠道病毒C109型(EV-C109)和肠道病毒C117型(EV-C117)。我们采用下一代测序(NGS)方法直接在来自格拉斯哥(英国苏格兰)的污水浓缩物中检测多种肠道病毒血清型,生成全衣壳核苷酸序列,并将其与来自该污水样本的细胞培养分离株序列以及来自GenBank的临床肠道病毒分离株序列进行比较。在污水浓缩物中鉴定出属于所有四个A、B、C和D肠道病毒种的13种不同血清型。鉴定出了与2016年在美国和欧洲报告的B3谱系的肠道病毒D68型流行株以及2015年在丹麦和荷兰发现的肠道病毒C109型呼吸道分离株密切相关的肠道病毒株。环境监测(ES)可以有效地检测人群中肠道病毒的传播。将NGS用于环境监测有助于克服传统细胞培养和测序方法的局限性,传统方法具有选择性和偏向性,并且有助于早期检测和评估新兴肠道病毒病原体的传播。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/12e0/6110882/ae5e797904a4/fmicb-09-01956-g001.jpg

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