Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom.
Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
mBio. 2023 Dec 19;14(6):e0146823. doi: 10.1128/mbio.01468-23. Epub 2023 Oct 25.
Most public health initiatives that monitor viruses in wastewater have utilized quantitative polymerase chain reaction (PCR) and whole genome PCR sequencing, mirroring techniques used for viral epidemiology in individuals. These techniques require prior knowledge of the target viral genome and are limited to monitoring individual or small groups of viruses. Metagenomic sequencing may offer an alternative strategy for monitoring a broad spectrum of viruses in wastewater, including novel and emerging pathogens. In this study, while amplicon sequencing gave high viral genome coverage, untargeted shotgun sequencing of total nucleic acid samples was unable to detect human pathogenic viruses with enough sensitivity for use in genomic epidemiology. Enrichment of shotgun libraries for respiratory viruses using hybrid-capture technology provided genotypic information on a range of viruses simultaneously, indicating strong potential for wastewater surveillance. This type of targeted metagenomics could be used for monitoring diverse targets, such as pathogens or antimicrobial resistance genes, in environmental samples.
大多数监测废水中病毒的公共卫生举措都利用了定量聚合酶链反应（PCR）和全基因组 PCR 测序，这反映了用于个体病毒流行病学的技术。这些技术需要事先了解目标病毒基因组，并且仅限于监测单个或少数几种病毒。宏基因组测序可能提供了一种替代策略，可以监测废水中的广泛病毒，包括新型和新兴病原体。在这项研究中，虽然扩增子测序提供了高病毒基因组覆盖率，但针对总核酸样本的非靶向鸟枪法测序无法以足够的灵敏度检测到用于基因组流行病学的人类致病病毒。使用杂交捕获技术对呼吸病毒的鸟枪法文库进行富集，可同时提供一系列病毒的基因型信息，表明在废水监测方面具有很强的潜力。这种靶向宏基因组学可用于监测环境样本中的多种目标，如病原体或抗微生物药物耐药性基因。
