Comparative assessment of Nanotrap and polyethylene glycol-based virus concentration in wastewater samples

K. Farkas, J. Kevill, Rachel C Williams, Igor Pântea, Nicola Ridding, Kathryn Lambert-Slosarska, Nick Woodhall, Jasmine M S Grimsley, Matthew J. Wade, Andrew C. Singer, Andrew J Weightman, Gareth Cross, Davey L Jones
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Abstract

Wastewater-based epidemiology is now widely used in many countries for the routine monitoring of SARS-CoV-2 and other viruses at a community level. However, efficient sample processing technologies are still under investigation. In this study, we compared the performance of the novel Nanotrap® Microbiome Particles (NMP) concentration method to the commonly used polyethylene glycol (PEG) precipitation method for concentrating viruses from wastewater and their subsequent quantification and sequencing. For this, we first spiked wastewater with SARS-CoV-2, influenza and measles viruses and norovirus and found that the NMP method recovered 0.4–21% of them depending on virus type, providing consistent and reproducible results. Using the NMP and PEG methods, we monitored SARS-CoV-2, influenza A and B viruses, RSV, enteroviruses and norovirus GI and GII and crAssphage in wastewater using quantitative PCR (qPCR)-based methods and next-generation sequencing. Good viral recoveries were observed for highly abundant viruses using both methods; however, PEG precipitation was more successful in the recovery of low-abundance viruses present in wastewater. Furthermore, samples processed with PEG precipitation were more successfully sequenced for SARS-CoV-2 than those processed with the NMP method. Virus recoveries were enhanced by high sample volumes when PEG precipitation was applied. Overall, our results suggest that the NMP concentration method is a rapid and easy virus concentration method for viral targets that are abundant in wastewater, whereas PEG precipitation may be more suited to the recovery and analysis of low-abundance viruses and for next generation sequencing.
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废水样本中纳米诱捕器和聚乙二醇病毒浓度的比较评估
以废水为基础的流行病学目前已在许多国家广泛应用,用于在社区一级对 SARS-CoV-2 和其他病毒进行常规监测。然而,高效的样本处理技术仍在研究之中。在本研究中,我们比较了新型 Nanotrap® 微生物组微粒(NMP)浓缩法与常用的聚乙二醇(PEG)沉淀法在浓缩废水中的病毒及其后续定量和测序方面的性能。为此,我们首先在废水中添加了 SARS-CoV-2、流感病毒、麻疹病毒和诺如病毒,结果发现,根据病毒类型的不同,NMP 方法可回收 0.4-21%的病毒,且结果一致、可重复。利用 NMP 和 PEG 方法,我们使用基于定量 PCR (qPCR) 的方法和新一代测序技术监测了废水中的 SARS-CoV-2、甲型和乙型流感病毒、RSV、肠道病毒、诺如病毒 GI 和 GII 以及 crAssphage。这两种方法都能很好地回收高丰度病毒,但 PEG 沉淀法在回收废水中低丰度病毒方面更为成功。此外,用 PEG 沉淀法处理的样本比用 NMP 法处理的样本更能成功地对 SARS-CoV-2 进行测序。使用 PEG 沉淀法时,样品量越大,病毒回收率越高。总之,我们的研究结果表明,NMP 浓缩法是一种快速简便的病毒浓缩方法,适用于废水中含量丰富的病毒目标物,而 PEG 沉淀法可能更适用于低含量病毒的回收和分析以及下一代测序。
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来源期刊
CiteScore
3.30
自引率
0.00%
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0
审稿时长
15 weeks
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