Abstract
This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was detected in sewage samples, with genogroup II being more prevalent. Interestingly, the pig-mucin capture enhanced not only the recovery of norovirus and rotavirus but also recovery of astrovirus, sapovirus and husavirus. Documenting sewage virome using these methods provides information for molecular epidemiology and may be useful in developing strategies to prevent further spread of viruses.
Highlights
Increasing human population leads to increased demand for agricultural products and water, wastewater re-use will be necessary, which will pose a risk for virus pollution of the environment and subsequent affects viral transmission (Sano et al 2016)
Norovirus genogroup I (GI) was detected in all samples, with concentrations 10 to 100 times lower compare to norovirus GII concentrations
There are several challenges when applying metagenomics deep sequencing to describe the total virome of sewage samples (Bibby et al 2013, Adriaenssens et al 2018)
Summary
Increasing human population leads to increased demand for agricultural products and water, wastewater re-use will be necessary, which will pose a risk for virus pollution of the environment and subsequent affects viral transmission (Sano et al 2016). Documenting viral prevalence and diversity in sewage may be a useful method for monitoring viruses circulating in the community (Smith et al 2016). Their detection by PCR approaches requires previously identified sequences for primer design and will not detect more distant viruses. Most of human enteric viruses have small RNA genomes making their detection difficult Their relative abundance if compared to bacteria, phage, parasites present in the environment challenge their detection and identification (Cotten and Koopmans 2016; Nieuwenhuijse and Koopmans, 2017; Adriaenssens et al 2018). Each sample type is unique and methods need to be adapted to account for
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