Optimization of metagenomic approach for sewage and stool

Human sewage may contain components of the microbiome of local population and this study aimed to optimize a method to identify human enteric viruses present using random primed next generation sequencing. To achieve this goal two methods using different enrichment steps were compared. Enrichment was based on the binding properties of viral capsid using pig-mucin capture, or by selecting viral RNA prior to library preparation using a capture array. A third method, non-specific biophysical precipitation with polyethylene glycol, was included for comparison. All three methods gave full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus or astrovirus. Many norovirus sequences were detected in all three sewage samples, with genogroup II being more prevalent. Surprisingly the pig-mucin capture increased not only recovery of norovirus and rotavirus but also of astrovirus, sapovirus and husavirus. Being able to document the virome of sewage will provide information for molecular epidemiology and will be useful in developing strategies to prevent further spread of viruses.