Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics.

ABSTRACT: Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preamplification pipelines (specific to RNA viruses, DNA viruses or both) for viral genome sequencing using spiked-in Phosphate Buffered Saline and sewage samples containing known concentrations of viruses. We found that compared to the pipeline targeting all genome types, the RNA pipeline performed better in detecting RNA viruses in both spiked and unspiked sewage samples, allowing the detection of various mammalian viruses including members from the Reoviridae, Picornaviridae, Astroviridae and Caliciviridae. However, the DNA-specific pipeline d

SUBMITTER: Fernandez-Cassi X 

PROVIDER: S-EPMC11422458 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature