Virus detection using metagenomic sequencing of swine nasal and rectal swabs

Advances in DNA sequencing have increased our ability to generate large amounts of sequence data at lower costs. These developments have enabled microbial detection and characterization directly from clinical specimens, known as metagenomic sequencing. Viral metagenomic sequencing was performed on five nasaland five fecal-swab pools collected from each of two primary and two secondary market slaughterhouses and a cull-swine buying station in the southeastern United States. Sequences were assembled de novo and analyzed by BLASTN to identify viruses present in the samples. Twenty seven different viruses were identified. Reads similar to a diverse family of single-stranded circular DNA viruses were identified in nearly every sample (47 of 50). Other viruses identified at all five sampling sites and in over half of the samples were bocavirus, torovirus, posavirus, torque teno virus, IAS virus, picobirnavirus, and teschovirus. Viruses identified in multiple sites in greater than 20% of the samples included enterovirus, parvovirus, influenza A virus, sapelovirus, and Senecavirus A. Other significant swine viruses detected less frequently include porcine circovirus type 2, porcine epidemic diarrhea virus, and porcine deltacoronavirus. Together, these results suggest that metagenomic sequencing is a powerful tool for virus detection and characterization.