Rapid detection and characterisation of PRRS resolving mixed infections

Porcine reproductive and respiratory syndrome virus (PRRSV) is a rapidly evolving, highly pathogenic porcine arterivirus, among the most common infectious agents of swine disease, affecting between 30% to 40% of the breeding herds in the US each year.

Traditionally, PRRSV diagnosis involves amplifying (reverse-transcription PCR) and Sanger sequencing of several conserved open reading frames (ORFs), to detect and classify the virus for outbreak management. Herds are often coinfected with both (pathogenic) wild-type viruses and (benign) modified live virus (MLV) vaccines, which are challenging to discriminate by Sanger sequencing.

However, long-read sequencing can rapidly generate full-length amplicon sequences from multiple strains in the same sample, allowing for greater discrimination, increased reliability, and improved turn-around time.

Here we evaluated the Oxford Nanopore platform, compared to Sanger sequencing, for PRRSV-2 amplicon sequencing.