Evaluating NGS-generated Contig Accuracy for Detection and Assignment of PRRSV against a reference genome in Experimentally Mixed PRRSV infection Samples
This project evaluated the performance of next-generation sequencing (NGS) for detecting and characterizing mixed infections of Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2). Controlled viral mixtures containing combinations of wild-type and commercial modified-live vaccine strains at different viral loads and relative abundances were generated in processing fluid to simulate field conditions. Sequencing data were produced to assess the sensitivity and accuracy of NGS for detecting multiple co-circulating PRRSV-2 strains, evaluate the effect of viral complexity on strain detection and contig assembly, and establish practical sequence identity thresholds for accurate strain assignment from partial genome recovery. The resulting data provide a benchmark dataset for improving interpretation of PRRSV NGS results in diagnostic and research applications.