Comparative ORF and whole genome sequencing analysis of the porcine reproductive and respiratory syndrome virus (PRRSV) in routine samples reveal a recombinant virus strain

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) causes one of the economically most important diseases in pig farming. In view of the particularly high level of genetic variation of this virus, molecular epidemiological methods are very well suited for the characterisation of virus strains. In our study, we present the results of PRRSV testing using RT-qPCR and following ORF5, ORF4–ORF6 and whole genome sequencing (WGS) in two pig farms, connected by purchase and both suffering from PRRSV outbreaks. Analyses based on ORF5 sequences detected only a field virus strain in farmA, despite vaccination with a modified live vaccine (MLV). In farmB, the MLV used in farmA and a field virus strain could be determined. However, the ORF4–ORF6 sequences confirmed the results from farmA, but revealed two different field virus strains in farmB. This phenomenon could be resolved using next generation sequencing (NGS) technologies for WGS analyses of two representative virus strains originating from farmB. WGS revealed two closely related field virus strains with a nucleotide sequence identity of 97.72%. One strain was a recombinant PRRSV strain, apparently created from the MLV used in farmA and a field virus strain. The fact that only the ORF5 region originated from the MLV explains the differences in the sequences of ORF5 compared to ORF4–ORF6 and WGS. Our study shows that ORF-based molecular characterisation of PRRSV strains might be deceptive due to mosaic recombination events requiring WGS to accurately reveal the molecular relationships between virus strains.

Keywords

• next generation sequencing
• molecular epidemiology
• modified live vaccine