PCR-Based Detection and Genetic Characterization of Parainfluenza Virus 5 Detected in Pigs in Korea from 2016 to 2018

Abstract

Simple Summary Parainfluenza virus 5 (PIV5) has been known for a long time. The virus is detected in various animals suffering from different clinical diseases. However, the pathogenicity of PIV5 is largely unconfirmed. Thus, it is necessary to continue researching for the prevalence, genetic diversity, and evolution characteristic of PIV5. The results of this study confirmed a permanent prevalence of PIV5 in Republic of Korea, identified three field strains with more divergence, and elucidated the evolutionary path of PIV5 in which a few codons of the F and HN genes had an elevated rate of non-synonymous substitutions. This study applied a molecular-based method to detect parainfluenza virus 5 (PIV5) collected from 2016 to 2018 in nine provinces of Republic of Korea. We demonstrated that PIV5 was detectable in both serum and pooled organs at an average positive rate of 1.78% (99/5566). Among these, the complete genome sequence of 15,246 nucleotides was obtained for 12 field strains. Three out of the 12 strains had the lowest genetic identity (96.20-96.68%) among the 21 porcine PIV5 genomes collected in Germany, China, India, and Republic of Korea from 1998 to 2017. By analyzing a large collection of complete genome sequences of the structural protein-coding F and HN genes, this study proposed a classification of PIV5 into two lineages, 1 and 2, and identified that group 2.2.2 within sub-lineage 2.2 was substantially divergent. The evolution of two structural protein-coding genes was largely under purifying selection. A few codons (6/9 for the F gene, 7/8 for the HN gene) had elevated dN/dS values, which were loaded on internal branches and were predicted to be related to beneficial trait(s) of the virus.