Characterization of porcine parainfluenza virus 1, a virus with possible association with respiratory disease, from deceased pigs.

Abstract

Objectives: Pigs, being farm animals and an important food source of humans, would also be a source of zoonotic disease pathogens, e.g. Influenenza virus A (HIN1) and Nipah virus, in humans. Therefore, understanding more about porcine pathogens is important in preparing for emerging diseases in humans. Recently, our research group has found a porcine paramyxovirus, named porcine parainfluenza 1 (PPIV-1) and detailed analysis was performed based on its genomic data in this study. Methods: The virus studied, PPIV-1, was found by RT-PCR of RNA extracted from samples of deceased pigs from a slaughter house with conserved primers. Complete genomes of three viruses were then sequenced with primer walking strategy. Potential of mRNA editing of phosphoprotein gene was checked by cloning. Characterisation of genomic features, phylogentic analysis and estimation of divergence time were performed using different bioinformatics software tools. Results: RT-PCR for paramyxovirus gene fragment was positive in nasopharyngeal (3.1%) and rectal (0.7%) swab samples, but negative in other samples, namely, liver, lung and blood samples. Annotation of complete genome sequences showed PPIV-1 contain six major genes similar to other paramyxoviruses. Amino acid identities of PPIV-1 were highest with respiroviruses, especially human parainfluenza virus 1 (HPIV-1) and Sendai virus (SeV). Characteristics of intergenic regions and proteins and phylogenetic analysis also suggested PPIV-1 as a member of the genus Respirovirus, with a closer relationship with SeV and HPIV-1 than other respiroviruses. Estimation of divergence dates suggested the divergence time of all respiroviruses were earlier than the group of viruses comprising HPIV-1, SeV and PPIV-1. The Ka/Ks ratios of most coding regions in PPIV-1 were low, suggesting these genes were under purifying selection. Conclusion: The presence of PPIV-1 in mainly respiratory samples suggested a possible association with respiratory disease. A number of common genome characteristics, the phylogenetic analysis and divergence time estimation showed that PPIV-1 is a respirovirus more closely related to HPIV-1 and SeV than other respiroviruses. This suggested that there should be a subtype of 'group 1' viruses in the respiroviruses. The purifying selection in most genes supported swine as the primary host of PPIV-1. To summarise, PPIV-1 should be classified as a 'group 1' respirovirus with a possible association with respiratory disease in swine, its possibly primary host.