Molecular evolutionary genetic analysis of emerging parvoviruses identified in pigs

Parvoviruses infect a wide variety of vertebrates and arthropods and are associated with various clinical manifestations. Due to the advent of new sequence-independent PCR methods and high-throughput sequencing, several novel members of parvoviruses within the subfamily Parvovirinae were recently described. Several of these viruses do not fit in the current classification and others now have confusing or contradictory nomenclature because two or more names were used for similar or identical groups of parvoviruses or identical names were used for distinct virus groups. In this study, recently described vertebrate parvoviruses with emphasis on those identified in pigs were classified through phylogenetic analyses based on the sequences of their complete or near complete genomes, open reading frame (ORF) 1 (non-structural protein, NS1), ORF2 (capsid protein, VP1), and ORF3 (nuclear phosphoprotein, NP1) genes by using Bayesian Markov chain Monte Carlo (MCMC), Maximum Likelihood (ML) and Neighbor-Joining (NJ) methods. Among all available vertebrate parvovirus sequences, eight distinct clades were identified, corresponding to the five well established genera Parvovirus, Erythrovirus, Denpendovirus, Amdovirus and Bocavirus. Moreover, three novel clades were identified and tentatively designated as PARV4-like virus, novel clade 1 and novel clade 2. Parvoviruses in pigs were found to be distributed across four different clades including Parvovirus, Bocavirus, PARV4-like virus and the novel clade 2. All pig parvoviruses identified to date were organized based on the current analysis. The present analysis will assist to clarify the nomenclature of parvoviruses in pigs and facilitate future uniform assignment of names for new parvoviruses within the subfamily Parvovirinae.