Identification and genomic characterization of a novel porcine parvovirus (PPV6) in China

Abstract

Background: Parvoviruses are classified into two subfamilies based on their host range: the Parvovirinae, which infect vertebrates, and the Densovirinae, which mainly infect insects and other arthropods. In recent years, a number of novel parvoviruses belonging to the subfamily Parvovirinae have been identified from various animal species and humans, including human parvovirus 4 (PARV4), porcine hokovirus, ovine partetravirus, porcine parvovirus 4 (PPV4), and porcine parvovirus 5 (PPV5).

Methods: Using sequence-independent single primer amplification (SISPA), a novel parvovirus within the subfamily Parvovirinae that was distinct from any known parvoviruses was identified and five full-length genome sequences were determined and analyzed.

Results: A novel porcine parvovirus, provisionally named PPV6, was initially identified from aborted pig fetuses in China. Retrospective studies revealed the prevalence of PPV6 in aborted pig fetuses and piglets(50% and 75%, respectively) was apparently higher than that in finishing pigs and sows (15.6% and 3.8% respectively). Furthermore, the prevalence of PPV6 in finishing pig was similar in affected and unaffected farms (i.e. 16.7% vs. 13.6%-21.7%). This finding indicates that animal age, perhaps due to increased innate immune resistance, strongly influences the level of PPV6 viremia. Complete genome sequencing and multiple alignments have shown that the nearly full-length genome sequences were approximately 6,100 nucleotides in length and shared 20.5%-42.6% DNA sequence identity with other members of the Parvovirinae subfamily. Phylogenetic analysis showed that PPV6 was significantly distinct from other known parvoviruses and was most closely related to PPV4.

Conclusion: Our findings and review of published parvovirus sequences suggested that a novel porcine parvovirus is currently circulating in China and might be classified into the novel genus Copiparvovirus within the subfamily Parvovirinae. However, the clinical manifestations of PPV6 are still unknown in that the prevalence of PPV6 was similar between healthy pigs and sick pigs in a retrospective epidemiological study. The identification of PPV6 within the subfamily Parvovirinae provides further insight into the viral and genetic diversity of parvoviruses.

Figure 1

Genome structure and phylogenetic analysis: bootstrapped neighbor-joining tree based on full-length genomes and NSP or VP amino acid sequences of PPV6 and the Parvoviridae . A. The solid line represents the DNA genome and the boxes represent the ORFs. The position and size of putative ORFs are indicated. B. A phylogenetic tree was constructed based on 5 near full-length genomes (6.1 kb) of PPV6 and 31 genomes from GenBank using amaximum-likelihood method (GTR + G + I) with bootstrap analysis of 1,000 replicates. C and D. Phylogenetic trees were constructed based on amino acid sequences of NSP and VP using a Poisson correction model with bootstrap analysis of 1,000 replicates. Phylogenetic analyses were conducted using the MEGA6.0 (www.megasoftware.net) program. Branches corresponding to partitions reproduced in <70% bootstrap replicates are collapsed. The evolutionary distance scale is shown at the bottom. The sequence of GM-densovirus (NC004286) is used as outgroup to root the tree. The asterisk indicates the new genus proposed by ICTV.

Figure 2

Sequence alignment of the putative phospholipase A2 motif of PPV6 with those of other parvoviruses. The conserved amino acids of the Ca²⁺ binding loop (YXGXR) and the catalytic residues (HD--Y) are indicated at the bottom of the alignment. The GenBank numbers of the sequences are indicated.