Genome Sequence of a Highly Prevalent Porcine Partetravirus in Mainland China

Abstract

Partetravirus is a novel defined genus of animal parvoviruses. Here, we first report the genome sequence of porcine partetravirus strain JSNJ62, which is highly prevalent in mainland China. It will help in understanding the epidemiology and molecular characteristics of the porcine partetravirus.

GENOME ANNOUNCEMENT

Parvoviruses are members of the family Parvoviridae, which are small, nonenveloped icosahedral viruses, and can cause a broad spectrum of diseases in animals (3). Based on their host range, the family Parvoviridae is classified into two subfamilies: the Parvovirinae subfamily and the Densovirinae subfamily. The partetraviruses are among parvoviruses in the subfamily Parvovirinae, which includes the human partetravirus, bovine partetravirus, ovine partetravirus, and porcine partetravirus (PPtV) (1, 4–7).

Porcine partetravirus (PtV, also known previously as hokovirus) has been described in Hong Kong, Germany, and Romania in recent years. It has been shown to have a prevalence of 22.8% to 50.5% in healthy and diseased pigs and wild boars (1, 2, 5). Phylogenetic analysis based on the near-full-length genome indicated that the PPtV sequences of German and Romanian wild boars were closely related to the isolates from Hong Kong.

In this study, a PPtV strain JSNJ62 was first discovered and identified in piglet liver samples from a farm with high fever syndrome in mainland China. It was worth noting that there was more than a 58.6% infection rate in the piglets, which were less than 20 days old. It is thus necessary to analyze the genome sequence of PPtV/JSNJ62 and understand its molecular characteristics.

The genome was generated with PCR using five primers, which were designed from alignments of available animal PtV genomes. The PCR products were purified and cloned into pMD18-T vector (TaKaRa), and sequenced with an automated sequencer (Genetic Analyzer 3730XL; Applied Biosystems). The terminal sequences were acquired by using a rapid amplification of cDNA ends (RACE) kit (Clontech, Japan).

Because of the presence of hairpin structures, the terminal sequences of all animal PtVs have not yet been acquired successfully (1, 2, 5, 7). The genome of PPtV/JSNJ62 is a single-stranded DNA molecule comprising 5,069 bp, with a GC content of 51.41%. It possessed a genome organization typical of parvoviruses. It encodes two open reading frames (ORFs), ORF1 and ORF2. ORF1 encodes nonstructural protein NS1, and ORF2 encodes overlapping capsid proteins (VP1/VP2) and a small conserved putative protein. Interestingly, a continuous deletion of 5 nucleotides was found in the small noncoding gap, which was between the ORFs. It was a novel sequence characteristic of the porcine partetravirus.

The genome of the PPtV/JSNJ62 exhibited 97.4 to 99.1% nucleotide identity to those of other PPtVs. Phylogenetic analyses, based on the genome and the ORFs of the parvoviruses, indicated that PPtV/JSNJ62 showed a close relationship to the PPtVs and formed a novel cluster with known PPtVs. This indicated that the PPtVs has undergone an evolution in the continuous transmission. These data will facilitate future investigations of evolutionary characteristics and molecular pathogenesis of PPtVs.

Nucleotide sequence accession number.

The genome sequence of PPtV strain JSNJ62 was deposited in GenBank under accession no. JN990269.