Genome characterization of a novel porcine bocavirus

Abstract

Using a high-throughput DNA sequencing method, one DNA sequence (contig01006), suspected to belong to a novel porcine bocavirus (PBoV), was found with a high rate of detection (19.6 %) in fecal samples from healthy piglets. Moreover, a novel PBoV (tentatively named PBoV3C) with a nearly complete genome sequence (5235 bp) was identified. PBoV3C exhibits typical genome characteristics of bocaviruses and shows the highest genomic sequence identity (78 % to 81 %) to PBoV3A/B (PBoV3/4-UK) and PBoV3D/E (PBoV3/4-HK), respectively. Phylogenetic and recombination analysis indicated high diversity, prevalence and complexity among the PBoVs. The phospholipase A2 (PLA2) site of VP1 and the secondary structure of VP2 of PBoV3C were also analyzed. Additionally, we propose a uniform method of PBoV nomenclature based on the VP1 gene.

Fig. 1

Prediction of the structure of VP2 of PBoV3C. (red, αA helix; blue, β-barrel; green, DE-loop and HI-loop, which form a channel on the surface; white, variable regions; yellow, bilateral terminus)

Fig. 2

Phylogenetic analysis of viruses in the family Parvoviridae. The phylogenetic tree was generated from nearly full-length nucleotide sequences from members of the subfamilies Parvovirinae (genera Parvovirus, Erythrovirus, Dependovirus, Amdovirus, and Bocavirus) and Densovirinae, using the MEGA 4.1 software (neighbor-joining method with 1,000 bootstrap replicates). PBoV3C is indicated by a black circle. MVC, minute virus of canines; BPV, bovine parvovirus; HBoV, human bocavirus; PBoV-WUH1, porcine boca-like virus; GBoV, gorilla bocavirus; CslBoV, California sea lion bocavirus

Fig. 3

Phylogenetic relationships of three protein sequences (NS1, NP1, VP1) encoded by ORFs of bocaviruses. Phylogenetic trees of NS1 (a), NP1 (b) and VP1 (c) based on amino acid sequences were constructed by MEGA ver. 4.1 software (neighbor-joining method with 1,000 bootstrap replicates). PBoV3C is labeled with a black circle. MVC, minute virus of canines; BPV, bovine parvovirus; HBoV, human bocavirus; PBoV-WUH1, porcine boca-like virus; 6 V/7 V, partial Chinese porcine bocavirus sequences; GBoV, gorilla bocavirus; CslBoV, California sea lion bocavirus

Fig. 4

Putative recombination in the bocavirus NP1 region. Bootscan analysis using the complete NP1 gene sequence of PBoV cluster1 (PBoV-WUH1 and PBoV-H18) as the query sequence (SimPlot 3.5.1, F84 model; window size, 200 bp; step, 10 bp) on a nucleotide alignment, generated using Clustal_X2. PBoV cluster3 (PBoV3C, PBoV3/4-UK and PBoV3/4-HK) is indicated by a red line, and PBoV cluster2 (PBoV1/2-CHN and PBoV-A6) is indicated by a deep blue line