Complete coding sequences and phylogenetic analysis of porcine bocavirus

Abstract

Here we report, for the first time, the nearly full-length genome sequence of porcine bocavirus (PBoV), a recently discovered parvovirus from pigs. Phylogenetic trees based on this genome sequence showed that PBoV belongs to the branch containing the genus Bocavirus, which comprises canine minute virus (CnMV), bovine parvovirus, gorilla bocavirus and human bocavirus (HBoV), and was most closely related to the group containing CnMV. PBoV was predicted to contain three potential ORFs encoding the non-structural protein NS1, the characteristic NP1 protein and the capsid protein VP1/VP2, with an organization similar to that of known bocaviruses. Interestingly, the NS1 gene of PBoV was more similar in length to the homogeneous gene found in HBoV than to those of other known bocaviruses. In addition, highly conserved unique splicedonor and -acceptor sites were identified in the NS1 gene of HBoV and PBoV.The family Parvoviridae is classified into two subfamilies: the subfamily Parvovirinae, which infects vertebrates, and the subfamily Densovirinae, which infects arthropods. Based on a report published by the International Committee on Taxonomy of Viruses (ICTV), the subfamily Parvovirinae is divided into five genera: Parvovirus, Erythrovirus, Dependovirus, Amdovirus and Bocavirus (Tattersall et al., 2005). Recently, Hokovirus was proposed as a new genus of the subfamily Parvovirinae (Adlhoch et al., 2010;Lau et al., 2008).Bocavirus, one genus of the subfamily Parvovirinae, is a non-enveloped, autonomously replicating, single-stranded DNA virus containing a genome of approximately 5 kb in length, and has close relationships with respiratory and enteric infections in humans and animals (Allander et al., 2005;Chen et al., 1986Chen et al., , 1988 Chen et al., , 2010 Kapoor et al., 2010a, b;Manteufel & Truyen, 2008;Schwartz et al., 2002). The genus Bocavirus comprises four members: bovine parvovirus (BPV), canine minute virus (CnMV), human bocavirus (HBoV) and gorilla bocavirus (GBoV), and has gained special attention because of HBoV, which causes respiratory diseases in children. In the field of veterinary medicine, BPV and CnMV were discovered in the 1960s and they share about 40 % sequence identity (Schwartz et al., 2002).Using random amplification and large-scale sequencing technology, a novel porcine parvovirus was recently discovered in Swedish pigs with post-weaning multisystemic wasting syndrome (PMWS) (Blomström et al., 2009). Based on partial nucleotide sequencing, this novel porcine parvovirus was proposed to be a porcine boca-like virus (PBoV-like). Subsequent studies revealed the high prevalence of this novel PBoV-like in weaning piglets with respiratory tract symptoms or PMWS, and even in pigs without PMWS (Blomström et al., 2010;Zhai et al., 2010). However, to date, the complete genomic sequence for PBoV-like has not been reported.In this study, we first detected the prevalence of this novel PBoV-like from clinical samples collected in central China. Using an established PCR, which amplifies a 496 bp fragme...

Genetic detection and analysis of porcine bocavirus type 1 (PoBoV1) in European wild boar (Sus scrofa)

“…The full genome of this virus was not obtained at that time, only a 1879 nucleotide (nt) long sequence, but based on similarities with the other bocavirus sequences it was named porcine boca-like virus (PBo-likeV). A very recent study of PBo-likeV reported the nearly full-length genome of this virus [13] and phylogenetic analysis confirmed that PBo-likeV belonged into the Bocavirus genus. A tentative classification of the newly discovered porcine bocaviruses was proposed by Zhang et al [14] grouping the six reported porcine bocaviruses into four species: PoBoV1 (porcine boca-like virus or PBoLV), PoBoV2 (porcine parvovirus 4 or PPV4), PoBoV3 (PBoV1/PBoV2), and PoBoV4 (6V/ 7V).…”

Evolutionary, epidemiological, demographical, and geographical dissection of porcine bocavirus in China and America

“…Individual infection of PBoV usually causes no apparent clinical signs, and the co-infection of PBoV could make the clinical signs more obvious (Kesebir et al, 2006). Many scientists have also reported that PBoV exhibit varying prevalence rates with a wide range from 1.5% to 88% in pig samples from different regions (Blomstrom et al, 2009(Blomstrom et al, , 2010Zhai et al, 2010;Cadar et al, 2011;Li et al, 2011;McKillen et al, 2011;Shan et al, 2011a;Zeng et al, 2011;Zhang et al, 2011). In the present manuscript, compared with other organs in Chinese samples, the spleen (20.8%) and inguinal lymph node (27.2%) have much higher positive rates, suggesting that they are organs in which PBoV replication likely easily takes place.…”

“…a highly conserved alternative splice site and a putative secretory phospholipase A2 (sPLA2) motif in the NS1 and VP1 genes, respectively Zeng et al, 2011). PBoV has a much higher infection rate in diseased pigs than in healthy pigs, and post-weaning piglets are often co-infected with PCV2, PRRSV and PTTV2, which had a significantly higher prevalence in the PBoVpositive samples than that in the PBoV-negative samples .…”

Complete Genome Sequence of a Novel Species of Porcine Bocavirus, PBoV5

“…Subsequent studies reported the nearly complete genome characterization of two species of PBoVs in China, PBoV1 and PBoV2 (7,12,(15)(16)(17). In recent studies, two new species of porcine bocaviruses (PBoV3 and PBoV4) were discovered in Northern Ireland and Hong Kong (11,14).…”