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. 2015 Jul 24:4:370.
doi: 10.1186/s40064-015-1155-8. eCollection 2015.

A novel porcine bocavirus harbors a variant NP gene

Sung J Yoo  1 , Sun Young Sunwoo  2 , Seong Sik Ko  1 , Sang H Je  1 , Dong Uk Lee  1 , Young S Lyoo  1
Affiliations

A novel porcine bocavirus harbors a variant NP gene

Sung J Yoo et al. Springerplus. .

Abstract

Background: Porcine bocavirus is classified within the genus Bocaparvovirus, family Parvoviridae. Unlike other parvoviruses, the members of genus Bocaparvovirus (bocaparvoviruses) encode an additional open reading frame (NP1). Many strains of PBoVs have been identified in domestic pigs and recognized as a potential emerging pathogen causing respiratory and gastrointestinal disease.

Findings: A new strain of porcine bocavirus (PBoV) that harbored the shortest NP1 gene among all currently characterized PBoVs (provisionally named as 'PBoV-KU14') was detected in domestic pigs. Almost the complete genome sequence was obtained, approximately 4,630 nucleotides in lengths with putative NS1, NP1, and VP1/2 genes of 1,908, 600, 1,851 bp, respectively. Phylogenetic and comparative analysis was performed using protein and nucleotide sequences. It was revealed that PBoV-KU14 belongs to the genus Bocaparvovirus and species Ungulate bocaparvovirus 4. However, phylogenetic incongruence was observed among species classifications based on the NS1, NP1 and VP1/2 proteins, which indicates a probability of crossover recombination. Conserved protein domains unique for genus Bocaparvovirus in NP1, VP1 protein were also detected.

Conclusion: NP1 gene truncation supposed to be caused by cross over recombination was detected in a new strain of PBoV (PBoV-KU14). Considering high rates of substitution and recombination in parvovirus, periodic surveillance study to monitor genomic variation and find new strainsof PBoVs seems to be needed.

Keywords: NP1 gene truncation; Phylogenetic incongruence; Porcine bocavirus; Recombination; Surveillance.

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Figures

Figure 1
Figure 1
Phylogenetic relationships between viruses belonged to the family Parvoviridae. The phylogenetic tree was generated based on nearly complete genome sequences from members of subfamilies Parvovirinae (genera Erythroparvovirus, Tetraparvovirus, Dependoparvovirus, Bocaparvovirus, Copiparvovirus, Aveparvovirus, Amdoparvovirus, Protoparvovirus), using the neighbor-joining method. Numbers at the nodes indicate the values of 1,000 bootstrap analysis. PBoV-KU14 is marked by a diamond. BPV Bovine parvovirus, CBoV canine bocavirus, CMV Canine minute virus, CslBoV California sea lion bocavirus, FBoV feline bocavirus, GboV bocavirus gorilla, HBoV human bocavirus and PBoV porcine bocavirus.
Figure 2
Figure 2
Phylogenetic relationships between viruses belonging to the genus Bocaparvovirus. The phylogenetic tree was generated based on protein sequences of NS1 (a), NP1 (b), VP1/2 (c), using the neighbor-joining method. Numbers at the nodes indicate the values of 1,000 bootstrap analysis. PBoV-KU14 is marked by a black diamond.
Figure 3
Figure 3
Conserved domain in NP1 protein (a) and expected protein motif in VP1u protein (b).
Figure 4
Figure 4
Comparison of PBoV-KU14 from 2,036 to 2,382 bp with the viruses of Ungulate bocaparvovirus3,4 using Bioedit with ClustalW. Conserved residues are indicated above the alignments. The numbers indicated by vertical bars indicate the sequences of PBoV-KU14; the location where the suspected original start codon was changed to ACA and the start codon of NP1 gene start are marked by asterisks.
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