Recombination analysis based on the complete genome of bocavirus
- Xingli Fu†1, 2,
- Xiaochun Wang†1,
- Bin Ni1,
- Hongxing Shen1,
- Hua Wang1,
- Xiaodan Zhang1,
- Shengxia Chen1,
- Shihe Shao1 and
- Wen Zhang1Email author
© Fu et al; licensee BioMed Central Ltd. 2011
Received: 15 November 2010
Accepted: 20 April 2011
Published: 20 April 2011
Bocavirus include bovine parvovirus, minute virus of canine, porcine bocavirus, gorilla bocavirus, and Human bocaviruses 1-4 (HBoVs). Although recent reports showed that recombination happened in bocavirus, no systematical study investigated the recombination of bocavirus. The present study performed the phylogenetic and recombination analysis of bocavirus over the complete genomes available in GenBank. Results confirmed that recombination existed among bocavirus, including the likely inter-genotype recombination between HBoV1 and HBoV4, and intra-genotype recombination among HBoV2 variants. Moreover, it is the first report revealing the recombination that occurred between minute viruses of canine.
Members of the genus Bocavirus are non-enveloped single-stranded DNA (ss-DNA) virus, which belong to the Parvoviridae family. The bocavirus genome is not segmented and contains a single molecule of linear, positive- or negative-sense DNA of 4,000-6,000 nucleotides in length . Known members of bocavirus include bovine parvovirus (BPV), minute virus of canine (MVC), porcine bocavirus (PBoV), gorilla bocavirus (GBoV), and Human bocaviruses 1-4 (HBoV1-4).
The MVC genome shares about 43% identity with BPV over the genome level [2, 3]. BPV was first identified in 1961 in samples from calves with diarrhea , while MVC was first isolated from canine fecal samples in 1970 . HBoV was first described in pooled nasopharyngeal aspirates from children with respiratory infections in 2005, and was provisionally categorized into the genus bocavirus . Subsequently, HBoV2, HBoV3, and HBoV4 were discovered, sharing a mean similarity of 80% with HBoV1, and all have been categorized into the genus bocavirus [6, 7]. Recently, new bocavirus species were isolated from gorilla and swine, and most closely related to HBoV [8, 9].
Although recently reports showed that recombination happened in bocavirus , no study has systematically investigated the recombination among bocavirus strains. In the present study, therefore, we analyzed the available complete bocavirus genome sequences in GenBank to elucidate the recombination among bocavirus strains.
The study sequences comprised all the 121 available complete genome sequences of bocavirus from GenBank dated September 2010. Sequences were firstly screened to exclude patented and artificial mutants, and then aligned in the ClustalW program . The alignment was manually adjusted for the correct reading frame. Sequences showing less than 1% divergence from each other were considered as the same. The remaining 54 BoV genomes included one GBoV, one BPV, two PBoVs, three MVCs, and 47 HBoVs.
Before phylogenetic analysis, multiple-alignment was performed in the ClustalW program. Phylogenetic trees were constructed using the neighbor-joining method and evaluated using the interior branch test method with Mega 4 software . Percent bootstrap support was indicated at each node. GenBank accession no. was indicated at each branch.
The remaining 54 bocavirus genomes were re-aligned in the ClustalW program. Detection of potential recombinant sequences, identification of potential parental sequences, and localization of possible recombination break points were determined using the Recombination Detection Program (RDP), GENECONV , BOOTSCAN , MaxChi , CHIMAERA , and SISCAN  methods embedded in RDP3 . A Multiple-comparison-corrected P-value cutoff of 0.05 was used throughout.
Results and Discussion
For RNA viruses, recombination has been shown to be an important feature of their evolution [21–23], and single-stranded DNA parvoviruses have been shown to have a mutation rate approaching that of RNA viruses . The HBoV sequences were previously considered to show very low protein and nucleotide sequence diversity . Recently, however, other 3 different genotypes (HBoV2-4) were discovered, which reveals that the HBoVs own the property of high sequence diversity. The present study provide the evidence that recombination was observed through complete bocavirus genome analyses, including the likely inter-genotype recombination between HBoV1 and HBoV4, and intra-genotype recombination between HBoV2 variants. As a matter of fact, a recent study indicated HBoVs coinfection was detected , which will increase the chance of recombination between baocavirus strains.
Taken together, this study confirmed that recombination existed among bocavirus, including the likely inter-genotype recombination between HBoV1 and HBoV4, and intra-genotype recombination among HBoV2 variants. It is the first report revealing the recombination that occurred between minute virus strains of canine.
This work was supported by the Professional Research Foundation for Advanced Talents of Jiangsu University under Grant No.10JDG044 and No.10JDG059.
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