title: Co-existence of multiple strains of two novel porcine bocaviruses in the same pig, a previously undescribed phenomenon in members of the family Parvoviridae, and evidence for inter- and intra-host genetic diversity and recombination.
abstract: Despite the recent discovery of novel bocaviruses from porcine samples, their genetic evolution and diversity are poorly understood. This study reports the identification and complete genome characterization of two novel parvoviruses, porcine bocavirus 3 (PBoV3) and porcine bocavirus 4 (PBoV4), from various porcine tissues/samples, displaying marked intra- and inter-host genetic diversity, with recombination events. Bocaviruses were detected by PCR among 16.5 % (55/333) of porcine samples (lymph nodes, serum, nasopharyngeal and faecal samples) from healthy, sick or deceased pigs from farms and a slaughterhouse in Hong Kong. As marked nucleotide polymorphisms were observed in the partial VP1 sequences, complete VP1 genes from one nasopharyngeal and three faecal specimens were cloned and sequenced, which suggested the presence of two different bocaviruses and demonstrated significant intra- and inter-host genetic diversity. Complete genome sequences revealed the presence of two bocaviruses, PBoV3 and PBoV4, in a faecal and nasopharyngeal specimen, respectively, with two genotypes, PBoV4-1 and PBoV4-2, in the latter. Their genomes encoded three ORFs, characteristic of bocaviruses. Phylogenetic analysis showed that they were distantly related to other bocaviruses, forming a distinct cluster within the genus. Recombination analysis showed possible recombination events among VP1 sequences of PBoV4 strains from a faecal specimen, with two breakpoints identified (with a 68 and 71 bp region), suggesting that different strains/variants within the same host could have arisen from recombination. This is the first report describing marked sequence diversity and the co-existence of two viruses of the family Parvoviridae within the same host, which may have originated from and, in turn, facilitated recombination.
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.|Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR.|State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR.|Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Susanna K P
authors.initials: SKP
authors.lastname: Lau
authors.affiliation: Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR.|Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR.|State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR.|Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Patrick C Y
authors.initials: PCY
authors.lastname: Woo
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Cyril C Y
authors.initials: CCY
authors.lastname: Yip
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Kenneth S M
authors.initials: KSM
authors.lastname: Li
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Clara T Y
authors.initials: CTY
authors.lastname: Fu
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Yi
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.|State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR.|Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR.|Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR.
authors.forename: Kwok-Hung
authors.initials: KH
authors.lastname: Chan
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong SAR.|State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR.|Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR.|Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR.
authors.forename: Kwok-Yung
authors.initials: KY
authors.lastname: Yuen
mesh_terms: D000818:Animals; D052660:Bocavirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D016000:Cluster Analysis; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D016679:Genome, Viral; D006723:Hong Kong; D008969:Molecular Sequence Data; D010322:Parvoviridae Infections / Q000662:veterinary* / Q000821:virology; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013552:Swine; D013553:Swine Diseases / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D004279:DNA, Viral; D014764:Viral Proteins