Identification and Nearly Full-Length Genome Characterization of Novel Porcine Bocaviruses

Abstract

The genus bocavirus includes bovine parvovirus (BPV), minute virus of canines (MVC), and a group of human bocaviruses (HBoV1-4). Using sequence-independent single primer amplification (SISPA), a novel bocavirus group was discovered with high prevalence (12.59%) in piglet stool samples. Two nearly full-length genome sequences were obtained, which were approximately 5,100 nucleotides in length. Multiple alignments revealed that they share 28.7–56.8% DNA sequence identity with other members of Parvovirinae. Phylogenetic analyses indicated their closest neighbors were members of the genus bocavirus. The new viruses had a putative non-structural NP1 protein, which was unique to bocaviruses. They were provisionally named porcine bocavirus 1 and 2 (PBoV1, PBoV2). PBoV1 and PBoV2 shared 94.2% nucleotide identity in NS1 gene sequence, suggesting that they represented two different bocavirus species. Two additional samples (6V, 7V) were amplified for 2,407 bp and 2,434 bp products, respectively, including a partial NP1 gene and the complete VP1 gene; Phylogenetic analysis indicated that 6Vand 7V grouped with PBoV1 and PBoV2 in the genus of bocavirus, but were in the separate clusters. Like other parvoviruses, PBoV1, PBoV2, 6Vand 7V also contained a putative secretory phospholipase A2 (sPLA2) motif in the VP1 unique region, with a conserved HDXXY motif in the catalytic center. The conserved motif YXGXF of the Ca2+-binding loop of sPLA2 identified in human bocavirus was also found in porcine bocavirus, which differs from the YXGXG motif carried by most other parvoviruses. The observation of PBoV and potentially other new bocavirus genus members may aid in molecular and functional characterization of the genus bocavirus.

The Fecal Viral Flora of California Sea Lions

“…Related species of human bocaviruses in feces have since been reported and associated with gastroenteritis (3,26,29). Recently, bocavirus species were also identified in swine (6,12), gorilla (27), and chimpanzee (52). Here, bocaviruses were identified in 18 of the 47 California sea lion samples and were abundant in 7 samples (Ͼ500 reads).…”

Identification and genomic characterization of a novel porcine parvovirus (PPV6) in china

“…Furthermore, the conserved motifs of the Ca 2+ binding loop of PLA2 is the "YXGXR" motif in PPV6, rather than the "YXGXG" or "YXGXF" motif found in most parvoviruses [6]. The PLA2 activity of the alternate motif found in PPV6 needs further study.…”

“…Random detection of unknown virus genomic DNA or RNA from serum samples was performed using SISPA as previously described with some modifications [6]. To detect viral RNA, first-strand cDNA synthesis was performed using SuperScript™ III reverse transcriptase (Invitrogen, Carlsbad, CA, USA) primed with 5 pmol random hexamer primer 42°C for 1 h. The second-strand cDNA was then synthesized by adding 1 U of RNase H and 30 U of DNA polymerase I (Invitrogen) at 12°C for 1 h followed by 1 h at 22°C.…”

“…An additional ORF; i.e., ORF3, encodes an accessory protein and has been identified in some parvoviruses, such as NP1, an NSP only found in bocavirus and PPV4 [6,7]. In recent years, with the use of molecular assays and pathogen discovery tools, a number of novel parvoviruses belonging to the subfamily Parvovirinae have been identified in various animal species and humans, including human parvovirus 4 (PARV4), porcine hokovirus (PPV3), ovine partetravirus, PPV4, and PPV5 [6][7][8][9][10][11][12][13]. Among them, PPV3 and ovine partetravirus have been shown to have a close relationship to PARV4, and currently have been proposed to be classified into the genus Tetraparvovirus by the ICTV [3,4].…”

Complete Genomes of Three Human Bocavirus Strains from Children with Gastroenteritis and Respiratory Tract Illnesses in Jiangsu, China

“…HBoV has four different genotypes, HBoV 1 to 4, according to phylogenetic analysis, among which HBoV1 was first described in children with respiratory infections (1) and HBoV2, HBoV3, and HBoV4 were discovered subsequently, sharing a mean similarity of 80% with HBoV1 (2, 7). Recently, new bocavirus species were isolated from gorilla and swine and were most closely related to HBoV (3,6). In this study, two cases of gastroenteritis and one case of respiratory tract illness in three children Ͻ6 years old in Jiangsu, China, were determined to be positive for HBoV.…”