GENOME ANNOUNCEMENT
Complete Genome Sequence of a Novel Species of Porcine Bocavirus, PBoV5 Bin Li,a Junjie Ma,a Shaobo Xiao,b Liurong Fang,b Songlin Zeng,b Libin Wen,a Xuehan Zhang,a Yanxiu Ni,a Rongli Guo,a Zhengyu Yu,a Junming Zhou,a Aihua Mao,a Lixin Lv,a Xiaoming Wang,a and Kongwang Hea Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, China,a and Division of Animal Infectious Diseases, State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Chinab
Porcine bocavirus 5 is a novel porcine bocavirus species found in a pig with clinical diarrhea from a farm in China. Here, we report the complete genome sequence of strain PBoV5/JS677, which will help toward understanding the molecular and evolutionary characteristics of the porcine bocavirus.
P
arvoviruses are members of the family Parvoviridae and can cause a broad spectrum of diseases in animals (8). The family Parvoviridae is classified into two subfamilies: the Parvovirinae subfamily and the Densovirinae subfamily. Bocaviruses are unique among parvoviruses in the subfamily Parvovirinae, which includes the bovine parvoviruses, canine minute viruses, gorilla bocavirus, four species of human bocaviruses, and porcine bocavirus (PBoV) (1, 2, 5, 6, 8, 9, 10, 13). In 2009, the porcine bocavirus was first discovered in Sweden (3, 4). Subsequent studies reported the nearly complete genome characterization of two species of PBoVs in China, PBoV1 and PBoV2 (7, 12, 15–17). In recent studies, two new species of porcine bocaviruses (PBoV3 and PBoV4) were discovered in Northern Ireland and Hong Kong (11, 14). In this study, a novel species of porcine bocavirus, PBoV5, was discovered and identified in piglet stool samples from a farm in China where a piglet had clinical diarrhea. Six pairs of oligonucleotide primers to amplify regions of the PBoV5/JS677 genomes were designed from alignments of available PBoV genomes. The PCR products were purified and cloned into the pMD18-T vector (TaKaRa) and sequenced with an ABI3730XL genome sequencer. The terminal sequences were acquired by using a kit for rapid amplification of cDNA ends (RACE) (Clontech, Japan). The genome of PBoV5/JS677 is a single-stranded DNA molecule comprising 5,076 bp, with a GC content of 50.69%. It had three putative open reading frames (ORFs) encoding two nonstructural proteins (NS1 and NP1) and two structural proteins (VP1 and VP2). Phylogenetic analyses based on the genome and the ORFs indicated that PBoV5/JS677 was distantly related to other porcine bocaviruses, forming a distinct cluster within the genus Bocavirus. Sequence analysis showed that the genome of PBoV5/JS677 was 48.7 to 86.3% homologous to other PBoVs. The NS1 and NP1 genes of the PBoV5/JS677 shared 48.7 to 86.2% and 31.9 to 82.1% sequence identity, respectively, with the nonstructural genes of other porcine bocaviruses. Under the existing criteria for classification of bocaviruses by the International Committee on Taxonomy of Viruses (ICTV), species are defined as ⬍95% homologous nonstructural gene DNA sequence (http://www. ictvdb.org/). Therefore, PBoV5/ JS677 should be classified as a prototype virus of a new porcine bocavirus species. These data will facilitate future investigations of evolutionary characteristics and molecular pathogenesis of PBoV.
1286
jvi.asm.org
Nucleotide sequence accession number. The complete genome sequence of PBoV5 strain JS677 was deposited in GenBank under accession no. JN831651. ACKNOWLEDGMENTS This work was supported by the Special Fund for Independent Innovation of Agricultural Science and Technology in Jiangsu Province [CX (11) 4043], the “863” Project (2011AA10A208), and the National Natural Sciences Foundation of China (31001066).
REFERENCES 1. Allander T, et al. 2005. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc. Natl. Acad. Sci. U. S. A. 102: 12891–12896. 2. Anderson LJ. 2007. Human bocavirus: a new viral pathogen. Clin. Infect. Dis. 44:911–912. 3. Blomstrom AL, et al. 2009. Detection of a novel porcine boca-like virus in the background of porcine circovirus type 2 induced postweaning multisystemic wasting syndrome. Virus Res. 146:125–129. 4. Blomstrom AL, et al. 2010. Studies of porcine circovirus type 2, porcine boca-like virus and torque teno virus indicate the presence of multiple viral infections in postweaning multisystemic wasting syndrome pigs. Virus Res. 152:59 – 64. 5. Carmichael L. 2004. Recent advances in canine infectious diseases, p 25–30. International Veterinary Information Service, Ithaca, NY. 6. Chen KC, et al. 1986. Complete nucleotide sequence and genome organization of bovine parvovirus. J. Virol. 60:1085–1097. 7. Cheng WX, et al. 2010. Identification and nearly full-length genome characterization of novel porcine bocaviruses. PLoS One 5:e13583. 8. Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (ed). 2005. Virus taxonomy. Eighth report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, San Diego, CA. 9. Kapoor A, et al. 2009. A newly identified bocavirus species in human stool. J. Infect. Dis. 199:196 –200. 10. Kapoor A, et al. 2010. Identification and characterization of a new bocavirus species in gorillas. PLoS One 5:e11948. 11. Lau SK, et al. 2011. 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 intrahost genetic diversity and recombination. J. Gen. Virol. 92:2047–2059.
Received 17 October 2011 Accepted 24 October 2011 Address correspondence to Kongwang He,
[email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JVI.06589-11
0022-538X/12/$12.00
Journal of Virology p. 1286 –1287
Genome Announcement
12. Li B, et al. 2011. Development of a novel TaqMan-based real-time PCR assay for the detection of porcine boca-like virus (Pbo-likeV). Virol. J. 8:357. 13. Manteufel J, Truyen U. 2008. Animal bocaviruses: a brief review. Intervirology 51:328 –334. 14. McKillen J, et al. 2011. Isolation in cell cultures and initial characterisation of two novel bocavirus species from swine in Northern Ireland. Vet. Microbiol. 152:39 – 45.
January 2012 Volume 86 Number 2
15. Shan TL, et al. 2011. Genomic characterization and high prevalence of bocaviruses in swine. PLoS One 6:e17292. 16. Zeng SL, et al. 2011. Complete coding sequences and phylogenetic analysis of porcine bocavirus (PBoV). J. Gen. Virol. 92:784 –788. 17. Zhai SL, et al. 2010. High prevalence of a novel porcine bocavirus in weanling piglets with respiratory tract symptoms in China. Arch. Virol. 155:1313–1317.
jvi.asm.org 1287
