GENOME ANNOUNCEMENT
Complete Genome Sequence of a Novel Porcine Parvovirus in China Xiao-Fang Dai,a,b Qiu-Ju Wang,a,b Shi-Jin Jiang,a,b and Zhi-Jing Xiea,b Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian, Shandong, China,a and Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, Shandong, Chinab
The porcine parvovirus JT strain (PPV-JT) was isolated from a piglet showing nonsuppurative myocarditis in Shandong, China, in 2010. The complete genomic sequence of PPV-JT, 4,941 bp long, was determined from clones made from replicative form (RF) DNA. The genomic analysis demonstrated that the PPV-JT might be involved in a recombination event, which will help us understand the molecular characteristics and evolutionary of PPV in China.
F
rom a worldwide perspective, porcine parvovirus (PPV) is considered a major cause of reproductive failure in swine and is found in almost all pig-breeding countries. Infection of pregnant gilts and sows with PPV results in embryonic death, mummification, stillbirths, and delayed return to estrus (3). Although infection with PPV is typically asymptomatic in swine of all ages, cutaneous lesions and nonsuppurative myocarditis in piglets also have been reported (2, 4). The JT strain of PPV (PPV-JT) was isolated from a piglet showing nonsuppurative myocarditis in Shandong, China. The fulllength genome of PPV-JT was determined from clones made from replicative form (RF) DNA and sequenced with an ABI Prism 3730 genetic analyzer, using the BigDye terminator cycle sequencing kit. The DNA sequences were compiled and edited using the Lasergene sequence analysis software package (DNASTAR, Madison, WI). Multiple sequence alignments were created with ClustalX version 2.1. Phylogenetic analyses were done using PHYLIP version 3.69. Neighbor-joining analysis was performed with the DNADIST and NEIGHBOR modules of PHYLIP version 3.69. Bootstrap analysis with 1,000⫻ replicates of the alignment was applied to the neighbor-joining method, using the SEQBOOT and CONSENSE modules of PHYLIP version 3.69. The trees were edited in MEGA4 (5). The nucleotide sequence of PPV was 4,941 bp long. Compared with NADL-2, PPV-JT was missing 67 bp in both the 3= end and the 5= terminal, respectively. A 127-bp direct repeat, which starts just 5 bases before the stop codon of the right open reading frame (ORF), was found in the gene sequence of PPV-JT. The region from bp 4475 to 4601 was identical to the region from bp 4602 to 4728, each containing 4 AATAA sites. We also found two small 24-bp repetitions (bp 4494 to 4518 and bp 4568 to 4591) inside the 127-bp repeat. Nucleotide sequence alignments, using the ClustalV method and a BLAST search in GenBank, demonstrated that the NS1 segment of PPV-JT had 98.2 to 99.9% identity among gene sequences available in GenBank, the NS2 segment had 97.9 to 100% identity, the NS3 segment 98.5 to 100% identity, the VP1 segment 98.6 to 99.9% identity, and the VP2 segment 98.3 to 99.8% identity, and all showed the highest homology with the corresponding genes from NADL-2 (1), respectively. The nucleotide sequences and the deduced amino acid sequences of each protein were investigated to examine the molecular characteristic of PPV-JT in detail. There was a Trp440Leu
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substitution in the NS1 coding region, and there was a Pro304Ser substitution in the VP2 coding region, corresponding to amino acid 454 of the VP1 protein. The NS1 gene phylogenetic analysis suggested that PPV-JT had a close relationship to the PPV China strain. However, the NS2 and NS3 genes had a close relationship to the PPV BQ strain. Phylogenetic analysis revealed that the VP1 and VP2 genes from PPV-JT were closely related to the corresponding genes from NADL-2. The phylogenetic analyses showed that the nonstructural coding genes had a different relationship to the reference genes, which suggested that the PPV-JT strain might be involved in a recombination event. This study has provided information that will perhaps help us gain further insight into the molecular and functional characterization of PPV. Nucleotide sequence accession number. The complete genome sequence of PPV-JT has been submitted to GenBank under accession no. JN968975. ACKNOWLEDGMENTS We thank Wang Guo-Ming and Wang Xiao-Wei for materials and helpful technical assistance and are grateful to Song Qian-Qian for excellent assistance with the preparation of the manuscript.
REFERENCES 1. Bergeron J, Menezes J, Tijssen P. 1993. Genome organization and mapping of transcription and translation products of the NADL-2 strain of porcine parvovirus. Virology 197:86 –98. 2. Bolt DM, Hani H, Müller E, Waldvogel AS. 1997. Non-suppurative myocarditis in piglets associated with porcine parvovirus infection. J. Comp. Pathol. 117:107–118. 3. Joo HS, Donaldson-Wood CR, Johnson RH. 1976. Observations of the pathogenesis of porcine parvovirus infection. Arch. Virol. 51:123–129. 4. Lager KM, Mengeling WL, Liu W. 1992. Comparison of the virulence of two isolates of porcine parvovirus in 72-day-old porcine fetuses. J. Vet. Diagn. Invest. 4:245–248. 5. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA 4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596 –1599.
Received 28 September 2012 Accepted 28 September 2012 Address correspondence to Zhi-Jing Xie,
[email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JVI.02689-12
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