Abstract
Here, we report a novel porcine circovirus type 2a (PCV2a) strain with 11 nucleotides (nt) inserted in the origin of genome replication (Ori). This is the first report of a PCV2a strain with nucleotide insertion in Ori. Our study will help further epidemiological studies and extend our knowledge of evolutionary characteristics of PCV2.
GENOME ANNOUNCEMENT
The essential etiological agent of porcine circovirus diseases (PCVD), porcine circovirus type 2 (PCV2), is a nonenveloped virus possessing a circular, single-stranded ambisense DNA genome of 1,766 to 1,768 nucleotides (nt) in length in general (8, 10). PCV2 strains are divided into three PCV2 genotypes, PCV2a, PCV2b, and PCV2c (7). The PCV2 genome contains two major open reading frames (ORFs), ORF1 encoding replication-related protein (Rep and Rep′) (2) and ORF2 encoding capsid protein (Cap) (6). As a circular genome, there are two intergenic regions between ORF1 and ORF2. The origin of PCV2 genome replication (Ori) was located in the larger intergenic region (4, 5). There are some motifs that are of significant importance for virus replication through interaction with Rep and Rep′ in Ori (3, 4, 9). Ori is also a relatively conserved region of the PCV2 genome. Here, we report the complete genomic sequence of a novel PCV2a strain, 10JS-2, that was characterized by 11-nt insertion.
PCV2 strain 10JS-2 was accidentally isolated from a serum sample in China. Total DNA was extracted from cell culture, and the whole genome of PCV2 was generated by the PCR method using a pair of primers (1). The PCR products were purified and cloned into pGEM-T Easy vector (Promega) and sequenced with an automated sequencer (genetic analyzer 3730XL; Applied Biosystems).
The complete genomic sequence of the 10JS-2 strain was found to be 1,779 nt in length. Phylogenetic analysis revealed that 10JS-2 belongs to genotype PCV2a. Therefore, we inferred that 10JS-2 is probably derived from PCV2a strains with the 11-nt insertion in Ori. PCV2 strain Fh16 (GenBank accession no. AY321993) (France) and PCV2 strain DK475case (GenBank accession no. EF565360) (Denmark) were also been reported to contain an 11-nt insertion in Ori. However, Fh16 and DK475case belonged to PCV2b genotype. Remarkably, 11-nt insertion in Ori was unique for 10JS-2 compared with the other PCV2a strains. Moreover, the 11-nt insertion of 10JS-2 was also different from that of Fh16 (GenBank accession no. AY321993) (France) and DK475case (GenBank accession no. EF565360) (Denmark).
Previous studies have indicated that the origin of PCV2 genome replication was located within the larger intergenic region between ORF1 and ORF2. A characteristic of PCV2 Ori is a stem-loop structure for rolling-circle melting-pot replication. Adjacent to the 3′ region downstream of the stem-loop structure, hexamer motifs serve as binding sites for the replicases. However, the insertion of 11 nt in strain 10JS-2 leads to one more hexamer motif in Ori region compared with normal PCV2a strains.
PCV2 strain 10JS-2 described here is the first complete genomic sequence containing 11-nt insertion, isolated from the naturally PCV2-infected pig, which will contribute to further studies focusing on the molecular evolution of emerging PCV2 strains.
Nucleotide sequence accession number.
The complete genome sequence of PCV2 strain 10JS-2 has been deposited in GenBank under accession no. JQ806749.
ACKNOWLEDGMENT
This study was supported by a grant from Modern Agricultural Industry Technology System Programs (GWZJ-2009-05).
REFERENCES
- 1. Cai L, et al. 2012. Identification of an emerging recombinant cluster in porcine circovirus type 2. Virus Res. 165:95–102 [DOI] [PubMed] [Google Scholar]
- 2. Cheung AK. 2003. The essential and nonessential transcription units for viral protein synthesis and DNA replication of porcine circovirus type 2. Virology 313:452–459 [DOI] [PubMed] [Google Scholar]
- 3. Cheung AK. 2004. Identification of an octanucleotide motif sequence essential for viral protein, DNA, and progeny virus biosynthesis at the origin of DNA replication of porcine circovirus type 2. Virology 324:28–36 [DOI] [PubMed] [Google Scholar]
- 4. Finsterbusch T, Mankertz A. 2009. Porcine circoviruses-small but powerful. Virus Res. 143:177–183 [DOI] [PubMed] [Google Scholar]
- 5. Mankertz A, Persson F, Mankertz J, Blaess G, Buhk HJ. 1997. Mapping and characterization of the origin of DNA replication of porcine circovirus. J. Gen. Virol. 71:2562–2566 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Nawagitgul P, et al. 2000. Open reading frame 2 of porcine circovirus type 2 encodes a major capsid protein. J. Gen. Virol. 81:2281–2287 [DOI] [PubMed] [Google Scholar]
- 7. Olvera A, Cortey M, Segales J. 2007. Molecular evolution of porcine circovirus type 2 genomes: phylogeny and clonality. Virology 357:175–185 [DOI] [PubMed] [Google Scholar]
- 8. Shang SB, et al. 2009. Fine mapping of antigenic epitopes on capsid proteins of porcine circovirus, and antigenic phenotype of porcine circovirus type 2. Mol. Immunol. 46:327–334 [DOI] [PubMed] [Google Scholar]
- 9. Steinfeldt T, Finsterbusch T, Mankertz A. 2001. Rep and Rep′ protein of porcine circovirus type 1 bind to the origin of replication in vitro. Virology 291:152–160 [DOI] [PubMed] [Google Scholar]
- 10. Todd D, et al. 2005. Family Circoviridae, p 327–334 In Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA. (ed), Virus taxonomy. Eighth report of the International Committee on Taxonomy of Viruses Elsevier, London, United Kingdom [Google Scholar]