Complete genome sequence of a porcine circovirus 2 strain isolated in central china.

We report here the complete genome sequence of the porcine circovirus type 2 (PCV2) XZBK strain, isolated from central China. This is the first report of a member of the 1B subgroup of PCV2b central China. This finding will help in understanding the epidemiology and molecular characteristics of PCV2.

GENOME ANNOUNCEMENT

Porcine circoviruses (PCVs) are circular single-stranded DNA viruses belonging to the genus Circovirus and the family Circoviridae, which contain porcine circovirus type 1 (PCV1) and type 2 (PCV2) (1). PCV1 does not induce disease in swine (2), while PCV2 is the etiological agent of postweaning multisystemic wasting syndrome (PMWS). This disease was first confirmed in Canada in 1997. Since then, it has brought great losses in pig production worldwide (3, 4). In 2001, PMWS associated with PCV2 infection in China occurred on many large pig farms in animals, and numerous PCV2 strains have been isolated since then (5–7).

PCV2 is one of the smallest DNA viruses infecting mammals, and its genome ranges from 1,766 to 1,768 nucleotides (nt). The PCV2 genome contains three major open reading frames (ORFs). ORF1 and ORF2 encode the replicase (Rep) protein and the viral capsid (Cap) protein, respectively, which perform two of the most elementary functions of the virus, copying and the successive packaging of the viral genome, and ORF3 encodes a protein that is involved in PCV2-induced apoptosis in vitro. PCV2 strains are divided into three PCV2 genotypes, PCV2a, PCV2b, and PCV2c (8). Recently, PCV2b has been the most prevalent strain in China (5, 7).

The PCV2 XZBK isolate was isolated from the intestine of a 4-week-old pig with naturally occurring diarrhea on a pig farm in Henan Province, central China. The whole genome of the PCV2 XZBK isolate was amplified by using the primers described by Fenaux et al. (9). The PCR products were purified and cloned into pMD18-T vector (TaKaRa Biotechnology, Dalian, China) and sequenced with an automated sequencer (3730xl Genetic Analyzer; Applied Biosystems). The result showed that the whole genome of the PCV2 XZBK strain is 1,767 nt in length, with a G+C content of 48.44%. XZBK contains at least three ORFs, encoding 2 major proteins (Rep and Cap). It has the sequence CCCCGC at nucleotides 262 to 267 of ORF2 and PR at amino acid positions 88 and 89 of ORF2. Thus, XZBK was classified in group 1. A comparison of genome sequences revealed that the PCV2 XZBK strain exhibited 95.8% to 99.3% nucleotide identity with other PCV2 strains in Henan Province and 95.6% to 99.2% with PCV2 genomes in other provinces in China. Phylogenetic analyses based on the genome of PCV2 strains indicated that XZBK together with PCV2b-1B (accession no. JF317566) from South Korea (10) was grouped in one cluster, and the genome of XZBK shared 99.7% nucleotide sequence identity to that of JF317566. There were only six nucleotide differences between the genomes of XZBK and JF317566. The nucleotide sequence and amino acid homologies between XZBK and PCV2b-1B (JF317566) were 99.6% and 100% in ORF1, respectively, while in ORF2, they shared 99.9% and 100% sequence homology at the nucleotide and amino acid levels, respectively. The results showed that the PCV2 XZBK strain belongs to the PCV2b-1B genotype.

Nucleotide sequence accession number.

The genome sequence of the PCV2 XZBK strain has been deposited in GenBank under accession no. KF926650.