Abstract
We report here the complete genomic sequence of a novel porcine circovirus type 2 (PCV2) strain, which is supposed to be the result of natural genetic recombination between the ORF1 gene of genotype PCV2b-1B and the ORF2 gene of PCV2b-1C. Further analyses revealed that this novel PCV2 strain arose from recombination between PCV2a and PCV2b strains within the ORF2 gene. To our knowledge, this is the first report of both inter- and intragenotype PCV2 gene rearrangement in the field, and it will help in understanding the epidemiology and molecular characteristics of porcine circovirus type 2(PCV2) in southern China.
GENOME ANNOUNCEMENT
Porcine circovirus type 2 (PCV2) has been associated with several disease outcomes in swine, primarily postweaning multisystemic wasting syndrome (PMWS) and porcine dermatitis nephropathy syndrome (PDNS) (1). PCV2b was the predominant genotype circulating in China from 2009 to 2010, and PCV2b-1C was an emerging predominant subtype (2). PCV2b is more prevalent than PCV2a in porcine circovirus-associated disease (PCVAD) cases, and in vaccinated herds PCV2b circulation is common (3).
In April 2012, PCV2 was isolated from a commercial swine farm with an outbreak of PDNS in nursery pigs in Guangdong Province, southern China. Subsequently, nucleotide sequences were amplified through reverse transcription-PCR (RT-PCR.) The complete sequence was obtained through sequencing. The isolate was identified as PCV2 and named PCV-Y4.
Sequence analysis showed that the full genomic length of PCV-Y4 is 1,767 nucleotides (nt). The coding region of PCV-Y4 includes three open reading frames (ORFs). PCV-Y4 has the sequence CCCCTC at nucleotides 262 to 267 of ORF2 and PL at amino acid positions 88 and 89 of ORF2. Thus, PCV-Y4 was classified in group 1, but it is located in neither PCV2b-1C nor PCV2b-1A1B. It is classified in a new gene cluster on a distinct branch that is located between PCV2b-1C and PCV2b-1A1B in the phylogenetic trees based on the complete genome. This novel cluster may result from recombination between the ORF1 gene of genotype PCV2b-1B and the ORF2 gene of PCV2b-1C.
The nucleotide sequence and amino acid homologies between PCV-Y4 and PCV2b-1B (JF317566.1) are 99.6% and 100% in ORF1, respectively, while in ORF2 they share 98.2% and 97.4% sequence homology at the nucleotide and amino acid levels, respectively.
Amino acid sequence analysis showed that the most variable region of the capsid protein of PCV-Y4 is encoded in ORF2. ORF2 of PCV-Y4 contains 702 nt, encoding a protein of 234 amino acids, one amino acid less than that of HM038030 (PCV2b-1C). Also, the cap of AF109398 (PCV2a-2A) and AB072302 (PCV2a-2A) has 233 amino acids. Positions 47 to 91, 121 to 136, and 185 to 206 are the hypervariable region of the cap. There are only five positions that differ between the cap of PCV-Y4 and that of HM038030 (PCV2b-1C). W and H are at positions 40 and 194, and the point mutations are reported the first time. More interestingly, G is present at position 169, which is different from the sequence of HM038030 (PCV2b-1C) but is the same as the sequences of AF109398 (PCV2a-2A) and AB072302 (PCV2a-2A). These results showed that both inter- and intragenotype recombination may exist in PCV-Y4.
Therefore, continuing surveillance of porcine circovirus type 2 in the field is critical to understanding the genesis and emergence of future pandemic strains in southern China.
Nucleotide sequence accession number.
The GenBank accession number for the genome sequence of PCV-Y4 is JX294717.
ACKNOWLEDGMENTS
This work was supported by the International Sci &Tech Cooperation Program (2010DFB33920) and the Modern Agricultural Industry Technology System (CARS-36).
The funding organizations had no role in the study design, data collection and analysis, ownership of the materials, or preparation of the manuscript.
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