Detection and genotyping of porcine circovirus in naturally infected pigs by oligo-microarray

A rapid and reliable method for the identification of porcine circovirus (PCV) genotypes based on oligonucleotide microarray hybridization has been developed. The genotype-specific oligonucleotides (22–30 mer) immobilized on the surface of glass slides were selected to bind to the multiple target sites within the replication gene that are conserved among individual PCV genotypes. Cy5-labeled DNA targets were amplified in a PCR with primers common to both genotypes. The identification of PCV genotype was based on hybridization with several individual genotype-specific oligonucleotides. This approach combines the high sensitivity of PCR with the selectivity of DNA–DNA hybridization. The utility and feasibility of oligonucleotide microarray hybridization was evaluated by testing standard and 87 clinical isolates. Analysis of the specimens showed that this microarray-based method is capable of unambiguous identification of both genotypes and fivefold more sensitive than gel electrophoresis. Our results indicated that the oligonucleotide array is useful for the identification and discrimination of PCV from clinical isolates and specimens in a clinical laboratory.