Polymerase chain reaction-based genetic typing of Japanese porcine reproductive and respiratory syndrome viruses

Porcine reproductive and respiratory syndrome viruses (PRRSVs) are classified into 2 distinct genotypes: the North American type and the European type. The Japanese PRRSVs were genotyped by reverse transcriptase-polymerase chain reaction using the reported primer pairs that were either reactive to both types, specific to the North American type or specific to the European type. All the PRRSV genomes from 66 tissue homogenates or sera and 55 infectious viruses were of the North American type, whereas no European-type viral genome was detected. Two PCR primers specific to the North American type showed different detection efficiency. Half of the tissue samples and 15% of the infectious viruses were not detected with one primer pair, although all of them were detected with the other primer pair. Nucleotide sequencing analysis of the forward- and reverse primer-binding sites of the nonreactive viruses indicated that all these viruses had nucleotide mismatches within the 4 bases corresponding to the 3' end of the reverse primer. These mismatches appeared to be responsible for the nonreactivity of the former primers to these viruses.