Analysis of open reading frame 5 in Japanese porcine reproductive and respiratory syndrome virus isolates by restriction fragment length polymorphism

For the epidemiological survey of porcine reproductive and respiratory syndromes virus (PRRSV) isolated in Japan, the open reading frame (ORF) 5 gene of 37 field isolates in Chiba prefecture from 1991 to 1999 were analyzed by restriction fragment length polymorphism (RFLP). Reverse tanscription-polymerase chain reaction (RT-PCR) amplifying the ORF 5 gene detected 35 field isolates except for 2 isolates. RFLP analysis with MluI, HincII, SacH, HaeIII and MspI demonstrated that 35 field isolates were divided into 14 distinct codes and 34 isolates were distinguished from VR2332-derived modified live PRRSV vaccine, indicating the existence of genetic diversity in PRRSV field isolates in Japan. Only one strain 98-4A had an RFLP pattern identical to the vaccine strain. Nine out of the 35 field isolates (25.7%) had the RFLP code 1-3-2-1-1 and these patterns occurred throughout the examination period. This suggests that these isolates are the prevailing strain of PRRS in Chiba prefecture. RFLP with 5 enzymes demonstrated that various strains existed in the same year, and that there were different codes on the same farm according to the year. These observations indicate that there is a genetic variation among field isolates in very limited regions and some viruses possess the ability to cause their own genomic substitutions within a herd in a short time.