Genetic analysis of the S1 gene of 4/91 type infectious bronchitis virus isolated in Japan.

S1 gene sequences for infectious bronchitis virus (IBV) strains of the 4/91 genotype (commonly called 793B) isolated from field outbreaks in Japan were analyzed to ascertain the relationship to 4/91 vaccine strain. Three field isolates (JP/Wakayama/2003, JP/Iwate/2005 and JP/Saitama/2006) from flocks not immunized with a 4/91 type live IBV vaccine and one isolate (JP/Wakayama-2/2004) from a flock immunized with a 4/91 type live vaccine were examined. The amino acid identities among JP/Wakayama/2003, JP/Iwate/2005 and JP/Saitama/2006 were about 98%, whereas the identities to the 4/91 vaccine strain and JP/Wakayama-2/2004 were about 90%. Three of the field isolates, JP/Wakayama/2003, JP/Iwate/2005 and JP/Saitama/2006, were classified into a cluster closely related to French and Spanish isolates, but different from the cluster including the vaccine and JP/Wakayama-2/2004. These results indicate that JP/Wakayama/2003, JP/Iwate/2005 and JP/Saitama/2006 were derived from foreign field isolates, but not from the vaccine strain. On the other hand, the S1 gene of JP/Wakayama-2/2004 revealed high sequence similarity with that of the 4/91 vaccine strain and appeared to be a vaccine-like virus derived from a vaccine. The field isolates of 4/91 genotype IBV could be distinguished from other genotypes by using the BalI and Pst I enzymes in addition to the polymerase chain reaction (PCR) -restriction fragment length polymorphism (RFLP) methods of Mase et al. [16] using Hae II and EcoR I enzymes. Furthermore, the 4/91 vaccine strain and vaccine-like isolate (JP/Wakayama-2/2004) could be differentiated from the other field isolates by Bgl II digestion. This method, therefore, would assist in identification of field isolates of the 4/91 genotype as outbreaks of IBV in vaccinated flocks.