Chronological and geographical variations in the small RNA segment of the teratogenic Akabane virus

Characterization of the small RNA segment of the teratogenic Akabane virus was performed to define the genetic heterogeneity and molecular epidemiology of the virus. The nucleotide and amino acid sequences were highly conserved among the Akabane virus isolates, irrespective of the year of isolation and geographical origin, except for a Kenyan strain MP496. On the basis of the nucleocapsid gene sequences of the segment, 170 field isolates were grouped into four distinct phylogenetic lineages. The Japanese isolates were divided into two major clusters, one containing the prototype strain JaGAr39 and strains isolated in the 1970s, 1988–1989, 1991, and 1994–1999, and the other containing strains isolated from 1982 to 1987, 1990, 1993, 1998, and 2000 to 2003 together with the Taiwanese and Israeli strains. The Asian strains seemed to have evolved in a common gene pool. The Australian and Kenyan strains were placed in the independent third and fourth clusters of the phylogenetic tree, respectively. No consecutive mutations have occurred on the small RNA segment of the Japanese isolates, indicating that the various genotypes of the virus might invade continuously from an exotic source and that certain viruses adaptable to the Japanese environment might spread transiently.