Emergence of a new strain of type O foot-and-mouth disease virus: its phylogenetic and evolutionary relationship with the PanAsia pandemic strain.

In India, Foot-and-mouth disease virus (FMDV) serotype O has been associated with more than 75% of the outbreaks. Previous studies with this serotype have indicated that the viruses circulating in India belong to a single genotype. Recent (February 2001) FMD epidemics in Europe have focussed global attention on the source of the virus and have been traced to a strain, PanAsia (serotype O), which is present in India since 1990. In this study, to further characterize the isolates belonging to the PanAsian strain, we sequenced the complete VP1-encoding (1 D) gene for 71 FMDV serotype O isolates from India recovered from the field outbreaks during the last 4 decades (1962-2001). All the isolates in the tree were distributed in to three major branches (designated as A, B and C); the branch C is further divided into four groups (I-IV), of which the group IV belongs to the PanAsia strain. Furthermore, we show that the PanAsia strain has been circulating endemically since 1982 (not 1990 as reported earlier) and has been the most dominant outbreak strain in the recent years and distributed at least in 17 states of the country. During the year 2001, another new group (group III) of virus with genetic divergence of 5.4-11.1% at nucleotide level from the PanAsia strain is found to co-circulate endemically, and is slowly replacing it. At amino acid level this strain differed from PanAsia strain at five amino acid positions in the VP1. Although these strains are divergent at nucleotide level, they maintained a good antigenic relationship with one of the vaccine strains (IND R2/75) widely used in the country. Given the ability of the PanAsia virus to persist, spread and to outcompete other strains, the present trend could be of serious concern as the newly emerging virus is replacing it. If this is true, then there is another equally divergent strain as PanAsia that may pose a serious threat to the global dairy and meat industries.