Molecular characterization of SAT-2 foot-and-mouth disease virus isolates obtained from cattle during a four-month period in 2001 in Limpopo Province, South Africa

Foot-and-mouth disease (FMD) is an acute, highly contagious viral infection of domestic and wild cloven-hoofed animals. The virus is a single-stranded RNA virus that has a high rate of nucleotide mutation and amino acid substitution. In southern Africa the South African Territories (SAT) 1-3 serotypes of FMD virus are maintained by large numbers of African buffaloes (Syncerus caffer), which provide a potential source of infection for domestic livestock and wild animals. During February 2001, an outbreak of SAT-2 was recorded in cattle in the FMD control zone of South Africa, adjacent to the Kruger National Park (KNP). They had not been vaccinated against the disease since they form the buffer between the vaccination and free zones but in the face of the outbreak, they were vaccinated as part of the control measures to contain the disease. The virus was, however, isolated from some of them on several occasions up to May 2001. These isolates were characterized to determine the rate of genetic change in the main antigenic determinant, the 1D/2A gene. Nucleotide substitutions at 12 different sites were identified of which five led to amino acid changes. Three of these occurred in known antigenic sites, viz. the GH-loop and C-terminal part of the protein, and two of these have previously been shown to be subject to positive selection. Likelihood models indicated that the ratio of non-synonymous to synonymous changes among the outbreak sequences recovered from cattle was four times higher than among comparable sequences isolated from wildlife, suggesting that the virus may be under greater selective pressure during rapid transmission events.