title: The implications of virus diversity within the SAT 2 serotype for control of foot-and-mouth disease in sub-Saharan Africa.
abstract: SAT 2 is the serotype most often associated with outbreaks of foot-and-mouth disease (FMD) in livestock in southern and western Africa and is the only SAT type to have been recorded outside the African continent in the last decade. Its epidemiology is complicated by the presence of African buffalo (Syncerus caffer), which play an important role in virus maintenance and transmission. To assess the level of genetic complexity of this serotype among viruses associated with both domestic livestock and wildlife, complete VP1 gene sequences of 53 viruses from 17 countries and three different host species were analysed. Phylogenetic analysis revealed eleven virus lineages, differing from each other by at least 20 % in pairwise nucleotide comparisons, four of which fall within the southern African region, two in West Africa and the remaining five in central and East Africa. No evidence of recombination between these lineages was detected, and thus we conclude that these are independently evolving virus lineages which occur primarily in discrete geographical localities in accordance with the FMD virus topotype concept. Applied to the whole phylogeny, rates of nucleotide substitution are significantly different between topotypes, but most individual topotypes evolve in accordance with a molecular clock at an average rate of approximately 0.002 substitutions per site per year. This study provides an indication of the intratypic complexity of the SAT 2 serotype at the continental level and emphasizes the value of molecular characterization of diverse FMD field strains for tracing the origin of outbreaks.
authors.affiliation: ARC-Onderstepoort Veterinary Institute, Exotic Diseases Division, Private Bag X5, Onderstepoort 0110, South Africa.|Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria 0002, South Africa.
authors.forename: A D S
authors.initials: ADS
authors.lastname: Bastos
authors.affiliation: Centre for Tropical Veterinary Medicine, University of Edinburgh, Edinburgh EH25 9RG, UK.
authors.forename: D T
authors.initials: DT
authors.lastname: Haydon
authors.affiliation: Laboratoire Central Veterinaire, BP 2295, Bamako, Mali.|ARC-Onderstepoort Veterinary Institute, Exotic Diseases Division, Private Bag X5, Onderstepoort 0110, South Africa.
authors.forename: O
authors.initials: O
authors.lastname: Sangaré
authors.affiliation: ARC-Onderstepoort Veterinary Institute, Exotic Diseases Division, Private Bag X5, Onderstepoort 0110, South Africa.
authors.forename: C I
authors.initials: CI
authors.lastname: Boshoff
authors.affiliation: Mammal Research Institute, Department of Zoology & Entomology, University of Pretoria, Pretoria 0002, South Africa.
authors.forename: J L
authors.initials: JL
authors.lastname: Edrich
authors.affiliation: Organization of African Unity/Inter-African Bureau for Animal Resources (OAU-IBR), PO Box 30786, Nairobi, Kenya.|ARC-Onderstepoort Veterinary Institute, Exotic Diseases Division, Private Bag X5, Onderstepoort 0110, South Africa.
authors.forename: G R
authors.initials: GR
authors.lastname: Thomson
mesh_terms: D017954:Africa South of the Sahara / Q000453:epidemiology; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002020:Buffaloes / Q000821:virology; D004279:DNA, Viral / Q000235:genetics; D004196:Disease Outbreaks / Q000662:veterinary; D019143:Evolution, Molecular; D005536:Foot-and-Mouth Disease / Q000453:epidemiology / Q000517:prevention & control / Q000821:virology; D029544:Foot-and-Mouth Disease Virus / Q000145:classification* / Q000235:genetics*; D014644:Genetic Variation; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D017386:Sequence Homology, Amino Acid; D012703:Serotyping; D014764:Viral Proteins / Q000235:genetics
chemical_list: D004279:DNA, Viral; D014764:Viral Proteins