title: Evolutionary analysis of serotype A foot-and-mouth disease viruses circulating in Pakistan and Afghanistan during 2002-2009.
abstract: Foot-and-mouth disease (FMD) is endemic in Pakistan and Afghanistan. Three different serotypes of the virus, namely O, A and Asia-1, are responsible for the outbreaks of this disease in these countries. In the present study, the nucleotide-coding sequences for the VP1 capsid protein (69 samples) or for all four capsid proteins (P1, seven representative samples) of the serotype A FMD viruses circulating in Pakistan and Afghanistan were determined. Phylogenetic analysis of the foot-and-mouth disease virus (FMDV) VP1-coding sequences from these countries collected between 2002 and 2009 revealed the presence of at least four lineages within two distinct genotypes, all belonging to the Asia topotype, within serotype A. The predominant lineage observed was A-Iran05 but three other lineages (a new one is named here A-Pak09) were also identified. The A-Iran05 lineage is still evolving as revealed by the presence of seven distinct variants, the dominant being the A-Iran05AFG-07 and A-Iran05BAR-08 sublineages. The rate of evolution of the A-Iran05 lineage was found to be about 1.2×10(-2) substitutions per nucleotide per year. This high rate of change is consistent with the rapid appearance of new variants of FMDV serotype A in the region. The A22/Iraq FMDV vaccine is antigenically distinct from the A-Iran05BAR-08 viruses. Mapping of the amino acid changes between the capsid proteins of the A22/Iraq vaccine strain and the A-Iran05BAR-08 viruses onto the A22/Iraq capsid structure identified candidate amino acid substitutions, exposed on the virus surface, which may explain this antigenic difference.
authors.affiliation: Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.|National Veterinary Laboratory, Park Road, 45500 Islamabad, Pakistan.|National Veterinary Institute, Technical University of Denmark, Lindholm, 4771 Kalvehave, Denmark.
authors.forename: Syed M
authors.initials: SM
authors.lastname: Jamal
authors.affiliation: Food and Agriculture Organization of the United Nations, Rome, Italy.
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Ferrari
authors.affiliation: Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
authors.forename: Safia
authors.initials: S
authors.lastname: Ahmed
authors.affiliation: National Veterinary Institute, Technical University of Denmark, Lindholm, 4771 Kalvehave, Denmark.
authors.forename: Preben
authors.initials: P
authors.lastname: Normann
authors.affiliation: Biophysics Section, Blackett Laboratory, Division of Cell and Molecular Biology, Imperial College London, London SW7 2AZ, UK.
authors.forename: Stephen
authors.initials: S
authors.lastname: Curry
authors.affiliation: National Veterinary Institute, Technical University of Denmark, Lindholm, 4771 Kalvehave, Denmark.
authors.forename: Graham J
authors.initials: GJ
authors.lastname: Belsham
mesh_terms: D000346:Afghanistan; D000595:Amino Acid Sequence; D000818:Animals; D036022:Capsid Proteins / Q000235:genetics / Q000378:metabolism; D004196:Disease Outbreaks; D019143:Evolution, Molecular; D005536:Foot-and-Mouth Disease / Q000453:epidemiology / Q000821:virology*; D029544:Foot-and-Mouth Disease Virus / Q000145:classification* / Q000235:genetics; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010154:Pakistan; D058974:Phylogeography; D011487:Protein Conformation; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012703:Serotyping / Q000379:methods
chemical_list: D036022:Capsid Proteins; D012367:RNA, Viral