title: Genetic diversity of foot-and-mouth disease virus serotype O in Pakistan and Afghanistan, 1997-2009.
abstract: Foot-and-mouth disease (FMD) is endemic in Pakistan and Afghanistan; serotypes O, A and Asia-1 of the virus are responsible for the outbreaks in these countries with FMDV type O usually being the most common. In the present study, the nucleotide sequences encoding the FMDV capsid protein VP1 from virus samples were determined. Phylogenetic analysis of the serotype O FMD viruses circulating in Pakistan and Afghanistan between 1997 and 2009 revealed the presence of at least three different lineages within the ME-SA (Middle East South Asia) topotype. The three lineages detected in this study are Pak98, Iran2001 and PanAsia. The PanAsia lineage is currently dominant in the area and is evolving with time as revealed by the appearance of distinct variants e.g. PanAsia-II and a new variant designated here as PanAsia-III. The rates of evolution of the O-PanAsia-II and III sublineages prevalent in the region were found to be 6.65 × 10(-3) (95% CI=5.49-7.80 × 10(-3)) and 7.80 × 10(-3) (95% CI=6.72-8.89 × 10(-3)) substitutions per nucleotide per year, respectively. The present study reveals the presence of multiple (sub-)lineages of FMDV serotype O co-circulating in the region and that significant new variants are frequently emerging.
authors.affiliation: National Veterinary Laboratory, Park Road, 45500 Islamabad, Pakistan. jamal115@yahoo.com
authors.forename: Syed M
authors.initials: SM
authors.lastname: Jamal
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Ferrari
authors.forename: Safia
authors.initials: S
authors.lastname: Ahmed
authors.forename: Preben
authors.initials: P
authors.lastname: Normann
authors.forename: Graham J
authors.initials: GJ
authors.lastname: Belsham
mesh_terms: D000346:Afghanistan; D000818:Animals; D002020:Buffaloes; D036022:Capsid Proteins / Q000235:genetics; D002417:Cattle; D005536:Foot-and-Mouth Disease / Q000821:virology*; D029544:Foot-and-Mouth Disease Virus / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D006041:Goats; D010154:Pakistan; D010802:Phylogeny; D058974:Phylogeography; D012044:Regression Analysis; D017422:Sequence Analysis, DNA; D012703:Serotyping; D012756:Sheep
chemical_list: D036022:Capsid Proteins; C442501:VP1 protein, Foot-and-mouth disease virus