Molecular characterisation of foot-and-mouth disease viruses from Pakistan, 2005-2008.
Foot-and-mouth disease (FMD), an economically important disease of cloven-hoofed animals, is endemic in Pakistan where three virus serotypes are present (O, A and Asia 1). Fifty-eight clinical samples collected between 2005 and 2008 from animals with suspected FMD in various locations in Pakistan were subjected to virus isolation on primary cell culture, antigen ELISA and real-time RT-PCR (rRT-PCR). Viruses were isolated from 32 of these samples and identified as FMDV type O (n = 31) or type A (n = 1). Foot-and-mouth disease virus (FMDV) genome was detected in a further 11 samples by real-time RT-PCR. Phylogenetic analyses of the VP1 nucleotide sequences showed that all of the type O viruses belonged to the MIDDLE EAST-SOUTH ASIA topotype with the majority belonging to the PanAsia-2 lineage; a single example of the older PanAsia lineage was identified. The single FMDV type A virus belonged to the ASIA topotype, but did not cluster with known strains that are currently circulating (such as Iran-05) and was not closely related to other type A viruses from the region. These findings demonstrate the widespread distribution of O-PanAsia-2 in Pakistan and the presence of undisclosed novel type A lineages in the region.
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan. 
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Waheed
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan Institute for Animal Health, Pirbright, Woking, Surrey, UK Food and Agriculture Organization (FAO), National Veterinary Laboratory, Islamabad, Pakistan.
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Parida
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan Institute for Animal Health, Pirbright, Woking, Surrey, UK Food and Agriculture Organization (FAO), National Veterinary Laboratory, Islamabad, Pakistan.
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QM
Khan
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan Institute for Animal Health, Pirbright, Woking, Surrey, UK Food and Agriculture Organization (FAO), National Veterinary Laboratory, Islamabad, Pakistan.
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Hussain
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan Institute for Animal Health, Pirbright, Woking, Surrey, UK Food and Agriculture Organization (FAO), National Veterinary Laboratory, Islamabad, Pakistan.
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Ebert
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan Institute for Animal Health, Pirbright, Woking, Surrey, UK Food and Agriculture Organization (FAO), National Veterinary Laboratory, Islamabad, Pakistan.
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Wadsworth
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan Institute for Animal Health, Pirbright, Woking, Surrey, UK Food and Agriculture Organization (FAO), National Veterinary Laboratory, Islamabad, Pakistan.
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Reid
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan Institute for Animal Health, Pirbright, Woking, Surrey, UK Food and Agriculture Organization (FAO), National Veterinary Laboratory, Islamabad, Pakistan.
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Hutchings
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan Institute for Animal Health, Pirbright, Woking, Surrey, UK Food and Agriculture Organization (FAO), National Veterinary Laboratory, Islamabad, Pakistan.
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Mahapatra
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan Institute for Animal Health, Pirbright, Woking, Surrey, UK Food and Agriculture Organization (FAO), National Veterinary Laboratory, Islamabad, Pakistan.
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King
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan Institute for Animal Health, Pirbright, Woking, Surrey, UK Food and Agriculture Organization (FAO), National Veterinary Laboratory, Islamabad, Pakistan.
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Paton
National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan Institute for Animal Health, Pirbright, Woking, Surrey, UK Food and Agriculture Organization (FAO), National Veterinary Laboratory, Islamabad, Pakistan.
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Knowles
D000818:Animals; D002020:Buffaloes; D036022:Capsid Proteins / Q000235:genetics / Q000378:metabolism; D002417:Cattle; D002418:Cattle Diseases / Q000453:epidemiology* / Q000821:virology; D005536:Foot-and-Mouth Disease / Q000453:epidemiology* / Q000821:virology; D029544:Foot-and-Mouth Disease Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D008969:Molecular Sequence Data; D010154:Pakistan / Q000453:epidemiology; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000662:veterinary
D036022:Capsid Proteins; C442501:VP1 protein, Foot-and-mouth disease virus
epidemiology; foot-and-mouth disease; molecular; phylogenetic