title: Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus.
abstract: Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT-PCR method was developed to amplify a 7.6kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal.
authors.affiliation: The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: King
authors.affiliation: The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
authors.forename: Graham L
authors.initials: GL
authors.lastname: Freimanis
authors.affiliation: Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK; MRC-University of Glasgow, Centre for Virus Research, University of Glasgow, 464 Bearsden Road, G61 1QH, UK.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Orton
authors.affiliation: The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
authors.forename: Ryan A
authors.initials: RA
authors.lastname: Waters
authors.affiliation: Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
authors.forename: Daniel T
authors.initials: DT
authors.lastname: Haydon
authors.affiliation: The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK. Electronic address: donald.king@pirbright.ac.uk.
authors.forename: Donald P
authors.initials: DP
authors.lastname: King
mesh_terms: D000818:Animals; D002417:Cattle; D002418:Cattle Diseases / Q000821:virology; D005536:Foot-and-Mouth Disease / Q000473:pathology / Q000821:virology*; D029544:Foot-and-Mouth Disease Virus / Q000235:genetics* / Q000472:pathogenicity; D014644:Genetic Variation; D054884:Host-Pathogen Interactions; D012367:RNA, Viral / Q000302:isolation & purification; D006113:United Kingdom
chemical_list: D012367:RNA, Viral
keywords: Foot-and-mouth disease; Next generation sequencing; Phylogenetics; Variant analysis; Viral diversity