title: Comparative genomics of foot-and-mouth disease virus.
abstract: Here we present complete genome sequences, including a comparative analysis, of 103 isolates of foot-and-mouth disease virus (FMDV) representing all seven serotypes and including the first complete sequences of the SAT1 and SAT3 genomes. The data reveal novel highly conserved genomic regions, indicating functional constraints for variability as well as novel viral genomic motifs with likely biological relevance. Previously undescribed invariant motifs were identified in the 5' and 3' untranslated regions (UTR), as was tolerance for insertions/deletions in the 5' UTR. Fifty-eight percent of the amino acids encoded by FMDV isolates are invariant, suggesting that these residues are critical for virus biology. Novel, conserved sequence motifs with likely functional significance were identified within proteins L(pro), 1B, 1D, and 3C. An analysis of the complete FMDV genomes indicated phylogenetic incongruities between different genomic regions which were suggestive of interserotypic recombination. Additionally, a novel SAT virus lineage containing nonstructural protein-encoding regions distinct from other SAT and Euroasiatic lineages was identified. Insights into viral RNA sequence conservation and variability and genetic diversity in nature will likely impact our understanding of FMDV infections, host range, and transmission.
authors.affiliation: Department of Pathobiology and Veterinary Science, University of Connecticut, 61 N. Eagleville Road, Unit-3089, Storrs, CT 06269-3089, USA.
authors.forename: C
authors.initials: C
authors.lastname: Carrillo
authors.forename: E R
authors.initials: ER
authors.lastname: Tulman
authors.forename: G
authors.initials: G
authors.lastname: Delhon
authors.forename: Z
authors.initials: Z
authors.lastname: Lu
authors.forename: A
authors.initials: A
authors.lastname: Carreno
authors.forename: A
authors.initials: A
authors.lastname: Vagnozzi
authors.forename: G F
authors.initials: GF
authors.lastname: Kutish
authors.forename: D L
authors.initials: DL
authors.lastname: Rock
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D036022:Capsid Proteins / Q000235:genetics; D029544:Foot-and-Mouth Disease Virus / Q000235:genetics*; D014644:Genetic Variation; D016679:Genome, Viral; D023281:Genomics; D014943:Global Health; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D017361:Viral Nonstructural Proteins / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D036022:Capsid Proteins; D017361:Viral Nonstructural Proteins