title: Primer design for specific diagnosis by PCR of highly variable RNA viruses: typing of foot-and-mouth disease virus.
abstract: A PCR assay for the specific detection and identification of viral sequences that correlate with established serotypes of foot-and-mouth disease virus (FMDV) has been developed. A new analysis based on homology profiles among reported sequences was used for primer design. RNA replicase (3D) gene regions that showed high homology among FMDVs, and low homology to other picornaviruses, were used for PCR amplification. Specific and highly sensitive detection was achieved for RNA of FMDV types C, A, and O, either purified or extracted from vesicular fluids of infected animals, under reaction conditions permissive for the detection of variants present in the virus population. Similarly, serotype-specific primers were designed to amplify the carboxy-terminal end of VP1 gene of FMDV types either C, A, or O. The results of PCR amplification of 15 different FMDV RNAs using type-specific primers are in agreement with the serological typing of the corresponding viruses and show that the primer-selection procedure developed for FMDV constitutes a reliable method of viral diagnosis.
authors.affiliation: Departamento de Sanidad Animal, CIT-INIA, Madrid, Spain.
authors.forename: A
authors.initials: A
authors.lastname: Rodríguez
authors.forename: E
authors.initials: E
authors.lastname: Martínez-Salas
authors.forename: J
authors.initials: J
authors.lastname: Dopazo
authors.forename: M
authors.initials: M
authors.lastname: Dávila
authors.forename: J C
authors.initials: JC
authors.lastname: Sáiz
authors.forename: F
authors.initials: F
authors.lastname: Sobrino
mesh_terms: D000818:Animals; D005537:Aphthovirus / Q000145:classification* / Q000235:genetics; D002213:Capsid / Q000235:genetics*; D036022:Capsid Proteins; D016384:Consensus Sequence; D004277:DNA, Single-Stranded / Q000235:genetics; D005536:Foot-and-Mouth Disease / Q000175:diagnosis*; D005814:Genes, Viral / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D012689:Sequence Homology, Nucleic Acid; D012703:Serotyping; D013045:Species Specificity; D015678:Viral Structural Proteins / Q000235:genetics
chemical_list: D036022:Capsid Proteins; D004277:DNA, Single-Stranded; C442501:VP1 protein, Foot-and-mouth disease virus; D015678:Viral Structural Proteins