TY - JOUR T1 - Diagnosis of foot-and-mouth disease by RT-PCR: use of phylogenetic data to evaluate primers for the typing of viral RNA in clinical samples. JF - Arch Virol Y1 - 2001 A1 - Reid, S M A1 - Ferris, N P A1 - Hutchings, G H A1 - Kris De Clercq A1 - Newman, B J A1 - Knowle, N J A1 - Samuel, A R KW - Animals KW - DNA Primers KW - Foot-and-Mouth Disease KW - Foot-and-Mouth Disease Virus KW - Phylogeny KW - Reverse Transcriptase Polymerase Chain Reaction KW - RNA, Viral KW - Sensitivity and Specificity KW - Sequence Analysis, DNA KW - Serotyping AB -

The results of type-specific RT-PCR diagnostic assays on foot-and-mouth disease (FMD) viruses in clinical samples were mapped onto serotype-specific dendrograms representing the degree of nucleotide sequence variation between the FMD virus isolates. This novel approach assisted the selection of suitable PCR primer sets for the diagnosis of FMD virus isolates belonging to different topotypes within each serotype. These interpretations were qualified by using a universal (FMD virus group) specific primer to confirm that FMD virus RNA had been extracted from the samples under investigation. The analyses showed that the design of primer sets for the detection of FMD virus serotypes O, A, Asia 1, SAT 1 and SAT 3 were generally satisfactory, as most virus isolates within the major virus sub-groupings were successfully detected. However, the FMD virus serotype C and SAT 2 specific primers were less efficient as certain virus sub-groups were not detected. This identified the need for additional or alternative primers to improve RT-PCR procedures for more comprehensive detection of divergent virus strains within these serotypes. There were some examples where not all virus isolates from the same outbreak reacted with particular type-specific primers which suggested that either further minor refinements may be necessary in the primer design or that there were shortcomings in the RT-PCR methodology.

VL - 146 CP - 12 U1 - http://www.ncbi.nlm.nih.gov/pubmed/11811689?dopt=Abstract ER -