Genetic Markers of the Cattle Foot and Mouth Disease Virus: Genomic Analysis

Abstract

Objective of this work was to search for genome loci of various types of foot and mouth disease (FMD) virus, characterized by the lowest variability, to be used as genetic markers in the PCR-indication of the virus.Materials and methods. The resources of the National Center for Biotechnology Information (NCBI) and BLAST and Vector NTI 9.1.0 software utilities were employed in the research. Plasmid DNA with marker insertion was utilized for PCR amplification.Results and discussion. The nucleotide sequences of FMD virus genomes, the types A, Asia-1, C, O and SAT (1, 2 and 3), were analyzed. In the process of aligning of isolate genomes of each type, potentially conservative sites were identified. The comparison between these loci has revealed one most conserved locus, and the subsequent BLAST analysis has established its high specificity to FMD virus genome. Primers and a probe were selected for this locus. In addition, the oligonucleotide primers were selected for the three genes included in the cattle genome that are least homologous to the specific oligonucleotides. The primers/probe were used as internal control of amplification. To control the progress of amplification, a positive control has been developed that has a nucleotide sequence of the marker region of FMD virus genome. It was found out that genomes of certain virus isolates show high level of polymorphism in relation to PCR-probe (12 isolates by A, Asia-1, SAT1, and SAT2 serotypes). However, modifications of the PCR-probe (Pas FMDV and Psat FMDV) allow for elimination of the effect of such variability on the number of virus isolates identification. Nucleotide sequences of the primers, probes and positive controls are presented in the tables.