Detection and serotyping of foot-and-mouth disease virus with laboratory and in silico methods

Abstract

Foot-and-mouth disease virus (FMDV) is a highly contagious animal pathogen and it has a variable genome and high antigenic variation. There are seven known serotypes of this virus: A, O, C, Asia1, SAT1, SAT2, and SAT3. The rapid detection and serotype characterization of the virus is instrumental for the prompt response by animal health authorities. This thesis presents the design and development of the first electronic microarray assay for the simultaneous detection and subtyping of FMDV. The assay was evaluated in silico and it was tested with 19 synthetic DNA constructs representing all 7 serotypes, followed by the testing with 23 viral RNA samples representing all 7 serotypes. Also, various in silico methods were compared for the classification of FMDV sequences using complete genomes and next generation sequencing (NGS) data. Finally, highly specific and highly sensitive single nucleotide variant signatures that distinguish the seven FMDV serotypes were discovered.