Evaluation of PCR primers targeting the VP2 region of the foot-and-mouth disease virus for improved serotype detection

Abstract

Frequently, a sequence from a single strain of a virus is used to design primers for PCR-based virus detection. However, high mutation rates in RNA viruses lead to failure of microorganism detection in clinical samples. Therefore, it is essential to find conserved regions within sequences to design primers for the detection of pathogen genomes in suspected clinical samples. The aim of the study was to find conserved regions of the genome for improved serotype detection. In the present study, primers were designed for serotype detection based on the VP2 coding region of foot-and-mouth disease virus (FMDV) after alignment of full genome (n = 375) sequences. These primer pairs and previously reported primer pairs were then compared using positive samples (n = 91) collected during 2010-2016 from Faisalabad District, Pakistan. The detection rate of newly designed primer pairs O-Wqs-F/Rev-Wqs (96.5%), As-Wqs-F/Rev-Wqs (90.4%), and A-Wqs-F/Rev-Wqs (100%) was better compared with previously reported primer pairs P38/P33 (81%), P74-77/P33 (47.6%), and P87-92/P33 (41.6%) in detecting FMDV serotypes O, Asia1, and A, respectively. The higher detection rates of the newly designed primer pairs appeared to be due to the selection of highly conserved sequences within the serotypes for designing primers. To the best of the authors' knowledge, this is the first study that describes serotype diagnosis of FMDV based on primers targeting the VP2 region. In conclusion, this new method offers an improved approach for the serotyping of FMDV compared to previous methods.