COMPARISON AND EVALUATION OF ONE-STEP REVERSE TRANSCRIPTASE-POLYMERASE CHAIN REACTION (RT-PCR) AND REVERSE TRANSCRIPTASE LOOP-MEDIATED ISOTHERMAL AMPLIFICATION ASSAY(RT-LAMP) FOR RAPID DETECTION OF FOOT-AND-MOUTH DISEASE VIRUS (FMDV)

Foot-and-mouth disease (FMD) is endemic in Pakistan and cause severe economic losses. Serotype O, A and Asia 1 is prevalent and their rapid detection for Pakistaniisolates is needed to determine the serotype prevalence in different areas of the country. One step reversetranscriptase-polymerase chain reaction (RT-PCR) and reverse transcriptase loop-mediated isothermal amplification (RT- LAMP) was compared for the rapid and sensitive detection of FMDV genome. FMDV genome was confirmed in 19/25clinically affected animals by sequencing. These positive samples (n=19) were also confirmed in both RT-PCR and RT-LAMP consensus assay.In theserotyping assay, RT-PCR detection rate was16.67%, 80%, and 50% and RT-LAMP detection rate was 50%, 60% and 50%for serotype Asia 1, O and type A respectively. In general detection of FMDV, RT-PCR assay and the RT-LAMP assay showed high concordance (k = 1.0). However, in serotype detection, RT-LAMP was found more sensitive as compared to RT-PCR for the detection of the FMDV serotype Asia1 and Vice Versa in the detection of serotype O. To the best of the author’s knowledge, this is thefirst document on thecomparison of RT-LAMP and one-step RT- PCR for FMDV using ESE-Quant Tube Scanner in Pakistan.The RT-LAMP assay has the potential for early and rapid clinical diagnosis, surveillance and serotyping of FMDV infection in endemic countries.