A reverse transcription-multiplex PCR strategy devised for concomitant detection and differentiation of foot and mouth disease virus serotypes O, A and Asia 1 in India

Jajati Keshari Mohapatra; Manoranjan Rout; Saravanan Subramaniam; Priyabrata Giri; Shyam Singh Dahiya; Sagar Sangam Rautaray; Jitendra Kumar Biswal; Nihar Ranjan Sahoo; Rabindra Prasad Singh

doi:10.1016/j.jviromet.2023.114829

A reverse transcription-multiplex PCR strategy devised for concomitant detection and differentiation of foot and mouth disease virus serotypes O, A and Asia 1 in India

J Virol Methods. 2023 Dec:322:114829. doi: 10.1016/j.jviromet.2023.114829. Epub 2023 Oct 1.

Authors

Jajati Keshari Mohapatra¹, Manoranjan Rout², Saravanan Subramaniam², Priyabrata Giri², Shyam Singh Dahiya², Sagar Sangam Rautaray², Jitendra Kumar Biswal², Nihar Ranjan Sahoo², Rabindra Prasad Singh²

Affiliations

¹ ICAR-National Institute on Foot and Mouth Disease, International Centre for FMD, Arugul, Bhubaneswar 752050, Odisha, India. Electronic address: jajati1@gmail.com.
² ICAR-National Institute on Foot and Mouth Disease, International Centre for FMD, Arugul, Bhubaneswar 752050, Odisha, India.

PMID: 37783396
DOI: 10.1016/j.jviromet.2023.114829

Abstract

Serotype identification occupies the central part of foot and mouth disease (FMD) diagnosis workflow and vaccination decision tree. In this study, a reverse transcription-multiplex PCR (RT-mPCR) strategy wherein three assays with unique combinations of serotype specific primers targeting the VP1 region was developed to differentiate FMD virus serotypes O, A and Asia 1 based on differential size of the PCR amplicons on agarose gel. Their diagnostic performance relative to the mPCR assay in use in India was evaluated on 169 clinical samples and 210 cell culture grown virus isolates. The relative diagnostic sensitivity was found to be 99.69%, 98.78% and 99.08% for primer combinations 1, 2 and 3, respectively. These assays proved their worth by detecting serotype in three FMD suspected specimens that went undiagnosed in the existing mPCR and also by identifying multiple serotypes in the same sample. Their detection limits varied from log₁₀ 2 to log₁₀ 4 viral RNA dilution and from 100 to 0.1 TCID₅₀ virus depending on the serotype. The validated novel mPCR assays show promise to be included in the routine diagnostic tool-box to augment the efficiency of diagnosis of FMD virus serotypes that display extreme genetic diversity and a tendency of transboundary dispersal.

Keywords: Differentiation; FMD virus; Multiplex PCR; Serotypes O, A, Asia 1.

MeSH terms

Animals
Cell Differentiation
Foot-and-Mouth Disease Virus*
Foot-and-Mouth Disease* / diagnosis
India
Multiplex Polymerase Chain Reaction
Reverse Transcription
Sensitivity and Specificity
Serogroup
Serotyping