The following tables provide details of the primers and probes used in various real time RT-PCR tests for detecting Foot-and-mouth disease virus

Primers and probes used for One step RT-PCR of Foot-and-mouth disease virus (Reid et al., 2001, and Callahan et al., 2002), these are the assays described in Chapter 2.1.8. Foot and mouth disease, of the OIE Manual of Diagnostic Tests and Vaccines for Terrestrial Animals.

RT-PCR Primer/Probe Oligo Name Sequence (5'-3') Working concentration
FMDV5'UTR Forward primer SA‑IR‑219‑246F CAC YTY AAG RTG ACA YTG RTA CTG GTA C 10 pmol/μl
FMDV5'UTR Reverse primer SA‑IR‑315‑293R CAG ATY CCR AGT GWC ICI TGT TA 10 pmol/μl
FMDV5'UTR Taqman probe SAmulti2‑P‑IR‑292‑269R CCT CGG GGT ACC TGA AGG GCA TCC 5 pmol/μl
FMD3D Forward primer 3DF ACT GGG TTT TAC AAA CCT GTG A 10 pmol/μl
FMD3D Reverse primer 3DR GCG AGT CCT GCC ACG GA 10 pmol/μl
FMD3D Taqman probe 3DP TCC TTT GCA CGC CGT GGG AC 5 pmol/μl

Callahan JD, Brown F, Osorio FA, Sur JH, Kramer E, Long GW, Lubroth J, Ellis SJ, Shoulars KS, Gaffney KL, Rock DL and Nelson WM (2002). Use of a portable real-time reverse transcriptase-polymerase chain reaction assay for rapid detection of Foot-and-mouth disease virus. Journal of the American Veterinary Medical Association 220(11):1636-1642.publication

Reid SM, Ferris NP, Hutchings GH, Zhang Z, Belsham GJ and Alexandersen S (2001). Diagnosis of foot-and-mouth disease by real-time fluorogenic PCR assay. The Veterinary record 149(20):621-623.publication

These real-time RT-PCR assays have been designed to detect different Foot-and-mouth disease virus lineages expected to be circulating in different geographical locations.

Full details of these assays can be found on

East Africa

This set of specific assays was designed for the detection of FMDV strains currently circulating in the region of East Africa especially Tanzania, Uganda and Kenya (Bachanek-Bankowska et al., 2016)

Designed to detect: O/EA-2, O/EA-4, A/Africa/G-I, SAT 1/I(NWZ) and SAT 2/IV

West Eurasia

This set of real-time RT-PCR type-specific as-says was designed for the detection of FMDV strains currently circulating in West Eurasia (Reid et al., 2014).

Designed to detect: O/ME-SA/PanAsia-2, A/ASIA/Iran- 05, Asia1/ASIA/Group 1, Asia1/ASIA/Group 2 and Asia1/ASIA/Group 6


This FMDV-O Ind-2001-specific real-time RT-PCR is a molecular tool for detection of foot-and-mouth Disease virus O/ME-SA/Ind2001 lineage (Knowles et al., 2014).
This lineage was originally detected on the Indian sub-continent, but has since spread westwards through the Middle East to North Africa and eastwards into Southeast Asia

Designed to detect: O/ME-SA/Ind-2001d

SAT 2 - Egypt

This real-time RT-PCR is a molecular tool for detection of Foot-and-mouth disease virus SAT 2/VII topotype and was developed in response to the SAT 2 outbreak in Egypt in 2012 (Ahmed et al., 2012).
Outside of Egypt this lineage has been detected in Libya, Palestinian Autonomous Territories, Eritrea and Cameroon.

Designed to detect: SAT 2/VII


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