Development of Reverse-transcriptase, Real-time PCR Assays to Distinguish the Southern African Territories (SAT) Serotypes 1 and 3 and Topotype VII of SAT2 of Foot-and-Mouth Disease Virus

Overview

Journal Front Vet Sci

Specialty Veterinary Medicine

Date 2022 Oct 7

PMID 36204292

Authors

Taeyo Chestley

Patrycja Sroga

Michelle Nebroski

Kate Hole

Hussaini Ularamu

Oliver Lung

Charles Nfon

Affiliations

Soon will be listed here.

Abstract

Foot-and-Mouth Disease Virus (FMDV), the causative agent of Foot-and-Mouth Disease, is a highly feared, economically devastating transboundary pathogen. This is due to the virus' extremely contagious nature and its ability to utilize multiple transmission routes. As such, rapid and accurate diagnostic testing is imperative to the control of FMD. Identification of the FMDV serotype is necessary as it provides the foundation for appropriate vaccine selection and aids in outbreak source tracing. With the vast genetic diversity, there is a desperate need to be able to characterize FMDV without relying on prior knowledge of viral serotypes. In this study, the Neptune bioinformatics tool was used to identify genetic signatures specific to each Southern African Territories (SAT) 1, 2 and 3 genomes but exclusionary to the other circulating FMDV serotypes (A, O, Asia1, and the heterologous SAT1, SAT2 and/or SAT3). Identification of these unique genomic regions allowed the design of TaqMan-based real-time reverse transcriptase PCR (rRT-PCR) primer/probe sets for SAT1, SAT2 and SAT3 viruses. These assays were optimized using prototypic FMDV cell culture isolates using the same reagents and thermocycling conditions as the FMDV pan-serotype 3D rRT-PCR assay. Cross-reactivity was evaluated in tandem with the FMDV pan-serotype 3D rRT-PCR utilizing representative strains from FMDV serotypes A, O, Asia1, SAT1, SAT2 and SAT3. The SAT1, SAT2, and SAT3 primer/probe sets were specific for the homologous serotype and exclusionary to all others. SAT1 and SAT3 primer/probe sets were able to detect several topotypes, whereas the SAT2 assay was revealed to be specific for topotype VII. The SAT2 topotype VII specificity was possibly due to the use of sequence data deposited post-2011to design the rRT-PCR primers and probes. Each assay was tested against a panel of 99 bovine tissue samples from Nigeria, where SAT2 topotype VII viruses were correctly identified and no cross-reactivity was exhibited by the SAT1 and 3 assays. These novel SAT1, SAT3 and SAT2 topotype VII rRT-PCR assays have the potential to detect and differentiate circulating FMD SAT viruses.

Citing Articles

A TaqMan-based RT-qPCR assay for serotyping of Southern African territories (SAT) 2 strains of Foot-and-Mouth disease virus (FMDV) in Southern Africa.

Kabelo T, Fana E, Kesamang M, Hyera J, Lebani K BMC Res Notes. 2023; 16(1):323.

PMID: 37941022 PMC: 10634033. DOI: 10.1186/s13104-023-06586-7.

References

Reid S, Mioulet V, Knowles N, Shirazi N, Belsham G, King D . Development of tailored real-time RT-PCR assays for the detection and differentiation of serotype O, A and Asia-1 foot-and-mouth disease virus lineages circulating in the Middle East. J Virol Methods. 2014; 207:146-53. DOI: 10.1016/j.jviromet.2014.07.002. View

Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth B, Remm M . Primer3--new capabilities and interfaces. Nucleic Acids Res. 2012; 40(15):e115. PMC: 3424584. DOI: 10.1093/nar/gks596. View

Bastos A, Haydon D, Sangare O, Boshoff C, Edrich J, Thomson G . The implications of virus diversity within the SAT 2 serotype for control of foot-and-mouth disease in sub-Saharan Africa. J Gen Virol. 2003; 84(Pt 6):1595-1606. DOI: 10.1099/vir.0.18859-0. View

Moniwa M, Embury-Hyatt C, Zhang Z, Hole K, Clavijo A, Copps J . Experimental foot-and-mouth disease virus infection in white tailed deer. J Comp Pathol. 2012; 147(2-3):330-42. DOI: 10.1016/j.jcpa.2012.01.010. View

Moniwa M, Clavijo A, Li M, Collignon B, Kitching P . Performance of a foot-and-mouth disease virus reverse transcription-polymerase chain reaction with amplification controls between three real-time instruments. J Vet Diagn Invest. 2007; 19(1):9-20. DOI: 10.1177/104063870701900103. View

Reid S, Hutchings G, Ferris N, De Clercq K . Diagnosis of foot-and-mouth disease by RT-PCR: evaluation of primers for serotypic characterisation of viral RNA in clinical samples. J Virol Methods. 1999; 83(1-2):113-23. DOI: 10.1016/s0166-0934(99)00113-5. View

Ferris N, Dawson M . Routine application of enzyme-linked immunosorbent assay in comparison with complement fixation for the diagnosis of foot-and-mouth and swine vesicular diseases. Vet Microbiol. 1988; 16(3):201-9. DOI: 10.1016/0378-1135(88)90024-7. View

Reid S, Ferris N, Hutchings G, Zhang Z, Belsham G, Alexandersen S . Detection of all seven serotypes of foot-and-mouth disease virus by real-time, fluorogenic reverse transcription polymerase chain reaction assay. J Virol Methods. 2002; 105(1):67-80. DOI: 10.1016/s0166-0934(02)00081-2. View

Knowles N, Samuel A . Molecular epidemiology of foot-and-mouth disease virus. Virus Res. 2003; 91(1):65-80. DOI: 10.1016/s0168-1702(02)00260-5. View

10.

Burman A, Clark S, Abrescia N, Fry E, Stuart D, Jackson T . Specificity of the VP1 GH loop of Foot-and-Mouth Disease virus for alphav integrins. J Virol. 2006; 80(19):9798-810. PMC: 1617245. DOI: 10.1128/JVI.00577-06. View

11.

Marinier E, Zaheer R, Berry C, Weedmark K, Domaratzki M, Mabon P . Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations. Nucleic Acids Res. 2017; 45(18):e159. PMC: 5737611. DOI: 10.1093/nar/gkx702. View

12.

Reid S, Ferris N, Hutchings G, De Clercq K, Newman B, Knowle N . Diagnosis of foot-and-mouth disease by RT-PCR: use of phylogenetic data to evaluate primers for the typing of viral RNA in clinical samples. Arch Virol. 2002; 146(12):2421-34. DOI: 10.1007/s007050170012. View

13.

El Bagoury G, Elhabashy R, Mahmoud A, Hagag N, El Zowalaty M . Development and evaluation of one-step real-time RT-PCR assay for improved detection of foot-and-mouth disease virus serotypes circulating in Egypt. J Virol Methods. 2022; 306:114525. DOI: 10.1016/j.jviromet.2022.114525. View

14.

Knowles N, Wadsworth J, Bachanek-Bankowska K, King D . VP1 sequencing protocol for foot and mouth disease virus molecular epidemiology. Rev Sci Tech. 2017; 35(3):741-755. DOI: 10.20506/rst.35.3.2565. View

15.

Ahmed H, Salem S, Habashi A, Arafa A, Aggour M, Salem G . Emergence of foot-and-mouth disease virus SAT 2 in Egypt during 2012. Transbound Emerg Dis. 2012; 59(6):476-81. DOI: 10.1111/tbed.12015. View

16.

Knowles N, Bachanek-Bankowska K, Wadsworth J, Mioulet V, Valdazo-Gonzalez B, Eldaghayes I . Outbreaks of Foot-and-Mouth Disease in Libya and Saudi Arabia During 2013 Due to an Exotic O/ME-SA/Ind-2001 Lineage Virus. Transbound Emerg Dis. 2014; 63(5):e431-5. DOI: 10.1111/tbed.12299. View

17.

Katoh K, Misawa K, Kuma K, Miyata T . MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002; 30(14):3059-66. PMC: 135756. DOI: 10.1093/nar/gkf436. View

18.

Lim D, Ryoo S, Kang H, Oh S, Jang S, Kang B . Enhanced detection and serotyping of foot-and-mouth disease virus serotype O, A, and Asia1 using a novel multiplex real-time RT-PCR. Transbound Emerg Dis. 2022; 69(5):e2578-e2589. PMC: 9796456. DOI: 10.1111/tbed.14603. View

19.

Verdaguer N, Mateu M, Andreu D, Giralt E, Domingo E, Fita I . Structure of the major antigenic loop of foot-and-mouth disease virus complexed with a neutralizing antibody: direct involvement of the Arg-Gly-Asp motif in the interaction. EMBO J. 1995; 14(8):1690-6. PMC: 398262. DOI: 10.1002/j.1460-2075.1995.tb07158.x. View

20.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View