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Mohapatra JK, Rout M, Subramaniam S, Giri P, Dahiya SS, Rautaray SS, Biswal JK, Sahoo NR, Singh RP. 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; 322:114829. [PMID: 37783396 DOI: 10.1016/j.jviromet.2023.114829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/19/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
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.
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Affiliation(s)
- Jajati Keshari Mohapatra
- ICAR-National Institute on Foot and Mouth Disease, International Centre for FMD, Arugul, Bhubaneswar 752050, Odisha, India.
| | - Manoranjan Rout
- ICAR-National Institute on Foot and Mouth Disease, International Centre for FMD, Arugul, Bhubaneswar 752050, Odisha, India
| | - Saravanan Subramaniam
- ICAR-National Institute on Foot and Mouth Disease, International Centre for FMD, Arugul, Bhubaneswar 752050, Odisha, India
| | - Priyabrata Giri
- ICAR-National Institute on Foot and Mouth Disease, International Centre for FMD, Arugul, Bhubaneswar 752050, Odisha, India
| | - Shyam Singh Dahiya
- ICAR-National Institute on Foot and Mouth Disease, International Centre for FMD, Arugul, Bhubaneswar 752050, Odisha, India
| | - Sagar Sangam Rautaray
- ICAR-National Institute on Foot and Mouth Disease, International Centre for FMD, Arugul, Bhubaneswar 752050, Odisha, India
| | - Jitendra Kumar Biswal
- ICAR-National Institute on Foot and Mouth Disease, International Centre for FMD, Arugul, Bhubaneswar 752050, Odisha, India
| | - Nihar Ranjan Sahoo
- ICAR-National Institute on Foot and Mouth Disease, International Centre for FMD, Arugul, Bhubaneswar 752050, Odisha, India
| | - Rabindra Prasad Singh
- ICAR-National Institute on Foot and Mouth Disease, International Centre for FMD, Arugul, Bhubaneswar 752050, Odisha, India
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Saduakassova MA, Wood BA, Henry E, Gray AR, Mioulet V, Sultanov AA, Wadsworth J, Knowles NJ, Di Nardo A, King DP, Bachanek-Bankowska K. Establishing a molecular toolbox of lineage-specific real-time RT-PCR assays for the characterization of foot-and-mouth disease viruses circulating in Asia. Front Vet Sci 2023; 10:1271690. [PMID: 38098997 PMCID: PMC10720594 DOI: 10.3389/fvets.2023.1271690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/20/2023] [Indexed: 12/17/2023] Open
Abstract
Foot-and-mouth disease (FMD) is endemic in many Asian countries, with outbreaks occurring regularly due to viruses from serotypes O, A, and Asia1 that co-circulate in the region. The ability to rapidly characterize new virus occurrences provides critical information to understand the epidemiology and risks associated with field outbreaks, and helps in the selection of appropriate vaccines to control the disease. FMD lineage-specific characterization is usually determined through sequencing; however, this capacity is not always readily available. In this study, we provide a panel of real-time RT-PCR (rRT-PCR) assays to allow differentiation of the FMD virus (FMDV) lineages known to have been co-circulating in Asia during 2020. This panel included five new rRT-PCR assays designed to detect lineages O/ME-SA/PanAsia-PanAsia-2, O/ME-SA/Ind-2001, O/SEA/Mya-98, O/CATHAY, and A/ASIA/Sea-97, along with three published rRT-PCR assays for A/ASIA/Iran-05, A/ASIA/G-VII, and Asia1 serotypes. Samples of known FMD lineage (n = 85) were tested in parallel with all eight lineage-specific assays and an established 3D pan-FMD rRT-PCR assay, and comparative limit of detection (LOD) experiments were conducted for the five newly developed assays. All samples (85/85) were assigned to the correct serotype, and the correct lineage was assigned for 70 out of 85 samples where amplification only occurred with the homologous assay. For 13 out of 85 of the samples, there was amplification in two assays; however, the correct lineage could be designated based on the strongest Ct values for 12 out of 13 samples. An incorrect lineage was assigned for 3 out of 85 samples. The amplification efficiencies for the five new rRT-PCR assays ranged between 79.7 and 100.5%, with nucleic acid dilution experiments demonstrating broadly equivalent limits of detection when compared to the 3D pan-FMD rRT-PCR assay. These new tests, together with other published lineage-specific rRT-PCR assays, constitute a panel of assays (or molecular toolbox) that can be selected for use in FMD endemic countries (individually or a subset of the assays depending on region/lineages known to be circulating) for rapid characterization of the FMDV lineages circulating in Asia at a relatively low cost. This molecular toolbox will enhance the ability of national laboratories in endemic settings to accurately characterize circulating FMDV strains and facilitate prompt implementation of control strategies, and may be particularly useful in settings where it is difficult to access sequencing capability.
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Affiliation(s)
- Meruyert A. Saduakassova
- FAO World Reference Laboratory for Foot-and-Mouth Disease, The Pirbright Institute, Woking, United Kingdom
- Virology Department, Kazakh Scientific Research Veterinary Institute, Almaty, Kazakhstan
| | - Britta A. Wood
- FAO World Reference Laboratory for Foot-and-Mouth Disease, The Pirbright Institute, Woking, United Kingdom
| | - Elisabeth Henry
- FAO World Reference Laboratory for Foot-and-Mouth Disease, The Pirbright Institute, Woking, United Kingdom
| | - Ashley R. Gray
- FAO World Reference Laboratory for Foot-and-Mouth Disease, The Pirbright Institute, Woking, United Kingdom
| | - Valérie Mioulet
- FAO World Reference Laboratory for Foot-and-Mouth Disease, The Pirbright Institute, Woking, United Kingdom
| | - Akhmetzhan A. Sultanov
- Virology Department, Kazakh Scientific Research Veterinary Institute, Almaty, Kazakhstan
| | - Jemma Wadsworth
- FAO World Reference Laboratory for Foot-and-Mouth Disease, The Pirbright Institute, Woking, United Kingdom
| | - Nick J. Knowles
- FAO World Reference Laboratory for Foot-and-Mouth Disease, The Pirbright Institute, Woking, United Kingdom
| | - Antonello Di Nardo
- FAO World Reference Laboratory for Foot-and-Mouth Disease, The Pirbright Institute, Woking, United Kingdom
| | - Donald P. King
- FAO World Reference Laboratory for Foot-and-Mouth Disease, The Pirbright Institute, Woking, United Kingdom
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Chestley T, Sroga P, Nebroski M, Hole K, Ularamu H, Lung O, Nfon C. 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. Front Vet Sci 2022; 9:977761. [PMID: 36204292 PMCID: PMC9530708 DOI: 10.3389/fvets.2022.977761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022] Open
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.
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Affiliation(s)
- Taeyo Chestley
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
- *Correspondence: Taeyo Chestley
| | - Patrycja Sroga
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Michelle Nebroski
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Kate Hole
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Hussaini Ularamu
- National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - Oliver Lung
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Charles Nfon
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
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Lim D, Ryoo S, Kang H, Oh SH, Jang S, Kang B, Park H, Hwang H, Kim J, Park C, Cha S. 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:e2578-e2589. [PMID: 35614493 PMCID: PMC9796456 DOI: 10.1111/tbed.14603] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/19/2022] [Accepted: 05/22/2022] [Indexed: 01/01/2023]
Abstract
Rapid and accurate detection and serotyping of foot-and-mouth disease (FMD) virus (FMDV) is essential for implementing control policies against emergent FMD outbreaks. Current serotyping assays, such as VP1 reverse transcription-polymerase chain reaction (RT-PCR)/sequencing (VP1 RT-PCR/sequencing) and antigen detection enzyme-linked immunosorbent assay (ELISA), have problems with increasing serotyping failure of FMDVs from FMD outbreaks. This study was conducted to develop a multiplex real-time RT-PCR for specific detection and differential serotyping of FMDV serotype O, A, and Asia 1 directly from field clinical samples. Primers and probes were designed based on 571 VP1 coding region sequences originated from seven pools. Multiplex real-time RT-PCR using these primers and probes demonstrated serotype-specific detection with enhanced sensitivity compared to VP1 RT-PCR/sequencing for reference FMDV (n = 24). Complete serotyping conformity between the developed multiplex real-time RT-PCR and previous VP1 RT-PCR/sequencing was demonstrated using FMDV field viruses (n = 113) prepared in cell culture. For FMDV field clinical samples (n = 55), the serotyping rates of multiplex real-time RT-PCR and VP1 RT-PCR/sequencing were 92.7% (51/55) and 72.7% (40/55), respectively. Moreover, the developed multiplex real-time RT-PCR demonstrated improved FMDV detection (up to 33.3%) and serotyping (up to 67.7%) capabilities for saliva samples when compared with 3D real-time RT-PCR and VP1 RT-PCR/sequencing, during 10 days of challenge infection with FMDV serotype O, A, and Asia 1. Collectively, this study suggests that the newly developed multiplex real-time RT-PCR assay may be useful for the detection and differential serotyping of FMDV serotype O, A, and Asia 1 in the field.
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Affiliation(s)
- Da‐Rae Lim
- Foot‐and‐Mouth‐Disease Research DivisionAnimal and Plant Quarantine AgencyGimcheon‐siGyeongsangbuk‐doRepublic of Korea,College of Veterinary Medicine & Animal Disease Intervention CenterKyungpook National UniversityDaeguRepublic of Korea
| | - Soyoon Ryoo
- Foot‐and‐Mouth‐Disease Research DivisionAnimal and Plant Quarantine AgencyGimcheon‐siGyeongsangbuk‐doRepublic of Korea
| | - Hyeonjeong Kang
- Foot‐and‐Mouth‐Disease Research DivisionAnimal and Plant Quarantine AgencyGimcheon‐siGyeongsangbuk‐doRepublic of Korea
| | - Su Hong Oh
- MedianDiagnostics Inc.Sunhwan‐daero, Dongnae‐myeonChuncheon‐siGangwon‐doRepublic of Korea
| | - Sang‐Ho Jang
- MedianDiagnostics Inc.Sunhwan‐daero, Dongnae‐myeonChuncheon‐siGangwon‐doRepublic of Korea
| | - BoKyu Kang
- MedianDiagnostics Inc.Sunhwan‐daero, Dongnae‐myeonChuncheon‐siGangwon‐doRepublic of Korea,Animal and Plant Quarantine AgencyGimcheon‐siGyeongsangbuk‐doRepublic of Korea
| | - Hye‐Jin Park
- Foot‐and‐Mouth‐Disease Research DivisionAnimal and Plant Quarantine AgencyGimcheon‐siGyeongsangbuk‐doRepublic of Korea
| | - Hyeonwoo Hwang
- Foot‐and‐Mouth‐Disease Research DivisionAnimal and Plant Quarantine AgencyGimcheon‐siGyeongsangbuk‐doRepublic of Korea
| | - Jae‐Myung Kim
- Foot‐and‐Mouth‐Disease Research DivisionAnimal and Plant Quarantine AgencyGimcheon‐siGyeongsangbuk‐doRepublic of Korea
| | - Choi‐Kyu Park
- College of Veterinary Medicine & Animal Disease Intervention CenterKyungpook National UniversityDaeguRepublic of Korea
| | - Sang‐Ho Cha
- Foot‐and‐Mouth‐Disease Research DivisionAnimal and Plant Quarantine AgencyGimcheon‐siGyeongsangbuk‐doRepublic of Korea
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El Bagoury GF, Elhabashy R, Mahmoud AH, Hagag NM, El Zowalaty ME. 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. [PMID: 35337855 DOI: 10.1016/j.jviromet.2022.114525] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 11/17/2022]
Abstract
Foot-and-mouth disease (FMD) is an extremely contagious and economically important viral disease affecting livestock. Rapid and precise diagnosis of FMD is critical for efficient control and surveillance strategies of the disease. In this study, one-step real-time reverse transcription-polymerase chain reaction (RT-qPCR) assays using newly designed primers/probe sets in the conserved regions within the VP1 coding sequence were developed for specific detection of FMDV serotypes SAT 2 and O with their different lineage circulating in Egypt. The assays were validated for the efficacy to detect different lineages of these endemic serotypes in Egypt; the detection limit was 10 genomic copies for serotype SAT 2 and one genomic copy for serotype O, with no cross-reactivity observed. These findings were confirmed by the specific and sensitive detection of FMDV in clinical samples obtained from different regions in Egypt and representing a range of subtypes within the SAT 2 and O serotypes. The results illustrate the potential of tailored RT-qPCR tools for the rapid detection and serotyping of FMDV belonging to different lineages of serotypes SAT 2 and O circulating in Egypt with high sensitivity and specificity. The developed assays could be easily deployed for routine surveillance and hence improving the disease control measures.
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Affiliation(s)
- Gabr F El Bagoury
- Department of Virology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Rawan Elhabashy
- Biotechnology Research Unit, Animal Health Research Institute, Agricultural Research Center, Dokki 12618, Giza, Egypt.
| | - Ayman H Mahmoud
- Biotechnology Research Unit, Animal Health Research Institute, Agricultural Research Center, Dokki 12618, Giza, Egypt
| | - Naglaa M Hagag
- Genome Research Unit, Animal Health Research Institute, Agricultural Research Center, Dokki 12618, Giza, Egypt.
| | - Mohamed E El Zowalaty
- Department of Microbiology and Immunology, Faculty of Pharmacy, El Saleheya El Gadida University, El Saleheya El Gadida, 44813, Ash Sharqia, Egypt; Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
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Foglia EA, Lembo T, Kazwala R, Ekwem D, Shirima G, Grazioli S, Brocchi E, Pezzoni G. Combining Multiple Assays Improves Detection and Serotyping of Foot-and-Mouth Disease Virus. A Practical Example with Field Samples from East Africa. Viruses 2021; 13:v13081583. [PMID: 34452448 PMCID: PMC8412026 DOI: 10.3390/v13081583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 01/26/2023] Open
Abstract
Multiple serotypes and topotypes of foot-and-mouth disease virus (FMDV) circulate in endemic areas, posing considerable impacts locally. In addition, introductions into new areas are of great concern. Indeed, in recent years, multiple FMDV outbreaks, caused by topotypes that have escaped from their original areas, have been recorded in various parts of the world. In both cases, rapid and accurate diagnosis, including the identification of the serotype and topotype causing the given outbreaks, plays an important role in the implementation of the most effective and appropriate measures to control the spread of the disease. In the present study, we describe the performance of a range of diagnostic and typing tools for FMDV on a panel of vesicular samples collected in northern Tanzania (East Africa, EA) during 2012–2018. Specifically, we tested these samples with a real-time RT-PCR targeting 3D sequence for pan-FMDV detection; an FMDV monoclonal antibody-based antigen (Ag) detection and serotyping ELISA kit; virus isolation (VI) on LFBKαVβ6 cell line; and a panel of four topotype-specific real-time RT-PCRs, specifically tailored for circulating strains in EA. The 3D real-time RT-PCR showed the highest diagnostic sensitivity, but it lacked typing capacity. Ag-ELISA detected and typed FMDV in 71% of sample homogenates, while VI combined with Ag-ELISA for typing showed an efficiency of 82%. The panel of topotype-specific real-time RT-PCRs identified and typed FMDV in 93% of samples. However, the SAT1 real-time RT-PCR had the highest (20%) failure rate. Briefly, topotype-specific real-time RT-PCRs had the highest serotyping capacity for EA FMDVs, although four assays were required, while the Ag-ELISA, which was less sensitive, was the most user-friendly, hence suitable for any laboratory level. In conclusion, when the four compared tests were used in combination, both the diagnostic and serotyping performances approached 100%.
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Affiliation(s)
- Efrem Alessandro Foglia
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (S.G.); (E.B.); (G.P.)
- Correspondence:
| | - Tiziana Lembo
- The Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; (T.L.); (D.E.)
| | - Rudovick Kazwala
- The Nelson Mandela African Institution of Science and Technology, Arusha 23306, Tanzania; (R.K.); (G.S.)
| | - Divine Ekwem
- The Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK; (T.L.); (D.E.)
| | - Gabriel Shirima
- The Nelson Mandela African Institution of Science and Technology, Arusha 23306, Tanzania; (R.K.); (G.S.)
| | - Santina Grazioli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (S.G.); (E.B.); (G.P.)
| | - Emiliana Brocchi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (S.G.); (E.B.); (G.P.)
| | - Giulia Pezzoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (S.G.); (E.B.); (G.P.)
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Khan S, Ali Shah SA, Jamal SM. Evaluation of Sandwich Enzyme-Linked Immunosorbent Assay and Reverse Transcription Polymerase Chain Reaction for the Diagnosis of Foot-and-Mouth Disease. Intervirology 2021; 64:209-214. [PMID: 34139693 DOI: 10.1159/000517003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 05/03/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Foot-and-mouth disease (FMD) is an infectious and highly contagious disease of cloven-hoofed domestic and wild animals, causing heavy economic losses to the livestock industry. Rapid and reliable diagnosis of the disease is essential for the implementation of effective control measures. This study compared sandwich enzyme-linked immunosorbent assay (S-ELISA) and conventional reverse transcription polymerase chain reaction (RT-PCR) for the diagnosis of FMD. METHODS A total of 60 epithelial samples from suspected cases of FMD were tested using both S-ELISA and RT-PCR assays. The level of agreement between the assays was assessed by calculating the Kappa value. RESULTS S-ELISA detected 38 (63%) samples positive for FMD virus (FMDV). Being predominant, serotype O was detected in 22 (57.9%) of the total samples tested positive, whereas 9 (23.7%) and 7 (18.4%) samples were found positive for serotypes A and Asia-1, respectively. RT-PCR detected viral genome in 51 (85%) of the samples using pan-FMDV primers set, 1F/1R. Thirty-six samples were found positive and 7 negative by both the tests. The level of agreement between the tests was assessed by calculating the Kappa value, which was found to be fair (Kappa value = 0.303 and 95% CI = 0.089; 0.517) and significant (p = 0.009). However, 2 samples, which were found positive on S-ELISA tested negative on RT-PCR. This may be attributed to the presence of nucleotide mismatch(es) in the primer-binding sites that may have resulted in failure of amplification of the viral genome. The serotype-specific RT-PCR assays not only confirmed serotyping results of S-ELISA but were also able to establish serotype in 9 S-ELISA-negative but pan-FMDV RT-PCR-positive samples. CONCLUSIONS The RT-PCR assay contributes significantly to establishing a quick, sensitive, and definitive diagnosis of FMD in resource-constrained countries. Samples giving negative results in S-ELISA should be tested in RT-PCR for the disease detection and virus typing.
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Affiliation(s)
- Salman Khan
- Department of Biotechnology, University of Malakand, Dir Lower, Pakistan
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8
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Grazioli S, Ferris NP, Dho G, Pezzoni G, Morris AS, Mioulet V, Brocchi E. Development and validation of a simplified serotyping ELISA based on monoclonal antibodies for the diagnosis of foot-and-mouth disease virus serotypes O, A, C and Asia 1. Transbound Emerg Dis 2020; 67:3005-3015. [PMID: 32530134 DOI: 10.1111/tbed.13677] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/13/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022]
Abstract
This study describes the development and validation of a simplified enzyme-linked immunosorbent assay (ELISA) for the detection and discrimination of foot-and-mouth disease virus (FMDV) serotypes O, A, C and Asia 1. The multiplex ELISA was designed using selected, type-specific monoclonal antibodies (MAbs) coated onto ELISA plates as catching antibodies and a unique pan-FMDV MAb (1F10) as detector conjugate. Capture MAbs with the broadest intratypic reactivity were selected for each of the four FMDV serotypes by screening large panels of candidate MAbs with a wide spectrum of representative FMDV isolates. An additional pan-FMDV ELISA using 1F10 MAb for both capture and detection was used to complement the specific typing ELISAs to detect virus isolates, which might escape binding to the selected serotype-specific MAbs. This multiplex ELISA was prepared in a stabilized format, with immunoplates pre-coated with six MAbs and positive antigen controls already trapped by the relevant MAb, with the view to make available a diagnostic kit. Diagnostic performance of the MAbs-multiplex ELISA was analysed using 299 FMDV-positive epithelial suspensions representative of the antigenic and genomic variability within each serotype. Overall, the results provided evidence that the diagnostic performance of this assay platform is improved compared to the more complex polyclonal-based antigen detection ELISA; combining data from different serotypes and referring to the gold standard tests (i.e. virus isolation and/or RT-PCR), the MAbs-multiplex ELISA showed a sensitivity of 79% for the serotype-specific ELISA, compared to 72% for the polyclonal ELISA. The absence of reactivity of a minority of FMDV strains using the MAbs-multiplex ELISA can largely be attributed to deteriorated or low antigen concentration in the sample. This multiplex ELISA is simple, rapid and stable. FMDV antigenic diversity was adequately covered by the selected MAbs. Therefore, it can be used to replace existing polyclonal ELISAs for FMDV detection and serotyping.
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Affiliation(s)
- Santina Grazioli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
| | | | - Giovanna Dho
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
| | - Giulia Pezzoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
| | | | | | - Emiliana Brocchi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
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9
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Howson ELA, Orton RJ, Mioulet V, Lembo T, King DP, Fowler VL. GoPrime: Development of an In Silico Framework to Predict the Performance of Real-Time PCR Primers and Probes Using Foot-and-Mouth Disease Virus as a Model. Pathogens 2020; 9:pathogens9040303. [PMID: 32326039 PMCID: PMC7238122 DOI: 10.3390/pathogens9040303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/07/2020] [Accepted: 04/16/2020] [Indexed: 11/16/2022] Open
Abstract
Real-time PCR (rPCR) is a widely accepted diagnostic tool for the detection and quantification of nucleic acid targets. In order for these assays to achieve high sensitivity and specificity, primer and probe-template complementarity is essential; however, mismatches are often unavoidable and can result in false-negative results and errors in quantifying target sequences. Primer and probe sequences therefore require continual evaluation to ensure they remain fit for purpose. This paper describes the development of a linear model and associated computational tool (GoPrime) designed to predict the performance of rPCR primers and probes across multiple sequence data. Empirical data were generated using DNA oligonucleotides (n = 90) that systematically introduced variation in the primer and probe target regions of a diagnostic assay routinely used to detect foot-and-mouth disease virus (FMDV); an animal virus that exhibits a high degree of sequence variability. These assays revealed consistent impacts of patterns of substitutions in primer and probe-sites on rPCR cycle threshold (CT) and limit of detection (LOD). These data were used to populate GoPrime, which was subsequently used to predict rPCR results for DNA templates (n = 7) representing the natural sequence variability within FMDV. GoPrime was also applicable to other areas of the FMDV genome, with predictions for the likely targets of a FMDV-typing assay consistent with published experimental data. Although further work is required to improve these tools, including assessing the impact of primer-template mismatches in the reverse transcription step and the broader impact of mismatches for other assays, these data support the use of mathematical models for rapidly predicting the performance of rPCR primers and probes in silico.
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Affiliation(s)
- Emma L A Howson
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (E.LAH.); (V.M.); (V.LF.)
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK; (R.JO.); (T.L.)
| | - Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK; (R.JO.); (T.L.)
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | - Valerie Mioulet
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (E.LAH.); (V.M.); (V.LF.)
| | - Tiziana Lembo
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary & Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK; (R.JO.); (T.L.)
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (E.LAH.); (V.M.); (V.LF.)
- Correspondence: ; Tel.: +44-(0)1483-232441
| | - Veronica L Fowler
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK; (E.LAH.); (V.M.); (V.LF.)
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10
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Gray AR, Wood BA, Henry E, Azhar M, King DP, Mioulet V. Evaluation of Cell Lines for the Isolation of Foot-and-Mouth Disease Virus and Other Viruses Causing Vesicular Disease. Front Vet Sci 2020; 7:426. [PMID: 32851014 PMCID: PMC7401924 DOI: 10.3389/fvets.2020.00426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/12/2020] [Indexed: 12/26/2022] Open
Abstract
The most sensitive cell culture system for the isolation of foot-and-mouth disease virus (FMDV) is primary bovine thyroid (BTY) cells. However, BTY cells are seldom used because of the challenges associated with sourcing thyroids from FMDV-negative calves (particularly in FMD endemic countries), and the costs and time required to regularly prepare batches of cells. Two continuous cell lines, a fetal goat tongue cell line (ZZ-R 127) and a fetal porcine kidney cell line (LFBK-αVβ6), have been shown to be highly sensitive to FMDV. Here, we assessed the sensitivity of ZZ-R 127 and LFBK-αVβ6 cells relative to primary BTY cells by titrating a range of FMDV original samples and isolates. Both the ZZ-R 127 and LFBK-αVβ6 cells were susceptible to FMDV for >100 passages, and there were no significant differences in sensitivity relative to primary BTY cells. Notably, the LFBK-αVβ6 cell line was highly sensitive to the O/CATHAY porcine-adapted FMDV strain. These results support the use of ZZ-R 127 and LFBK-αVβ6 as sensitive alternatives to BTY cells for the isolation of FMDV, and highlight the use of LFBK-αVβ6 cells as an additional tool for the isolation of porcinophilic viruses.
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Affiliation(s)
- Ashley R Gray
- Vesicular Disease Reference Laboratory, The Pirbright Institute, Surrey, United Kingdom
| | - Britta A Wood
- Vesicular Disease Reference Laboratory, The Pirbright Institute, Surrey, United Kingdom
| | - Elisabeth Henry
- Vesicular Disease Reference Laboratory, The Pirbright Institute, Surrey, United Kingdom
| | - Mehreen Azhar
- Vesicular Disease Reference Laboratory, The Pirbright Institute, Surrey, United Kingdom
| | - Donald P King
- Vesicular Disease Reference Laboratory, The Pirbright Institute, Surrey, United Kingdom
| | - Valérie Mioulet
- Vesicular Disease Reference Laboratory, The Pirbright Institute, Surrey, United Kingdom
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11
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Wang H, Hou P, Zhao G, Yu L, Gao YW, He H. Development and evaluation of serotype-specific recombinase polymerase amplification combined with lateral flow dipstick assays for the diagnosis of foot-and-mouth disease virus serotype A, O and Asia1. BMC Vet Res 2018; 14:359. [PMID: 30458768 PMCID: PMC6245561 DOI: 10.1186/s12917-018-1644-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/09/2018] [Indexed: 11/10/2022] Open
Abstract
Background Foot-and-mouth disease (FMD) caused by foot-and-mouth disease virus (FMDV) is one of the most highly infectious diseases in livestock, and leads to huge economic losses. Early diagnosis and rapid differentiation of FMDV serotype is therefore integral to the prevention and control of FMD. In this study, a series of serotype-specific reverse transcription recombinase polymerase amplification assays combined with lateral flow dipstick (RPA-LFD) were establish to differentiate FMDV serotypes A, O or Asia 1, respectively. Results The serotype-specific primers and probes of RPA-LFD were designed to target conserved regions of the FMDV VP1 gene sequence, and three primer and probe sets of serotype-specific RPA-LFD were selected for amplification of FMDV serotypes A, O or Asia 1, respectively. Following incubation at 38 °C for 20 min, the RPA amplification products could be visualized by LFD. Analytical sensitivity of the RPA assay was then determined with ten-fold serial dilutions of RNA of VP1 gene and the recombinant vector respectively containing VP1 gene from FMDV serotypes A, O or Asia1, the detection limits of these assays were 3 copies of plasmid DNA or 50 copies of viral RNA per reaction. Moreover, the specificity of the assay was assessed, and there was no cross reactions with other viruses leading to bovine vesicular lesions. Furthermore, 126 clinical samples were respectively detected with RPA-LFD and real-time PCR (rPCR), there was 98.41% concordance between the two assays, and two samples were positive by RPA-LFD but negative in rPCR, these were confirmed as FMDV-positive through viral isolation in BHK-21 cells. It showed that RPA-LFD assay was more sensitive than the rPCR method in this study. Conclusion The development of serotype-specific RPA-LFD assay provides a rapid, sensitive, and specific method for differentiation of FMDV serotype A, O or Asia1, respectively. It is possible that the serotype-specific RPA-LFD assay may be used as a integral protocol for field detection of FMDV.
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Affiliation(s)
- Hongmei Wang
- Ruminant Diseases Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Peili Hou
- Ruminant Diseases Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Guimin Zhao
- Ruminant Diseases Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Li Yu
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, 150001, China
| | - Yu-Wei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute of Academy of Military Medical Sciences, Changchun, 130122, China.
| | - Hongbin He
- Ruminant Diseases Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China.
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12
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Lim DR, Kim HR, Park MJ, Chae HG, Ku BK, Nah JJ, Ryoo S, Wee SH, Park CK. A tailored reverse transcription loop-mediated isothermal amplification for sensitive and specific detection of serotype A foot-and-mouth disease virus circulating in pool 1 region countries. Transbound Emerg Dis 2018; 65:1898-1908. [PMID: 30054975 DOI: 10.1111/tbed.12971] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/07/2018] [Accepted: 07/02/2018] [Indexed: 11/29/2022]
Abstract
Rapid and accurate diagnosis of foot-and-mouth disease viruses (FMDV) is essential for the prompt control of FMD outbreaks. Reverse transcription polymerase chain reaction (RT-PCR) and real-time quantitative RT-PCR (qRT-PCR) are used for routine FMDV diagnosis as World Organisation for Animal Health-recommended diagnostic assays. However, these PCR-based assays require sophisticated equipment, specialized labour, and complicated procedures for the detection of amplified products, making them unsuitable for under-equipped laboratories in developing countries. In this study, to overcome these shortcomings, a simple, rapid, and cost-effective reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the sensitive and specific detection of serotype A FMDV circulating in the pool 1 region. The amplification could be completed in 40 min at 62°C, and the results could be visually detected by the naked eye without any additional detection systems. The assay specifically amplified the VP1 gene of the Sea-97 genotype of serotype A FMDV, but it did not amplify other viral nucleic acids. The limit of detection of the assay was 102 TCID50 /ml, which is 10 times more sensitive than RT-PCR and is comparable to the sensitivity of qRT-PCR. Evaluation of the assay using different FMDV strain serotypes showed 100% agreement with the results of RT-PCR. Surprisingly, the previously reported RT-LAMP assay did not detect all eight tested strains of serotype A FMDVs, due to multiple mismatches between primer and template sequences, demonstrating that it is not suitable for detecting serotype A FMDVs circulating in pool 1-region countries. Conversely, the newly developed RT-LAMP assay using improved primers can rapidly and accurately diagnose the genotype of Sea-97 strains of serotype A FMDVs from the pool 1 region. The established RT-LAMP assay in this study is a simple, rapid, specific, sensitive, and cost-effective tool for the detection of serotype A FMDV in the resource-limited pool 1-region countries.
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Affiliation(s)
- Da-Rae Lim
- College of Veterinary Medicine and Animal Disease Intervention Center, Kyungpook National University, Daegu, Korea
| | - Hye-Ryung Kim
- College of Veterinary Medicine and Animal Disease Intervention Center, Kyungpook National University, Daegu, Korea
| | - Min-Ji Park
- College of Veterinary Medicine and Animal Disease Intervention Center, Kyungpook National University, Daegu, Korea
| | - Ha-Gyeong Chae
- College of Veterinary Medicine and Animal Disease Intervention Center, Kyungpook National University, Daegu, Korea
| | - Bok-Kyung Ku
- Foot-and-Mouth Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Jin-Ju Nah
- Foot-and-Mouth Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Soyoon Ryoo
- Foot-and-Mouth Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Sung-Hwan Wee
- Foot-and-Mouth Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Korea
| | - Choi-Kyu Park
- College of Veterinary Medicine and Animal Disease Intervention Center, Kyungpook National University, Daegu, Korea
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13
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Lim DR, Kim HR, Park MJ, Chae HG, Ku BK, Nah JJ, Ryoo SY, Wee SH, Park YR, Jeon HS, Kim JJ, Jeon BY, Lee HW, Yeo SG, Park CK. An improved reverse transcription loop-mediated isothermal amplification assay for sensitive and specific detection of serotype O foot-and-mouth disease virus. J Virol Methods 2018; 260:6-13. [PMID: 29964077 DOI: 10.1016/j.jviromet.2018.06.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 11/25/2022]
Abstract
A sensitive and specific swarm primer-based reverse transcription loop-mediated isothermal amplification (sRT-LAMP) assay for the detection of serotype O foot-and-mouth disease virus (FMDV) was developed and evaluated. The assay specifically amplified the VP3 gene of serotype O FMDV, but did not amplify the VP3 gene of other serotype FMDVs or any other viruses. The limit of detection of the assay was 102 TCID50/mL or 103 RNA copies/μL, which is 100 times lower than that of the RT-LAMP assay without swarm primers. The new assay is 10 times more sensitive than reverse transcription-polymerase chain reaction (RT-PCR) and is comparable to the sensitivity of real time RT-PCR (qRT-PCR). Evaluation of the assay using different serotypes of FMDV strains showed 100% agreement with the RT-PCR results. The previously reported serotype O FMDV-specific RT-LAMP assay did not detect 20 out of 22 strains of serotype O FMDVs, probably due to multiple mismatches between the primer and template sequences, showing that it is not suitable for detecting the serotype O FMDVs circulating in Pool 1 region countries, including Korea. In contrast, the developed sRT-LAMP assay with improved primers can rapidly and accurately diagnose serotype O FMDVs circulating in Pool 1 region countries and will be a useful alternative to RT-PCR and qRT-PCR.
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Affiliation(s)
- Da-Rae Lim
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hye-Ryung Kim
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Min-Ji Park
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ha-Gyeong Chae
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Bok-Kyung Ku
- Foot-and-Mouth Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbuk-do 39660, Republic of Korea
| | - Jin-Ju Nah
- Foot-and-Mouth Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbuk-do 39660, Republic of Korea
| | - So-Yoon Ryoo
- Foot-and-Mouth Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbuk-do 39660, Republic of Korea
| | - Sung-Hwan Wee
- Foot-and-Mouth Disease Research Division, Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbuk-do 39660, Republic of Korea
| | - Yu-Ri Park
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu 41566, Republic of Korea; Avian Influenza Research & Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, Gyeongsangbuk-do 39660, Republic of Korea
| | | | | | - Bo-Young Jeon
- Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, Wonju 26493, Republic of Korea
| | - Hyeong-Woo Lee
- Institute of Research and Development, Scorpiogen Co., Hankyong National University, Anseong, Gyeonggi-do 17579, Republic of Korea
| | - Sang-Geon Yeo
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Choi-Kyu Park
- College of Veterinary Medicine & Animal Disease Intervention Center, Kyungpook National University, Daegu 41566, Republic of Korea.
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14
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Howson ELA, Armson B, Lyons NA, Chepkwony E, Kasanga CJ, Kandusi S, Ndusilo N, Yamazaki W, Gizaw D, Cleaveland S, Lembo T, Rauh R, Nelson WM, Wood BA, Mioulet V, King DP, Fowler VL. Direct detection and characterization of foot-and-mouth disease virus in East Africa using a field-ready real-time PCR platform. Transbound Emerg Dis 2018; 65:221-231. [PMID: 28758346 PMCID: PMC5811823 DOI: 10.1111/tbed.12684] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Indexed: 12/21/2022]
Abstract
Effective control and monitoring of foot-and-mouth disease (FMD) relies upon rapid and accurate disease confirmation. Currently, clinical samples are usually tested in reference laboratories using standardized assays recommended by The World Organisation for Animal Health (OIE). However, the requirements for prompt and serotype-specific diagnosis during FMD outbreaks, and the need to establish robust laboratory testing capacity in FMD-endemic countries have motivated the development of simple diagnostic platforms to support local decision-making. Using a portable thermocycler, the T-COR™ 8, this study describes the laboratory and field evaluation of a commercially available, lyophilized pan-serotype-specific real-time RT-PCR (rRT-PCR) assay and a newly available FMD virus (FMDV) typing assay (East Africa-specific for serotypes: O, A, Southern African Territories [SAT] 1 and 2). Analytical sensitivity, diagnostic sensitivity and specificity of the pan-serotype-specific lyophilized assay were comparable to that of an OIE-recommended laboratory-based rRT-PCR (determined using a panel of 57 FMDV-positive samples and six non-FMDV vesicular disease samples for differential diagnosis). The FMDV-typing assay was able to correctly identify the serotype of 33/36 FMDV-positive samples (no cross-reactivity between serotypes was evident). Furthermore, the assays were able to accurately detect and type FMDV RNA in multiple sample types, including epithelial tissue suspensions, serum, oesophageal-pharyngeal (OP) fluid and oral swabs, both with and without the use of nucleic acid extraction. When deployed in laboratory and field settings in Tanzania, Kenya and Ethiopia, both assays reliably detected and serotyped FMDV RNA in samples (n = 144) collected from pre-clinical, clinical and clinically recovered cattle. These data support the use of field-ready rRT-PCR platforms in endemic settings for simple, highly sensitive and rapid detection and/or characterization of FMDV.
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Affiliation(s)
- E. L. A. Howson
- The Pirbright InstitutePirbrightSurreyUK
- Institute of Biodiversity, Animal Health and Comparative MedicineCollege of Medical Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
| | - B. Armson
- The Pirbright InstitutePirbrightSurreyUK
- Institute of Biodiversity, Animal Health and Comparative MedicineCollege of Medical Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
| | - N. A. Lyons
- The Pirbright InstitutePirbrightSurreyUK
- European Commission for the Control of Foot‐and‐Mouth Disease (EuFMD)Animal Production and Health DivisionFAORomeItaly
| | - E. Chepkwony
- Foot‐and‐Mouth Disease Laboratory, EmbakasiMinistry of Agriculture, Livestock, Fisheries and Blue EconomyNairobiKenya
| | - C. J. Kasanga
- Department of Biochemistry, Molecular Biology and BiotechnologyCollege of Veterinary and Medical SciencesSokoine University of Agriculture, Chuo KikuuMorogoroTanzania
| | - S. Kandusi
- Department of Biochemistry, Molecular Biology and BiotechnologyCollege of Veterinary and Medical SciencesSokoine University of Agriculture, Chuo KikuuMorogoroTanzania
| | - N. Ndusilo
- Department of Biochemistry, Molecular Biology and BiotechnologyCollege of Veterinary and Medical SciencesSokoine University of Agriculture, Chuo KikuuMorogoroTanzania
| | - W. Yamazaki
- Department of Veterinary ScienceFaculty of AgricultureUniversity of MiyazakiMiyazakiJapan
| | - D. Gizaw
- National Animal Health Diagnostic & Investigation CentreSebetaOromiaEthiopia
| | - S. Cleaveland
- Institute of Biodiversity, Animal Health and Comparative MedicineCollege of Medical Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
| | - T. Lembo
- Institute of Biodiversity, Animal Health and Comparative MedicineCollege of Medical Veterinary & Life SciencesUniversity of GlasgowGlasgowUK
| | | | | | - B. A. Wood
- The Pirbright InstitutePirbrightSurreyUK
| | - V. Mioulet
- The Pirbright InstitutePirbrightSurreyUK
| | - D. P. King
- The Pirbright InstitutePirbrightSurreyUK
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15
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Saduakassova MA, Sultanov AA, Kutumbetov LB, Wadsworth J, A Wood B, Knowles NJ, King DP, Bachanek-Bankowska K. Development and evaluation of a novel real-time RT-PCR to detect foot-and-mouth disease viruses from the emerging A/ASIA/G-VII lineage. J Virol Methods 2018; 252:37-41. [PMID: 29113733 PMCID: PMC5764150 DOI: 10.1016/j.jviromet.2017.10.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/10/2017] [Accepted: 10/30/2017] [Indexed: 11/24/2022]
Abstract
A new lineage of foot-and-mouth disease virus (FMDV), called A/ASIA/G-VII, emerged from the Indian subcontinent in 2015 and continues to spread in Western Asia. Currently, the distribution of viruses belonging to this lineage is defined using sequencing approaches, but other cheaper and faster diagnostic methods are urgently needed. Thus, this study describes the development and validation of a novel A/ASIA/G-VII lineage-specific real-time RT-PCR (rRT-PCR). Diagnostic sensitivity and specificity were evaluated using representative field specimens and isolates from the A/ASIA/G-VII lineage, as well as samples comprising other FMDV lineages that co-circulate in Asia (n=54). This lineage-specific assay accurately detected all A/ASIA/G-VII samples tested (n=29), and no detection was observed for samples belonging to other FMDV lineages (n=25), namely A/ASIA/Sea-97, A/ASIA/Iran-05SIS-10, A/ASIA/Iran-05FAR-11, Asia1/ASIA/Sindh-08, O/CATHAY, O/ME-SA/PanAsia-2ANT-10, O/ME-SA/Ind-2001d, O/SEA/Mya-98. Additionally, the limit of detection was found to be at least equivalent to a pan-serotypic rRT-PCR assay. Therefore, these data indicate that this newly developed rRT-PCR assay can be applied to characterise field isolates in countries where the A/ASIA/G-VII lineage is endemic, as well as to monitor new incursions and outbreaks due to this lineage.
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Affiliation(s)
- Meruyert A Saduakassova
- Kazakh Scientific Research Veterinary Institute, 223 Raimbek Avenue, Almaty, 050016, Kazakhstan
| | - Akhmetzhan A Sultanov
- Kazakh Scientific Research Veterinary Institute, 223 Raimbek Avenue, Almaty, 050016, Kazakhstan
| | - Lespek B Kutumbetov
- Kazakh Scientific Research Veterinary Institute, 223 Raimbek Avenue, Almaty, 050016, Kazakhstan
| | - Jemma Wadsworth
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, United Kingdom
| | - Britta A Wood
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, United Kingdom
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, United Kingdom
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, United Kingdom
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16
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Bachanek-Bankowska K, Mero HR, Wadsworth J, Mioulet V, Sallu R, Belsham GJ, Kasanga CJ, Knowles NJ, King DP. Development and evaluation of tailored specific real-time RT-PCR assays for detection of foot-and-mouth disease virus serotypes circulating in East Africa. J Virol Methods 2016; 237:114-120. [PMID: 27575682 DOI: 10.1016/j.jviromet.2016.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 11/27/2022]
Abstract
Rapid, reliable and accurate diagnostic methods provide essential support to programmes that monitor and control foot-and-mouth disease (FMD). While pan-specific molecular tests for FMD virus (FMDV) detection are well established and widely used in endemic and FMD-free countries, current serotyping methods mainly rely either on antigen detection ELISAs or nucleotide sequencing approaches. This report describes the development of a panel of serotype-specific real-time RT-PCR assays (rRT-PCR) tailored to detect FMDV lineages currently circulating in East Africa. These assays target sequences within the VP1-coding region that share high intra-lineage identity, but do not cross-react with FMD viruses from other serotypes that circulate in the region. These serotype-specific assays operate with the same thermal profile as the pan-diagnostic tests making it possible to run them in parallel to produce CT values comparable to the pan-diagnostic test detecting the 3D-coding region. These assays were evaluated alongside the established pan-specific molecular test using field samples and virus isolates collected from Tanzania, Kenya and Ethiopia that had been previously characterised by nucleotide sequencing. Samples (n=71) representing serotype A (topotype AFRICA, lineage G-I), serotype O (topotypes EA-2 and EA-4), serotype SAT 1 (topotype I (NWZ)) and serotype SAT2 (topotype IV) were correctly identified with these rRT-PCR assays. Furthermore, FMDV RNA from samples that did not contain infectious virus could still be serotyped using these assays. These serotype-specific real-time RT-PCR assays can detect and characterise FMDVs currently circulating in East Africa and hence improve disease control in this region.
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Affiliation(s)
| | - Herieth R Mero
- Department of Microbiology and Parasitology & Southern African Centre for Infectious diseases Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Jemma Wadsworth
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Valerie Mioulet
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Raphael Sallu
- Tanzania Veterinary Laboratory Agency, P. O. Box 9252, Dar es Salaam, Tanzania
| | - Graham J Belsham
- National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave DK-4771, Denmark
| | - Christopher J Kasanga
- Department of Microbiology and Parasitology & Southern African Centre for Infectious diseases Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
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17
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Ullah A, Jamal SM, Romey A, Gorna K, Kakar MA, Abbas F, Ahmad J, Zientara S, Bakkali Kassimi L. Genetic Characterization of Serotypes A and Asia-1 Foot-and-mouth Disease Viruses in Balochistan, Pakistan, in 2011. Transbound Emerg Dis 2016; 64:1569-1578. [DOI: 10.1111/tbed.12548] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Indexed: 11/29/2022]
Affiliation(s)
- A. Ullah
- Center for Advanced Studies in Vaccinology and Biotechnology (CASVAB); University of Balochistan; Quetta Pakistan
- Department of Biotechnology and Informatics; Faculty of Life Sciences and Informatics; Balochistan University of Information Technology, Engineering and Management Sciences; Beleli Quetta
| | - S. M. Jamal
- Department of Biotechnology; University of Malakand; Chakdara Khyber Pakhtunkhwa Pakistan
| | - A. Romey
- ANSES; Laboratory for Animal Health; UMR 1161 Virology (ANSES, INRA, ENVA); University of Paris EST; Maisons-Alfort France
| | - K. Gorna
- ANSES; Laboratory for Animal Health; UMR 1161 Virology (ANSES, INRA, ENVA); University of Paris EST; Maisons-Alfort France
| | - M. A. Kakar
- Livestock and Dairy Development Department; Quetta Balochistan
| | - F. Abbas
- Center for Advanced Studies in Vaccinology and Biotechnology (CASVAB); University of Balochistan; Quetta Pakistan
| | - J. Ahmad
- Department of Biotechnology and Informatics; Faculty of Life Sciences and Informatics; Balochistan University of Information Technology, Engineering and Management Sciences; Beleli Quetta
| | - S. Zientara
- ANSES; Laboratory for Animal Health; UMR 1161 Virology (ANSES, INRA, ENVA); University of Paris EST; Maisons-Alfort France
| | - L. Bakkali Kassimi
- ANSES; Laboratory for Animal Health; UMR 1161 Virology (ANSES, INRA, ENVA); University of Paris EST; Maisons-Alfort France
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18
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Knight-Jones TJD, Robinson L, Charleston B, Rodriguez LL, Gay CG, Sumption KJ, Vosloo W. Global Foot-and-Mouth Disease Research Update and Gap Analysis: 4 - Diagnostics. Transbound Emerg Dis 2016; 63 Suppl 1:42-8. [DOI: 10.1111/tbed.12523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2016] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - L. L. Rodriguez
- Plum Island Animal Disease Center; ARS; USDA; Greenport NY USA
| | - C. G. Gay
- Agricultural Research Service; USDA; National Program 103-Animal Health; Beltsville MD USA
| | - K. J. Sumption
- European Commission for the Control of FMD (EuFMD); FAO; Rome Italy
| | - W. Vosloo
- Australian Animal Health Laboratory; CSIRO-Biosecurity Flagship; Geelong VIC Australia
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19
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Mei Y, He C, Deng W, Ba D, Yang M, Zhang J, Zhang S, Shen P, Chen X. A Real-Time PCR Method to Detect the Population Level of Halovirus SNJ1. PLoS One 2016; 11:e0155642. [PMID: 27192212 PMCID: PMC4871410 DOI: 10.1371/journal.pone.0155642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 05/02/2016] [Indexed: 11/21/2022] Open
Abstract
Although viruses of haloarchaea are the predominant predator in hypersaline ecosystem, the culture studies about halovirus-host systems are infancy. The main reason is the tradition methodology (plaque assay) for virus-host interaction depends on culturable and susceptible host. Actually, more than 90% of haloarchaea are unculturable. Therefore, it is necessary to establish an approach for detecting the dynamics of virus in hypersaline environment without culture. In this study, we report a convenient method to determine the dynamics of halovirus SNJ1 based on quantitative real-time PCR (qPCR). All findings showed that the qPCR method was specific (single peak in melt curves), accurate (a good linear relationship between the log of the PFU and the Ct values, R2 = 0.99), reproducible (low coefficient of variations, below 1%). Additionally, the physicochemical characteristics of the samples tested did not influence the stability of qPCR. Therefore, the qPCR method has the potential value in quantifying and surveying haloviruses in halophilic ecological system.
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Affiliation(s)
- Yunjun Mei
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, Hubei, China
- * E-mail:
| | - Congcong He
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Wei Deng
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Dala Ba
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Ming Yang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Jian Zhang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Shunxi Zhang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Ping Shen
- State Key Laboratory of Virology, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Science, Wuhan University, Wuhan, Hubei, China
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