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Singanallur NB, Anderson DE, Sessions OM, Kamaraj US, Bowden TR, Horsington J, Cowled C, Wang LF, Vosloo W. Probe capture enrichment next-generation sequencing of complete foot-and-mouth disease virus genomes in clinical samples. J Virol Methods 2019; 272:113703. [PMID: 31336142 DOI: 10.1016/j.jviromet.2019.113703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/04/2019] [Accepted: 07/17/2019] [Indexed: 01/02/2023]
Abstract
Next-generation sequencing (NGS) techniques offer an unprecedented "step-change" increase in the quantity and quality of sequence data rapidly generated from a sample and can be applied to obtain ultra-deep coverage of viral genomes. This is not possible with the routinely used Sanger sequencing method that gives the consensus reads, or by cloning approaches. In this study, a targeted-enrichment methodology for the simultaneous acquisition of complete foot-and-mouth disease virus (FMDV) genomes directly from clinical samples is presented. Biotinylated oligonucleotide probes (120 nt) were used to capture and enrich viral RNA following library preparation. To create a virus capture panel targeting serotype O and A simultaneously, 18 baits targeting the highly conserved regions of the 8.3 kb FMDV genome were synthesised, with 14 common to both serotypes, 2 specific to serotype O and 2 specific to serotype A. These baits were used to capture and enrich FMDV RNA (as cDNA) from samples collected during one pathogenesis and two vaccine efficacy trials, where pigs were infected with serotype O or A viruses. After enrichment, FMDV-specific sequencing reads increased by almost 3000-fold. The sequence data were used in variant call analysis to identify single nucleotide polymorphisms (SNPs). This methodology was robust in its ability to capture diverse sequences, was shown to be highly sensitive, and can be easily scaled for large-scale epidemiological studies.
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Affiliation(s)
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - October M Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore
| | - Uma S Kamaraj
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Timothy R Bowden
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Jacquelyn Horsington
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Christopher Cowled
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wilna Vosloo
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
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2
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King DP, Ferris NP, Shaw AE, Reid SM, Hutchings GH, Giuffre AC, Robida JM, Callahan JD, Nelson WM, Beckham TR. Detection of Foot-and-Mouth Disease Virus: Comparative Diagnostic Sensitivity of Two Independent Real-Time Reverse Transcription-Polymerase Chain Reaction Assays. J Vet Diagn Invest 2016; 18:93-7. [PMID: 16566264 DOI: 10.1177/104063870601800114] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Rapid and accurate diagnosis is central to the effective control of foot-and-mouth disease (FMD). It is now recognized that reverse-transcription polymerase chain reaction (RT-PCR) assays can play an important role in the routine detection of FMD virus (FMDV) in clinical samples. The aim of this study was to compare the ability of 2 independent real-time RT-PCR (rRT-PCR) assays targeting the 5′ untranslated region (5′UTR) and RNA polymerase (3D) to detect FMDV in clinical samples. There was concordance between the results generated by the 2 assays for 88.1% (347 of 394) of RNA samples extracted from suspensions of epithelial tissue obtained from suspect FMD cases. The comparison between the 2 tests highlighted 19 FMDV isolates (13 for the 5′UTR and 6 for the 3D assay), which failed to produce a signal in 1 assay but gave a positive signal in the other. The sequence of the genomic targets of selected isolates highlighted nucleotide substitutions in the primer or probe regions, thereby providing an explanation for negative results generated in the rRT-PCR assays. These data illustrate the importance of the continuous monitoring of circulating FMDV field strains to ensure the design of the rRT-PCR assay remains fit for purpose and suggest that the use of multiple diagnostic targets could further enhance the sensitivity of molecular methods for the detection of FMDV
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Affiliation(s)
- Donald P King
- Institute for Animal Health, Pirbright Laboratory, Surrey, UK.
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Gorna K, Relmy A, Romey A, Zientara S, Blaise-Boisseau S, Bakkali-Kassimi L. Establishment and validation of two duplex one-step real-time RT-PCR assays for diagnosis of foot-and-mouth disease. J Virol Methods 2016; 235:168-175. [PMID: 27317973 DOI: 10.1016/j.jviromet.2016.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 11/19/2022]
Abstract
Two duplex one-step TaqMan-based RT-PCR protocols for detection of foot-and-mouth disease virus (FMDV) were established and validated. Each RT-PCR test consists of a ready-to-use master mix for simultaneous detection of the well established 3D or IRES FMDV targets and incorporates the host β-actin mRNA as an internal control target, in a single-tube assay. The two real-time RT-PCR 3D/β-actin and IRES/β-actin tests are highly sensitive and able to detect up to 7TCID50/ml of FMDV and 10 copies/1μl of viral RNA. In field epithelium samples, the diagnostic sensitivity was 100% (95% CI; 91-100%) for the 3D/β-actin test and 97% (95% CI; 87-100%) for the IRES/β-actin test. The diagnostic specificity was 100% (95% CI; 95-100%) for both RT-PCRs. In addition, the two protocols proved to be robust, showing inter-assay coefficients of variation ranging from 1.94% to 6.73% for the IRES target and from 2.33% to 5.42% for the 3D target for different RNA extractions and different RT-PCR conditions. The internally controlled one-step real-time RT-PCR protocols described in this study provide a rapid, effective and reliable method for the detection of FMDV and thus may improve the routine diagnosis for foot-and-mouth disease.
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Affiliation(s)
- K Gorna
- Université Paris EST, ANSES, Laboratoire de Santé Animale, UMR Virologie 1161 (ANSES INRA ENVA), Laboratoire National et OIE de référence pour la fièvre aphteuse, 14 rue Pierre et Marie Curie, 94706 Maisons-Alfort, France
| | - A Relmy
- Université Paris EST, ANSES, Laboratoire de Santé Animale, UMR Virologie 1161 (ANSES INRA ENVA), Laboratoire National et OIE de référence pour la fièvre aphteuse, 14 rue Pierre et Marie Curie, 94706 Maisons-Alfort, France
| | - A Romey
- Université Paris EST, ANSES, Laboratoire de Santé Animale, UMR Virologie 1161 (ANSES INRA ENVA), Laboratoire National et OIE de référence pour la fièvre aphteuse, 14 rue Pierre et Marie Curie, 94706 Maisons-Alfort, France
| | - S Zientara
- Université Paris EST, ANSES, Laboratoire de Santé Animale, UMR Virologie 1161 (ANSES INRA ENVA), Laboratoire National et OIE de référence pour la fièvre aphteuse, 14 rue Pierre et Marie Curie, 94706 Maisons-Alfort, France
| | - S Blaise-Boisseau
- Université Paris EST, ANSES, Laboratoire de Santé Animale, UMR Virologie 1161 (ANSES INRA ENVA), Laboratoire National et OIE de référence pour la fièvre aphteuse, 14 rue Pierre et Marie Curie, 94706 Maisons-Alfort, France
| | - L Bakkali-Kassimi
- Université Paris EST, ANSES, Laboratoire de Santé Animale, UMR Virologie 1161 (ANSES INRA ENVA), Laboratoire National et OIE de référence pour la fièvre aphteuse, 14 rue Pierre et Marie Curie, 94706 Maisons-Alfort, France.
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Nagendrakumar SB, Hong NTT, Geoffrey FT, Jacqueline MM, Andrew D, Michelle G, Van Phuc K, Ngon QV, Phuong LTT, Phuc NNH, Hanh TX, Van Hung V, Quynhanh LT, Tan TM, Long NT, Wilna V. A Malaysia 97 monovalent foot-and-mouth disease vaccine (>6PD50/dose) protects pigs against challenge with a variant FMDV A SEA-97 lineage virus, 4 and 7 days post vaccination. Vaccine 2015; 33:4513-9. [PMID: 26192355 DOI: 10.1016/j.vaccine.2015.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/30/2015] [Accepted: 07/07/2015] [Indexed: 11/16/2022]
Abstract
Pigs play a significant role during outbreaks of foot-and-mouth disease (FMD) due to their ability to amplify the virus. It is therefore essential to determine what role vaccination could play to prevent clinical disease and lower virus excretion into the environment. In this study we investigated the efficacy of the double oil emulsion A Malaysia 97 vaccine (>6PD50/dose) against heterologous challenge with an isolate belonging to the A SEA-97 lineage at 4 and 7 days post vaccination (dpv). In addition, we determined whether physical separation of pigs in the same room could prevent virus transmission. Statistically there was no difference in the level of protection offered by 4 and 7 dpv. However, no clinical disease or viral RNA was detected in the blood of pigs challenged 4 dpv, although three of the pigs had antibodies to the non-structural proteins (NSPs), indicating viral replication. Viral RNA was also detected in nasal and saliva swabs, but on very few occasions. Two of the pigs vaccinated seven days prior to challenge had vesicles distal from the injection site, but on the inoculated foot, and two pigs had viral RNA detected in the blood. One pig sero-converted to the NSPs. In contrast, all unvaccinated and inoculated pigs had evidence of infection. No infection occurred in any of the susceptible pigs in the same room, but separated from the infected pigs, indicating that strict biosecurity measures were sufficient under these experimental conditions to prevent virus transmission. However, viral RNA was detected in the nasal swabs of one group of pigs, but apparently not at sufficient levels to cause clinical disease. Vaccination led to a significant decrease in viral RNA in vaccinated pigs compared to unvaccinated and infected pigs, even with this heterologous challenge, and could therefore be considered as a control option during outbreaks.
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Affiliation(s)
| | | | - Fosgate T Geoffrey
- Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | | | - Davis Andrew
- Australian Animal Health Laboratory, CSIRO-Biosecurity Flagship, Geelong, Australia
| | - Giles Michelle
- Australian Animal Health Laboratory, CSIRO-Biosecurity Flagship, Geelong, Australia
| | - Kim Van Phuc
- National Veterinary Company, Ho Chi Minh City, Vietnam
| | - Quach Vo Ngon
- National Veterinary Company, Ho Chi Minh City, Vietnam
| | | | | | | | - Vo Van Hung
- Center for Veterinary Diagnostics, Regional Animal Health Office 6, Ho Chi Minh City, Vietnam
| | - Le Thi Quynhanh
- Center for Veterinary Diagnostics, Regional Animal Health Office 6, Ho Chi Minh City, Vietnam
| | - Tran Minh Tan
- Center for Veterinary Diagnostics, Regional Animal Health Office 6, Ho Chi Minh City, Vietnam
| | - Ngo Thanh Long
- Center for Veterinary Diagnostics, Regional Animal Health Office 6, Ho Chi Minh City, Vietnam
| | - Vosloo Wilna
- Australian Animal Health Laboratory, CSIRO-Biosecurity Flagship, Geelong, Australia.
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Efficacy of a high potency O1 Manisa monovalent vaccine against heterologous challenge with a FMDV O Mya98 lineage virus in pigs 4 and 7 days post vaccination. Vaccine 2015; 33:2778-85. [PMID: 25917677 DOI: 10.1016/j.vaccine.2015.04.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 04/02/2015] [Accepted: 04/13/2015] [Indexed: 11/20/2022]
Abstract
Early protection with a high potency (>6PD50) foot-and-mouth disease (FMD) O1 Manisa (Middle-East South Asia lineage) vaccine against challenge with O/VIT/2010 (O Mya98 lineage) was tested in pigs. Only two pigs that were vaccinated seven days prior to challenge had any demonstrable antibodies as a result of vaccination at the time of challenge. However, 80% and 60% of pigs that were vaccinated seven and four days prior to coronary band challenge were protected. Vaccination significantly reduced the amount of virus excreted in nasal swabs, saliva and faeces compared to unvaccinated and infected controls. Virus and viral RNA could be detected in some pigs until termination of the experiment 14 days after challenge. Antibodies to the non-structural proteins (NSP) were detected in only one pig that was challenged four days post vaccination (dpv) and transiently in two pigs that were challenged sevendpv at only one time point. For each vaccine and control group, a group of unvaccinated pigs were kept in the same room but with no direct contact with the infected pigs to determine whether vaccination prevented transmission. Despite the presence of live virus and viral RNA in these indirect contact pigs, the groups in contact with the vaccinated and infected pigs did not develop clinical signs nor did they sero-convert. Contact pigs in the same room as unvaccinated challenged controls did show signs of disease and virus infection that resulted in sero-conversion to the NSP. A breach of the wall that separated the two groups at nine days post challenge might have contributed to this finding. This study showed that high potency vaccine can provide protection to pigs soon after vaccination and that aerosol transmission within rooms is a rare event.
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Vosloo W, Morris J, Davis A, Giles M, Wang J, Nguyen HTT, Kim PV, Quach NV, Le PTT, Nguyen P, Dang H, Tran HX, Vu PP, Hung VV, Le QT, Tran TM, Mai TMT, Le QTV, Singanallur NB. Collection of Oral Fluids Using Cotton Ropes as a Sampling Method to Detect Foot-and-Mouth Disease Virus Infection in Pigs. Transbound Emerg Dis 2013; 62:e71-5. [DOI: 10.1111/tbed.12196] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Indexed: 11/27/2022]
Affiliation(s)
- W. Vosloo
- CSIRO-Australian Animal Health Laboratory; Geelong Vic. Australia
| | - J. Morris
- CSIRO-Australian Animal Health Laboratory; Geelong Vic. Australia
| | - A. Davis
- CSIRO-Australian Animal Health Laboratory; Geelong Vic. Australia
| | - M. Giles
- CSIRO-Australian Animal Health Laboratory; Geelong Vic. Australia
| | - J. Wang
- CSIRO-Australian Animal Health Laboratory; Geelong Vic. Australia
| | | | - P. V. Kim
- National Veterinary Company; Ho Chi Minh City Vietnam
| | - N. V. Quach
- National Veterinary Company; Ho Chi Minh City Vietnam
| | - P. T. T. Le
- National Veterinary Company; Ho Chi Minh City Vietnam
| | - P.H.N. Nguyen
- National Veterinary Company; Ho Chi Minh City Vietnam
| | - H. Dang
- National Veterinary Company; Ho Chi Minh City Vietnam
| | - H. X. Tran
- National Veterinary Company; Ho Chi Minh City Vietnam
| | - P. P. Vu
- Center for Veterinary Diagnostics; Ho Chi Minh City Vietnam
| | - V. V. Hung
- Center for Veterinary Diagnostics; Ho Chi Minh City Vietnam
| | - Q. T. Le
- Center for Veterinary Diagnostics; Ho Chi Minh City Vietnam
| | - T. M. Tran
- Center for Veterinary Diagnostics; Ho Chi Minh City Vietnam
| | - T. M. T. Mai
- Center for Veterinary Diagnostics; Ho Chi Minh City Vietnam
| | - Q. T. V. Le
- Center for Veterinary Diagnostics; Ho Chi Minh City Vietnam
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Reid SM, Ebert K, Bachanek-Bankowska K, Batten C, Sanders A, Wright C, Shaw AE, Ryan ED, Hutchings GH, Ferris NP, Paton DJ, King DP. Performance of real-time reverse transcription polymerase chain reaction for the detection of foot-and-mouth disease virus during field outbreaks in the United Kingdom in 2007. J Vet Diagn Invest 2009; 21:321-30. [PMID: 19407083 DOI: 10.1177/104063870902100303] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Rapid and accurate diagnosis is essential for effective control of foot-and-mouth disease (FMD). The present report describes the practical steps undertaken to deploy a real-time reverse transcription polymerase chain reaction (real-time RT-PCR) to process the samples received during the outbreaks of FMD in the United Kingdom in 2007. Two independent real-time RT-PCR assays targeting different regions (5'UTR and 3D) of the FMD virus (FMDV) genome were used to confirm the presence of FMDV in clinical samples collected from the first infected premises. Once the FMDV strain responsible had been sequenced, a single real-time RT-PCR assay (3D) was selected to test a total of 3,216 samples, including material from all 8 infected premises. Using a 96-well automated system to prepare nucleic acid template, up to 84 samples could be processed within 5 hr of submission, and up to 269 samples were tested per working day. A conservative cut-off was used to designate positive samples, giving rise to an assay specificity of 99.9% or 100% for negative control material or samples collected from negative premises, respectively. For the first time, real-time RT-PCR results were used to recognize preclinical FMD in a cattle herd. Furthermore, during the later stages of the outbreaks, the real-time RT-PCR assay supported an active surveillance program within high-risk cattle herds. To the authors' knowledge, this is the first documented use of real-time RT-PCR as a principal laboratory diagnostic tool following introduction of FMD into a country that was FMD-free (without vaccination) and highlights the advantages of this assay to support control decisions during disease outbreaks.
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Affiliation(s)
- Scott M Reid
- Institute for Animal Health, Pirbright, Woking, Surrey, United Kingdom.
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Hoffmann B, Beer M, Reid SM, Mertens P, Oura CAL, van Rijn PA, Slomka MJ, Banks J, Brown IH, Alexander DJ, King DP. A review of RT-PCR technologies used in veterinary virology and disease control: sensitive and specific diagnosis of five livestock diseases notifiable to the World Organisation for Animal Health. Vet Microbiol 2009; 139:1-23. [PMID: 19497689 DOI: 10.1016/j.vetmic.2009.04.034] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 04/15/2009] [Accepted: 04/28/2009] [Indexed: 12/31/2022]
Abstract
Real-time, reverse transcription polymerase chain reaction (rRT-PCR) has become one of the most widely used methods in the field of molecular diagnostics and research. The potential of this format to provide sensitive, specific and swift detection and quantification of viral RNAs has made it an indispensable tool for state-of-the-art diagnostics of important human and animal viral pathogens. Integration of these assays into automated liquid handling platforms for nucleic acid extraction increases the rate and standardisation of sample throughput and decreases the potential for cross-contamination. The reliability of these assays can be further enhanced by using internal controls to validate test results. Based on these advantageous characteristics, numerous robust rRT-PCRs systems have been developed and validated for important epizootic diseases of livestock. Here, we review the rRT-PCR assays that have been developed for the detection of five RNA viruses that cause diseases that are notifiable to the World Organisation for Animal Health (OIE), namely: foot-and-mouth disease, classical swine fever, bluetongue disease, avian influenza and Newcastle disease. The performance of these tests for viral diagnostics and disease control and prospects for improved strategies in the future are discussed.
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Affiliation(s)
- Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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Paixão TA, Neta AVC, Paiva NO, Reis JR, Barbosa MS, Serra CV, Silva RR, Beckham TR, Martin BM, Clarke NP, Adams LG, Santos RL. Diagnosis of foot-and mouth disease by real time reverse transcription polymerase chain reaction under field conditions in Brazil. BMC Vet Res 2008; 4:53. [PMID: 19117507 PMCID: PMC2631516 DOI: 10.1186/1746-6148-4-53] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 12/31/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Foot-and-mouth disease (FMD) is an economically important and highly contagious viral disease that affects cloven-hoofed domestic and wild animals. Virus isolation and enzyme-linked immunosorbent assay (ELISA) are the gold standard tests for diagnosis of FMD. As these methods are time consuming, assays based on viral nucleic acid amplification have been developed. RESULTS A previously described real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay with high sensitivity and specificity under laboratorial and experimental conditions was used in the current study. To verify the applicability of this assay under field conditions in Brazil, 460 oral swabs from cattle were collected in areas free of FMD (n = 200) and from areas with outbreaks of FMD (n = 260). Three samples from areas with outbreaks of FMD were positive by real-time RT-PCR, and 2 of those samples were positive by virus isolation and ELISA. Four other samples were considered inconclusive by real-time RT-PCR (threshold cycle [Ct] > 40); whereas all 200 samples from an area free of FMD were real-time RT-PCR negative. CONCLUSION real-time RT-PCR is a powerful technique for reliable detection of FMDV in a fraction of the time required for virus isolation and ELISA. However, it is noteworthy that lack of infrastructure in certain areas with high risk of FMD may be a limiting factor for using real-time RT-PCR as a routine diagnostic tool.
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Affiliation(s)
- Tatiane A Paixão
- Departamento de Clínica e Cirurgia Veterinária, Escola de Veterinária da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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Diagnostic evaluation of multiplexed reverse transcription-PCR microsphere array assay for detection of foot-and-mouth and look-alike disease viruses. J Clin Microbiol 2008; 46:1081-9. [PMID: 18216216 DOI: 10.1128/jcm.01740-07] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A high-throughput multiplexed assay was developed for the differential laboratory detection of foot-and-mouth disease virus (FMDV) from viruses that cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses by using multiplexed reverse transcription-PCR (mRT-PCR) amplification coupled with a microsphere hybridization array and flow-cytometric detection. Two of the 17 primer-probe sets included in this multiplex assay were adopted from previously characterized real-time RT-PCR (rRT-PCR) assays for FMDV. The diagnostic accuracy of the mRT-PCR assay was evaluated using 287 field samples, including 247 samples (213 true-positive samples and 35 true-negative samples) from suspected cases of foot-and-mouth disease collected from 65 countries between 1965 and 2006 and 39 true-negative samples collected from healthy animals. The mRT-PCR assay results were compared to those of two singleplex rRT-PCR assays, using virus isolation with antigen enzyme-linked immunosorbent assays as the reference method. The diagnostic sensitivity of the mRT-PCR assay for FMDV was 93.9% (95% confidence interval [CI], 89.8 to 96.4%), and the sensitivity was 98.1% (95% CI, 95.3 to 99.3%) for the two singleplex rRT-PCR assays used in combination. In addition, the assay could reliably differentiate between FMDV and other vesicular viruses, such as swine vesicular disease virus and vesicular exanthema of swine virus. Interestingly, the mRT-PCR detected parapoxvirus (n = 2) and bovine viral diarrhea virus (n = 2) in clinical samples, demonstrating the screening potential of this mRT-PCR assay to identify viruses in FMDV-negative material not previously recognized by using focused single-target rRT-PCR assays.
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Schembri N, Hart K, Petersen R, Whittington R. Assessment of the management practices facilitating the establishment and spread of exotic diseases of pigs in the Sydney region. Aust Vet J 2006; 84:341-8. [PMID: 17359469 DOI: 10.1111/j.1751-0813.2006.00035.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
OBJECTIVE To assess management factors that would influence the establishment and spread of exotic diseases in pigs in the Sydney region. DESIGN Saleyard and pig producer practices that could assist the initiation and subsequent spread of exotic diseases in pigs were surveyed and assessed over a 12 month period. PROCEDURE Two saleyards in the Sydney region selling pigs were attended weekly for 12 months (2002-2003) to collect details on vendors and purchasers of pigs. Pig producer locations were mapped. All pig farmers on the Department of Primary Industries temporary brand register were surveyed to record management practices and knowledge of exotic diseases. Swine brands were inspected to determine their quality as a tracing mechanism. RESULTS There were 101 pig sale days during the survey period with 13,869 pigs sold. There were 305 vendors, of whom 95% were identifiable through saleyard records. However, only 40% of the 377 purchasers were identifiable. More than one third of the 1749 transactions were for cash without the identity of the purchaser being recorded at the saleyards. Some 3% of pigs failed to sell and were returned to the property of origin. A total of 64 of 132 pig producers in the Sydney region were surveyed and 52 responded with survey information. The production systems of pig producers were predominately intensive or semi-intensive (88%) with 69% of these operators being small hobby producers. Pigs were mostly fed household and commercial scraps that were free of meat scraps, however, 2 producers were found to be feeding meat scraps (swill) illegally. Some 56% of producers surveyed did not have a tattoo swine brand and of the 23 producers with registered brands, 3 were not available for inspection or were not functional and 2 used the brand irregularly. CONCLUSION This survey has identified factors that would assist the establishment and spread of vesicular and other exotic diseases in pigs. The factors included feeding meat scraps (swill), poor farmer knowledge of exotic diseases, ineffective pig owner identification at saleyards, the practice of cash sales that precluded the collection of purchaser details, and inadequate identification of pigs. Tracing the movements of pigs under these circumstances would be difficult.
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