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Chen W, Wang W, Wang X, Li Z, Wu K, Li X, Li Y, Yi L, Zhao M, Ding H, Fan S, Chen J. Advances in the differential molecular diagnosis of vesicular disease pathogens in swine. Front Microbiol 2022; 13:1019876. [PMID: 36386633 PMCID: PMC9641196 DOI: 10.3389/fmicb.2022.1019876] [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: 08/15/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV), Senecavirus A (SVA) and swine vesicular disease virus (SVDV) are members of the family Picornaviridae, which can cause similar symptoms - vesicular lesions in the tissues of the mouth, nose, feet, skin and mucous membrane of animals. Rapid and accurate diagnosis of these viruses allows for control measures to prevent the spread of these diseases. Reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR are traditional and reliable methods for pathogen detection, while their amplification reaction requires a thermocycler. Isothermal amplification methods including loop-mediated isothermal amplification and recombinase polymerase amplification developed in recent years are simple, rapid and do not require specialized equipment, allowing for point of care diagnostics. Luminex technology allows for simultaneous detection of multiple pathogens. CRISPR-Cas diagnostic systems also emerging nucleic acid detection technologies which are very sensitivity and specificity. In this paper, various nucleic acid detection methods aimed at vesicular disease pathogens in swine (including FMDV, SVA and SVDV) are summarized.
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Affiliation(s)
- Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Weijun Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xinyan Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhaoyao Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaowen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yuwan Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Shuangqi Fan, ; Jinding Chen,
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- *Correspondence: Shuangqi Fan, ; Jinding Chen,
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Abendaño N, Esparza-Baquer A, Bernales I, Reina R, de Andrés D, Jugo BM. Gene Expression Profiling Reveals New Pathways and Genes Associated with Visna/Maedi Viral Disease. Animals (Basel) 2021; 11:ani11061785. [PMID: 34203742 PMCID: PMC8232142 DOI: 10.3390/ani11061785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Visna/Maedi is a disease caused by a small ruminant lentivirus (SRLV), with different symptoms in adult sheep such as pneumonia, arthritis, encephalitis and mastitis. SRLV infection in sheep is widespread across the world, with Europe showing the highest individual prevalence. There is currently no effective treatment for SRLV infections and, due to their constant changes, effective vaccine development has been and is still challenging. The dynamics of the sheep immune response to these virus infections is unclear, and changes in gene expression can help to explain the processes occurring in infected sheep. In this study, a gene expression microarray was used to identify the differentially expressed genes in infected and diseased sheep by comparing animals with different serologic statuses and with the presence of VM-characteristic clinical lesions in the lungs. The expression profile analysis revealed many interesting genes that may be associated with the viral infection process (such as OXT and a number of genes implicated in the Toll Like Receptors signaling network and complement pathway). This work improves our understanding of the sheep immune response against SRLVs. Abstract Visna/Maedi virus (VMV) is a lentivirus that infects the cells of the monocyte/macrophage lineage in sheep, goats and wild ruminants. Infection with VMV causes a multisystemic inflammatory disorder, which includes pneumonia, encephalitis, mastitis or arthritis. The immune response to VMV infection is complex, and the infection and pathogenesis of this virus are not totally characterized yet. In this work, a gene expression microarray was used to identify the differentially expressed genes in VMV infection and disease development by comparing sheep with different serologic status and with presence of VM-characteristic clinical lesions. The expression profile analysis has revealed many interesting genes that may be associated with the viral infection process. Among them, the OXT gene appeared significantly up-regulated, so the oxytocin-secreting system could play an essential role in VM disease. Moreover, some of the most significantly enriched functions in up-regulated genes appeared the complement pathway, which (in combination with the Toll-like receptor signaling network) could compose a mechanism in the VMV pathogenesis. Identifying the host genetic factors associated with VMV infection can be applied to develop strategies for preventing infection and develop effective vaccines that lead to therapeutic treatments.
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Affiliation(s)
- Naiara Abendaño
- Genetics, Physical Anthropology and Animal Physiology Department, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (N.A.); (A.E.-B.)
| | - Aitor Esparza-Baquer
- Genetics, Physical Anthropology and Animal Physiology Department, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (N.A.); (A.E.-B.)
| | - Irantzu Bernales
- Gene Expression Unit, Genomics Facility of General Research Services (SGIker), Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - Ramsés Reina
- Instituto de Agrobiotecnología (CSIC-Gobierno de Navarra), 31192 Mutilva Baja, Spain; (R.R.); (D.d.A.)
| | - Damián de Andrés
- Instituto de Agrobiotecnología (CSIC-Gobierno de Navarra), 31192 Mutilva Baja, Spain; (R.R.); (D.d.A.)
| | - Begoña M. Jugo
- Genetics, Physical Anthropology and Animal Physiology Department, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (N.A.); (A.E.-B.)
- Correspondence:
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3
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Wong CL, Yong CY, Ong HK, Ho KL, Tan WS. Advances in the Diagnosis of Foot-and-Mouth Disease. Front Vet Sci 2020; 7:477. [PMID: 32974392 PMCID: PMC7473413 DOI: 10.3389/fvets.2020.00477] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/26/2020] [Indexed: 11/13/2022] Open
Abstract
Foot-and-mouth disease (FMD) is a devastating livestock disease caused by foot-and-mouth disease virus (FMDV). Outbreaks of this disease in a country always result in conspicuous economic losses to livestock industry and subsequently lead to serious socioeconomic damages due to the immediate imposition of trade embargo. Rapid and accurate diagnoses are imperative to control this infectious virus. In the current review, enzyme-linked immunosorbent assay (ELISA)-based methods used in FMD diagnosis are extensively reviewed, particularly the sandwich, liquid-phase blocking, and solid-phase competition ELISA. The differentiation of infected animals from vaccinated animals using ELISA-based methods is also highlighted, in which the role of 3ABC polyprotein as a marker is reviewed intensively. Recently, more studies are focusing on the molecular diagnostic methods, which detect the viral nucleic acids based on reverse transcription-polymerase chain reaction (RT-PCR) and RT-loop-mediated isothermal amplification (RT-LAMP). These methods are generally more sensitive because of their ability to amplify a minute amount of the viral nucleic acids. In this digital era, the RT-PCR and RT-LAMP are progressing toward the mobile versions, aiming for on-site FMDV diagnosis. Apart from RT-PCR and RT-LAMP, another diagnostic assay specifically designed for on-site diagnosis is the lateral flow immunochromatographic test strips. These test strips have some distinct advantages over other diagnostic methods, whereby the assay often does not require the aid of an external device, which greatly lowers the cost per test. In addition, the on-site diagnostic test can be easily performed by untrained personnel including farmers, and the results can be obtained in a few minutes. Lastly, the use of FMDV diagnostic assays for progressive control of the disease is also discussed critically.
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Affiliation(s)
- Chuan Loo Wong
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Chean Yeah Yong
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia.,Laboratory of Vaccines and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Hui Kian Ong
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Wen Siang Tan
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia.,Laboratory of Vaccines and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
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4
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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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5
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Yadav BS, Pokhriyal M, Ratta B, Kumar A, Saxena M, Sharma B. Viral diagnosis in Indian livestock using customized microarray chips. Bioinformation 2015; 11:489-92. [PMID: 26912948 PMCID: PMC4748017 DOI: 10.6026/97320630011489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/09/2015] [Indexed: 01/18/2023] Open
Abstract
Viral diagnosis in Indian livestock using customized microarray chips is gaining momentum in recent years. Hence, it is possible to design customized microarray chip for viruses infecting livestock in India. Customized microarray chips identified Bovine herpes virus-1 (BHV-1), Canine Adeno Virus-1 (CAV-1), and Canine Parvo Virus-2 (CPV-2) in clinical samples. Microarray identified specific probes were further confirmed using RT-PCR in all clinical and known samples. Therefore, the application of microarray chips during viral disease outbreaks in Indian livestock is possible where conventional methods are unsuitable. It should be noted that customized application requires a detailed cost efficiency calculation.
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Affiliation(s)
- Brijesh S Yadav
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
| | - Mayank Pokhriyal
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
| | - Barkha Ratta
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
| | - Ajay Kumar
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
| | - Meeta Saxena
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
| | - Bhaskar Sharma
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, India - 243122
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6
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Maree FF, Kasanga CJ, Scott KA, Opperman PA, Melanie C, Sangula AK, Raphael S, Yona S, Wambura PN, King DP, Paton DJ, Rweyemamu MM. Challenges and prospects for the control of foot-and-mouth disease: an African perspective. VETERINARY MEDICINE-RESEARCH AND REPORTS 2014; 5:119-138. [PMID: 32670853 PMCID: PMC7337166 DOI: 10.2147/vmrr.s62607] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/23/2014] [Indexed: 11/23/2022]
Abstract
The epidemiology of foot-and-mouth disease (FMD) in Africa is unique in the sense that six of the seven serotypes of FMD viruses (Southern African Territories [SAT] 1, SAT2, SAT3, A, O, and C), with the exception of Asia-1, have occurred in the last decade. Due to underreporting of FMD, the current strains circulating throughout sub-Saharan Africa are in many cases unknown. For SAT1, SAT2, and serotype A viruses, the genetic diversity is reflected in antigenic variation, and indications are that vaccine strains may be needed for each topotype. This has serious implications for control using vaccines and for choice of strains to include in regional antigen banks. The epidemiology is further complicated by the fact that SAT1, SAT2, and SAT3 viruses are maintained and spread by wildlife, persistently infecting African buffalo in particular. Although the precise mechanism of transmission of FMD from buffalo to cattle is not well understood, it is facilitated by direct contact between these two species. Once cattle are infected they may maintain SAT infections without the further involvement of buffalo. No single strategy for control of FMD in Africa is applicable. Decision on the most effective regional control strategy should focus on an ecosystem approach, identification of primary endemic areas, animal husbandry practices, climate, and animal movement. Within each ecosystem, human behavior could be integrated in disease control planning. Different regions in sub-Saharan Africa are at different developmental stages and are thus facing unique challenges and priorities in terms of veterinary disease control. Many science-based options targeting improved vaccinology, diagnostics, and other control measures have been described. This review therefore aims to emphasize, on one hand, the progress that has been achieved in the development of new technologies, including research towards improved tailored vaccines, appropriate vaccine strain selection, vaccine potency, and diagnostics, and how it relates to the conditions in Africa. On the other hand, we focus on the unique epidemiological, ecological, livestock farming and marketing, socioeconomic, and governance issues that constrain effective FMD control. Any such new technologies should have the availability of safe livestock products for trade as the ultimate goal.
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Affiliation(s)
- Francois F Maree
- Transboundary Animal Diseases Programme, Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort, Pretoria, South Africa.,Department of Microbiology and Plant Pathology, Faculty of Agricultural and Natural Sciences, University of Pretoria, Pretoria, South Africa
| | - Christopher J Kasanga
- Southern African Centre for Infectious Diseases Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Katherine A Scott
- Transboundary Animal Diseases Programme, Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort, Pretoria, South Africa
| | - Pamela A Opperman
- Transboundary Animal Diseases Programme, Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort, Pretoria, South Africa.,Department of Microbiology and Plant Pathology, Faculty of Agricultural and Natural Sciences, University of Pretoria, Pretoria, South Africa
| | - Chitray Melanie
- Transboundary Animal Diseases Programme, Onderstepoort Veterinary Institute, Agricultural Research Council, Onderstepoort, Pretoria, South Africa.,Department of Microbiology and Plant Pathology, Faculty of Agricultural and Natural Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Sallu Raphael
- Southern African Centre for Infectious Diseases Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sinkala Yona
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Philemon N Wambura
- Southern African Centre for Infectious Diseases Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | | | - Mark M Rweyemamu
- Southern African Centre for Infectious Diseases Surveillance, Sokoine University of Agriculture, Morogoro, Tanzania
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Challenges and economic implications in the control of foot and mouth disease in sub-saharan Africa: lessons from the zambian experience. Vet Med Int 2014; 2014:373921. [PMID: 25276472 PMCID: PMC4158296 DOI: 10.1155/2014/373921] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 07/27/2014] [Accepted: 07/28/2014] [Indexed: 11/17/2022] Open
Abstract
Foot and mouth disease is one of the world's most important livestock diseases for trade. FMD infections are complex in nature and there are many epidemiological factors needing clarification. Key questions relate to the control challenges and economic impact of the disease for resource-poor FMD endemic countries like Zambia. A review of the control challenges and economic impact of FMD outbreaks in Zambia was made. Information was collected from peer-reviewed journals articles, conference proceedings, unpublished scientific reports, and personal communication with scientists and personal field experiences. The challenges of controlling FMD using mainly vaccination and movement control are discussed. Impacts include losses in income of over US$ 1.6 billion from exports of beef and sable antelopes and an annual cost of over US$ 2.7 million on preventive measures. Further impacts included unquantified losses in production and low investment in agriculture resulting in slow economic growth. FMD persistence may be a result of inadequate epidemiological understanding of the disease and ineffectiveness of the control measures that are being applied. The identified gaps may be considered in the annual appraisal of the FMD national control strategy in order to advance on the progressive control pathway.
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8
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Guan H, Li Z, Yin X, Zhang Y, Gao P, Bai Y, Liu J. Rapid Detection and Differentiation of Foot and Mouth Disease Virus Serotypes by Antigen-capture Reverse Transcriptase Loop-mediated Isothermal Amplification. ACTA ACUST UNITED AC 2013. [DOI: 10.3923/ajava.2013.647.654] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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9
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A New Generation Microarray for the Simultaneous Detection and Identification of Yersinia pestis and Bacillus anthracis in Food. J Pathog 2012; 2012:627036. [PMID: 23125935 PMCID: PMC3483683 DOI: 10.1155/2012/627036] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 08/02/2012] [Accepted: 08/05/2012] [Indexed: 11/17/2022] Open
Abstract
The use of microarrays as a multiple analytic system has generated increased interest and provided a powerful analytical tool for the simultaneous detection of pathogens in a single experiment. A wide array of applications for this technology has been reported. A low density oligonucleotide microarray was generated from the genetic sequences of Y. pestis and B. anthracis and used to fabricate a microarray chip. The new generation chip, consisting of 2,240 spots in 4 quadrants with the capability of stripping/rehybridization, was designated as “Y-PESTIS/B-ANTHRACIS 4x2K Array.” The chip was tested for specificity using DNA from a panel of bacteria that may be potentially present in food. In all, 37 unique Y. pestis-specific and 83 B. anthracis-specific probes were identified. The microarray assay distinguished Y. pestis and B. anthracis from the other bacterial species tested and correctly identified the Y. pestis-specific oligonucleotide probes using DNA extracted from experimentally inoculated milk samples. Using a whole genome amplification method, the assay was able to detect as low as 1 ng genomic DNA as the start sample. The results suggest that oligonucleotide microarray can specifically detect and identify Y. pestis and B. anthracis and may be a potentially useful diagnostic tool for detecting and confirming the organisms in food during a bioterrorism event.
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10
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Differentiation of the seven major lyssavirus species by oligonucleotide microarray. J Clin Microbiol 2011; 50:619-25. [PMID: 22189108 DOI: 10.1128/jcm.00848-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An oligonucleotide microarray, LyssaChip, has been developed and verified as a highly specific diagnostic tool for differentiation of the 7 major lyssavirus species. As with conventional typing microarray methods, the LyssaChip relies on sequence differences in the 371-nucleotide region coding for the nucleoprotein. This region was amplified using nested reverse transcription-PCR primers that bind to the 7 major lyssaviruses. The LyssaChip includes 57 pairs of species typing and corresponding control oligonucleotide probes (oligoprobes) immobilized on glass slides, and it can analyze 12 samples on a single slide within 8 h. Analysis of 111 clinical brain specimens (65 from animals with suspected rabies submitted to the laboratory and 46 of butchered dog brain tissues collected from restaurants) showed that the chip method was 100% sensitive and highly consistent with the "gold standard," a fluorescent antibody test (FAT). The chip method could detect rabies virus in highly decayed brain tissues, whereas the FAT did not, and therefore the chip test may be more applicable to highly decayed brain tissues than the FAT. LyssaChip may provide a convenient and inexpensive alternative for diagnosis and differentiation of rabies and rabies-related diseases.
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11
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Multiplex RT-PCR detection and microarray typing of vesicular disease viruses. J Virol Methods 2011; 175:236-45. [DOI: 10.1016/j.jviromet.2011.05.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 05/12/2011] [Accepted: 05/12/2011] [Indexed: 11/17/2022]
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12
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Longjam N, Deb R, Sarmah AK, Tayo T, Awachat VB, Saxena VK. A Brief Review on Diagnosis of Foot-and-Mouth Disease of Livestock: Conventional to Molecular Tools. Vet Med Int 2011; 2011:905768. [PMID: 21776357 PMCID: PMC3135314 DOI: 10.4061/2011/905768] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 03/25/2011] [Accepted: 04/20/2011] [Indexed: 12/31/2022] Open
Abstract
Foot-and-mouth disease (FMD) is one of the highly contagious diseases of domestic animals. Effective control of this disease needs sensitive, specific, and quick diagnostic tools at each tier of control strategy. In this paper we have outlined various diagnostic approaches from old to new generation in a nutshell. Presently FMD diagnosis is being carried out using techniques such as Virus Isolation (VI), Sandwich-ELISA (S-ELISA), Liquid-Phase Blocking ELISA (LPBE), Multiplex-PCR (m-PCR), and indirect ELISA (DIVA), and real time-PCR can be used for detection of antibody against nonstructural proteins. Nucleotide sequencing for serotyping, microarray as well as recombinant antigen-based detection, biosensor, phage display, and nucleic-acid-based diagnostic are on the way for rapid and specific detection of FMDV. Various pen side tests, namely, lateral flow, RT-LAMP, Immunostrip tests, and so forth. are also developed for detection of the virus in field condition.
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Affiliation(s)
- Neeta Longjam
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati 781022, India
| | - Rajib Deb
- Division of Animal Biotechnology, Indian Veterinary Research Institute (IVRI), Izatnagar 243122, India
| | - A. K. Sarmah
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati 781022, India
| | - Tilling Tayo
- Division of Animal Nutrition, Indian Veterinary Research Institute (IVRI), Izatnagar 243122, India
| | - V. B. Awachat
- Division of Poultry Science, Central Avian Research Institute (CARI), Izatnagar 243122, India
| | - V. K. Saxena
- Division of Veterinary Biochemistry and Physiology, Central Sheep and Wool Research Institute (CSWRI), Avikanagar, India
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Lopez CA, Daaboul GG, Vedula RS, Ozkumur E, Bergstein DA, Geisbert TW, Fawcett HE, Goldberg BB, Connor JH, Unlü MS. Label-free multiplexed virus detection using spectral reflectance imaging. Biosens Bioelectron 2011; 26:3432-7. [PMID: 21342761 DOI: 10.1016/j.bios.2011.01.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Revised: 12/21/2010] [Accepted: 01/14/2011] [Indexed: 10/18/2022]
Abstract
We demonstrate detection of whole viruses and viral proteins with a new label-free platform based on spectral reflectance imaging. The Interferometric Reflectance Imaging Sensor (IRIS) has been shown to be capable of sensitive protein and DNA detection in a real time and high-throughput format. Vesicular stomatitis virus (VSV) was used as the target for detection as it is well-characterized for protein composition and can be modified to express viral coat proteins from other dangerous, highly pathogenic agents for surrogate detection while remaining a biosafety level 2 agent. We demonstrate specific detection of intact VSV virions achieved with surface-immobilized antibodies acting as capture probes which is confirmed using fluorescence imaging. The limit of detection is confirmed down to 3.5 × 10(5)plaque-forming units/mL (PFUs/mL). To increase specificity in a clinical scenario, both the external glycoprotein and internal viral proteins were simultaneously detected with the same antibody arrays with detergent-disrupted purified VSV and infected cell lysate solutions. Our results show sensitive and specific virus detection with a simple surface chemistry and minimal sample preparation on a quantitative label-free interferometric platform.
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Affiliation(s)
- Carlos A Lopez
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215, USA
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14
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Goris N, Vandenbussche F, Herr C, Villers J, Van der Stede Y, De Clercq K. Validation of two real-time RT-PCR methods for foot-and-mouth disease diagnosis: RNA-extraction, matrix effect, uncertainty of measurement and precision. J Virol Methods 2009; 160:157-62. [PMID: 19447138 DOI: 10.1016/j.jviromet.2009.05.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 05/03/2009] [Accepted: 05/06/2009] [Indexed: 11/30/2022]
Abstract
Real-time reverse transcription polymerase chain reaction (rRT-PCR) assays are being used routinely for diagnosing foot-and-mouth disease virus (FMDV). Although most laboratories determine analytical and diagnostic sensitivity and specificity, a thorough validation in terms of establishing optimal RNA-extraction conditions, matrix effect, uncertainty of measurement and precision is not performed or reported generally. In this study, different RNA-extraction procedures were compared for two FMDV rRT-PCRs. The NucleoSpin columns available commercially combined high extraction efficiency with ease-of-automation. Furthermore, six different FMDV-negative matrices were spiked with a dilution series of FMDV SAT1 ZIM 25/89. Compared to cell-culture-spiked viral control samples, no matrix effect on the analytical sensitivity was found for blood or foot epithelium. Approximately 1log(10) reduction in detection limit was noted for faecal and tongue epithelium samples, whereas a 3log(10) decrease was observed for spleen samples. By testing the same dilution series in duplicate on 10 different occasions, an estimation of uncertainty of measurement and precision was obtained using blood as matrix. Both rRT-PCRs produced highly precise results emphasising their potential to replace conventional virological methods. The uncertainty measurement, as described in this study, proved to be a useful tool to evaluate the probability of making a wrong decision.
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Affiliation(s)
- Nesya Goris
- Veterinary and Agrochemical Research Centre, Virology Department, Brussels, Belgium.
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15
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Jack PJM, Amos-Ritchie RN, Reverter A, Palacios G, Quan PL, Jabado O, Briese T, Lipkin WI, Boyle DB. Microarray-based detection of viruses causing vesicular or vesicular-like lesions in livestock animals. Vet Microbiol 2009; 133:145-53. [PMID: 18621489 PMCID: PMC4310687 DOI: 10.1016/j.vetmic.2008.05.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Revised: 05/12/2008] [Accepted: 05/26/2008] [Indexed: 10/22/2022]
Abstract
Definitive diagnosis of vesicular or vesicular-like lesions in livestock animals presents challenges both for veterinary clinicians and diagnostic laboratories. It is often impossible to diagnose the causative disease agent on a clinical basis alone and difficult to collect ample vesicular epithelium samples. Due to restrictions of time and sample size, once laboratory tests have ruled out foot-and-mouth disease, vesicular stomatitis and swine vesicular disease a definitive diagnosis may remain elusive. With the ability to test a small quantity of sample for a large number of pathogens simultaneously, DNA microarrays represent a potential solution to this problem. This study describes the application of a long oligonucleotide microarray assay to the identification of viruses known to cause vesicular or vesicular-like lesions in livestock animals. Eighteen virus isolates from cell culture were successfully identified to genus level, including representatives of each foot-and-mouth disease virus serotype, two species of vesicular stomatitis virus (VSV), swine vesicular disease virus, vesicular exanthema of swine virus (VESV), bovine herpesvirus 1, orf virus, pseudocowpox virus, bluetongue virus serotype 1 and bovine viral diarrhoea virus 1. VSV and VESV were also identified in vesicular epithelium samples, with varying levels of sensitivity. The results indicate that with further development this microarray assay could be a valuable tool for the diagnosis of vesicular and vesicular-like diseases.
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Affiliation(s)
- Philippa J. M. Jack
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Private Bag 24, Geelong, Victoria 3220, Australia
| | - Rachel N. Amos-Ritchie
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Private Bag 24, Geelong, Victoria 3220, Australia
| | - Antonio Reverter
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | - Gustavo Palacios
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Phuong-Lan Quan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Omar Jabado
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - David B. Boyle
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Private Bag 24, Geelong, Victoria 3220, Australia
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16
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Genotyping Arrays. MICROARRAYS 2009. [PMCID: PMC7123720 DOI: 10.1007/978-0-387-72719-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Although the most common use of DNA microarrays is gene expression profiling, microarrays are also used for many other applications, including genotyping, resequencing, SNP analysis, and DNA methylation assays. Here we describe genotyping arrays for Influenza A subtype identification and for upper respiratory pathogen diagnostics using standard hybridization techniques and we also describe resequencing, SNP, and methylation assays using an enzyme-based strategy [25, 26].
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17
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De Clercq K, Goris N, Barnett PV, MacKay DK. The Importance of Quality Assurance/Quality Control of Diagnostics to Increase the Confidence in Global Foot-and-Mouth Disease Control. Transbound Emerg Dis 2008; 55:35-45. [DOI: 10.1111/j.1865-1682.2007.01011.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Ojha S, Kostrzynska M. Examination of animal and zoonotic pathogens using microarrays. Vet Res 2007; 39:4. [DOI: 10.1051/vetres:2007042] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 07/27/2007] [Indexed: 01/13/2023] Open
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19
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Lodes MJ, Suciu D, Wilmoth JL, Ross M, Munro S, Dix K, Bernards K, Stöver AG, Quintana M, Iihoshi N, Lyon WJ, Danley DL, McShea A. Identification of upper respiratory tract pathogens using electrochemical detection on an oligonucleotide microarray. PLoS One 2007; 2:e924. [PMID: 17895966 PMCID: PMC1976596 DOI: 10.1371/journal.pone.0000924] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 08/31/2007] [Indexed: 11/19/2022] Open
Abstract
Bacterial and viral upper respiratory infections (URI) produce highly variable clinical symptoms that cannot be used to identify the etiologic agent. Proper treatment, however, depends on correct identification of the pathogen involved as antibiotics provide little or no benefit with viral infections. Here we describe a rapid and sensitive genotyping assay and microarray for URI identification using standard amplification and hybridization techniques, with electrochemical detection (ECD) on a semiconductor-based oligonucleotide microarray. The assay was developed to detect four bacterial pathogens (Bordetella pertussis, Streptococcus pyogenes, Chlamydia pneumoniae and Mycoplasma pneumoniae) and 9 viral pathogens (adenovirus 4, coronavirus OC43, 229E and HK, influenza A and B, parainfluinza types 1, 2, and 3 and respiratory syncytial virus. This new platform forms the basis for a fully automated diagnostics system that is very flexible and can be customized to suit different or additional pathogens. Multiple probes on a flexible platform allow one to test probes empirically and then select highly reactive probes for further iterative evaluation. Because ECD uses an enzymatic reaction to create electrical signals that can be read directly from the array, there is no need for image analysis or for expensive and delicate optical scanning equipment. We show assay sensitivity and specificity that are excellent for a multiplexed format.
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MESH Headings
- Adenoviridae/genetics
- Adenoviridae/isolation & purification
- Bacterial Infections/diagnosis
- Bacterial Infections/microbiology
- Bordetella pertussis/genetics
- Bordetella pertussis/isolation & purification
- Chlamydophila pneumoniae/genetics
- Chlamydophila pneumoniae/isolation & purification
- Coronavirus 229E, Human/genetics
- Coronavirus 229E, Human/isolation & purification
- Coronavirus OC43, Human/genetics
- Coronavirus OC43, Human/isolation & purification
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Electrochemistry/methods
- Humans
- Influenza A virus/genetics
- Influenza A virus/isolation & purification
- Influenza B virus/genetics
- Influenza B virus/isolation & purification
- Mycoplasma pneumoniae/genetics
- Mycoplasma pneumoniae/isolation & purification
- Oligonucleotide Array Sequence Analysis/methods
- Parainfluenza Virus 1, Human/genetics
- Parainfluenza Virus 1, Human/isolation & purification
- Parainfluenza Virus 2, Human/genetics
- Parainfluenza Virus 2, Human/isolation & purification
- Parainfluenza Virus 3, Human/genetics
- Parainfluenza Virus 3, Human/isolation & purification
- Polymerase Chain Reaction
- Reproducibility of Results
- Respiratory Syncytial Viruses/genetics
- Respiratory Syncytial Viruses/isolation & purification
- Respiratory System/microbiology
- Respiratory System/virology
- Sensitivity and Specificity
- Sequence Analysis, DNA
- Streptococcus pyogenes/genetics
- Streptococcus pyogenes/isolation & purification
- Virus Diseases/diagnosis
- Virus Diseases/virology
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20
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Lodes MJ, Suciu D, Elliott M, Stover AG, Ross M, Caraballo M, Dix K, Crye J, Webby RJ, Lyon WJ, Danley DL, McShea A. Use of semiconductor-based oligonucleotide microarrays for influenza a virus subtype identification and sequencing. J Clin Microbiol 2006; 44:1209-18. [PMID: 16597840 PMCID: PMC1448669 DOI: 10.1128/jcm.44.4.1209-1218.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the face of concerns over an influenza pandemic, identification of virulent influenza A virus isolates must be obtained quickly for effective responses. Rapid subtype identification, however, is difficult even in well-equipped virology laboratories or is unobtainable in the field under more austere conditions. Here we describe a genome assay and microarray design that can be used to rapidly identify influenza A virus hemagglutinin subtypes 1 through 15 and neuraminidase subtypes 1 through 9. Also described is an array-based enzymatic assay that can be used to sequence portions of both genes or any other sequence of interest.
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Affiliation(s)
- Michael J Lodes
- CombiMatrix Corporation, 6500 Harbour Heights Parkway, Suite 301, Mukilteo, WA 98275, USA.
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21
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Martín V, Perales C, Abia D, Ortíz AR, Domingo E, Briones C. Microarray-based identification of antigenic variants of foot-and-mouth disease virus: a bioinformatics quality assessment. BMC Genomics 2006; 7:117. [PMID: 16709242 PMCID: PMC1481559 DOI: 10.1186/1471-2164-7-117] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Accepted: 05/18/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of viral quasispecies can influence viral pathogenesis and the response to antiviral treatments. Mutant clouds in infected organisms represent the first stage in the genetic and antigenic diversification of RNA viruses, such as foot and mouth disease virus (FMDV), an important animal pathogen. Antigenic variants of FMDV have been classically diagnosed by immunological or RT-PCR-based methods. DNA microarrays are becoming increasingly useful for the analysis of gene expression and single nucleotide polymorphisms (SNPs). Recently, a FMDV microarray was described to detect simultaneously the seven FMDV serotypes. These results encourage the development of new oligonucleotide microarrays to probe the fine genetic and antigenic composition of FMDV for diagnosis, vaccine design, and to gain insight into the molecular epidemiology of this pathogen. RESULTS A FMDV microarray was designed and optimized to detect SNPs at a major antigenic site of the virus. A screening of point mutants of the genomic region encoding antigenic site A of FMDV C-S8c1 was achieved. The hybridization pattern of a mutant includes specific positive and negative signals as well as crosshybridization signals, which are of different intensity depending on the thermodynamic stability of each probe-target pair. Moreover, an array bioinformatic classification method was developed to evaluate the hybridization signals. This statistical analysis shows that the procedure allows a very accurate classification per variant genome. CONCLUSION A specific approach based on a microarray platform aimed at distinguishing point mutants within an important determinant of antigenicity and host cell tropism, namely the G-H loop of capsid protein VP1, was developed. The procedure is of general applicability as a test for specificity and discriminatory power of microarray-based diagnostic procedures using multiple oligonucleotide probes.
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Affiliation(s)
- Verónica Martín
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Celia Perales
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - David Abia
- Bioinformatics Unit, Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Angel R Ortíz
- Bioinformatics Unit, Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Carlos Briones
- Centro de Astobiología (CSIC-INTA), Torrejón de Ardoz, 28850, Madrid, Spain
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