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Wang C, Hou B, Shao G, Wan C. Development of a One-Step Real-Time TaqMan Reverse Transcription Polymerase Chain Reaction (RT-PCR) Assay for the Detection of the Novel Variant Infectious Bursal Disease Virus (nVarIBDV) Circulating in China. Viruses 2023; 15:1453. [PMID: 37515141 PMCID: PMC10383243 DOI: 10.3390/v15071453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The novel variant IBDV (nVarIBDV, especially genotype A2dB1) mainly affects broilers in China. It causes an infection characterized by the atrophy of the bursa, a decrease in the level of lymphocytes, proliferation of fibrous tissue around the follicle, and severe atrophy of the follicle in the bursa. Poultry vaccinated with live IBDV vaccines do not have the challenge present with bursa atrophy, which is misdiagnosed for nVarIBDV because of the lack of other gross clinical symptoms. The present study sought to explore the potential and reliability of the real-time TaqMan analysis method for the detection and discrimination of the nVarIBDV genotype from that of the non-nVarIBDV, especially in live vaccine strains. This method will help monitor vaccinated poultry to control and manage infection with the nVarIBDV IBDVs. The nucleotide polymorphism in the 5'-UTR region and the vp5/vp2 overlapping region of the segment A sequences of IBDV were used to establish a one-step real-time TaqMan reverse transcription polymerase chain reaction (RT-PCR) method in this study. The results showed that the method accurately distinguished the nVarIBDV and non-nVarIBDV strains (especially live vaccine strains), and there were no cross-reactions with the infectious bronchitis virus (IBV), Newcastle disease virus (NDV), avian influenza virus (AIV), infectious laryngotracheitis virus (ILTV), fowlpox virus (FPV), Mycoplasma gallisepticum (M. gallisepticum), Mycoplasma synoviae (M. synoviae), and IBDV-negative field samples. The method showed a linear dynamic range between 102 and 107 DNA copies/reaction, with an average R2 of 0.99 and an efficiency of 93% for nVarIBDV and an average R2 of 1.00 and an efficiency of 94% for non-nVarIBDV. The method was also used for the detection of 84 clinical bursae of chickens vaccinated with the live vaccine. The results showed that this method accurately distinguished the nVarIBDV and non-nVarIBDV strains (vaccine strains), compared with a strategy based on the sequence analysis of HVRs at the vp2 gene or the reverse transcription PCR (RT-PCR) for the vp5 gene. These findings showed that this one-step real-time TaqMan RT-PCR method provides a rapid, sensitive, specific, and simple approach for detection of infections caused by nVarIBDV and is a useful clinical diagnostic tool for identifying and distinguishing nVarIBDV from non-nVarIBDV, especially live vaccine strains.
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Affiliation(s)
- Chenyan Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
| | - Bo Hou
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
| | - Guoqing Shao
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, National Research Center for Engineering and Technology of Veterinary Bio-Products, Nanjing 210014, China
| | - Chunhe Wan
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
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Ghorashi MS, Pant SD, Ghorashi SA. Comparison of colourimetric loop-mediated isothermal amplification (LAMP), PCR and high-resolution melt curve analysis and culture based diagnostic assays in the detection of three salmonella serotypes in poultry. Avian Pathol 2022; 51:476-487. [PMID: 35833568 DOI: 10.1080/03079457.2022.2101916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The accuracy of two molecular tests, PCR and loop-mediated isothermal amplification (LAMP) assay were compared with bacterial culture in detection of salmonella in poultry clinical samples. The icIR family transcriptional regulator gene was targeted and out of 56 clinical specimens, 20 poultry field isolates were found positive for salmonella. Along with human isolates, reference strains of three different serovars, Salmonella Enteritidis (S. Enteritidis), S. Typhimurium and S. Infantis, were also tested. Eight different but genetically closely related bacterial genera (Klebsiella, Pseudomonas, Enterobacter, Campylobacter, Staphylococcus, Streptococcus, Escherichia and Pasteurella) were also used to evaluate the specificity of assay. The LAMP assay showed 80.8% sensitivity (95% CI, 0.66-0.95) and 100% specificity (95% CI, 0.71-1.00) when compared with microbiological culture and PCR, both with 100% sensitivity (95% CI, 0.87-1.00) and 100% specificity (95% CI, 0.71-1.00). High-resolution melt (HRM) curve analysis following PCR was able to differentiate between salmonella isolates based on their melting points, and all specimens were genotyped in three distinct HRM curve profiles. Each normalised melt curve profile represented one salmonella serotype and differences between the three melt profiles were correlated with nucleotide variations in the target gene sequences which demonstrated high discriminatory power of this technique. The colourimetric LAMP assay provided an alternative detection method capable of being used in the field and showed analytical sensitivity for detection of 1 pg of salmonella DNA per reaction. The advantages and disadvantages of each test in detection of salmonella are discussed.
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Affiliation(s)
- Mojdeh Sadat Ghorashi
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia,
| | - Sameer Dinkar Pant
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia: .,Graham Centre for Agricultural Innovation, Wagga Wagga, Australia:
| | - Seyed Ali Ghorashi
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia: .,Graham Centre for Agricultural Innovation, Wagga Wagga, Australia:
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Young P, Tarce P, Adhikary S, Connolly J, Crawshaw T, Ghorashi SA. Evaluation of high-resolution melt curve analysis for rapid differentiation of Campylobacter hepaticus from other species in birds. PLoS One 2021; 16:e0251328. [PMID: 33984000 PMCID: PMC8118346 DOI: 10.1371/journal.pone.0251328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/24/2021] [Indexed: 11/18/2022] Open
Abstract
Spotty liver disease (SLD) is a bacterial disease of chicken, causing mortalities and reduction in egg production, hence, contributing to economic loss in the poultry industry. The causative agent of SLD has only recently been identified as a novel Campylobacter species, Campylobacter hepaticus. Specific primers were designed from the hsp60 gene of Campylobacter hepaticus and PCR followed by high-resolution melt curve analysis was optimised to detect and differentiate three species of Campylobacter (Campylobacter coli, Campylobacter jejuni and Campylobacter hepaticus). The three Campylobacter species produced a distinct curve profile and was differentiated using HRM curve analysis. The potential of the PCR-HRM curve analysis was shown in the genotyping of 37 Campylobacter isolates from clinical specimens from poultry farms. PCR-HRM curve analysis of DNA extracts from bile samples or cultures from bile samples, were identified as Campylobacter hepaticus and confirmed by DNA sequencing. The DNA sequence analysis of selected samples from each of the three HRM distinctive curves patterns showed that each DNA sequence was associated with a unique melt profile. The potential of the PCR-HRM curve analysis in genotyping of Campylobacter species was also evaluated using faecal specimens from 100 wild birds. The results presented in this study indicate that PCR followed by HRM curve analysis provides a rapid and robust technique for genotyping of Campylobacter species using either bacterial cultures or clinical specimens.
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Affiliation(s)
- Petrina Young
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Pol Tarce
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Sadhana Adhikary
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Joanne Connolly
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Tim Crawshaw
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- School of Veterinary Sciences, Massey University, Tennent Drive, Palmerston North, New Zealand
| | - Seyed A. Ghorashi
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- * E-mail:
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Wang J, Yang J, Gao S, Liu A, Rashid M, Li Y, Liu Z, Liu J, Liu G, Luo J, Guan G, Yin H. Rapid detection and differentiation of Theileria annulata, T. orientalis and T. sinensis using high-resolution melting analysis. Ticks Tick Borne Dis 2019; 11:101312. [PMID: 31645296 DOI: 10.1016/j.ttbdis.2019.101312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/24/2019] [Accepted: 10/09/2019] [Indexed: 11/18/2022]
Abstract
Bovine theileriosis, caused by protozoan parasites of the genus Theileria, presents with various clinical symptoms. In cattle, clinical presentations and outcomes of bovine theileriosis are closely correlated with the causative Theileria spp. Thus, accurate detection and discrimination of Theileria spp. are essential for epidemiological studies and for provision of clinical management strategies. High-resolution melting (HRM) analyses of two amplicons targeting the 18S rRNA indicated that T. annulata, T. orientalis, and T. sinensis isolated from China can be accurately detected and discriminated with the lowest detection limit of 1-10 copy numbers of plasmid bearing the 18S rRNA sequence. The approach was verified with DNA samples from experimentally infected cattle and field samples. Thus, this assay is useful for diagnosis of bovine theileriosis in field samples and experimentally infected animals, and could also be applicable for the survey of parasite dynamics, epidemiological studies.
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Affiliation(s)
- Jinming Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Jifei Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Shandian Gao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Aihong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Muhammad Rashid
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Zhijie Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China.
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping 1, Lanzhou, Gansu, 730046, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou 225009, PR China.
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Banowary B, Dang VT, Sarker S, Connolly JH, Chenu J, Groves P, Raidal S, Ghorashi SA. Evaluation of Two Multiplex PCR-High-Resolution Melt Curve Analysis Methods for Differentiation of Campylobacter jejuni and Campylobacter coli Intraspecies. Avian Dis 2019; 62:86-93. [PMID: 29620472 DOI: 10.1637/11739-080417-reg.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Campylobacter infection is a common cause of bacterial gastroenteritis in humans and remains a significant global public health issue. The capability of two multiplex PCR (mPCR)-high-resolution melt (HRM) curve analysis methods (i.e., mPCR1-HRM and mPCR2-HRM) to detect and differentiate 24 poultry isolates and three reference strains of Campylobacter jejuni and Campylobacter coli was investigated. Campylobacter jejuni and C. coli were successfully differentiated in both assays, but the differentiation power of mPCR2-HRM targeting the cadF gene was found superior to that of mPCR1-HRM targeting the gpsA gene or a hypothetical protein gene. However, higher intraspecies variation within C. coli and C. jejuni isolates was detected in mPCR1-HRM when compared with mPCR2-HRM. Both assays were rapid and required minimum interpretation skills for discrimination between and within Campylobacter species when using HRM curve analysis software.
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Affiliation(s)
- Banya Banowary
- A School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia 2678
| | - Van Tuan Dang
- A School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia 2678
| | - Subir Sarker
- A School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia 2678.,C School of Life Sciences, La Trobe University, Melbourne, Victoria, Australia 3086
| | - Joanne H Connolly
- A School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia 2678.,B Graham Centre for Agricultural Innovation, New South Wales Department of Primary Industries and Charles Sturt University, Wagga Wagga, New South Wales, Australia 2678
| | - Jeremy Chenu
- D Birling Avian Laboratories, Bringelly, New South Wales, Australia 2556
| | - Peter Groves
- E University of Sydney, Sydney, New South Wales, Australia 2006
| | - Shane Raidal
- A School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia 2678.,B Graham Centre for Agricultural Innovation, New South Wales Department of Primary Industries and Charles Sturt University, Wagga Wagga, New South Wales, Australia 2678
| | - Seyed Ali Ghorashi
- A School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia 2678.,B Graham Centre for Agricultural Innovation, New South Wales Department of Primary Industries and Charles Sturt University, Wagga Wagga, New South Wales, Australia 2678
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Techera C, Tomás G, Panzera Y, Banda A, Perbolianachis P, Pérez R, Marandino A. Development of real-time PCR assays for single and simultaneous detection of infectious bursal disease virus and chicken anemia virus. Mol Cell Probes 2018; 43:58-63. [PMID: 30447279 DOI: 10.1016/j.mcp.2018.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/15/2018] [Accepted: 11/13/2018] [Indexed: 11/29/2022]
Abstract
Infectious bursal disease virus (IBDV) and chicken anemia virus (CAV) cause relevant immunosuppressive diseases in poultry. Clinical diagnosis of these viruses is challenging given the different disease presentations and the frequent occurrence of co-infections with other pathogens. Here, we standardized and validated simplex and duplex RT-qPCR assays for the straightforward detection of IBDV and CAV. The qPCR assays are based on primers and hydrolysis probes that target highly conserved regions of IBDV and CAV genomes. Analytical sensitivity tests on 10-fold serial dilutions containing 100-108 viral genomes indicated that the simplex assays have good determination coefficients and efficiency and detect a wide range of virus doses (102 to 108 molecules copies/reactions). The relatively small values of intra- and inter-assay variability ensure the repeatability and support its reproducibility in different diagnostic and research facilities. The assays are also efficient tools for absolute quantification as indicated by the analytical performance analysis. The assays have an excellent specificity and absence of cross-reactivity with negative samples, or with other common avian viruses. The simplex IBDV and CAV assays use probes labelled with different dyes (FAM and HEX) and can be multiplexed for the simultaneous detection of both viruses. The determination coefficients, PCR efficiencies, and relatively small intra- and inter-assay variability were comparable to the simplex assays. This duplex assay is the first to simultaneously detect IBDV and CAV using the same RNA extraction from the bursa of Fabricius in a single and straightforward step. Therefore, this method is time saving, provides quantitative results for both targets without any cross-reaction, and reduces the risk of carrying-over contaminations. The qPCR assays here developed can be used in simplex and duplex formats for detection and quantification of large number of samples with reliable sensitivity and specificity. These tools are expected to improve surveillance and control of these ubiquitous viruses.
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Affiliation(s)
- Claudia Techera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Yanina Panzera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Alejandro Banda
- Poultry Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University, P.O. Box 97813, Pearl, MS39288, USA
| | - Paula Perbolianachis
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.
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Hashemi S, Mahzounieh M, Sheikhi N, Ebrahimi A. Application of high-resolution melting-curve analysis on pvpA gene for detection and classification of Mycoplasma gallisepticum strains. Microb Pathog 2018; 124:365-371. [PMID: 29959042 DOI: 10.1016/j.micpath.2018.06.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 11/25/2022]
Abstract
Mycoplasma gallisepticum (MG) is an avian species pathogen which causes heavy economic losses in the poultry industry. The purpose of this study was to determine genomic diversity of 14 MG field strains from chicken, Chuker partridge and peacock collected during 2009-2012 in Iran by polymerase chain reaction and partial sequencing of the pvpA gene. A High-Resolution Melting (HRM) technique was also developed and applied to differentiate between field and vaccine strains. Sequencing of the pvpA gene revealed a 51 nucleotide deletion, within DR-1 and DR-2, among MG strains from chicken and partridge whilst 63 nucleotides were deleted in MG strain from peacock. One nucleotide substitution was also observed among chicken MG strains. Phylogenetic analysis of the sequences clustered all of the Iranian MG strains into two clades or phylogeny groups; the strains from chicken and partridge in one group (group 1) and the strain from peacock into another group (group 4). HRM analysis has also produced comparable outcome to those of sequencing; four distinct melting curves which correspond to the three MG strains from chicken, Chukar partridge and peacock and ts-11 vaccine strain. Overall, findings of this study point towards a single source of infection for the chicken and partridge MG strains and likelihood of the strains being native and endemic in Iran. Peacock considered as an exotic species in Iran, hence the genetic distance for the pvpA gene. MG can be transmitted easily among different avian species and this distinct peacock strain may pose a threat to poultry industry. Our findings also show that molecular variation among pvpA gene of MG strains could be revealed using the relatively rapid and affordable HRM technique.
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Affiliation(s)
- Shabnam Hashemi
- Research Institute for Zoonotic Diseases and Department of Pathobiology, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran.
| | - Mohammadreza Mahzounieh
- Research Institute for Zoonotic Diseases and Department of Pathobiology, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Nariman Sheikhi
- Department of Clinical Sciences, Faculty of Specialized Veterinary Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Azizollah Ebrahimi
- Research Institute for Zoonotic Diseases and Department of Pathobiology, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
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Sayhi M, Ouerghi O, Belgacem K, Arbi M, Tepeli Y, Ghram A, Anik Ü, Österlund L, Laouini D, Diouani MF. Electrochemical detection of influenza virus H9N2 based on both immunomagnetic extraction and gold catalysis using an immobilization-free screen printed carbon microelectrode. Biosens Bioelectron 2018; 107:170-177. [DOI: 10.1016/j.bios.2018.02.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/03/2018] [Accepted: 02/05/2018] [Indexed: 01/25/2023]
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Tomás G, Hernández M, Marandino A, Techera C, Grecco S, Hernández D, Banda A, Panzera Y, Pérez R. Development of an RT-qPCR assay for the specific detection of a distinct genetic lineage of the infectious bursal disease virus. Avian Pathol 2016; 46:150-156. [PMID: 27924642 DOI: 10.1080/03079457.2016.1228827] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The infectious bursal disease virus (IBDV) is a major health threat to the world's poultry industry despite intensive controls including proper biosafety practices and vaccination. IBDV (Avibirnavirus, Birnaviridae) is a non-enveloped virus with a bisegmented double-stranded RNA genome. The virus is traditionally classified into classic, variant and very virulent strains, each with different epidemiological relevance and clinical implications. Recently, a novel worldwide spread genetic lineage was described and denoted as distinct (d) IBDV. Here, we report the development and validation of a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay for the specific detection of dIBDVs in the global poultry industry. The assay employs a TaqMan-MGB probe that hybridizes with a unique molecular signature of dIBDV. The assay successfully detected all the assessed strains belonging to the dIBDV genetic lineage, showing high specificity and absence of cross-reactivity with non-dIBDVs, IBDV-negative samples and other common avian viruses. Using serial dilutions of in vitro-transcribed RNA we obtained acceptable PCR efficiencies and determination coefficients, and relatively small intra- and inter-assay variability. The assay demonstrated a wide dynamic range between 103 and 108 RNA copies/reaction. This rapid, specific and quantitative assay is expected to improve IBDV surveillance and control worldwide and to increase our understanding of the molecular epidemiology of this economically detrimental poultry pathogen.
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Affiliation(s)
- Gonzalo Tomás
- a Sección Genética Evolutiva, Departamento de Biología Animal , Instituto de Biología, Facultad de Ciencias, Universidad de la República , Montevideo , Uruguay
| | - Martín Hernández
- a Sección Genética Evolutiva, Departamento de Biología Animal , Instituto de Biología, Facultad de Ciencias, Universidad de la República , Montevideo , Uruguay
| | - Ana Marandino
- a Sección Genética Evolutiva, Departamento de Biología Animal , Instituto de Biología, Facultad de Ciencias, Universidad de la República , Montevideo , Uruguay
| | - Claudia Techera
- a Sección Genética Evolutiva, Departamento de Biología Animal , Instituto de Biología, Facultad de Ciencias, Universidad de la República , Montevideo , Uruguay
| | - Sofia Grecco
- a Sección Genética Evolutiva, Departamento de Biología Animal , Instituto de Biología, Facultad de Ciencias, Universidad de la República , Montevideo , Uruguay
| | - Diego Hernández
- a Sección Genética Evolutiva, Departamento de Biología Animal , Instituto de Biología, Facultad de Ciencias, Universidad de la República , Montevideo , Uruguay
| | - Alejandro Banda
- b Poultry Research and Diagnostic Laboratory, College of Veterinary Medicine , Mississippi State University , Pearl , MS , USA
| | - Yanina Panzera
- a Sección Genética Evolutiva, Departamento de Biología Animal , Instituto de Biología, Facultad de Ciencias, Universidad de la República , Montevideo , Uruguay
| | - Ruben Pérez
- a Sección Genética Evolutiva, Departamento de Biología Animal , Instituto de Biología, Facultad de Ciencias, Universidad de la República , Montevideo , Uruguay
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Banowary B, Dang VT, Sarker S, Connolly JH, Chenu J, Groves P, Ayton M, Raidal S, Devi A, Vanniasinkam T, Ghorashi SA. Differentiation of Campylobacter jejuni and Campylobacter coli Using Multiplex-PCR and High Resolution Melt Curve Analysis. PLoS One 2015; 10:e0138808. [PMID: 26394042 DOI: 10.1371/journal.pone.0138808] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 09/03/2015] [Indexed: 01/30/2023] Open
Abstract
Campylobacter spp. are important causes of bacterial gastroenteritis in humans in developed countries. Among Campylobacter spp. Campylobacter jejuni (C. jejuni) and C. coli are the most common causes of human infection. In this study, a multiplex PCR (mPCR) and high resolution melt (HRM) curve analysis were optimized for simultaneous detection and differentiation of C. jejuni and C. coli isolates. A segment of the hippuricase gene (hipO) of C. jejuni and putative aspartokinase (asp) gene of C. coli were amplified from 26 Campylobacter isolates and amplicons were subjected to HRM curve analysis. The mPCR-HRM was able to differentiate between C. jejuni and C. coli species. All DNA amplicons generated by mPCR were sequenced. Analysis of the nucleotide sequences from each isolate revealed that the HRM curves were correlated with the nucleotide sequences of the amplicons. Minor variation in melting point temperatures of C. coli or C. jejuni isolates was also observed and enabled some intraspecies differentiation between C. coli and/or C. jejuni isolates. The potential of PCR-HRM curve analysis for the detection and speciation of Campylobacter in additional human clinical specimens and chicken swab samples was also confirmed. The sensitivity and specificity of the test were found to be 100% and 92%, respectively. The results indicated that mPCR followed by HRM curve analysis provides a rapid (8 hours) technique for differentiation between C. jejuni and C. coli isolates.
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Sarker S, Ghorashi SA, Forwood JK, Raidal SR. Rapid genotyping of beak and feather disease virus using high-resolution DNA melt curve analysis. J Virol Methods 2014; 208:47-55. [DOI: 10.1016/j.jviromet.2014.07.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/21/2014] [Accepted: 07/25/2014] [Indexed: 11/21/2022]
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Huang SW, Ho CF, Chan KW, Cheng MC, Shien JH, Liu HJ, Wang CY. The genotyping of Infectious bronchitis virus in Taiwan by a multiplex amplification refractory mutation system reverse transcription polymerase chain reaction. J Vet Diagn Invest 2014; 26:721-33. [DOI: 10.1177/1040638714547735] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Infectious bronchitis virus (IBV; Avian coronavirus) causes acute respiratory and reproductive and urogenital diseases in chickens. Following sequence alignment of IBV strains, a combination of selective primer sets was designed to individually amplify the IBV wild-type and vaccine strains using a multiplex amplification refractory mutation system reverse transcription polymerase chain reaction (ARMS RT-PCR) approach. This system was shown to discriminate the IBV wild-type and vaccine strains. Moreover, an ARMS real-time RT-PCR (ARMS qRT-PCR) was combined with a high-resolution analysis (HRMA) to establish a melt curve analysis program. The specificity of the ARMS RT-PCR and the ARMS qRT-PCR was verified using unrelated avian viruses. Different melting temperatures and distinct normalized and shifted melting curve patterns for the IBV Mass, IBV H120, IBV TW-I, and IBV TW-II strains were detected. The new assays were used on samples of lung and trachea as well as virus from allantoic fluid and cell culture. In addition to being able to detect the presence of IBV vaccine and wild-type strains by ARMS RT-PCR, the IBV Mass, IBV H120, IBV TW-I, and IBV TW-II strains were distinguished using ARMS qRT-PCR by their melting temperatures and by HRMA. These approaches have acceptable sensitivities and specificities and therefore should be able to serve as options when carrying out differential diagnosis of IBV in Taiwan and China.
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Affiliation(s)
- Shr-Wei Huang
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Chia-Fang Ho
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Kun-Wei Chan
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Min-Chung Cheng
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Jui-Hung Shien
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Hung-Jen Liu
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Chi-Young Wang
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
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Abstract
Technology for infectious agent detection continues to evolve, particularly molecular methods that first emerged in the mid-1970s. The goals of new technology in diagnostics, whether in humans or in animals, including poultry, are to achieve the highest sensitivity and specificity possible to accurately identify the infection status of an individual or flock in the shortest time possible. Ease of use, low cost and increased information from a single test (e.g. multiplexing) are also critical areas frequently targeted for improvement. New tests and modifications of current tests are reported often, and diagnostic tests are now commonly developed by commercial companies. As one would expect, most advances in diagnostic technology are applied first to human health, and then may be adapted to animal health if practical. In the present review the trends and novel innovative technologies in primarily viral diagnostics are reviewed and the practicality of these methods and application for poultry health are discussed briefly. Also, influenza will seem to be over-represented in viral diagnostics since it is frequently used as a proof-of-concept target for novel technology due to its importance for animal and public health. Finally, the review is intended to be a brief survey of some of the innovative diagnostic technologies reported in recent years. It is not entirely comprehensive of all technology and the author makes no claims or endorsements of any of the technology or products mentioned.
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Affiliation(s)
- Erica Spackman
- Southeast Poultry Research Laboratory, USDA-ARS, Athens, GA 30605, USA.
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Tomás G, Hernández M, Marandino A, Panzera Y, Maya L, Hernández D, Pereda A, Banda A, Villegas P, Aguirre S, Pérez R. Development and validation of a TaqMan-MGB real-time RT-PCR assay for simultaneous detection and characterization of infectious bursal disease virus. J Virol Methods 2012; 185:101-7. [PMID: 22728272 DOI: 10.1016/j.jviromet.2012.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 05/26/2012] [Accepted: 06/13/2012] [Indexed: 10/28/2022]
Abstract
Rapid and reliable detection and classification of infectious bursal disease viruses (IBDVs) is of crucial importance for disease surveillance and control. This study presents the development and validation of a real-time RT-PCR assay to detect and discriminate very virulent (vv) from non-vv (classic and variant) IBDV strains. The assay uses two fluorogenic, minor groove-binding (MGB) TaqMan probes targeted to a single nucleotide polymorphism (SNP) embedded in a highly conserved genomic region. The analytical sensitivity of the assay was determined using serial dilutions of in vitro-transcribed RNA. The assay demonstrated a wide dynamic range between 10(2) and 10(8) standard RNA copies per reaction. Good reproducibility was also detected, with intra- and inter-assay coefficients of variation ranging from 0.13% to 2.23% and 0.26% to 1.92%, respectively. The assay detected successfully all the assessed vv, classical, and variant field and vaccine strains and correctly discriminated all vvIBDV strains from non-vvIBDV strains. Other common avian RNA viruses tested negative, indicating high specificity of the assay. The high sensitivity, rapidity, reproducibility, and specificity of the real-time RT-PCR assay make this method suitable for general and genotype-specific detection and quantitation.
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Affiliation(s)
- Gonzalo Tomás
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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Sepúlveda D, Cárdenas C, Carmona M, Marshall SH. Novel strategy to evaluate infectious salmon anemia virus variants by high resolution melting. PLoS One 2012; 7:e37265. [PMID: 22719837 PMCID: PMC3373561 DOI: 10.1371/journal.pone.0037265] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 04/18/2012] [Indexed: 12/29/2022] Open
Abstract
Genetic variability is a key problem in the prevention and therapy of RNA-based virus infections. Infectious Salmon Anemia virus (ISAv) is an RNA virus which aggressively attacks salmon producing farms worldwide and in particular in Chile. Just as with most of the Orthomyxovirus, ISAv displays high variability in its genome which is reflected by a wider infection potential, thus hampering management and prevention of the disease. Although a number of widely validated detection procedures exist, in this case there is a need of a more complex approach to the characterization of virus variability. We have adapted a procedure of High Resolution Melting (HRM) as a fine-tuning technique to fully differentiate viral variants detected in Chile and projected to other infective variants reported elsewhere. Out of the eight viral coding segments, the technique was adapted using natural Chilean variants for two of them, namely segments 5 and 6, recognized as virulence-associated factors. Our work demonstrates the versatility of the technique as well as its superior resolution capacity compared with standard techniques currently in use as key diagnostic tools.
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Affiliation(s)
- Dagoberto Sepúlveda
- Laboratorio de Patógenos Acuícolas, Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Constanza Cárdenas
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Marisela Carmona
- Laboratorio de Patógenos Acuícolas, Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Sergio H. Marshall
- Laboratorio de Patógenos Acuícolas, Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- * E-mail:
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Hu J, Li W, Wang T, Lin Z, Jiang M, Hu F. Development of a label-free and innovative approach based on surface plasmon resonance biosensor for on-site detection of infectious bursal disease virus (IBDV). Biosens Bioelectron 2012; 31:475-9. [DOI: 10.1016/j.bios.2011.11.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 11/10/2011] [Accepted: 11/10/2011] [Indexed: 11/17/2022]
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