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El-Tholoth M, Bau HH. Molecular Detection of Respiratory Tract Viruses in Chickens at the Point of Need by Loop-Mediated Isothermal Amplification (LAMP). Viruses 2024; 16:1248. [PMID: 39205222 PMCID: PMC11359210 DOI: 10.3390/v16081248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
Accurate and timely molecular diagnosis of respiratory diseases in chickens is essential for implementing effective control measures, preventing the spread of diseases within poultry flocks, minimizing economic loss, and guarding food security. Traditional molecular diagnostic methods like polymerase chain reaction (PCR) require expensive equipment and trained personnel, limiting their use to centralized labs with a significant delay between sample collection and results. Loop-mediated isothermal amplification (LAMP) of nucleic acids offers an attractive alternative for detecting respiratory viruses in broiler chickens with sensitivity comparable to that of PCR. LAMP's main advantages over PCR are its constant incubation temperature (∼65 °C), high amplification efficiency, and contaminant tolerance, which reduce equipment complexity, cost, and power consumption and enable instrument-free tests. This review highlights effective LAMP methods and variants that have been developed for detecting respiratory viruses in chickens at the point of need.
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Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
- Veterinary Sciences Program, Health Sciences Division, Al Ain Men’s Campus, Higher Colleges of Technology, Al Ain 17155, United Arab Emirates
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA;
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2
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Zhang T, Tang J, Zhang Y, Jin Y, Lin Z, Chen J, Huang J, Mo M. Establishment of a rapid real-time fluorescence-based recombinase-aided amplification method for detection of avian infectious bronchitis virus. J Virol Methods 2024; 328:114955. [PMID: 38768869 DOI: 10.1016/j.jviromet.2024.114955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
Abstract
Infectious bronchitis (IB) is an acute, highly contagious contact respiratory disease of chickens caused by infectious bronchitis virus (IBV). IBV is very prone to mutation, which brings great difficulties to the prevention and control of the disease. Therefore, there is a pressing need for a method that is fast, sensitive, specific, and convenient for detecting IBV. In this study, a real-time fluorescence-based recombinase-aided amplification (RF-RAA) method was established. Primers and probe were designed based on the conserved regions of the IBV M gene and the reaction concentrations were optimized, then the specificity, sensitivity, and reproducibility of this assay were tested. The results showed that the RF-RAA method could be completed at 39℃ within 20 min, during which the results could be interpreted visually in real-time. The RF-RAA method had good specificity, no cross-reaction with common poultry pathogens, and it detected a minimum concentration of template of 2 copies/μL for IBV. Besides, its reproducibility was stable. A total of 144 clinical samples were tested by RF-RAA and real-time quantitative PCR (qPCR), 132 samples of which were positive and 12 samples were negative, and the coincidence rate of the two methods was 100 %. In conclusion, the developed RF-RAA detection method is rapid, specific, sensitive, reproducible, and convenient, which can be utilized for laboratory detection and clinical diagnosis of IBV.
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Affiliation(s)
- Taoni Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jinwen Tang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yu Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yinghao Jin
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Zixue Lin
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jiming Chen
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jianni Huang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Meilan Mo
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China; Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning 530004, China; Guangxi Colleges and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning 530004, China.
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3
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Padzil F, Mariatulqabtiah AR, Tan WS, Ho KL, Isa NM, Lau HY, Abu J, Chuang KP. Loop-Mediated Isothermal Amplification (LAMP) as a Promising Point-of-Care Diagnostic Strategy in Avian Virus Research. Animals (Basel) 2021; 12:ani12010076. [PMID: 35011181 PMCID: PMC8744981 DOI: 10.3390/ani12010076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/02/2021] [Accepted: 12/04/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Many of the existing screening methods of avian viruses depend on clinical symptoms and pathological gross examinations that still necessitate confirmatory microscopic testing. Confirmation of a virus is often conducted at centralized laboratories that are well-equipped with instruments for virus isolation, hemagglutinin inhibition, virus neutralization, ELISA, PCR and qPCR. These assays are known for their great accuracy and sensitivity, and hence are set as standard practices. Nevertheless, limitations arise due to the time, cost and on-site applicability. As the technology progresses, molecular diagnostics should be more accessible to isolated areas and even practicable for use by non-skilled personnel such as farmers and private breeders. One of the point-of-care diagnostic strategies to consider for such matters is loop-mediated isothermal amplification (LAMP). Abstract Over the years, development of molecular diagnostics has evolved significantly in the detection of pathogens within humans and their surroundings. Researchers have discovered new species and strains of viruses, while mitigating the viral infections that occur, owing to the accessibility of nucleic acid screening methods such as polymerase chain reaction (PCR), quantitative (real-time) polymerase chain reaction (qPCR) and reverse-transcription qPCR (RT-qPCR). While such molecular detection methods are widely utilized as the benchmark, the invention of isothermal amplifications has also emerged as a reliable tool to improvise on-field diagnosis without dependence on thermocyclers. Among the established isothermal amplification technologies are loop-mediated isothermal amplification (LAMP), recombinant polymerase amplification (RPA), strand displacement activity (SDA), nucleic acid sequence-based amplification (NASBA), helicase-dependent amplification (HDA) and rolling circle amplification (RCA). This review highlights the past research on and future prospects of LAMP, its principles and applications as a promising point-of-care diagnostic method against avian viruses.
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Affiliation(s)
- Faiz Padzil
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Institute for Medical Research, National Institute of Health, Setia Alam, Shah Alam 40170, Selangor, Malaysia
| | - Abdul Razak Mariatulqabtiah
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +60-297-691-938
| | - Wen Siang Tan
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Nurulfiza Mat Isa
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Han Yih Lau
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Persiaran MARDI-UPM, Serdang 43400, Selangor, Malaysia;
| | - Jalila Abu
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Kuo-Pin Chuang
- International Degree Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 912, Taiwan;
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- School of Dentistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Molecular Detection of Infectious Laryngotracheitis Virus in Chickens with a Microfluidic Chip. Animals (Basel) 2021; 11:ani11113203. [PMID: 34827935 PMCID: PMC8614514 DOI: 10.3390/ani11113203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Infectious laryngotracheitis (ILT) presents a major risk to the chicken industry. Rapid, specific, simple, and point-of-need molecular detection of the virus is crucial to enable chicken farms to take timely action and contain the spread of infection. The current study describes an isothermal amplification assay for infectious laryngotracheitis virus (ILTV) infection and the implementation of this assay in a microfluidic chip suitable for molecular detection and quasi-quantification of ILTV in diagnostic veterinary laboratories with low resources and poultry farms. Our assay performance was compared and favorably agreed with quantitative PCR (qPCR). Clinical tests of our assay and chip with samples from diseased chickens demonstrated good concordance with the gold-standard benchtop qPCR assay. Abstract Infectious laryngotracheitis (ILT) is a viral disease of chickens’ respiratory system that imposes considerable financial burdens on the chicken industry. Rapid, simple, and specific detection of this virus is crucial to enable proper control measures. Polymerase chain reaction (PCR)-based molecular tests require relatively expensive instruments and skilled personnel, confining their application to centralized laboratories. To enable chicken farms to take timely action and contain the spread of infection, we describe a rapid, simple, semi-quantitative benchtop isothermal amplification (LAMP) assay, and a field-deployable microfluidic device for the diagnosis of ILTV infection in chickens. Our assay performance was compared and favorably agreed with quantitative PCR (qPCR). The sensitivity of our real-time LAMP test is 250 genomic copies/reaction. Clinical performance of our microfluidic device using samples from diseased chickens showed 100% specificity and 100% sensitivity in comparison with benchtop LAMP assay and the gold-standard qPCR. Our method facilitates simple, specific, and rapid molecular ILTV detection in low-resource veterinary diagnostic laboratories and can be used for field molecular diagnosis of suspected ILT cases.
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Parkhe P, Verma S. Evolution, Interspecies Transmission, and Zoonotic Significance of Animal Coronaviruses. Front Vet Sci 2021; 8:719834. [PMID: 34738021 PMCID: PMC8560429 DOI: 10.3389/fvets.2021.719834] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/07/2021] [Indexed: 12/18/2022] Open
Abstract
Coronaviruses are single-stranded RNA viruses that affect humans and a wide variety of animal species, including livestock, wild animals, birds, and pets. These viruses have an affinity for different tissues, such as those of the respiratory and gastrointestinal tract of most mammals and birds and the hepatic and nervous tissues of rodents and porcine. As coronaviruses target different host cell receptors and show divergence in the sequences and motifs of their structural and accessory proteins, they are classified into groups, which may explain the evolutionary relationship between them. The interspecies transmission, zoonotic potential, and ability to mutate at a higher rate and emerge into variants of concern highlight their importance in the medical and veterinary fields. The contribution of various factors that result in their evolution will provide better insight and may help to understand the complexity of coronaviruses in the face of pandemics. In this review, important aspects of coronaviruses infecting livestock, birds, and pets, in particular, their structure and genome organization having a bearing on evolutionary and zoonotic outcomes, have been discussed.
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Affiliation(s)
| | - Subhash Verma
- Department of Veterinary Microbiology, DGCN College of Veterinary and Animal Sciences, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
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Soroka M, Wasowicz B, Rymaszewska A. Loop-Mediated Isothermal Amplification (LAMP): The Better Sibling of PCR? Cells 2021; 10:1931. [PMID: 34440699 PMCID: PMC8393631 DOI: 10.3390/cells10081931] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/11/2022] Open
Abstract
In 1998, when the PCR technique was already popular, a Japanese company called Eiken Chemical Co., Ltd. designed a method known as the loop-mediated isothermal amplification of DNA (LAMP). The method can produce up to 109 copies of the amplified DNA within less than an hour. It is also highly specific due to the use of two to three pairs of primers (internal, external, and loop), which recognise up to eight specific locations on the DNA or RNA targets. Furthermore, the Bst DNA polymerase most used in LAMP shows a high strand displacement activity, which eliminates the DNA denaturation stage. One of the most significant advantages of LAMP is that it can be conducted at a stable temperature, for instance, in a dry block heater or an incubator. The products of LAMP can be detected much faster than in standard techniques, sometimes only requiring analysis with the naked eye. The following overview highlights the usefulness of LAMP and its effectiveness in various fields; it also considers the superiority of LAMP over PCR and presents RT-LAMP as a rapid diagnostic tool for SARS-CoV-2.
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Affiliation(s)
| | - Barbara Wasowicz
- Department of Genetics and Genomics, Institute of Biology, University of Szczecin, 3c Felczaka St., 71-412 Szczecin, Poland; (M.S.); (A.R.)
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Bhuiyan MSA, Amin Z, Bakar AMSA, Saallah S, Yusuf NHM, Shaarani SM, Siddiquee S. Factor Influences for Diagnosis and Vaccination of Avian Infectious Bronchitis Virus (Gammacoronavirus) in Chickens. Vet Sci 2021; 8:47. [PMID: 33809420 PMCID: PMC8001924 DOI: 10.3390/vetsci8030047] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 11/16/2022] Open
Abstract
Infectious bronchitis virus (IBV) is a major economic problem in commercial chicken farms with acute multiple-system infection, especially in respiratory and urogenital systems. A live-attenuated and killed vaccine is currently immunized to control IBV infection; however, repeated outbreaks occur in both unvaccinated and vaccinated birds due to the choice of inadequate vaccine candidates and continuous emergence of novel infectious bronchitis (IB) variants and failure of vaccination. However, similar clinical signs were shown in different respiratory diseases that are essential to improving the diagnostic assay to detect IBV infections. Various risk factors involved in the failure of IB vaccination, such as various routes of application of vaccination, the interval between vaccinations, and challenge with various possible immunosuppression of birds are reviewed. The review article also highlights and updates factors affecting the diagnosis of IBV disease in the poultry industry with differential diagnosis to find the nature of infections compared with non-IBV diseases. Therefore, it is essential to monitor the common reasons for failed IBV vaccinations with preventive action, and proper diagnostic facilities for identifying the infective stage, leading to earlier control and reduced economic losses from IBV disease.
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Affiliation(s)
- Md. Safiul Alam Bhuiyan
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jln UMS, Kota Kinabalu 88400, Sabah, Malaysia; (M.S.A.B.); (Z.A.); (S.S.); (N.H.M.Y.)
| | - Zarina Amin
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jln UMS, Kota Kinabalu 88400, Sabah, Malaysia; (M.S.A.B.); (Z.A.); (S.S.); (N.H.M.Y.)
| | - Ag Muhammad Sagaf Abu Bakar
- Jabatan Perkhidmatan Veterinar Sabah, Makamal Diagnosa Veterinar Kota Kinabalu, Peti Surat No 59, Tanjung Aru 89457, Sabah, Malaysia;
| | - Suryani Saallah
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jln UMS, Kota Kinabalu 88400, Sabah, Malaysia; (M.S.A.B.); (Z.A.); (S.S.); (N.H.M.Y.)
| | - Noor Hydayaty Md. Yusuf
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jln UMS, Kota Kinabalu 88400, Sabah, Malaysia; (M.S.A.B.); (Z.A.); (S.S.); (N.H.M.Y.)
| | - Sharifudin Md. Shaarani
- Food Biotechnology Program, Faculty of Science and Technology, Universiti Sains Islam Malaysia, Bandar Baru Nilai, Nilai 71800, Negeri, Malaysia;
| | - Shafiquzzaman Siddiquee
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jln UMS, Kota Kinabalu 88400, Sabah, Malaysia; (M.S.A.B.); (Z.A.); (S.S.); (N.H.M.Y.)
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Abstract
Sensitive, specific and rapid molecular diagnosis of respiratory diseases in animals and humans is critical to facilitate appropriate control measures and treatment. Conventional polymerase chain reaction (PCR)-based molecular diagnostics requires relatively expensive equipment and trained staff, restricting its use to centralized laboratories with significant delays between sample collection and test results. Herein, we report a highly sensitive, rapid, point-of-need, two-stage-molecular test that requires minimal instrumentation and training. Our test, dubbed Penn-RAMP, combines recombinase polymerase amplification (RPA, 38 °C) and loop-mediated isothermal amplification (LAMP, 63 °C) in one tube, enabling nested, two-stage isothermal amplification. We demonstrate Penn-RAMP's efficacy by testing for two common viral respiratory diseases of chickens: infectious laryngotracheitis (ILT) and infectious bronchitis (IB) that impose great economic burden worldwide. Test results of clinical samples with our closed-tube Penn-RAMP assays concord with the gold standard quantitative PCR (qPCR) assay; with 10-fold better limit of detection than LAMP and qPCR. Our closed-tube Penn-RAMP assays have the potential to greatly reduce false negatives while requiring minimal instrumentation and training.
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Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt.
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M. Najimudeen S, H. Hassan MS, C. Cork S, Abdul-Careem MF. Infectious Bronchitis Coronavirus Infection in Chickens: Multiple System Disease with Immune Suppression. Pathogens 2020; 9:pathogens9100779. [PMID: 32987684 PMCID: PMC7598688 DOI: 10.3390/pathogens9100779] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/21/2020] [Accepted: 09/21/2020] [Indexed: 12/11/2022] Open
Abstract
In the early 1930s, infectious bronchitis (IB) was first characterized as a respiratory disease in young chickens; later, the disease was also described in older chickens. The etiology of IB was confirmed later as being due to a coronavirus: the infectious bronchitis virus (IBV). Being a coronavirus, IBV is subject to constant genome change due to mutation and recombination, with the consequence of changing clinical and pathological manifestations. The potential use of live attenuated vaccines for the control of IBV infection was demonstrated in the early 1950s, but vaccine breaks occurred due to the emergence of new IBV serotypes. Over the years, various IBV genotypes associated with reproductive, renal, gastrointestinal, muscular and immunosuppressive manifestations have emerged. IBV causes considerable economic impacts on global poultry production due to its pathogenesis involving multiple body systems and immune suppression; hence, there is a need to better understand the pathogenesis of infection and the immune response in order to help developing better management strategies. The evolution of new strains of IBV during the last nine decades against vaccine-induced immune response and changing clinical and pathological manifestations emphasize the necessity of the rational development of intervention strategies based on a thorough understanding of IBV interaction with the host.
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Augustine R, Hasan A, Das S, Ahmed R, Mori Y, Notomi T, Kevadiya BD, S. Thakor A. Loop-Mediated Isothermal Amplification (LAMP): A Rapid, Sensitive, Specific, and Cost-Effective Point-of-Care Test for Coronaviruses in the Context of COVID-19 Pandemic. BIOLOGY 2020; 9:E182. [PMID: 32707972 PMCID: PMC7464797 DOI: 10.3390/biology9080182] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022]
Abstract
The rampant spread of COVID-19 and the worldwide prevalence of infected cases demand a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. The most common molecular tests approved by regulatory bodies across the world for COVID-19 diagnosis are based on Polymerase Chain Reaction (PCR). While PCR-based tests are highly sensitive, specific, and remarkably reliable, they have many limitations ranging from the requirement of sophisticated laboratories, need of skilled personnel, use of complex protocol, long wait times for results, and an overall high cost per test. These limitations have inspired researchers to search for alternative diagnostic methods that are fast, economical, and executable in low-resource laboratory settings. The discovery of Loop-mediated isothermal Amplification (LAMP) has provided a reliable substitute platform for the accurate detection of low copy number nucleic acids in the diagnosis of several viral diseases, including epidemics like Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). At present, a cocktail of LAMP assay reagents along with reverse transcriptase enzyme (Reverse Transcription LAMP, RT-LAMP) can be a robust solution for the rapid and cost-effective diagnosis for COVID-19, particularly in developing, and low-income countries. In summary, the development of RT-LAMP based diagnostic tools in a paper/strip format or the integration of this method into a microfluidic platform such as a Lab-on-a-chip may revolutionize the concept of PoCT for COVID-19 diagnosis. This review discusses the principle, technology and past research underpinning the success for using this method for diagnosing MERS and SARS, in addition to ongoing research, and the prominent prospect of RT-LAMP in the context of COVID-19 diagnosis.
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Affiliation(s)
- Robin Augustine
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Suvarthi Das
- Department of Medicine, Stanford University Medical Center, Palo Alto, CA 94304, USA;
| | - Rashid Ahmed
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar;
- Biomedical Research Center (BRC), Qatar University, Doha PO Box 2713, Qatar
| | - Yasuyoshi Mori
- Eiken Chemical Co., Ltd., Research and Development Division, Taito-ku 110-8408, Japan; (Y.M.); (T.N.)
| | - Tsugunori Notomi
- Eiken Chemical Co., Ltd., Research and Development Division, Taito-ku 110-8408, Japan; (Y.M.); (T.N.)
| | - Bhavesh D. Kevadiya
- Interventional Regenerative Medicine and Imaging Laboratory, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; (B.D.K.); (A.S.T.)
| | - Avnesh S. Thakor
- Interventional Regenerative Medicine and Imaging Laboratory, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA; (B.D.K.); (A.S.T.)
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11
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El-Tholoth M, Mauk MG, Anis E, Bau HH. A closed-tube, single-step, real time, reverse transcription-loop-mediated isothermal amplification assay for infectious bronchitis virus detection in chickens. J Virol Methods 2020; 284:113940. [PMID: 32687868 PMCID: PMC7367007 DOI: 10.1016/j.jviromet.2020.113940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 11/24/2022]
Abstract
A closed tube, single-step-real-time-RT-LAMP assay was developed for detection and semi-quantification of IBV in closed tube. The least limit of detection of our assay is 1 EID50/ ml. Clinical evaluation of samples from diseased chickens using our assay shows a very good concordance with RT-qPCR assay.
Infectious bronchitis (IB) is a viral infection of the chicken respiratory tract that causes substantial economic burden on the industry. Simple, specific and rapid diagnosis of this disease is critical for the initiation of appropriate control measures. Conventional molecular diagnostic methods require a relatively sophisticated equipment and skilled staff. Here we describe a rapid, simple, semi-quantative, closed-tube, single-step, real-time- reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for IB and compare our assay with quantative, reverse transcription- polymerase chain reaction (RT-qPCR). The limit of detection (LOD) of our RT-LAMP assay is 1 EID50/ ml. Clinical evaluation of samples from diseased chickens with our RT-LAMP showed a very good concordance with RT-qPCR. Our assay enables simple, specific, rapid molecular detection and semi-quantification of the infectious bronchitis virus (IBV) in veterinary diagnostic laboratories. Furthermore, our RT-LAMP detection is carried out in a sealed tube, eliminating the risk of false-positive results in subsequent tests because of any contamination of the work area as in the case of lateral flow strip or gel electrophoresis-based amplicon detection.
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Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt; Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, United States.
| | - Michael G Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Eman Anis
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA 19348, United States
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, United States
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12
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Wu X, Song Z, Zhai X, Zuo L, Mei X, Xiang R, Kang Z, Zhou L, Wang H. Simultaneous and visual detection of infectious bronchitis virus and Newcastle disease virus by multiple LAMP and lateral flow dipstick. Poult Sci 2020; 98:5401-5411. [PMID: 31265112 PMCID: PMC7107193 DOI: 10.3382/ps/pez372] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/09/2019] [Indexed: 12/12/2022] Open
Abstract
Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV) are both important viruses seriously affecting poultry industry worldwide. In this study, reverse-transcription LAMP (RT-LAMP) was combined with lateral flow dipstick (LFD) forming a novel detection tool which could simultaneously detect IBV and NDV visually. Primers targeted the 5'-untranslated region (5'-UTR) of IBV genome and the conserved region of NDV large polymerase gene (LP). The specificity and sensitivity of this multiple reverse transcription-LAMP-LFD (mRT-LAMP-LFD) assay were compared with those of conventional RT-PCR, nested RT-PCR (nRT-PCR), quantification RT-PCR (qRT-PCR), and RT-LAMP monitored by electrophoresis. No non-specific amplifications were observed when the assays were tested with unrelated viruses. According to the sensitivity study, when detecting IBV or NDV alone, the lowest detection limits of mRT-LAMP-LFD were 100.8 IBV RNA copies/reaction and 100.7 NDV RNA copies/reaction. Furthermore, when detecting IBV and NDV simultaneously, the lowest detection limit was the same as that of the single detection assays. In the clinical sample study, mRT-LAMP-LFD performed the best among these assays. When tested with IBV or NDV single infected samples, the mean detection rates were 98.65% and 97.25%, respectively. In the IBV and NDV co-infected sample study, the mean detection rates of IBV and NDV were both 95%. This study showed that mRT-LAMP-LFD was a promising qualitative detection tool suitable for field single or multiple IBV and NDV detection.
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Affiliation(s)
- Xuan Wu
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Zengxu Song
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Xiwen Zhai
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Lei Zuo
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Xueran Mei
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Rong Xiang
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Zhuangzhuang Kang
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Long Zhou
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
| | - Hongning Wang
- School of Life Science, Sichuan University, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, "985 Project" Science Innovative Platform for Resource and Environment Protection of Southwestern, Key Laboratory of Bio-resources and Eco-environment, Ministry of Education,29# Wangjiang Road, Chengdu 610065, China
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Recombinase polymerase amplification-nucleic acid lateral flow immunoassays for Newcastle disease virus and infectious bronchitis virus detection. Mol Biol Rep 2019; 46:6391-6397. [PMID: 31549369 PMCID: PMC7089497 DOI: 10.1007/s11033-019-05085-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 09/18/2019] [Indexed: 12/15/2022]
Abstract
Newcastle disease virus (NDV) and infectious bronchitis virus (IBV) are two poultry pathogens affecting the respiratory tract of chickens, and cause major economic losses in the industry. Rapid detection of these viruses is crucial to inform implementation of appropriate control measures. The objective of our study is developing a simple, rapid and field applicable recombinase polymerase amplification (RPA)–nucleic acid lateral flow (NALF) immunoassay for detection of NDV and IBV. Isothermal amplification of the matrix protein (M) gene of NDV and the nucleoprotein (N) gene of IBV was implemented via recombinase polymerase amplification at 38 °C for 40 min and 20 min, respectively using modified labeled primers. NALF device used in this study utilizes antibodies for detection of labeled RPA amplicons. The results revealed that RPA-NALF immunoassays can detect both viruses after 40 min at 38 °C and only NDV after 20 min. The limit of detection (LOD) was 10 genomic copies/RPA reaction. The assays results on clinical samples collected from diseased chicken farms demonstrated a good performance in comparison with quantitative real time reverse transcription polymerase chain reaction (qRT-PCR). The assays established in this study can facilitate rapid, on-site molecular diagnosis of suspected cases of ND and IB viral infections as the results can be detected by the naked eye without the need for measuring fluorescence. Furthermore, the NALF device could be adapted to detect other infectious agents.
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Zhai X, Mei X, Wu X, Zuo L, Zhou L, Tian Y, Han X, Yang X, Wang H. A loop-mediated isothermal amplification coupling with a lateral flow dipstick for rapid and specific detection of fowl adenovirus serotype-4. J Virol Methods 2019; 270:79-86. [PMID: 31054280 DOI: 10.1016/j.jviromet.2019.04.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 11/26/2022]
Abstract
Fowl adenovirus serotype-4 (FAdV-4) has been recognized as a predominant threat to the broilers aged from three to five weeks. Hydropericardium syndrome (HPS) is one of its major clinical diseases by FAdV-4 resulting in heavy economic losses. In this study, a loop-mediated isothermal amplification coupling with a lateral flow dipstick (LAMP-LFD) was developed for rapid and specific detection of fowl adenovirus serotype-4. The optimized LAMP-LFD can be completed in 60 min at 65 °C. The minimum detection limits of PCR, real-time PCR, nested PCR and LAMP-LFD are 1 × 104 copies/μl, 1 × 102 copies/μl, 10 copies/μl and 10 copies/μl respectively. Moreover, the specificity of the LAMP-LFD assay is satisfactory and does not produce cross reactions with other species. In field samples, 150 samples were assayed by PCR and LAMP-LFD. They agreed on the diagnosis "positive" in 13% of clinical samples, and they agreed on the diagnosis "negative" in 85% of clinical samples. Their probability of agreement is p0 = 147/150 = 13% + 85% = 98%. LAMP-LFD can potentially be modified and applied as a diagnostic tool for FAdV-4 infection especially in resource-limited areas, such as small breeding farms and basic veterinary labs to offer an affordable diagnostic.
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Affiliation(s)
- Xiwen Zhai
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Xueran Mei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Xuan Wu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Lei Zuo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Long Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Yiming Tian
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Xiaoxiao Han
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China; Department of Biomedical Sciences, Chengdu Medical College, Chengdu, Sichuan, PR China
| | - Xin Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - HongNing Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China.
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Current loop-mediated isothermal amplification (LAMP) technologies for the detection of poultry pathogens. WORLD POULTRY SCI J 2018. [DOI: 10.1017/s004393391700109x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Domanska-Blicharz K, Lisowska A, Pikuła A, Sajewicz-Krukowska J. Specific detection of GII-1 lineage of infectious bronchitis virus. Lett Appl Microbiol 2017; 65:141-146. [PMID: 28493279 PMCID: PMC7165721 DOI: 10.1111/lam.12753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/21/2017] [Accepted: 04/28/2017] [Indexed: 01/01/2023]
Abstract
Infectious bronchitis virus (IBV) is a worldwide prevalent RNA virus that causes highly contagious and economically devastating disease in chicken. The virus exists in many different genetic forms which made the disease control very difficult. The present study describes the development and validation of TaqMan probe‐based real‐time reverse transcription‐polymerase chain reaction (real‐time RT‐PCR) targeting the S1 coding region of S gene characteristic for the GII‐1 lineage (formerly the D1466‐like variant) of IBV. These strains are quite different from other European IBV belonging to different lineages of the GI genotype. The developed method was 30‐fold more sensitive than used so far for standard nested RT‐PCR with detection limit of 56 RNA copies per reaction. The specificity of the assay was also evaluated with a panel of different poultry pathogens. Repeatability and reproducibility of the method was very high with coefficients of variation lower than 4%. One hundred and twenty‐seven IBV‐positive samples were tested by this method and GII‐1 strains were detected in four of them (3·15%) which indicate a decrease in the GII‐1 IBV prevalence in Poland. The assay was proven to be a valuable tool for rapid diagnosis of GII‐1 lineage of IBV strains and moreover it enabled the monitoring of viral loads which can be used to assess disease progression. Significance and Impact of the Study This study reports a TaqMan probe‐based real‐time reverse transcription‐polymerase chain reaction (real‐time RT‐PCR) for rapid and accurate identification of GII‐1 lineage (formerly D1466‐like variant) of infectious bronchitis virus (IBV). The assay revealed to be more sensitive than standard nested RT‐PCR assay, previously used for this purpose. The developed assay has been tested on numerous field samples and revealed 3·15% prevalence of this lineage of IBV in Polish chicken population. Moreover, this new assay enables the assessment of viral load measurement which might be useful for epidemiology and pathogenesis studies.
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Affiliation(s)
- K Domanska-Blicharz
- Department of Poultry Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - A Lisowska
- Department of Poultry Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - A Pikuła
- Department of Poultry Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - J Sajewicz-Krukowska
- Department of Poultry Diseases, National Veterinary Research Institute, Pulawy, Poland
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Marandino A, Tomás G, Hernández M, Panzera Y, Craig MI, Vagnozzi A, Vera F, Techera C, Grecco S, Banda A, Hernández D, Pérez R. Development of RT-qPCR assays for the specific identification of two major genotypes of avian infectious bronchitis virus. J Virol Methods 2016; 235:21-25. [PMID: 27181213 DOI: 10.1016/j.jviromet.2016.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 11/30/2022]
Abstract
Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus (27.6kb) that causes one of the most persistent respiratory disease in poultry. The virus is classified in genotypes with different epidemiological relevance and clinical implications. The present study reports the development and validation of specific RT-qPCR assays for the detection of two major IBV genotypes: South America I (SAI) and Asia/South America II (A/SAII). The SAI genotype is an exclusive and widespread South American lineage while the A/SAII genotype is distributed in Asia, Europe and South America. Both identification assays employ TaqMan probes that hybridize with unique sequences in the spike glycoprotein gene. The assays successfully detected all the assessed strains belonging to both genotypes, showing high specificity and absence of cross-reactivity. Using serial dilutions of in vitro-transcribed RNA we obtained acceptable determination coefficients, PCR efficiencies and relatively small intra- and inter-assay variability. The assays demonstrated a wide dynamic range between 10(1)-10(7) and 10(2)-10(7) RNA copies/reaction for SAI and A/SAII strains, respectively. The possibility to characterize a large number of samples in a rapid, sensitive and reproducible way makes these techniques suitable tools for routine testing, IBV control, and epidemiological research in poultry.
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Affiliation(s)
- Ana Marandino
- 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
| | - Martín Hernández
- 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
| | - María Isabel Craig
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25 (1712) Castelar, Buenos Aires, Argentina
| | - Ariel Vagnozzi
- Instituto de Virología, CICVyA, INTA-Castelar, CC 25 (1712) Castelar, Buenos Aires, Argentina
| | - Federico Vera
- Laboratorio Sanidad Aviar, INTA- E.E.A, Concepción del Uruguay, Entre Ríos, Argentina
| | - Claudia Techera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Sofía Grecco
- 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, Pearl, MS 39288, USA
| | - Diego Hernández
- 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.
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Pathogenesis and Diagnostic Approaches of Avian Infectious Bronchitis. Adv Virol 2016; 2016:4621659. [PMID: 26955391 PMCID: PMC4756178 DOI: 10.1155/2016/4621659] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/05/2016] [Indexed: 02/06/2023] Open
Abstract
Infectious bronchitis (IB) is one of the major economically important poultry diseases distributed worldwide. It is caused by infectious bronchitis virus (IBV) and affects both galliform and nongalliform birds. Its economic impact includes decreased egg production and poor egg quality in layers, stunted growth, poor carcass weight, and mortality in broiler chickens. Although primarily affecting the respiratory tract, IBV demonstrates a wide range of tissues tropism, including the renal and reproductive systems. Thus, disease outcome may be influenced by the organ or tissue involved as well as pathotypes or strain of the infecting virus. Knowledge on the epidemiology of the prevalent IBV strains in a particular region is therefore important to guide control and preventions. Meanwhile previous diagnostic methods such as serology and virus isolations are less sensitive and time consuming, respectively; current methods, such as reverse transcription polymerase chain reaction (RT-PCR), Restriction Fragment Length Polymorphism (RFLP), and sequencing, offer highly sensitive, rapid, and accurate diagnostic results, thus enabling the genotyping of new viral strains within the shortest possible time. This review discusses aspects on pathogenesis and diagnostic methods for IBV infection.
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Zhang F, Bao S, Yu S, Cheng J, Tan L, Qiu X, Song C, Dai Y, Fei R, Ding C. Development of a loop-mediated isothermal amplification targeting a gene within the pyruvate dehydrogenase complex, the pdhA gene, for rapid detection of Mycoplasma gallisepticum. J Vet Diagn Invest 2016; 27:260-7. [PMID: 26038479 DOI: 10.1177/1040638715584155] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mycoplasma gallisepticum infections impose a significant economic burden on the poultry industry. In the current study, a loop-mediated isothermal amplification (LAMP) assay was developed and optimized to detect M. gallisepticum based on a gene within the pyruvate dehydrogenase complex, the pdhA gene, which codes for the major subunit (E1α) in the complex. The reaction conditions were optimized, and the specificity was confirmed by successful amplification of several M. gallisepticum strains, while no amplification was detected with 20 other major bacterial and viral pathogens of poultry. Additionally, the LAMP assay achieved 10-fold higher sensitivity than an existing polymerase chain reaction (PCR) method. The LAMP assay was applied to swab samples collected from poultry farms and compared with PCR. The positive detection rate was 20.2% (37/183) by LAMP and 13.1% (24/183) by PCR. The LAMP assay could provide a cost-effective, quick, and sensitive method for the detection of M. gallisepticum.
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Affiliation(s)
- Fanqing Zhang
- Department of Poultry Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China (Zhang, Bao, Yu, Cheng, Tan, Qiu, Song, Ding)College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China (Zhang, Fei)Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China (Dai)
| | - Shijun Bao
- Department of Poultry Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China (Zhang, Bao, Yu, Cheng, Tan, Qiu, Song, Ding)College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China (Zhang, Fei)Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China (Dai)
| | - Shengqing Yu
- Department of Poultry Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China (Zhang, Bao, Yu, Cheng, Tan, Qiu, Song, Ding)College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China (Zhang, Fei)Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China (Dai)
| | - Jinghua Cheng
- Department of Poultry Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China (Zhang, Bao, Yu, Cheng, Tan, Qiu, Song, Ding)College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China (Zhang, Fei)Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China (Dai)
| | - Lei Tan
- Department of Poultry Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China (Zhang, Bao, Yu, Cheng, Tan, Qiu, Song, Ding)College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China (Zhang, Fei)Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China (Dai)
| | - Xvsheng Qiu
- Department of Poultry Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China (Zhang, Bao, Yu, Cheng, Tan, Qiu, Song, Ding)College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China (Zhang, Fei)Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China (Dai)
| | - Cuiping Song
- Department of Poultry Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China (Zhang, Bao, Yu, Cheng, Tan, Qiu, Song, Ding)College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China (Zhang, Fei)Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China (Dai)
| | - Yabin Dai
- Department of Poultry Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China (Zhang, Bao, Yu, Cheng, Tan, Qiu, Song, Ding)College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China (Zhang, Fei)Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China (Dai)
| | - Rongmei Fei
- Department of Poultry Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China (Zhang, Bao, Yu, Cheng, Tan, Qiu, Song, Ding)College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China (Zhang, Fei)Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China (Dai)
| | - Chan Ding
- Department of Poultry Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China (Zhang, Bao, Yu, Cheng, Tan, Qiu, Song, Ding)College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China (Zhang, Fei)Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, China (Dai)
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Dhama K, Singh SD, Barathidasan R, Desingu PA, Chakraborty S, Tiwari R, Kumar MA. Emergence of Avian Infectious Bronchitis Virus and its variants need better diagnosis, prevention and control strategies: a global perspective. Pak J Biol Sci 2015; 17:751-67. [PMID: 26035949 DOI: 10.3923/pjbs.2014.751.767] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Growth in poultry sector is being challenged due to increased incidence and re-emergence of diseases caused due to evolution of several viral pathogens and use of live vaccines. Piles of economic losses are encountered due to these diseases. Avian Infectious Bronchitis (IB), caused by Corona virus, is OIE-listed disease and characterized by respiratory, renal and urogenital involvements, causing high mortality. Economic losses are encountered due to loss of productive performance of both egg and meat-type chickens. Variant viruses evolve due to spontaneous mutations and recombinations, causing disease in vaccinated flocks of all ages. Serotyping and genotyping are the common methods of classification of IBV strains. The virus has 4 clusters, grouped into 7 serotypes and the most important strains are Massachusetts, Connecticut, Arkansas, Gray, Holte and Florida along with numerous others, distributed round the globe. Several conventional and molecular diagnostic methods have been described for the diagnosis of IB in chickens. 'All-in/all-out' operations of rearing along with good biosafety measures forms the basis of prevention, whereas vaccination forms the backbone of IB control programme. Both live and inactivated (oil emulsified) conventional vaccines are available. The new generation vaccines (recombinant and vector-based) developed against locally prevailing IBV strains may be more helpful and avoid the reversion of virulence in live vaccine viruses. The present review deals with all these perspectives of this important emerging poultry pathogen.
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Loop-mediated isothermal amplification for diagnosis of 18 World Organization for Animal Health (OIE) notifiable viral diseases of ruminants, swine and poultry. Anim Health Res Rev 2015; 16:89-106. [PMID: 25900363 DOI: 10.1017/s1466252315000018] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a simple, powerful state-of-the-art gene amplification technique used for the rapid diagnosis and early detection of microbial diseases. Many LAMP assays have been developed and validated for important epizootic diseases of livestock. We review the LAMP assays that have been developed for the detection of 18 viruses deemed notifiable of ruminants, swine and poultry by the World Organization for Animal Health (OIE). LAMP provides a fast (the assay often takes less than an hour), low cost, highly sensitive, highly specific and less laborious alternative to detect infectious disease agents. The LAMP procedure can be completed under isothermal conditions so thermocyclers are not needed. The ease of use of the LAMP assay allows adaptability to field conditions and works well in developing countries with resource-limited laboratories. However, this technology is still underutilized in the field of veterinary diagnostics despite its huge capabilities.
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Chandrasekar A, Raja A, Dhinakar Raj G, Thangavelu A, Kumanan K. Rapid Detection of Avian Infectious Bronchitis Virus by Reverse Transcriptase-Loop Mediated Isothermal Amplification. ACTA ACUST UNITED AC 2015; 85:815-820. [PMID: 32226206 PMCID: PMC7100760 DOI: 10.1007/s40011-015-0490-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 10/30/2014] [Accepted: 01/22/2015] [Indexed: 11/24/2022]
Abstract
A reverse-transcription loop mediated isothermal amplification (RT-LAMP) was developed for rapid diagnosis of infectious bronchitis (IB) in poultry by targeting the spike protein 2 gene (S2). RT-LAMP primers were designed for IBV-S2 targets and optimized to run at 60 °C for 45 min. As compared with RT-PCR, RT-LAMP was 100 times more sensitive for IBV-S2 gene. RT-LAMP showed specific amplification with IB viral genome but not with other avian respiratory pathogens due to their mismatching with IBV-S2-RT-LAMP primers. RT-LAMP reaction products were visually detected by the addition of propidium iodide stain. Out of 102 field samples tested for detection of IBV, RT-LAMP detected IBV in 12 samples for S2 gene whereas RT-PCR detected IBV in six samples for S2 gene. The sensitivity of the RT-LAMP was 100 % and the specificity was 94 % for S2 gene. Since the developed RT-LAMP to detect IBV is simple, rapid, sensitive and specific, it can be a useful diagnostic tool for detection of IB in poultry in less equipped laboratories and in field conditions.
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Affiliation(s)
- A Chandrasekar
- 1Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, 600007 Tamil Nadu India
| | - A Raja
- 1Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Chennai, 600007 Tamil Nadu India
| | - G Dhinakar Raj
- 2Translational Research Platform for Veterinary Biologicals, TANUVAS, Chennai, 600051 Tamil Nadu India
| | - A Thangavelu
- 3Department of Veterinary Microbiology, Madras Veterinary College, TANUVAS, Chennai, 60007 Tamil Nadu India
| | - K Kumanan
- 4TANUVAS, Chennai, 600051 Tamil Nadu India
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23
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Application of cross-priming amplification (CPA) for detection of fowl adenovirus (FAdV) strains. Arch Virol 2015; 160:1005-13. [PMID: 25655263 PMCID: PMC4369288 DOI: 10.1007/s00705-015-2355-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/28/2015] [Indexed: 02/03/2023]
Abstract
Fowl adenoviruses (FAdVs) are widely distributed among chickens. Detection of FAdVs is mainly accomplished by virus isolation, serological assays, various polymerase chain reaction (PCR) assays, and loop-mediated isothermal amplification (LAMP). To increase the diagnostic capacity of currently applied techniques, cross-priming amplification (CPA) for the detection of the FAdV hexon gene was developed. The single CPA assay was optimised to detect all serotypes 1-8a-8b-11 representing the species Fowl aviadenovirus A-E. The optimal temperature and incubation time were determined to be 68 °C for 2 h. Using different incubation temperatures, it was possible to differentiate some FAdV serotypes. The results were recorded after addition of SYBR Green I(®) dye, which produced a greenish fluorescence under UV light. The CPA products separated by gel electrophoresis showed different "ladder-like" patterns for the different serotypes. The assay was specific for all serotypes of FAdV, and no cross-reactivity was observed with members of the genus Atadenovirus, duck atadenovirus A (egg drop syndrome virus EDS-76 [EDSV]) or control samples containing Marek's disease virus (MDV), infectious laryngotracheitis virus (ILTV) or chicken anaemia virus (CAV). The results of the newly developed FAdV-CPA were compared with those of real-time PCR. The sensitivity of CPA was equal to that of real-time PCR and reached 10(-2.0) TCID50, but the CPA method was more rapid and cheaper than the PCR systems. CPA is a highly specific, sensitive, efficient, and rapid tool for detection of all FAdV serotypes. This is the first report on the application of CPA for detection of FAdV strains.
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24
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Li C, Chen Z, Meng C, Liu G. Rapid detection of duck hepatitis A virus genotype C using reverse transcription loop-mediated isothermal amplification. J Virol Methods 2013; 196:193-8. [PMID: 24291148 DOI: 10.1016/j.jviromet.2013.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 11/13/2013] [Accepted: 11/19/2013] [Indexed: 01/20/2023]
Abstract
A one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was used and optimized to develop a rapid and sensitive detection system for duck hepatitis A virus genotype C (DHAV-C) RNA. A set of four specific primers was designed against highly conserved sequences located within the 3D gene from DHAV (strain GX1201). Under optimal reaction conditions, the sensitivity of DHAV-C-specific RT-LAMP was 100-fold higher than that of reverse transcriptase-polymerase chain reaction (RT-PCR), with a detection limit of 0.3pg (6.59×10(4) copies) per reaction. No cross-reactivity was observed from the samples of other duck viruses, which is in good accordance with RT-PCR. Furthermore, a positive reaction can be visually inspected by observing turbidity or color change after the addition of SYBR green I dye. The DHAV-C-specific RT-LAMP assay was applied to the samples and compared with RT-PCR. The positive-sample ratios were 26.7% (12 of 45) by RT-LAMP and 20% (9 of 45) by RT-PCR. Therefore, the newly developed RT-LAMP assay is a rapid, specific, sensitive, and cost-effective method of DHAV-C detection. This assay has potential applications in both clinical diagnosis and field surveillance of DHAV-C infection.
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Affiliation(s)
- Chuanfeng Li
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Zongyan Chen
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Chunchun Meng
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Guangqing Liu
- Division of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
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25
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Salar R, Gahlawat S, Siwach P, Duhan J, Gahlawat SK. Rapid Detection of Viruses Using Loop-Mediated Isothermal Amplification (LAMP): A Review. BIOTECHNOLOGY: PROSPECTS AND APPLICATIONS 2013. [PMCID: PMC7122297 DOI: 10.1007/978-81-322-1683-4_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most of the diseases caused by viral infection are found to be fatal, and the diagnosis is difficult due to confusion with other causative agents. So, a highly efficient molecular-based advance detection technique, i.e., loop-mediated isothermal amplification (LAMP) method, is developed for diagnosis of viral infections by various workers. It is based on amplification of DNA at very low level under isothermal conditions, using a set of four specifically designed primers and a DNA polymerase with strand displacement activity. This technique is found to be superior than most of the molecular techniques like PCR, RT-PCR, and real-time PCR due to its high specificity, sensitivity, and rapidity. Major advantage of LAMP method is its cost-effectiveness as it can be done simply by using water bath or dry bath. Here, in this review information regarding almost all the effective LAMP techniques which is developed so far for diagnosis of numerous viral pathogens is presented.
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Affiliation(s)
- R.K. Salar
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - S.K. Gahlawat
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
| | - P. Siwach
- grid.448811.0Department of Biotechnology, Chaudhary Devi lal University, Sirsa, Haryana India
| | - J.S. Duhan
- grid.448811.0Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana India
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26
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Acevedo AM, Perera CL, Vega A, Ríos L, Coronado L, Relova D, Frías MT, Ganges L, Núñez JI, Pérez LJ. A duplex SYBR Green I-based real-time RT-PCR assay for the simultaneous detection and differentiation of Massachusetts and non-Massachusetts serotypes of infectious bronchitis virus. Mol Cell Probes 2013; 27:184-92. [PMID: 23810983 DOI: 10.1016/j.mcp.2013.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/13/2013] [Accepted: 06/17/2013] [Indexed: 12/22/2022]
Abstract
Infectious bronchitis is a highly contagious viral disease of poultry caused by infectious bronchitis virus (IBV) and is considered one of the most economically important viral diseases of chickens. Control of IBV has been attempted using live attenuated and inactivated vaccines. Live attenuated vaccines of the Massachusetts (Mass.) serotype are the most commonly used for this purpose. Due to the continuous emergence of new variants of the infectious bronchitis virus, the identification of the type of IBV causing an outbreak in commercial poultry is important in the selection of the appropriate vaccine(s) capable of inducing a protective immune response. The present work was aimed at developing and evaluating a duplex SYBR Green I-based real-time RT-PCR (rRT-PCR) assay for the simultaneous detection and differentiation of Mass. and non-Mass. serotypes of IBV. The duplex rRT-PCR yielded curves of amplification with two specific melting curves (Tm1 = 83 °C ± 0.5 °C and Tm2 = 87 °C ± 0.5 °C) and only one specific melting peak (Tm = 87 °C ± 0.5 °C) when the IBV Mass. serotype and IBV non-Mass. serotype strains were evaluated, respectively. The detection limit of the assay was 8.2 gene copies/μL based on in vitro transcribed RNA and 0.1 EID50/mL. The assay was able to detect all the IBV strains assessed and discriminated well among the IBV Mass. and the IBV non-Mass. serotypes strains. In addition, amplification curves were not obtained with any of the other viruses tested. From the 300 field samples tested, the duplex rRT-PCR yielded a total of 80 samples that were positive for IBV (26.67%), 73 samples identified as the IBV Mass. serotype and seven samples as identified as the IBV non-Mass. serotype. A comparison of the performance of test as assessed with field samples revealed that the duplex rRT-PCR detected a higher number of IBV-positive samples than when conventional RT-PCR or virus isolation tests were used. The duplex rRT-PCR presented here is a useful tool for the rapid identification of outbreaks and for surveillance programmes during IB-suspected cases, particularly in countries with a vaccination control programme.
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Affiliation(s)
- Ana M Acevedo
- Centro Nacional de Sanidad Agropecuaria (CENSA), OIE Collaborating Centre for Diagnosis and Risk Analysis of The Caribean Region, Carretera de Jamaica, San José de las Lajas, La Habana 32700, Cuba
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27
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Ding YZ, Chen HT, Zhang J, Zhou JH, Ma LN, Zhang L, Gu Y, Liu YS. An overview of control strategy and diagnostic technology for foot-and-mouth disease in China. Virol J 2013; 10:78. [PMID: 23497282 PMCID: PMC3601015 DOI: 10.1186/1743-422x-10-78] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 02/26/2013] [Indexed: 11/23/2022] Open
Abstract
Foot-and-mouth disease (FMD) is one of most contagious animal diseases. It affects millions of cloven-hoofed animals and causes huge economic losses in many countries of the world. There are seven serotypes of which three (O, A and Asia 1) are endemic in China. Efficient control of FMD in China is crucial for the prevention and control of FMD in Asia and throughout the world. For the control of FMD, a powerful veterinary administration, a well-trained veterinary staff, a system of rapid and accurate diagnostic procedures and, in many countries, compulsory vaccination of susceptible animals are indispensable. This article strives to outline the Chinese animal disease control and prevention system, in particular for FMD, with the emphasis on diagnostic procedures applied in Chinese laboratories. In addition, new technologies for FMD diagnosis, which are currently in the phase of development or in the process of validation in Chinese laboratories, are described, such as lateral flow devices (LFD), Mab-based ELISAs, reverse transcription loop-mediated isothermal amplification (RT-LAMP) and gold nanopariticle immuno-PCR (GNP-IPCR).
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Affiliation(s)
- Yao-Zhong Ding
- OIE/China National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
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28
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Hanaki KI, Ike F, Hatakeyama R, Hirano N. Reverse transcription-loop-mediated isothermal amplification for the detection of rodent coronaviruses. J Virol Methods 2013; 187:222-7. [PMID: 23123121 PMCID: PMC7112798 DOI: 10.1016/j.jviromet.2012.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 10/11/2012] [Accepted: 10/22/2012] [Indexed: 11/20/2022]
Abstract
Mouse hepatitis virus (MHV) is one of the most prevalent viruses detected in laboratory mouse colonies. Enterotropic strains predominate in natural infections, and molecular techniques for the detection of MHV shedding in feces are powerful enough to diagnose active infections. A reverse transcription-loop-mediated isothermal amplification (RT-LAMP) technique was developed for the detection of rodent coronaviruses within 90 min. The specificity of this technique was confirmed by its ability to detect all 17 different strains of MHV and 6 strains of rat coronaviruses as well as its failure to detect human, bovine, and porcine coronaviruses nonspecifically. The sensitivity of RT-LAMP was 3.2-fold higher than that of reverse transcription-polymerase chain reaction (RT-PCR) and 31.6-fold lower than that of nested RT-PCR. An evaluation of the diagnostic performance of RT-LAMP performed in duplicate using mouse fecal specimens showed that the sensitivity and specificity with respect to nested RT-PCR were 85.7% and 100%, respectively. RT-LAMP assays would be suitable for monitoring active MHV infection in mouse colonies.
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Affiliation(s)
- Ken-Ichi Hanaki
- Department of Laboratory Animal Medicine, Institute for Biomedical Sciences, Iwate Medical University, 2-1-1 Nishi-Tokuda, Yahaba, Iwate 028-3694, Japan.
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29
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Rapid detection of the Marek's disease viral genome in chicken feathers by loop-mediated isothermal amplification. J Clin Microbiol 2011; 50:961-5. [PMID: 22170920 DOI: 10.1128/jcm.05408-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A loop-mediated isothermal amplification (LAMP) method for the rapid detection of serotype 1 Marek's disease virus (MDV) was developed. The method used a set of three pairs of primers to amplify the MEQ gene for detecting serotype 1 MDV. The MDV LAMP method did not cross-react with serotype 2 and serotype 3, nor did the LAMP primers have binding sites for the common avian DNA viruses (reticuloendotheliosis virus, chicken anemia virus, subgroup J of the avian leukosis virus). Additionally, the assay could detect up to 10 copies of the MEQ gene in the MD viral genome, and it had 10 times higher sensitivity than the traditional PCR methods. The LAMP master mix was stable for 90 days at -20°C. Furthermore, the efficiency of LAMP for detection of serotype 1 MDV in clinical samples was comparable to those of PCR and viral isolation. The LAMP procedure is simple and does not rely on any special equipment. The detection of serotype 1 MDV by LAMP will be useful for detecting and controlling oncogenic Marek's disease.
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30
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Chen HT, Zhang J, Liu YS, Liu XT. Detection of foot-and-mouth disease virus RNA by reverse transcription loop-mediated isothermal amplification. Virol J 2011; 8:510. [PMID: 22070774 PMCID: PMC3222687 DOI: 10.1186/1743-422x-8-510] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 11/09/2011] [Indexed: 12/29/2022] Open
Abstract
A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for foot-and-mouth disease virus (FMDV) RNA. The amplification was able to finish in 45 min under isothermal condition at 64°C by employing a set of four primers targeting FMDV 2B. The assay showed higher sensitivity than RT-PCR. No cross reactivity was observed from other RNA viruses including classical swine fever virus, swine vesicular disease, porcine reproductive and respiratory syndrome virus, Japanese encephalitis virus. Furthermore, the assay correctly detected 84 FMDV positive samples but not 65 FMDV negative specimens. The result indicated the potential usefulness of the technique as a simple and rapid procedure for the detection of FMDV infection.
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Affiliation(s)
- Hao-tai Chen
- State Key Laboratory of Veterinary Etiologic Biology, National Foot-and-Mouth Disease Reference Laboratory of China, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, P.R. China
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31
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Pyrc K, Milewska A, Potempa J. Development of loop-mediated isothermal amplification assay for detection of human coronavirus-NL63. J Virol Methods 2011; 175:133-6. [PMID: 21545810 PMCID: PMC7112811 DOI: 10.1016/j.jviromet.2011.04.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 04/18/2011] [Accepted: 04/20/2011] [Indexed: 11/24/2022]
Abstract
Human coronavirus NL63 was identified in 2004 in the Netherlands. Due to the high prevalence and world-wide distribution of this pathogen, it is essential to develop a sensitive and specific detection assay suitable for use in a routine diagnostic laboratory. Techniques based on PCR or real-time PCR are laborious and expensive. Detailed analysis of the HCoV-NL63 genome permitted the identification of a conserved nucleic acid sequential motif, which was sufficient for the design of a loop-mediated isothermal amplification (LAMP) assay. Evaluation of the method showed that the test is specific to HCoV-NL63 and that it does not cross-react with other respiratory viruses. The detection limit was found to be 1 copy of RNA template per reaction in cell culture supernatants and clinical specimens.
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Affiliation(s)
- Krzysztof Pyrc
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
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32
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Cardoso TC, Ferrari HF, Bregano LC, Silva-Frade C, Rosa ACG, Andrade AL. Visual detection of turkey coronavirus RNA in tissues and feces by reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynaphthol blue dye. Mol Cell Probes 2010; 24:415-7. [PMID: 20732411 PMCID: PMC7125592 DOI: 10.1016/j.mcp.2010.08.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 08/04/2010] [Accepted: 08/09/2010] [Indexed: 12/22/2022]
Abstract
A sensitive reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the rapid visual detection of turkey coronavirus (TCoV) infection. The reaction is performed in one step in a single tube at 65 °C for 45 min, with hydroxynaphthol blue (HNB) dye added prior to amplification. The detection limit of the RT-LAMP assay was approximately 102 EID50/50 μl TCoV genome, and no cross-reaction with other avian viruses was observed. The assay was evaluated further in tissue suspensions prepared from the ileum and ileum–caecal junctions of infected turkey embryos; 100% of these samples were positive in the RT-LAMP assay. All individual feces samples collected in the field were considered positive by both conventional RT-PCR and RT-LAMP. In conclusion, RT-LAMP with HNB dye was shown to be a sensitive, simple assay for the rapid diagnosis of TCoV infection, either directly from feces or in association with virus isolation methods.
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Affiliation(s)
- Tereza C Cardoso
- UNESP - São Paulo State University, Laboratory of Animal Virology, Campus de Araçatuba, São Paulo, Brazil.
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