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Flores-Contreras EA, Carrasco-González JA, Linhares DCL, Corzo CA, Campos-Villalobos JI, Henao-Díaz A, Melchor-Martínez EM, Iqbal HMN, González-González RB, Parra-Saldívar R, González-González E. Emergent Molecular Techniques Applied to the Detection of Porcine Viruses. Vet Sci 2023; 10:609. [PMID: 37888561 PMCID: PMC10610968 DOI: 10.3390/vetsci10100609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/16/2023] [Accepted: 09/17/2023] [Indexed: 10/28/2023] Open
Abstract
Molecular diagnostic tests have evolved very rapidly in the field of human health, especially with the arrival of the recent pandemic caused by the SARS-CoV-2 virus. However, the animal sector is constantly neglected, even though accurate detection by molecular tools could represent economic advantages by preventing the spread of viruses. In this regard, the swine industry is of great interest. The main viruses that affect the swine industry are described in this review, including African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), and porcine circovirus (PCV), which have been effectively detected by different molecular tools in recent times. Here, we describe the rationale of molecular techniques such as multiplex PCR, isothermal methods (LAMP, NASBA, RPA, and PSR) and novel methods such as CRISPR-Cas and microfluidics platforms. Successful molecular diagnostic developments are presented by highlighting their most important findings. Finally, we describe the barriers that hinder the large-scale development of affordable, accessible, rapid, and easy-to-use molecular diagnostic tests. The evolution of diagnostic techniques is critical to prevent the spread of viruses and the development of viral reservoirs in the swine industry that impact the possible development of future pandemics and the world economy.
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Affiliation(s)
- Elda A. Flores-Contreras
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | | | - Daniel C. L. Linhares
- Veterinary Diagnostic and Production Animal Medicine Department, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA;
| | - Cesar A. Corzo
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55455, USA;
| | | | | | - Elda M. Melchor-Martínez
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Reyna Berenice González-González
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Roberto Parra-Saldívar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
- Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Nuevo Leon, Mexico
| | - Everardo González-González
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo Leon, Mexico; (E.A.F.-C.); (E.M.M.-M.); (H.M.N.I.)
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Yadav P, Dhankher S, Sharma S. Simplified visual detection of Kyasanur Forest Disease virus employing Reverse Transcriptase-Polymerase Spiral Reaction (RT-PSR). Virus Res 2023; 335:199180. [PMID: 37482135 PMCID: PMC10412856 DOI: 10.1016/j.virusres.2023.199180] [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: 06/08/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Among recently prevalent tick-borne infections in India, Kyasanur Forest Virus Disease (KFD) is an important public health concern. During last decade the emergence of cases apart from endemic zone raised concern about case positivity. Early diagnosis is therefore very important in disease management and primary containment. This study, aimed to develop a simplified viral RNA extraction in combination to dry down format of novel isothermal assay for (Reverse Transcription- Polymerase Spiral reaction) specific and rapid identification of Kyasanur Forest Disease Virus targeting viral envelope gene. The one step method was optimized by magnetic bead based viral RNA extraction followed by isothermal RT-PSR assay in heat bath at 63⁰C for 60 minutes. Further, visual results interpretation was done by color change of Hydroxy Naphthol Blue dye. The detection limit of the assay was found 10 RNA copies/rxn with comparable to silica column based viral RNA combined real time qPCR. No cross reactivity was observed with other closely related flaviviruses. The assay was evaluated with clinical samples has shown >99% concordance between two methods. This is the first report of sample extraction coupled isothermal detection of KFD in a simplified manner without a need of any hi-end equipment. The assay developed here has potential to use as an alternate for field-based detection in resource limited settings for KFD.
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Affiliation(s)
- Pooja Yadav
- Virology Division, Defence Research Development Establishment, Jhansi Road, Gwalior, 474002, India
| | - Suman Dhankher
- Virology Division, Defence Research Development Establishment, Jhansi Road, Gwalior, 474002, India
| | - Shashi Sharma
- Virology Division, Defence Research Development Establishment, Jhansi Road, Gwalior, 474002, India.
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Prerana S, Ashwini P, Anupama KP, Prajna VS, Prithvisagar KS, Nayak A, Rai P, Rohit A, Karunasagar I, Karunasagar I, Maiti B. Evaluation of reverse transcriptase-polymerase spiral reaction assay for rapid and sensitive detection of severe acute respiratory syndrome coronavirus 2. Clin Chim Acta 2023; 539:144-150. [PMID: 36528050 PMCID: PMC9750508 DOI: 10.1016/j.cca.2022.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIM Existing real-time reverse transcriptase PCR (RT-qPCR) has certain limitations for the point-of-care detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since it requires sophisticated instruments, reagents and skilled laboratory personnel. In this study, we evaluated an assay termed the reverse transcriptase-polymerase spiral reaction (RT-PSR) for rapid and visual detection of SARS-CoV-2. METHODS The RT-PSR assay was optimized using RdRp gene and evaluated for the detection of SARS-CoV-2. The time of 60min and a temperature of 63°C was optimized for targeting the RNA-dependent RNA polymerase gene of SARS-CoV-2. The sensitivity of the assay was evaluated by diluting the in-vitro transcribed RNA, which amplifies as low as ten copies. RESULTS The specific primers designed for this assay showed 100% specificity and did not react when tested with other lung infection-causing viruses and bacteria. The optimized assay was validated with 190 clinical samples in two phases, using automated RTPCR based TrueNat test, and the results were comparable. CONCLUSIONS The RT-PSR assay can be considered for rapid and sensitive detection of SARS-CoV-2, particularly in resource-limited settings. To our knowledge, there is as yet no RT-PSR-based kit developed for SARS-CoV-2.
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Affiliation(s)
- Sharan Prerana
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Pai Ashwini
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Karanth Padyana Anupama
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Valakkunja Shankaranarayana Prajna
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Kattapuni Suresh Prithvisagar
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Ashwath Nayak
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India
| | - Praveen Rai
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India.
| | - Anusha Rohit
- Madras Medical Mission, Department of Microbiology, Dr. J. J. Nagar, Mogappair, Chennai 600037, India
| | - Indrani Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangalore 575018, India
| | - Iddya Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangalore 575018, India
| | - Biswajit Maiti
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangalore 575018, India.
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Li R, Tian X, Pang J, Li L, Yuan J, Tian Z, Wang Z. Point-of-Care Tests for Rapid Detection of Porcine Epidemic Diarrhea Virus: A Systematic Review and Meta-Analysis. Viruses 2022; 14:v14071355. [PMID: 35891337 PMCID: PMC9321219 DOI: 10.3390/v14071355] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/07/2022] [Accepted: 06/17/2022] [Indexed: 12/21/2022] Open
Abstract
The timely and accurate diagnosis of porcine epidemic diarrhea virus (PEDV) infection is crucial to reduce the risk of viral transmission. Therefore, the objective of this review was to evaluate the overall diagnostic accuracy of rapid point-of-care tests (POCTs) for PEDV. Studies published before 7 January 2022 were identified by searching PubMed, EMBASE, Springer Link, and Web of Science databases, using subject headings or keywords related to point of care and rapid test diagnostic for PEDV and PED. Two investigators independently extracted data, rated risk of bias, and assessed the quality using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. The bivariate model and the hierarchical summary receiver operating characteristic (HSROC) model were used for performing the meta-analysis. Threshold effect, subgroup analysis, and meta-regression were applied to explore heterogeneity. Of the 2908 records identified, 24 eligible studies involving 3264 specimens were enrolled in the meta-analysis, including 11 studies on evaluation of lateral flow immunochromatography assay (ICA)-based, and 13 on nucleic acid isothermal amplification (NAIA)-based POCTs. The overall pooled sensitivity, specificity and diagnostic odds ratio (DOR) were 0.95 (95% CI: 0.92–0.97), 0.96 (95% CI 0.88–0.99) and 480 (95% CI 111–2074), respectively; for ICA-based POCTs and the corresponding values for NAIA-based, POCTs were 0.97 (95% CI 0.94–0.99), 0.98 (95% CI 0.91–0.99) and 1517 (95% CI 290–7943), respectively. The two tests showed highly comparable and satisfactory diagnostic performance in clinical utility. These results support current recommendations for the use of rapid POC tests when PEDV is suspected.
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Affiliation(s)
- Renfeng Li
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China; (R.L.); (J.P.); (L.L.); (J.Y.); (Z.W.)
| | - Xiangqin Tian
- Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang Medical University, Xinxiang 453003, China
- Correspondence:
| | - Junzeng Pang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China; (R.L.); (J.P.); (L.L.); (J.Y.); (Z.W.)
| | - Linyue Li
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China; (R.L.); (J.P.); (L.L.); (J.Y.); (Z.W.)
| | - Jiakang Yuan
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China; (R.L.); (J.P.); (L.L.); (J.Y.); (Z.W.)
| | - Zhuangzhuang Tian
- School of International Education, Xinxiang Medical University, Xinxiang 453003, China;
| | - Ziliang Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China; (R.L.); (J.P.); (L.L.); (J.Y.); (Z.W.)
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Maiti B, Anupama KP, Rai P, Karunasagar I, Karunasagar I. Isothermal amplification-based assays for rapid and sensitive detection of severe acute respiratory syndrome coronavirus 2: Opportunities and recent developments. Rev Med Virol 2021; 32:e2274. [PMID: 34216498 PMCID: PMC8420443 DOI: 10.1002/rmv.2274] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/27/2021] [Indexed: 12/21/2022]
Abstract
The coronavirus disease 2019 (COVID‐19) is a global pandemic caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). To date, the virus has been detected in 219 countries of the world. Therefore, managing the disease becomes the priority, in which detecting the presence of the virus is a crucial step. Presently, real‐time RT polymerase chain reaction (RT‐qPCR) is considered a gold standard nucleic acid amplification test (NAAT). The test protocol of RT‐qPCR is complicated, places high demands on equipment, testing reagents, research personnel skills and is expensive. Therefore, simpler point‐of‐care (POC) tests are needed to accelerate clinical decision‐making and take some of the workload from centralized test laboratories. Various isothermal amplification‐based assays have been developed for the sensitive detection of different microorganisms, and recently some of them have been applied for detection of SARS‐CoV‐2. These do not require any programable thermocycler, can produce the results in a single temperature, and therefore, are considered simple. Unlike RT‐qPCR, these methods are highly sensitive, specific, less time‐consuming, simple and affordable, and can be used as POC diagnostic kit for COVID‐19. In this review, we have discussed the potential of isothermal amplification‐based assays as an alternative to RT‐qPCR for the detection of SARS‐CoV‐2.
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Affiliation(s)
- Biswajit Maiti
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Mangaluru, Karnataka, India
| | - Karanth Padyana Anupama
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Mangaluru, Karnataka, India
| | - Praveen Rai
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Mangaluru, Karnataka, India
| | - Indrani Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Mangaluru, Karnataka, India
| | - Iddya Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Mangaluru, Karnataka, India
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Ji J, Chen Q, Yu Z, Xu X, Mu X, Tian X, Fu X, Yao L, Bi Y, Xie Q. Simple and Visible Detection of Novel Astroviruses Causing Fatal Gout in Goslings Using One-Step Reverse Transcription Polymerase Spiral Reaction Method. Front Vet Sci 2020; 7:579432. [PMID: 33363231 PMCID: PMC7758545 DOI: 10.3389/fvets.2020.579432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/30/2020] [Indexed: 11/29/2022] Open
Abstract
In this study, a one-step isothermal method combining polymerase spiral reaction (PSR) with reverse transcription (RT-PSR) was established for rapid and specific detection of novel astroviruses causing fatal gout in goslings (N-GoAstV). The one-step RT-PSR was accomplished at the optimal temperature of 62°C and time of 40 min and used primers simply designed as conventional PCR primers, and the results of detection were visible to the naked eye. The detection limit of PSR was above 34.7 copies/μL at a 95% probability level according to probit regression analysis. The assay specifically detected N-GoAstV, and no other reference viruses were detected. These results suggest that the newly established RT-PSR assay could, in one step, accomplish reverse-transcription, amplification, and result determination providing a visible, convenient, rapid, and cost-effective test that can be carried out onsite, in order to ensure timely quarantine of N-GoAstV-infected birds, leading to effective disease control.
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Affiliation(s)
- Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, China
| | - Qinxi Chen
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, China
| | - Zhengli Yu
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, China
| | - Xinhao Mu
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, China
| | - Xiang Tian
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, China
| | - Xiaoge Fu
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bioreactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, China
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou, China
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Ji J, Chen Q, Sui C, Hu W, Yu Z, Zhang Z, Mu X, Xu X, Yao L, Kan Y, Xie Q. Rapid and visual detection of novel astroviruses causing fatal gout in goslings using one-step reverse transcription loop-mediated isothermal amplification. Poult Sci 2020; 99:4259-4264. [PMID: 32867970 PMCID: PMC7305742 DOI: 10.1016/j.psj.2020.05.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/02/2020] [Accepted: 05/22/2020] [Indexed: 01/03/2023] Open
Abstract
To visually and rapidly detect a novel goose astrovirus (N-GoAstV) causing fatal gout in goslings, an isothermal detection method based on one-step reverse transcription loop-mediated isothermal amplification (one-step RT-LAMP) was established. The one-step RT-LAMP assay for N-GoAstV detection, using Bst 3.0 DNA polymerase with strong reverse transcription activity and primer sets targeting the opening reading frame 1b (ORF1b) of N-GoAstV, could be completed in 30 min using a water bath at 61°C; the detection results could be visually observed by adding a pH-sensitive dye containing phenol red and cresol red. The detection limit of the one-step RT-LAMP assay was 57.8 copies, which was similar to that of reverse transcription–quantitative polymerase chain reaction. The assay specifically detected N-GoAstV without any cross-reaction with other reference viruses, and this was further confirmed using enzyme digestion. These results indicated that the newly established RT-LAMP assay could accomplish reverse transcription, amplification, and visual result determination in one step, and the results obtained via this rapid and cost-effective method could be used to support disease control on farms in terms of N-GoAstV infection.
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Affiliation(s)
- Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China.
| | - Qinxi Chen
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Chaoge Sui
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Wen Hu
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Zhengli Yu
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Zhibin Zhang
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Xinhao Mu
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China.
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China.
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou 510642, PR China
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Li Y, Huang T, Bai C, Fu J, Chen L, Liang Y, Wang K, Liu J, Gong X, Liu J. Reduction, Prevention, and Control of Salmonella enterica Viable but Non-culturable Cells in Flour Food. Front Microbiol 2020; 11:1859. [PMID: 32973696 PMCID: PMC7472744 DOI: 10.3389/fmicb.2020.01859] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/15/2020] [Indexed: 02/05/2023] Open
Abstract
The processing and storage conditions of flour food inevitably pose environmental stress, which promote bacteria to enter a viable but non-culturable (VBNC) state. The existence of VBNC cells causes false-negative detection in traditional culture-based detection methods, resulting in food quality and safety issues. This study aimed at investigating the influence factors including nutrition, acid, salt, and temperature for the entry into a VBNC state of Salmonella enterica and an efficient detection method. During induction with multi-stress conditions, nutrition starvation antagonizes with low-level acidity. Besides, high-level acidity was considered as an inhibitor for VBNC induction. Four inducers including nutrition starvation, salt stress, low-level acidity, and low temperature were concluded for a VBNC state. In addition, the keynote conditions for S. enterica entering a VBNC state included (i) nutrient-rich acidic environment, (ii) oligotrophic low-acidity environment, and (iii) oligotrophic refrigerated environment. Based on the keynote conditions, the environmental conditions of high acidity (1.0% v/v acetate) with low temperature (-20°C) could successfully eliminate the formation of S. enterica VBNC cells in flour food. In addition, combining with propidium monoazide pretreatment, PCR technology was applied to detect S. enterica VBNC cells. The sensitivity of the PMA-PCR technology was 105 CFU/ml in an artificially simulated food system. The results derived from this study might aid in the detection and control of VBNC state S. enterica in flour food products.
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Affiliation(s)
- Yanmei Li
- Department of Haematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Tengyi Huang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Caiying Bai
- Guangdong Women and Children Hospital, Guangzhou, China
| | - Jie Fu
- Department of Haematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ling Chen
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, China
| | - Yi Liang
- Guangdong Zhongqing Font Biochemical Science and Technology Co., Ltd., Maoming, China
| | - Kan Wang
- Research Center of Translational Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jun Liu
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, China
| | - Xiangjun Gong
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, China
- *Correspondence: Xiangjun Gong,
| | - Junyan Liu
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, United States
- Junyan Liu,
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Wang Y, Jiao WW, Wang Y, Sun L, Li JQ, Wang ZM, Xiao J, Shen C, Xu F, Qi H, Wang YH, Guo YJ, Shen AD. Simultaneous Nucleic Acids Detection and Elimination of Carryover Contamination With Nanoparticles-Based Biosensor- and Antarctic Thermal Sensitive Uracil-DNA-Glycosylase-Supplemented Polymerase Spiral Reaction. Front Bioeng Biotechnol 2019; 7:401. [PMID: 31921806 PMCID: PMC6923221 DOI: 10.3389/fbioe.2019.00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/22/2019] [Indexed: 11/17/2022] Open
Abstract
The current report devised a novel isothermal diagnostic assay, termed as nanoparticle-based biosensor (NB)- and antarctic thermal sensitive uracil-DNA-glycosylase (ATSU)-supplemented polymerase spiral reaction (PSR; NB-ATSU-PSR). The technique merges enzymatic digestion of carryover contaminants and isothermal nucleic acid amplification technique (PSR) for simultaneous detection of nucleic acid sequences and elimination of carryover contamination. In particular, nucleic acid amplification and elimination of carryover contamination are conducted in a single pot and, thus, the use of a closed-tube reaction can remove undesired results due to carryover contamination. For demonstration purpose, Klebsiella pneumoniae is employed as the model to demonstrate the usability of NB-ATSU-PSR assay. The assay's sensitivity, specificity, and practical feasibility were successfully evaluated using the pure cultures and sputum samples. The amplification products were detectable from as little as 100 fg of genomic DNAs and from ~550 colony-forming unit (CFU) in 1 ml of spiked sputum samples. All K. pneumoniae strains examined were positive for NB-ATSU-PSR detection, and all non-K. pneumoniae strains tested were negative for the NB-ATSU-PSR technique. The whole process, including rapid template preparation (20 min), PSR amplification (60 min), ATSU treatment (5 min), and result reporting (within 2 min), can be finished within 90 min. As a proof-of-concept methodology, NB-ATSU-PSR technique can be reconfigured to detect various target nucleic acid sequences by redesigning the PSR primer set.
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Affiliation(s)
- Yi Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Wei-Wei Jiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yacui Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Lin Sun
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Jie-Qiong Li
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Ze-Ming Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Jing Xiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chen Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Fang Xu
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Hui Qi
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yong-Hong Wang
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Ya-Jie Guo
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - A-Dong Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics (Capital Medical University), National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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10
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Malik YS, Verma AK, Kumar N, Touil N, Karthik K, Tiwari R, Bora DP, Dhama K, Ghosh S, Hemida MG, Abdel-Moneim AS, Bányai K, Vlasova AN, Kobayashi N, Singh RK. Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field. Front Microbiol 2019; 10:1957. [PMID: 31608017 PMCID: PMC6758846 DOI: 10.3389/fmicb.2019.01957] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.
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Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Atul Kumar Verma
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Naveen Kumar
- ICAR-National Institute of High Security Animal Diseases, OIE Reference Laboratory for Avian Influenza, Bhopal, India
| | - Nadia Touil
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d’Instruction Mohammed V, Rabat, Morocco
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology & Immunology, College of Veterinary Sciences, DUVASU, Mathura, India
| | - Durlav Prasad Bora
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Maged Gomaa Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Beni Suef University, Beni Suef, Egypt
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, CFAES, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | | | - Raj Kumar Singh
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
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11
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Ji J, Xu X, Wang X, Zuo K, Li Z, Leng C, Kan Y, Yao L, Bi Y. Novel polymerase spiral reaction assay for the visible molecular detection of porcine circovirus type 3. BMC Vet Res 2019; 15:322. [PMID: 31492192 PMCID: PMC6731610 DOI: 10.1186/s12917-019-2072-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 09/02/2019] [Indexed: 03/21/2023] Open
Abstract
Background Porcine circovirus type 3 (PCV3) is a newly emerging circovirus that might be associated with porcine dermatitis and nephropathy syndrome, reproductive failure, and cardiac and multisystemic inflammation. To aid the prevention and control of the infectious disease caused by PCV3, we developed a novel isothermal amplification assay using polymerase spiral reaction (PSR), which allows the visual detection of preserved strains and clinical samples. Results This assay precisely amplified the PCV3 genome with the use of a water bath at 62 °C for 50 min. The detection limit was found to be 1.13 × 102 copies/μL by gel electrophoresis or with the use of a visible dye (an indicator comprising phenol red and cresol red). No cross-reaction with other porcine infectious viruses was observed. The detection results for 23 PCV3-positive samples by PSR were in accordance with loop-mediated isothermal amplification (LAMP) assay. The detection rate of the PSR assay for PCV3 positivity of clinical samples was 68/97, which was higher than LAMP assay (67/97). Conclusions These results indicated that the PSR assay provides an accurate and rapid method for the detection of PCV3 with high sensitivity and specificity. It is particularly suited for use in a simple laboratory setting without a thermal cycler or gel electrophoresis equipment.
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Affiliation(s)
- Jun Ji
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China.
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China
| | - Xueyu Wang
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China
| | - Kejing Zuo
- Veterinary Laboratory, Guangzhou Zoo, Guangzhou, 510642, People's Republic of China
| | - Zhili Li
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Chaoliang Leng
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insect Bio-reactor and Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, Hena, 473061, People's Republic of China.
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China
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