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Uddin MA, Hossain MT, Rahman AKMA, Siddique MP, Kafi MA, Hossain MG, Chakraborty S, Rahman MM, Khasruzzaman AKM, Ward MP, Islam MA. Characterization, histopathology and immunogenicity of the lumpy skin disease virus isolated during 2019-20 in Bangladesh. Front Microbiol 2024; 15:1324243. [PMID: 38725689 PMCID: PMC11081030 DOI: 10.3389/fmicb.2024.1324243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/26/2024] [Indexed: 05/12/2024] Open
Abstract
Introduction Lumpy skin disease (LSD) is a highly contagious vector-borne viral disease of cattle. LSD has emerged in Bangladesh in 2019, causing significant economic losses due to its high morbidity and mortality. This research was designed to isolate, identify, and assess the immunogenicity of LSD virus (LSDV) using nodular tissue samples obtained from affected cattle during the 2019-20 outbreak across nine districts of Bangladesh. Methods To determine the presence of LSDV in nodular tissues, we initially used iiPCR and PCR, followed by histopathological examination. 151 were positive via iiPCR and PCR among the 180 collected samples. The PCR positive 151 samples were then inoculated into 10-day-old embryonated chicken eggs via the CAM route to isolate LSDV, confirmed through PCR. Subsequently, partial sequencing and phylogenetic analysis of the P32 gene were performed to determine the origin of the circulating LSDV strain. The immunogenicity of selected LSDV strains was assessed through an ELISA test. Results The PCR results revealed a distinct positive band at 192 bp in both the nodular tissue samples and the LSDV isolated from chicken embryo inoculations. Microscopic analysis of the nodular lesions revealed thickening of the epidermis, ballooning degeneration of keratinocytes, and proliferation of follicular epithelia. Additionally, mononuclear infiltration was observed at the demarcation line between infected and healthy tissue, with necrosis of muscular tissues beneath the epidermis. The LSDV isolate from Bangladesh exhibited a close genetic relationship with LSDV strains isolated from neighboring and other regional countries including India, Myanmar, and Mongolia. This observation strongly suggests the possibility of a transboundary spread of the LSD outbreak in Bangladesh during 2019-2020. The results of the immunogenicity test showed that the serum antibody titer remained at a protective level for up to 18 months following secondary immunization with inactivated LSDV antigen. This finding suggests that the inactivated LSDV antigen could be a potential vaccine candidate to protect cattle in Bangladesh against LSDV. Conclusion In conclusion, our research successfully isolated, identified, and characterized LSDV in cattle nodular tissues from the 2019-20 outbreak in Bangladesh. Furthermore, it provided insights into the probable origin of the circulating strain and investigated a potential vaccine candidate to protect cattle in the region from LSDV.
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Affiliation(s)
- Mohammad Asir Uddin
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | | | - Mahbubul Pratik Siddique
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Abdul Kafi
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Golbar Hossain
- Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Sourav Chakraborty
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohummad Muklesur Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - A. K. M. Khasruzzaman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Michael P. Ward
- Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - Md. Alimul Islam
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
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Trujillo JD, Wilson WC, Craig A, Van den Bergh C, Wang T, Thompson P, Swanepoel R, Morozov I, Richt JA. Rift Valley Fever virus M and L genome segment detection: a comparison of field-deployable reverse transcription insulated isothermal PCR (RT-iiPCR) and laboratory-based multiplex reverse transcription real-time PCR. J Clin Microbiol 2024; 62:e0043023. [PMID: 38305205 PMCID: PMC10935642 DOI: 10.1128/jcm.00430-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 11/21/2023] [Indexed: 02/03/2024] Open
Abstract
Rift Valley Fever phlebovirus (RVFV) is a mosquito-borne zoonotic pathogen that causes major agricultural and public health problems in Africa and the Arabian Peninsula. It is considered a potential agro-bioterrorism agent for which limited countermeasures are available. To address diagnostic needs, here we describe a rapid and sensitive molecular method immediately employable at sites of suspected outbreaks in animals that commonly precede outbreaks in humans. The strategy involves the concurrent detection of two of the three RVFV genome segments (large and medium) using reverse transcription insulated isothermal PCR (RT-iiPCR) performed on a portable, touch screen nucleic acid analyzer, POCKIT. The analytical sensitivity for both the RT-iiPCR and a laboratory-based L and M multiplex reverse transcription real-time PCR assay was estimated at approximately 0.1-3 copies/reaction using synthetic RNA or viral RNA. The diagnostic sensitivity and specificity of detection of RVFV on the POCKIT, determined using sera from sheep and cattle (n = 181) experimentally infected with two strains of RVFV (SA01 and Ken06), were 93.8% and 100% (kappa = 0.93), respectively. Testing of ruminant field sera (n = 193) in two locations in Africa demonstrated 100% diagnostic sensitivity and specificity. We conclude that the POCKIT dual-gene RVFV detection strategy can provide reliable, sensitive, and specific point-of-need viral RNA detection. Moreover, the field detection of RVFV in vectors or susceptible animal species can aid in the surveillance and epidemiological studies to better understand and control RVFV outbreaks. IMPORTANCE The content of this manuscript is of interest to the diverse readership of the Journal of Clinical Microbiology, including research scientists, diagnosticians, healthcare professionals, and policymakers. Rift Valley Fever virus (RVFV) is a zoonotic mosquito-borne pathogen that causes major agricultural and public health problems. Current and most sensitive diagnostic approaches that are molecular-based are performed in highly specialized molecular diagnostic laboratories. To address diagnostic needs, we developed a novel, rapid, and sensitive molecular method using a portable PCR machine, POCKIT, capable of immediate deployment at sites of suspected outbreaks. Here, we demonstrate that field-deployable RVFV detection can provide reliable, sensitive, and specific point-of-need viral RNA detection that could be used for diagnostic investigations and epidemiological studies, and can be performed in the field.
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Affiliation(s)
- Jessie D. Trujillo
- Center of Excellence for Emerging and Zoonotic Animal Diseases, Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - William C. Wilson
- Foreign Arthropod-Borne Animal Diseases Research Unit (FABADRU), USDA Agricultural Research Service (ARS), Manhattan, Kansas, USA
| | - Anthony Craig
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Vectors and Vector-Borne Diseases Research Programme, Pretoria, South Africa
| | - Carien Van den Bergh
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Vectors and Vector-Borne Diseases Research Programme, Pretoria, South Africa
| | - Thomas Wang
- Research and development, GeneReach USA, Lexington, Massachusetts, USA
| | - Peter Thompson
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Robert Swanepoel
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Vectors and Vector-Borne Diseases Research Programme, Pretoria, South Africa
| | - Igor Morozov
- Center of Excellence for Emerging and Zoonotic Animal Diseases, Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - Juergen A. Richt
- Center of Excellence for Emerging and Zoonotic Animal Diseases, Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, Kansas, USA
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Vectors and Vector-Borne Diseases Research Programme, Pretoria, South Africa
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Wang L, Liu L, Zhang H. Development and validation of an insulated isothermal polymerase chain reaction assay for the rapid detection of Mycoplasma synoviae. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2024; 15:7-12. [PMID: 38464611 PMCID: PMC10921137 DOI: 10.30466/vrf.2022.554037.3474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/01/2022] [Indexed: 03/12/2024]
Abstract
Mycoplasma synoviae, which causes the disease known as chicken synovitis, causes serious immunosuppression. We developed a rapid insulated isothermal polymerase chain reaction (iiPCR) assay for on-site detection of M. synoviae using a primer and probe set targeting the variable lipoprotein and haemagglutinin (vlhA) gene. In addition, the specificity, sensitivity, repeatability, and clinical detection of this method were evaluated. Our iiPCR assay detected M. synoviae clinical isolates and samples successfully and produced negative results on Mycoplasma galliscepticum, avian viral arthritis, Escherichia coli, Salmonella, Staphylococcus aureus and Corynebacterium, indicating that the PCR reactions were specific. Additionally, our iiPCR assay detected the prepared positive standard plasmid diluted 10 times (1.00 × 10-1 - 1.00 × 10-10) as a template. The undiluted positive plasmid was positive and double distilled water was negative indicating that the PCR reactions were sensitive, respectively. Finally, the vlhA positive standard plasmid with dilution multiple of 1.00 × 10-4 - 1.00 × 10-6 was repeatedly detected three times to evaluate the repeatability of the iiPCR method established in this experiment showing that the iiPCR of M. synoviae is repeatable. The established iiPCR was also used to detect 50 chicken joint enlargement samples. The thermostatic detection PCR established in this experiment was comparable to a reference real-time PCR (qPCR).
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Affiliation(s)
| | | | - Huanrong Zhang
- Department of Veterinary Medicine, College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu, China
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Zhu JH, Tai CH, Ping CF, Chou PH, Tsai YL, Chung S, Bradner L, Pentella M, Gauger P, Zhang J. Evaluation of a Sample-to-Result POCKIT Central SARS-CoV-2 PCR System. Diagnostics (Basel) 2023; 13:2219. [PMID: 37443612 DOI: 10.3390/diagnostics13132219] [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: 04/25/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
The emergence of COVID-19 has caused unprecedented impacts on global public health and many other aspects. Meanwhile, many types of methods have been developed to detect the causative agent, SARS-CoV-2; this has greatly advanced the technologies in the diagnostic field. Here, we describe the development and validation of a sample-in-result-out POCKIT Central SARS-CoV-2 PCR system for detecting SARS-CoV-2 in comparison with a commercial reference real-time RT-PCR assay (TaqPath COVID-19 Combo Kit). Both assays were specific and did not cross-react with non-SARS-CoV-2 agents. Both assays were able to detect various SARS-CoV-2 strains including some variants. Based on testing serial dilutions of SARS-CoV-2 USA-WA1/2020 isolate, the limit of detection was 0.8 TCID50/mL (1.87 × 103 genomic copies/mL) for POCKIT Central SARS-CoV-2 PCR and 0.16 TCID50/mL (3.75 × 102 genomic copies/mL) for the reference PCR. Subsequently, 183 clinical samples were tested by both assays and the diagnostic sensitivity, specificity, and agreement of the POCKIT Central SARS-CoV-2 PCR were 91.7%, 100%, and 94.0%, respectively, when compared to the reference PCR. The compact sample-to-result POCKIT Central SARS-CoV-2 PCR system is a simplified and efficient point-of-care tool for SARS-CoV-2 detection. In addition, this platform can be readily adapted to detect other human and animal viruses.
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Affiliation(s)
- Jin-Hui Zhu
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Chia-Hsing Tai
- GeneReach Biotechnology Corporation, Taichung 407, Taiwan
| | - Chia-Fong Ping
- GeneReach Biotechnology Corporation, Taichung 407, Taiwan
| | - Pin-Hsing Chou
- GeneReach Biotechnology Corporation, Taichung 407, Taiwan
| | - Yun-Long Tsai
- GeneReach Biotechnology Corporation, Taichung 407, Taiwan
| | - Simon Chung
- GeneReach Biotechnology Corporation, Taichung 407, Taiwan
| | - Laura Bradner
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Michael Pentella
- State Hygienic Laboratory, University of Iowa, Coralville, IA 52241, USA
| | - Phillip Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
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Yao SM, Wu ML, Hung TH. On-site detection system of Candidatus Liberibacter asiaticus by using TaqMan probe-based insulated isothermal polymerase chain reaction (iiPCR). PLoS One 2023; 18:e0287699. [PMID: 37352328 PMCID: PMC10289410 DOI: 10.1371/journal.pone.0287699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/09/2023] [Indexed: 06/25/2023] Open
Abstract
Citrus Huanglongbing (HLB) is one of the most destructive diseases of citrus plants caused by the obligate and phloem-limiting bacterium Candidatus Liberibacter asiaticus (Las). Reliable detection methods are important for successful control of the disease. This study was aimed to develop a rapid and user-friendly on-site detection system for Las using the TaqMan probe-based insulated isothermal polymerase chain reaction (iiPCR) assay. The Las-specific on-site detection system could be completed within one hour by simple DNA extraction coupled with a portable POCKIT device, which can perform PCR amplification and automatically provide qualitative results derived from fluorescence signals. The sensitivity of the TaqMan probe-iiPCR assay could be as low as single copy of Las, comparable to a real-time PCR method. Further testing of the field citrus samples showed 100% agreement between the TaqMan probe-iiPCR assay and the real-time PCR method, and the on-site detection system also demonstrated a great performance of Las detection. With high specificity and sensitivity, the on-site detection system developed in this study becomes a simple, rapid and powerful tool for detecting Las in fields.
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Affiliation(s)
- Shun-Min Yao
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Meng-Ling Wu
- Division of Forest Protection, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Ting-Hsuan Hung
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
- Research Center for Plant Medicine, National Taiwan University, Taipei, Taiwan
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Rapid Detection of Fusarium oxysporum Using Insulated Isothermal PCR and a Rapid, Simple DNA Preparation Protocol. Int J Mol Sci 2022; 23:ijms232113253. [PMID: 36362048 PMCID: PMC9659253 DOI: 10.3390/ijms232113253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/18/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Abstract
We developed an insulated isothermal PCR (iiPCR) method for the efficient and rapid detection of Fusarium oxysporum (Fo), which is a fungus that infects various hosts and causes severe crop losses. The Fo iiPCR method was sensitive enough to detect up to 100 copies of standard DNA template and 10 fg of Fo genomic DNA. In addition, it could directly detect 1 pg of mycelium and 10 spores of Fo without DNA extraction. Our study compared the performance of Fo iiPCR to that of three published in planta molecular detection methods—conventional PCR, SYBR green-based real-time PCR, and hydrolysis probe-based real-time PCR—in field detection of Fo. All diseased field samples yielded positive detection results with high reproducibility when subjected to an Fo iiPCR test combined with a rapid DNA extraction protocol compared to Fo iiPCR with an automated magnetic bead-based DNA extraction protocol. Intraday and interday assays were performed to ensure the stability of this new rapid detection method. The results of detection of Fo in diseased banana pseudostem samples demonstrated that this new rapid detection method was suitable for field diagnosis of Fusarium wilt and had high F1 scores for detection (the harmonic mean of precision and recall of detection) for all asymptomatic and symptomatic Fo-infected banana samples. In addition, banana samples at four growth stages (seedling, vegetative, flowering and fruiting, and harvesting) with mild symptoms also showed positive detection results. These results indicate that this new rapid detection method is a potentially efficient procedure for on-site detection of Fo.
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Song R, Liu P, Yang Y, Lee HS, Chen C, Wu X, Li X. Development of a Duplex Insulated Isothermal PCR Assay for Rapid On-Site Detection and Differentiation of Genotypes 1 and 2 of African Swine Fever Virus. Front Cell Infect Microbiol 2022; 12:948771. [PMID: 35873169 PMCID: PMC9300913 DOI: 10.3389/fcimb.2022.948771] [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: 05/20/2022] [Accepted: 06/16/2022] [Indexed: 11/25/2022] Open
Abstract
Genotype II African swine fever virus (ASFV) has been plaguing Asian pig industry since 2018. Recently, genotype I ASFV was reported for the first time in China. Since there is no commercial vaccine available against ASFV, early onsite detection and quick culling procedures are commonly used by many countries all over the world. It is important that the above two genotypes of ASFV could be quickly differentiated during onsite detection at the same time. In this study, we established a sensitive and simple Fluorescent Probe Hydrolysis-Insulated isothermal PCR (iiPCR) that can detect and differentiate two genotypes of ASFV within 40 minutes. The positive or negative results of tested samples were displayed on the screen of the device automatically after PCR amplification was complete. The detection limit of the iiPCR was tested to be 20 copies for both genotype I and genotype II ASFVs. There was no cross-reactivity with other swine viruses by using the established iiPCR. Fifty-eight ASFV positive samples confirmed by National ASF Reference Laboratory were subjected to the established duplex iiPCR for genotype differentiation. The results showed that all these ASFV-positive samples belong to genotype II. At last, we found serum samples could be directly used as the templates for iiPCR without comprising sensitivity and specificity. Therefore, the duplex iiPCR established in study provide a useful tool for ASFV onsite detection and genotype differentiation.
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Affiliation(s)
- Ruilong Song
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Penggang Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yang Yang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Hu Suk Lee
- International Livestock Research Institute (ILRI), Hanoi, Vietnam
| | - Changhai Chen
- Jiangsu Provincial Center for Animal Disease Control and Prevention, Nanjing, China
| | - Xiaodong Wu
- National African Swine Fever (ASF) Reference Laboratory, National Exotic Animal Disease Center, China Animal Health and Epidemiology Center, Qingdao, China
- *Correspondence: Xiaodong Wu, ; Xiangdong Li,
| | - Xiangdong Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- *Correspondence: Xiaodong Wu, ; Xiangdong Li,
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Chiu SC, Hu SC, Liao LM, Chen YH, Liao HW, Cheng JC, Lin JH. Evaluation of a New Norovirus Genogroups GI and GII In Vitro Molecular Diagnostic Assay Using Clinical Specimens Collected from Acute Diarrheal Outbreaks. Foodborne Pathog Dis 2022; 19:311-315. [PMID: 35404143 DOI: 10.1089/fpd.2021.0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Norovirus is a leading cause of acute gastroenteritis (AGE) in Taiwan. To improve diagnosis as part of laboratory surveillance, AGE surveillance was conducted using a new fluorescent probe hydrolysis-based insulated isothermal polymerase chain reaction (PCR) method, the POCKIT system, and the results were compared with those obtained from conventional methods. A total of 119 clinical stool samples from reported AGE outbreaks were collected for this study. From 83 real-time reverse transcription PCR (rRT-PCR) norovirus-positive cases, the POCKIT system identified 78 with a sensitivity of 90.3% in GI genogroup and 96.7% in GII genogroup. The specificity for both GI and GII genogroups was 100%. Overall, the POCKIT system is faster and easier to use than the conventional rRT-PCR method, and because of its high sensitivity and specificity, this system is a promising alternative for the detection of norovirus in patients with AGE, and would benefit public health laboratories for near real-time surveillance of AGE epidemic outbreaks.
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Affiliation(s)
- Shu-Chun Chiu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Szu-Chieh Hu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Ling-Min Liao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Yu-Hua Chen
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Hui-Wen Liao
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
| | - Ju-Chien Cheng
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Jih-Hui Lin
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taiwan, Taipei, Taiwan
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Zou T, Deng J, Li X, Zhang S, Chen L, Hao L, Zhuang J, Wang H, Zhang G, Ge S, Tian K. Development of a fluorescent probe hydrolysis-insulated isothermal PCR for rapid and sensitive on-site detection of African swine fever virus. Virol Sin 2022; 37:462-464. [PMID: 35257964 PMCID: PMC9243616 DOI: 10.1016/j.virs.2022.03.002] [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: 11/11/2021] [Accepted: 03/01/2022] [Indexed: 12/22/2022] Open
Abstract
A probe-based insulated isothermal PCR (iiPCR) assay was developed for rapid and onsite detection of ASFV. The developed iiPCR showed similar sensitivity and specificity with OIE recommended real-time PCR. Blood samples could be directly applied as PCR template in iiPCR without DNA extraction.
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Affiliation(s)
- Tianli Zou
- Beijing Wantai Biopharmaceutical Co., Ltd, Beijing, 102206, China
| | - Junhua Deng
- Luoyang Putai Bio-Tech Co. Ltd, Luoyang, 471003, China
| | - Xiangdong Li
- National Research Center for Veterinary Medicine, Luoyang, 471003, China
| | - Shiyin Zhang
- School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Lingyan Chen
- Luoyang Putai Bio-Tech Co. Ltd, Luoyang, 471003, China
| | - Liying Hao
- Luoyang Putai Bio-Tech Co. Ltd, Luoyang, 471003, China
| | | | - Heng Wang
- ASFV Regional Reference Laboratory in Guangzhou, South China Agricultural University, Guangzhou, 510642, China
| | - Guihong Zhang
- ASFV Regional Reference Laboratory in Guangzhou, South China Agricultural University, Guangzhou, 510642, China
| | - Shengxiang Ge
- School of Public Health, Xiamen University, Xiamen, 361102, China.
| | - Kegong Tian
- Luoyang Putai Bio-Tech Co. Ltd, Luoyang, 471003, China; National Research Center for Veterinary Medicine, Luoyang, 471003, China.
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Kalendar R. A Guide to Using FASTPCR Software for PCR, In Silico PCR, and Oligonucleotide Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2392:223-243. [PMID: 34773626 DOI: 10.1007/978-1-0716-1799-1_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The FastPCR software is an integrated tool environment for PCR primer and probe design and for prediction of oligonucleotide properties. The software provides comprehensive tools for designing primers for most PCR and perspective applications, including standard, multiplex, long-distance, inverse, real-time with TaqMan probe, Xtreme Chain Reaction (XCR), group-specific, overlap extension PCR for multifragment assembling cloning, and isothermal amplification (Loop-mediated Isothermal Amplification). A program is available to design specific oligonucleotide sets for long sequence assembly by ligase chain reaction and to design multiplexed of overlapping and nonoverlapping DNA amplicons that tile across a region(s) of interest for targeted next-generation sequencing, competitive allele-specific PCR (KASP)-based genotyping assay for single-nucleotide polymorphisms and insertions and deletions at specific loci, among other features. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. FastPCR includes various bioinformatics tools for analysis and searching of sequences, restriction I-II-III-type enzyme endonuclease analysis, and pattern searching. The program also supports the assembly of a set of contiguous sequences, consensus sequence generation, and sequence similarity and conservancy analysis. FastPCR performs efficient and complete detection of various repeat types with visual display. FastPCR allows for sequence file batch processing that is essential for automation. The software is available for download at https://primerdigital.com/fastpcr.html and online version at https://primerdigital.com/tools/pcr.html .
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Affiliation(s)
- Ruslan Kalendar
- PrimerDigital Ltd, Biocentre 3, Helsinki, Finland. .,National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
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Tran HNT, Le NCT, Pham BP, Luu VQ, Nguyen VL. Evaluation of an automated insulated isothermal polymerase chain reaction system for rapid and reliable, on-site detection of African swine fever virus. J Am Vet Med Assoc 2021; 259:662-668. [PMID: 34448618 DOI: 10.2460/javma.259.6.662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
OBJECTIVE To evaluate the utility of an automated insulated isothermal PCR (iiPCR) system for rapid and reliable on-site detection of African swine fever virus (ASFV) in swine biological samples. SAMPLE Lymph node, tissue homogenate, whole blood, serum, spleen, and tonsil samples collected from swine in North and South Vietnam. PROCEDURES Analytic sensitivity of the iiPCR system was determined by serial dilution and analysis of 2 samples (swine tissue homogenate and blood) predetermined to be positive for ASFV. Analytic specificity was assessed by analysis of 2 samples predetermined to be negative for ASFV and positive or negative for other swine pathogens (classical swine fever virus, porcine reproductive and respiratory syndrome virus, foot-and-mouth disease virus, and porcine circovirus type 2). Diagnostic performance of the iiPCR system for detection of ASFV was determined by analysis of the various tissue sample types. For all tests, a real-time PCR assay was used as the reference method. RESULTS The iiPCR system was able to detect ASFV in swine blood or tissue homogenate at dilutions up to 106, whereas the real-time PCR assay was able to detect dilutions of up to 105 or 106. The iiPCR system had high analytic specificity for detection of ASFV versus other swine pathogens. Between 97% and 100% agreement was found between results of the iiPCR system for the various tissue samples and results of real-time PCR assay. CONCLUSIONS AND CLINICAL RELEVANCE The evaluated iiPCR system was found to be a rapid, reliable, and sample-flexible method for ASFV detection and may be useful for disease surveillance and quarantine in national strategies for early ASF control.
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Knox A, Beddoe T. Isothermal Nucleic Acid Amplification Technologies for the Detection of Equine Viral Pathogens. Animals (Basel) 2021; 11:ani11072150. [PMID: 34359278 PMCID: PMC8300645 DOI: 10.3390/ani11072150] [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: 06/30/2021] [Revised: 07/17/2021] [Accepted: 07/18/2021] [Indexed: 01/25/2023] Open
Abstract
Simple Summary Equine viral diseases remain a prominent concern for human and equine health globally. Many of these viruses are of primary biosecurity concern to countries that import equines where these viruses are not present. In addition, several equine viruses are zoonotic, which can have a significant impact on human health. Current diagnostic techniques are both time consuming and laboratory-based. The ability to accurately detect diseases will lead to better management, treatment strategies, and health outcomes. This review outlines the current modern isothermal techniques for diagnostics, such as loop-mediated isothermal amplification and insulated isothermal polymerase chain reaction, and their application as point-of-care diagnostics for the equine industry. Abstract The global equine industry provides significant economic contributions worldwide, producing approximately USD $300 billion annually. However, with the continuous national and international movement and importation of horses, there is an ongoing threat of a viral outbreak causing large epidemics and subsequent significant economic losses. Additionally, horses serve as a host for several zoonotic diseases that could cause significant human health problems. The ability to rapidly diagnose equine viral diseases early could lead to better management, treatment, and biosecurity strategies. Current serological and molecular methods cannot be field-deployable and are not suitable for resource-poor laboratories due to the requirement of expensive equipment and trained personnel. Recently, isothermal nucleic acid amplification technologies, such as loop-mediated isothermal amplification (LAMP) and insulated isothermal polymerase chain reaction (iiPCR), have been developed to be utilized in-field, and provide rapid results within an hour. We will review current isothermal diagnostic techniques available to diagnose equine viruses of biosecurity and zoonotic concern and provide insight into their potential for in-field deployment.
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13
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Mori A, Pomari E, Deiana M, Perandin F, Caldrer S, Formenti F, Mistretta M, Orza P, Ragusa A, Piubelli C. Molecular techniques for the genomic viral RNA detection of West Nile, Dengue, Zika and Chikungunya arboviruses: a narrative review. Expert Rev Mol Diagn 2021; 21:591-612. [PMID: 33910444 DOI: 10.1080/14737159.2021.1924059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Molecular technology has played an important role in arboviruses diagnostics. PCR-based methods stand out in terms of sensitivity, specificity, cost, robustness, and accessibility, and especially the isothermal amplification (IA) method is ideal for field-adaptable diagnostics in resource-limited settings (RLS).Areas covered: In this review, we provide an overview of the various molecular methods for West Nile, Zika, Dengue and Chikungunya. We summarize literature works reporting the assessment and use of in house and commercial assays. We describe limitations and challenges in the usage of methods and opportunities for novel approaches such as NNext-GenerationSequencing (NGS).Expert opinion: The rapidity and accuracy of differential diagnosis is essential for a successful clinical management, particularly in co-circulation area of arboviruses. Several commercial diagnostic molecular assays are available, but many are not affordable by RLS and not usable as Point-of-care/Point-of-need (POC/PON) such as RReal-TimeRT-PCR, Array-based methods and NGS. In contrast, the IA-based system fits better for POC/PON but it is still not ideal for the multiplexing detection system. Improvement in the characterization and validation of current molecular assays is needed to optimize their translation to the point of care.
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Affiliation(s)
- Antonio Mori
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy.,Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elena Pomari
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Michela Deiana
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Francesca Perandin
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Sara Caldrer
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Fabio Formenti
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Manuela Mistretta
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Pierantonio Orza
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Andrea Ragusa
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Chiara Piubelli
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
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14
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Mobed A, Sepehri Shafigh E. Biosensors promising bio-device for pandemic screening "COVID-19". Microchem J 2021; 164:106094. [PMID: 33623173 PMCID: PMC7892310 DOI: 10.1016/j.microc.2021.106094] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 01/12/2023]
Abstract
Undoubtedly, the coronavirus pandemic is one of the most influential events not only in medicine but also in the economic field in the world. Rapid transmission and high mortality rates, as well as prolonged and asymptomatic communal periods, are the most important reasons for the global panic due to coronavirus. Since coronavirus treatment and specific vaccines are not yet available, early detection of the virus is critical. A rapid and accurate diagnosis can play a crucial role in the treatment and control of the COVID 19 disease. Serological, ELISA, and molecular-based tests, including PCR and RT-PCR, are among the most important routine methods for detecting coronaviruses. False-positive/negative results, low sensitivity and specificity, and the need for advanced equipment are among the disadvantages and problems of routine methods. To eliminate the drawbacks of routine methods, new technologies are being developed. Biosensors are one of the most important ones. This paper is a summary of the up-to-date states of innovative bio-sensing tools for the ultrasensitive detection of coronaviruses (COVID 19) with encouraging uses for future challenges in disease diagnosis.
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Affiliation(s)
- Ahmad Mobed
- Aging Research Institute, Faculty of Medicine, Tabriz University of Medical Sciences, Iran,Physical Medicine and Rehabilitation Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Corresponding author at: Aging Research Institute, Faculty of Medicine, Tabriz University of Medical Sciences, Iran
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15
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Lee J, Cho AY, Ko HH, Ping JF, Ma LJ, Chai CF, Noh JY, Jeong J, Jeong S, Kim Y, Kim J, Kim K, Lee S, Lee JB, Park SY, Choi IS, Lee SW, Song CS. Evaluation of insulated isothermal PCR devices for the detection of avian influenza virus. J Virol Methods 2021; 292:114126. [PMID: 33711374 DOI: 10.1016/j.jviromet.2021.114126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 02/17/2021] [Accepted: 03/08/2021] [Indexed: 12/26/2022]
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) and low pathogenic avian influenza viruses (LPAIVs) represent important threats to the poultry industry and global human health. Due to the high rates of avian influenza virus (AIV) transmission, controlling AIV outbreaks is challenging. HPAIV is known to be transmitted from wild birds to domestic ducks, from which it can be transmitted to layer and broiler chickens. Therefore, surveillance of AIV in domestic ducks and chickens in advance of outbreaks can prevent its spread and enable timely implementation of disease control measures. Certain molecular diagnostic tools can be applied in the field for faster AIV detection. In this study, we evaluated the AIV-detection ability of two insulated isothermal PCR (iiPCR) devices, POCKIT™Micro DUO Nucleic Acid Analyzer (POCKIT DUO) and POCKIT™ Central Nucleic Acid Analyzer (POCKIT Central). We found that the analytical, in vivo and clinical performances of the two POCKIT devices were comparable to those of real-time reverse transcription PCR. Due to their brief protocols and short detection times, POCKIT DUO and POCKIT Central represent promising molecular diagnostic devices for the reliable detection of AIV.
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Affiliation(s)
- Jiho Lee
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Andrew Y Cho
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | | | | | - Li-Juan Ma
- GeneReach Biotechnology, Taichung, Taiwan, ROC
| | | | | | - Jeihyun Jeong
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Sol Jeong
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Yujin Kim
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Junbeom Kim
- KCAV Co., Ltd., Seoul, 05029, Republic of Korea
| | - Kyujik Kim
- KCAV Co., Ltd., Seoul, 05029, Republic of Korea
| | - Sunhak Lee
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Joong-Bok Lee
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seung-Yong Park
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - In-Soo Choi
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Sang-Won Lee
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea
| | - Chang-Seon Song
- Department of Veterinary Medicine, Konkuk University, Seoul, 05029, Republic of Korea.
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16
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Shabani E, Dowlatshahi S, Abdekhodaie MJ. Laboratory detection methods for the human coronaviruses. Eur J Clin Microbiol Infect Dis 2021; 40:225-246. [PMID: 32984911 PMCID: PMC7520381 DOI: 10.1007/s10096-020-04001-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
Coronaviruses are a group of envelop viruses which lead to diseases in birds and mammals as well as human. Seven coronaviruses have been discovered in humans that can cause mild to lethal respiratory tract infections. HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 are the low-risk members of this family and the reason for some common colds. Besides, SARS-CoV, MERS-CoV, and newly identified SARS-CoV-2, which is also known as 2019-nCoV, are the more dangerous viruses. Due to the rapid spread of this novel coronavirus and its related disease, COVID-19, a reliable, simple, fast, and low-cost detection method is necessary for patient diagnosis and tracking worldwide. Human coronaviruses detection methods were classified and presented in this article. The laboratory detection techniques include RT-PCR, RT-LAMP, electrochemical and optical biosensors for RNA detection, and whole virus or viral proteins detection assays.
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Affiliation(s)
- Ehsan Shabani
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Sayeh Dowlatshahi
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Mohammad J Abdekhodaie
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran.
- Yeates School of Graduate Studies, Ryerson University, Toronto, ON, Canada.
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17
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Development and Evaluation of an iiPCR Assay for Salmonella and Shigella Detection on a Field-Deployable PCR System. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2020; 2020:9373984. [PMID: 32963655 PMCID: PMC7492956 DOI: 10.1155/2020/9373984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/07/2020] [Accepted: 08/27/2020] [Indexed: 11/18/2022]
Abstract
Background Salmonella and Shigella are often associated with fecal-oral transmission and cause large-scale outbreaks in centralized catering units and, therefore, should be frequently and strictly monitored, especially among food handlers. However, no specific and sensitive on-site detection method is available until now. Methods In this study, an insulated isothermal PCR assay for the detection of Salmonella and Shigella on a field-deployable PCR system was developed. Specificity, sensitivity, reproducibility, and clinical accuracy of the assay were characterized and evaluated. Results The insulated isothermal PCR assay could be completed within 58 minutes with minimal pretreatment needed. The assay was specific and with good reproducibility. The limit of detection was 103 CFU/mL and 101 CFU/mL for Salmonella and Shigella, respectively, which was comparable to multiplex real-time PCR. Mock on-site clinical evaluation results showed that the analytical sensitivity and specificity of the insulated isothermal PCR assay were 100% and 96.6%, while the positive predictive value and negative predictive value were 94.1% and 100%, respectively. Conclusion Based on our results, we believe that the assay developed herein could serve as an alternative method for preliminary screening and provide a valuable platform for the on-site detection of Salmonella and Shigella, especially in resource-limited and developing countries.
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18
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Mokhtar MH, Giribabu N, Salleh N. Testosterone Reduces Tight Junction Complexity and Down-regulates Expression of Claudin-4 and Occludin in the Endometrium in Ovariectomized, Sex-steroid Replacement Rats. In Vivo 2020; 34:225-231. [PMID: 31882482 DOI: 10.21873/invivo.11764] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/07/2019] [Accepted: 11/12/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND/AIM It was hypothesized that endometrial tight junction morphology and expression of tight junction proteins i.e., claudin-4 and occludin in the uterus, are affected by testosterone. Therefore, the effects of testosterone on these parameters in the uterus during receptivity period were investigated. MATERIALS AND METHODS Ovariectomized adult female rats were given testosterone (1 mg/kg/day) alone or in combination with flutamide or finasteride between days 6 to 8 of sex-steroid replacement treatment, which was considered the period of uterine receptivity. Ultramorphology of tight junctions was visualized by transmission electron microscopy while distribution and expression of claudin-4 and occludin were examined by immunofluorescence and real-time polymerase chain reaction respectively. RESULTS Administration of testosterone caused loss of tight junction complexity and down-regulated expression of claudin-4 and occludin in the uterus. CONCLUSION Decreased endometrial tight junction complexity and expression of claudin-4 and occludin in the uterus during receptivity period by testosterone may interfere with embryo attachment and subsequent implantation.
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Affiliation(s)
- Mohd Helmy Mokhtar
- Department of Physiology, Faculty of Medicine, University Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia
| | - Nelli Giribabu
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Naguib Salleh
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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19
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Stittleburg V, Rojas A, Cardozo F, Muñoz FM, Asturias EJ, Olson D, Paniaga-Avila A, Abeynayake J, Anderson EJ, Waggoner JJ. Dengue Virus and Yellow Fever Virus Detection Using Reverse Transcription-Insulated Isothermal PCR and Comparison with Real-Time RT-PCR. Am J Trop Med Hyg 2020; 103:157-159. [PMID: 32458782 DOI: 10.4269/ajtmh.19-0892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Real-time reverse transcriptase PCR (rRT-PCR) is the most accurate method for the detection of dengue virus (DENV) and yellow fever virus (YFV) in acute illness. However, performing rRT-PCR is not feasible for many laboratories in regions of endemicity. The current study compared new reverse transcription-insulated isothermal PCRs (the POCKIT DENV and YFV reagent sets) with laboratory-developed rRT-PCRs for both viruses using clinical samples and viral strains from different endemic regions. Sensitivity and specificity of the POCKIT DENV Reagent Set were 87.2% (68/78 samples) and 98.2% of samples (54/55), respectively. The YFV reagent set demonstrated sensitive detection of YFV RNA from six viral strains down to an estimated concentration of 2.5 log10 copies/mL and proved to be specific for YFV. Although the POCKIT assays require RNA extraction, they may provide accurate and less-complex options for molecular testing in laboratory settings where rRT-PCR is not practical.
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Affiliation(s)
- Victoria Stittleburg
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia
| | - Alejandra Rojas
- Departamento de Producción, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Fátima Cardozo
- Departamento de Salud Pública, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Flor M Muñoz
- Departments of Pediatrics and Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Edwin J Asturias
- Fundación para la Salud Integral de los Guatemaltecos, FUNSALUD, Quetzaltenango, Guatemala.,Division of Infectious Diseases and Epidemiology, Department of Pediatrics, University of Colorado at Denver, Aurora, Colorado
| | - Daniel Olson
- Division of Infectious Diseases and Epidemiology, Department of Pediatrics, University of Colorado at Denver, Aurora, Colorado
| | | | | | - Evan J Anderson
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, Georgia.,Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia
| | - Jesse J Waggoner
- Department of Global Health, Rollins School of Public Health, Atlanta, Georgia.,Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia
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20
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Miao G, Zhang L, Zhang J, Ge S, Xia N, Qian S, Yu D, Qiu X. Free convective PCR: From principle study to commercial applications-A critical review. Anal Chim Acta 2020; 1108:177-197. [PMID: 32222239 DOI: 10.1016/j.aca.2020.01.069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/11/2022]
Abstract
Polymerase chain reaction (PCR) is an extremely important tool for molecular diagnosis, as it can specifically amplify nucleic acid templates for sensitive detection. As another division of PCR, free convective PCR was invented in 2001, which can be performed in a capillary tube pseudo-isothermally within a significantly short time. Convective PCR thermal cycling is implemented by inducing thermal convection inside the capillary tube, which stratifies the reaction into spatially separate and stable melting, annealing, and extension zones created by the temperature gradient. Convective PCR is a promising tool that can be used for nucleic acid diagnosis as a point-of-care test (POCT) due to the significantly simplified heating strategy, reduced cost, and shortened detection time without sacrificing sensitivity and accuracy. Here, we review the history of free convective PCR from its invention to development and its commercial applications.
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Affiliation(s)
- Guijun Miao
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Lulu Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Jing Zhang
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China.
| | - Ningshao Xia
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361005, China.
| | - Shizhi Qian
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA, 23529, USA.
| | - Duli Yu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing, 100029, China.
| | - Xianbo Qiu
- Institute of Microfluidic Chip Development in Biomedical Engineering, College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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21
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Balasuriya UBR. Type A Influenza Virus Detection from Horses by Real-Time RT-qPCR and Insulated Isothermal RT-PCR. Methods Mol Biol 2020; 2123:383-392. [PMID: 32170704 DOI: 10.1007/978-1-0716-0346-8_29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Equine influenza (EI) is a highly contagious disease of horses caused by the equine influenza virus (EIV) H3N8 subtype. EI is the most important respiratory virus infection of horses and can disrupt major equestrian events and cause significant economic losses to the equine industry worldwide. Influenza H3N8 virus spreads rapidly in susceptible horses and can result in very high morbidity within 24-48 h after exposure to the virus. Therefore, rapid and accurate diagnosis of EI is critical for implementation of prevention and control measures to avoid the spread of EIV and to reduce the economic impact of the disease. The probe-based real-time reverse transcriptase polymerase chain reaction (RT-qPCR) assays targeting various EIV genes are reported to be highly sensitive and specific compared to the Directigen Flu-A® test and virus isolation in embryonated hens' eggs. Recently, a TaqMan® probe-based insulated isothermal RT-PCR (iiRT-PCR) assay for the detection of EIV H3N8 subtype has been described. These molecular-based diagnostic assays provide a fast and reliable means of EIV detection and disease surveillance.
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Affiliation(s)
- Udeni B R Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA.
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22
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Comparative analysis of different molecular and serological methods for detection of Xylella fastidiosa in blueberry. PLoS One 2019; 14:e0221903. [PMID: 31479482 PMCID: PMC6719857 DOI: 10.1371/journal.pone.0221903] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/08/2019] [Indexed: 12/28/2022] Open
Abstract
Bacterial leaf scorch, caused by Xylella fastidiosa, is a major threat to blueberry production in the southeastern United States. Management of this devastating disease is challenging and often requires early detection of the pathogen to reduce major loss. There are several different molecular and serological detection methods available to identify the pathogen. Knowing the efficiency and suitability of these detection techniques for application in both field and laboratory conditions is important when selecting the appropriate detection tool. Here, we compared the efficiency and the functionality of four different molecular detection techniques (PCR, real-time PCR, LAMP and AmplifyRP® Acceler8™) and one serological detection technique (DAS-ELISA). The most sensitive method was found to be real-time PCR with the detection limit of 25 fg of DNA molecules per reaction (≈9 genome copies), followed by LAMP at 250 fg per reaction (≈90 copies), AmplifyRP® Acceler8™ at 1 pg per reaction (≈350 copies), conventional PCR with nearly 1.25 pg per reaction (≈ 440 copies) and DAS-ELISA with 1x105 cfu/mL of Xylella fastidiosa. Validation between assays with 10 experimental samples gave consistent results beyond the variation of the detection limit. Considering robustness, portability, and cost, LAMP and AmplifyRP® Acceler8™ were not only the fastest methods but also portable to the field and didn’t require any skilled labor to carry out. Among those two, AmplifyRP® Acceler8™ was faster but more expensive and less sensitive than LAMP. On the other hand, real-time PCR was the most sensitive assay and required comparatively lesser time than C-PCR and DAS-ELISA, which were the least sensitive assays in this study, but all three assays are not portable and needed skilled labor to proceed. These findings should enable growers, agents, and diagnosticians to make informed decisions regarding the selection of an appropriate diagnostic tool for X. fastidiosa on blueberry.
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Ren Y, Yue H, Zhu L, Tang C, Zhang B. Development and evaluation of reverse transcription-insulated isothermal PCR assay to detect duck hepatitis A virus type A in liver samples using the POCKIT TM system. J Vet Med Sci 2019; 81:1533-1539. [PMID: 31406032 PMCID: PMC6863721 DOI: 10.1292/jvms.18-0759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Duck hepatitis A virus (DHAV) infection is characterized by severe hepatitis. In recent
years, DHAV-A has become widespread in Asia and has led to economic losses. Conventional
methods of DHAV-A detection must often be performed in the laboratory with inconvenience
equipment. We have developed a rapid reverse transcription insulated isothermal (RT-iiPCR)
technique for the on-site detection of DHAV-A based on the POCKITTM system in a
convenient minitype device. We optimized the PCR primers and probes for the amplification
of the DHAV-A 3C/3D genes, and successfully amplified a specific fragment of DHAV-A, but
no fragment from 18 other duck pathogens. The limit of detection for viral RNA was 49
copies per reaction, and the sensitivity and specificity were each 100% in the analysis of
60 liver samples. By comparison, the sensitivities of RT-iiPCR was comparable in
sensitivity to existing rRT-PCR. Furthermore, the RT-iiPCR results were 98.3% in agreement
with those of the rRT-PCR, with a kappa value of 0.938. In conclusion, this new method not
only offers a higher sensitivity and specificity than existing techniques, but also
time-saving and better suited to field diagnoses because device is portable.
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Affiliation(s)
- Yupeng Ren
- College of Life Science and Technology, Southwest Minzu University, South Section 4, First Ring Rd, Wuhou District, Chengdu City, Sichuan Province, 610041, P.R. China.,College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, P.R. China
| | - Hua Yue
- College of Life Science and Technology, Southwest Minzu University, South Section 4, First Ring Rd, Wuhou District, Chengdu City, Sichuan Province, 610041, P.R. China
| | - Lin Zhu
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang District, Chengdu City, Sichuan Province, 611130, P.R. China
| | - Cheng Tang
- College of Life Science and Technology, Southwest Minzu University, South Section 4, First Ring Rd, Wuhou District, Chengdu City, Sichuan Province, 610041, P.R. China
| | - Bin Zhang
- College of Life Science and Technology, Southwest Minzu University, South Section 4, First Ring Rd, Wuhou District, Chengdu City, Sichuan Province, 610041, P.R. China
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24
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Tsai JJ, Liu WL, Lin PC, Huang BY, Tsai CY, Lee PYA, Tsai YL, Chou PH, Chung S, Liu LT, Chen CH. A fully automated sample-to-answer PCR system for easy and sensitive detection of dengue virus in human serum and mosquitos. PLoS One 2019; 14:e0218139. [PMID: 31291289 PMCID: PMC6619671 DOI: 10.1371/journal.pone.0218139] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/25/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The insulated isothermal PCR (iiPCR) technology enables consistent PCR amplification and detection in a simple heating device. A pan-dengue virus (DENV) RT-iiPCR, targeting the 5' untranslated region, was validated previously on the semi-automated POCKIT combo system (involving separate devices for nucleic acid extraction and PCR amplification/detection) to offer performance comparable to a laboratory real-time PCR. Working on the same technologies, a compact automated sample-in-answer-out system (POCKIT Central Nucleic Acid Analyser) has been available commercially for iiPCR, minimizing human error risks and allowing easy molecular bio-detection near points of need. Here, we evaluated the analytical and clinical performance of the pan-DENV RT-iiPCR on the fully automated system by comparison to those on the semi-automated system. METHODOLOGY/PRINCIPAL FINDINGS Testing sera containing serial diluted DENV-1, -2, -3, or -4 cell culture stock, the pan-DENV RT-iiPCR system had similar 100% detection endpoints on the two systems; i.e. at 1, 10, 1 and 10 PFU/ml, respectively, on the fully automated system, and at 10, 1, 10 and 10 PFU/ml, respectively, on the semi-automated system. Furthermore, both fully automated and semi-automated PCR system can detect all four DENV serotypes in mosquitos. Clinical performance of the reagent on the two systems was evaluated by testing 60 human serum samples. Both systems detected the same 40 samples (ten DENV-1, -2, -3, and -4 positive each) and did not detect the other 20; 100% agreement (κ = 1) was found between the two systems. CONCLUSIONS/SIGNIFICANCE With performance comparable to a previously validated system, the fully-automated PCR system allows applications of the pan-DENV reagent as a useful tool near points of need to facilitate easy, fast and effective detection of dengue virus and help mitigate versatile public health challenges in the control and management of dengue disease.
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Affiliation(s)
- Jih-Jin Tsai
- Center for Dengue Fever Control and Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsing Medical University, Kaohsiung, Taiwan
- * E-mail: (JJT); (CHC)
| | - Wei-Liang Liu
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Ping-Chang Lin
- Center for Dengue Fever Control and Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Bo-Yi Huang
- Center for Dengue Fever Control and Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ching-Yi Tsai
- Center for Dengue Fever Control and Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | | | | | | | | | - Li-Teh Liu
- Center for Dengue Fever Control and Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung-Hwa University of Medical Technology, Tainan City, Taiwan
| | - Chun-Hong Chen
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- * E-mail: (JJT); (CHC)
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Zhang J, Nfon C, Tsai CF, Lee CH, Fredericks L, Chen Q, Sinha A, Bade S, Harmon K, Piñeyro P, Gauger P, Tsai YL, Wang HTT, Lee PYA. Development and evaluation of a real-time RT-PCR and a field-deployable RT-insulated isothermal PCR for the detection of Seneca Valley virus. BMC Vet Res 2019; 15:168. [PMID: 31126297 PMCID: PMC6534938 DOI: 10.1186/s12917-019-1927-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 05/20/2019] [Indexed: 12/17/2022] Open
Abstract
Background Seneca Valley virus (SVV) has emerged in multiple countries in recent years. SVV infection can cause vesicular lesions clinically indistinguishable from those caused by other vesicular disease viruses, such as foot-and-mouth disease virus (FMDV), swine vesicular disease virus (SVDV), vesicular stomatitis virus (VSV), and vesicular exanthema of swine virus (VESV). Sensitive and specific RT-PCR assays for the SVV detection is necessary for differential diagnosis. Real-time RT-PCR (rRT-PCR) has been used for the detection of many RNA viruses. The insulated isothermal PCR (iiPCR) on a portable POCKIT™ device is user friendly for on-site pathogen detection. In the present study, SVV rRT-PCR and RT-iiPCR were developed and validated. Results Neither the SVV rRT-PCR nor the RT-iiPCR cross-reacted with any of the vesicular disease viruses (20 FMDV, two SVDV, six VSV, and two VESV strains), classical swine fever virus (four strains), and 15 other common swine viruses. Analytical sensitivities of the SVV rRT-PCR and RT-iiPCR were determined using serial dilutions of in vitro transcribed RNA as well as viral RNA extracted from a historical SVV isolate and a contemporary SVV isolate. Diagnostic performances were further evaluated using 125 swine samples by two approaches. First, nucleic acids were extracted from the 125 samples using the MagMAX™ kit and then tested by both RT-PCR methods. One sample was negative by the rRT-PCR but positive by the RT-iiPCR, resulting in a 99.20% agreement (124/125; 95% CI: 96.59–100%, κ = 0.98). Second, the 125 samples were tested by the taco™ mini extraction/RT-iiPCR and by the MagMAX™ extraction/rRT-PCR system in parallel. Two samples were positive by the MagMAX™/rRT-PCR system but negative by the taco™ mini/RT-iiPCR system, resulting in a 98.40% agreement (123/125; 95% CI: 95.39–100%, κ = 0.97). The two samples with discrepant results had relatively high CT values. Conclusions The SVV rRT-PCR and RT-iiPCR developed in this study are very sensitive and specific and have comparable diagnostic performances for SVV RNA detection. The SVV rRT-PCR can be adopted for SVV detection in laboratories. The SVV RT-iiPCR in a simple field-deployable system could serve as a tool to help diagnose vesicular diseases in swine at points of need.
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Affiliation(s)
- Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA.
| | - Charles Nfon
- National Center for Foreign Animal Diseases, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | | | | | - Lindsay Fredericks
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Qi Chen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Avanti Sinha
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Sarah Bade
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Karen Harmon
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Pablo Piñeyro
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
| | - Phillip Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA, 50011, USA
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Ren Y, Yue H, Zhu L, Kan R, Tang C, Zhang B. A reverse transcription-insulated isothermal PCR assay for the detection of duck hepatitis A virus type 3 based on the POCKIT™ system. J Virol Methods 2019; 270:126-130. [PMID: 31100286 DOI: 10.1016/j.jviromet.2019.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 05/07/2019] [Accepted: 05/13/2019] [Indexed: 11/27/2022]
Abstract
Duck hepatitis A virus type 3 (DHAV-3) infection is characterized by severe hepatitis. In recent years, DHAV-3 has become widespread in Asia and has led to economic losses. Conventional methods for DHAV-3 detection usually depend on the use of larger equipment that is not portable and is not fit for on-site diagnoses. In this study, a rapid reverse transcription insulated isothermal (RT-iiPCR) technique was developed for the on-site detection of DHAV-3 based on the POCKIT™ system in a convenient device. The concentration of primer pairs and probes were optimized for amplification of the DHAV-3 VP3 gene of DHAV-3, with no amplification of 12 other duck pathogens. The detection limit of viral RNA was 3.85 × 101 copies/μL, and the analytical sensitivity and specificity levels were both 100% in the detection of 40 liver samples. Furthermore, 97.5% of the RT-iiPCR results were in agreement with those of rRT-PCR, with a kappa value of 0.93. This method is time-saving and better suited to field diagnoses because of its portable device.
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Affiliation(s)
- Yupeng Ren
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China; College of Life Science and Technology, Southwest University for Nationalities, Chengdu City, Sichuan Province, 610041, PR China.
| | - Hua Yue
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu City, Sichuan Province, 610041, PR China.
| | - Lin Zhu
- College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu City, Sichuan Province, 611130, PR China.
| | - Ruici Kan
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu City, Sichuan Province, 610041, PR China.
| | - Cheng Tang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu City, Sichuan Province, 610041, PR China.
| | - Bin Zhang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu City, Sichuan Province, 610041, PR China.
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Tsai JJ, Liu WL, Lin PC, Huang BY, Tsai CY, Chou PH, Lee FC, Ping CF, Lee PYA, Liu LT, Chen CH. An RT-PCR panel for rapid serotyping of dengue virus serotypes 1 to 4 in human serum and mosquito on a field-deployable PCR system. PLoS One 2019; 14:e0214328. [PMID: 30908535 PMCID: PMC6433249 DOI: 10.1371/journal.pone.0214328] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/11/2019] [Indexed: 12/29/2022] Open
Abstract
Background Dengue fever, a mosquito-borne disease, is caused by dengue virus (DENV) which includes four major serotypes (DENV-1, -2, -3, and -4). Some serotypes cause more severe diseases than the other; severe dengue is associated with secondary infections by a different serotype. Timely serotyping can provide early warning of dengue epidemics to improve management of patients and outbreaks. A mobile insulated isothermal PCR (iiPCR) system is available to allow molecular detection of pathogens near points of need. Methodology/Principle findings In this study, side-by-side comparison with the CDC DENV-1-4 Real Time RT-PCR (qRT-PCR) was performed to evaluate the performance of four singleplex DENV-1–4 serotyping reverse transcription-iiPCR (RT-iiPCR) reagents for DENV subtyping on the mobile PCR system. The four RT-iiPCRs did not react with Zika virus and chikungunya virus; tests with serial dilutions of the four DENV serotypes made in human serum showed they had detection endpoints comparable to those of the reference method, indicating great analytical sensitivity and specificity. Clinical performance of the RT-iiPCR reagents was evaluated by testing 40 serum samples each (around 20 target serotype-positive and 20 DENV-negative); all four reagents had high agreement (97.5–100%) with the reference qRT-PCR. Moreover, testing of mosquitoes separately infected experimentally with each serotype showed that the four reagents detected specifically their target DENV serotypes in mosquito. Conclusions/Significance With analytical and clinical performance comparable to the reference qRT-PCR assay, the four index RT-iiPCR reagents on the field-deployable PCR system can serve as a useful tool for DENV detection near points of needs.
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Affiliation(s)
- Jih-Jin Tsai
- Center for Dengue Fever Control and Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- * E-mail: (JJT); (CHC)
| | - Wei-Liang Liu
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Ping-Chang Lin
- Center for Dengue Fever Control and Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Bo-Yi Huang
- Center for Dengue Fever Control and Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ching-Yi Tsai
- Center for Dengue Fever Control and Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | | | | | | | | | - Li-Teh Liu
- Center for Dengue Fever Control and Research, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medical Technology, Chung-Hwa University of Medical Technology, Tainan City, Taiwan
| | - Chun-Hong Chen
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Zhunan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
- * E-mail: (JJT); (CHC)
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28
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Cook RF, Barrandeguy M, Lee PYA, Tsai CF, Shen YH, Tsai YL, Chang HFG, Wang HTT, Balasuriya UBR. Rapid detection of equine infectious anaemia virus nucleic acid by insulated isothermal RT-PCR assay to aid diagnosis under field conditions. Equine Vet J 2018; 51:489-494. [PMID: 30353944 DOI: 10.1111/evj.13032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/24/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Control of equine infectious anaemia (EIA) currently depends on serological diagnosis of infected equids. However, recently infected equids may not produce detectable anti-EIAV antibodies up to 157 days post infection and so present a high transmission risk. Therefore, direct nucleic acid detection methods are urgently needed to improve EIAV surveillance and management programs in counties where the disease is endemic. OBJECTIVES To evaluate a field-deployable, reverse transcription-insulated isothermal PCR (RT-iiPCR) assay targeting the conserved 5' untranslated region (5' UTR)/exon 1 of the tat gene of EIAV. STUDY DESIGN The analytical and clinical performance of the newly developed EIAV RT-iiPCR was evaluated by comparison with a EIAV real-time RT-PCR (RT-qPCR) along with the AGID test. METHODS Analytical sensitivity was determined using in vitro transcribed RNA containing the target area of the 5' UTR/tat gene and samples from two EIAV-positive horses. Specificity was verified using nine common equine viruses. Clinical performance was evaluated by comparison with EIAV RT-qPCR and AGID using samples derived from 196 inapparent EIAV carrier horses. RESULTS EIAV RT-iiPCR did not react with other commonly encountered equine viruses and had equivalent sensitivity (95% detection limit of eight genome equivalents), with a concordance of 95.41% to conventional EIAV RT-qPCR. However, the RT-qPCR and RT-iiPCR had sensitivities of 43.75 and 50.00%, respectively, when compared to the AGID test. MAIN LIMITATIONS Low viral loads commonly encountered in inapparent EIAV carriers may limit the diagnostic sensitivity of RT-PCR-based tests. CONCLUSIONS Although EIAV RT-iiPCR is not sufficiently sensitive to replace the current AGID test, it can augment control efforts by identifying recently exposed or "serologically silent" equids, particularly as the latter often represent a significant transmission risk because of high viral loads. Furthermore, the relatively low cost and field-deployable design enable utilisation of EIAV RT-iiPCR even in remote regions.
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Affiliation(s)
- R F Cook
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - M Barrandeguy
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología, Argentina
| | - P-Y A Lee
- GeneReach USA, Lexington, Massachusetts, USA
| | - C-F Tsai
- GeneReach USA, Lexington, Massachusetts, USA
| | - Y-H Shen
- GeneReach USA, Lexington, Massachusetts, USA
| | - Y-L Tsai
- GeneReach USA, Lexington, Massachusetts, USA
| | - H-F G Chang
- GeneReach USA, Lexington, Massachusetts, USA
| | - H-T T Wang
- GeneReach USA, Lexington, Massachusetts, USA
| | - U B R Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
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29
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Wood SA, Pochon X, Ming W, von Ammon U, Woods C, Carter M, Smith M, Inglis G, Zaiko A. Considerations for incorporating real-time PCR assays into routine marine biosecurity surveillance programmes: a case study targeting the Mediterranean fanworm ( Sabella spallanzanii) and club tunicate ( Styela clava) 1. Genome 2018; 62:137-146. [PMID: 30278148 DOI: 10.1139/gen-2018-0021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular techniques may provide effective tools to enhance marine biosecurity surveillance. Prior to routine implementation, evidence-based consideration of their benefits and limitations is needed. In this study, we assessed the efficiency and practicality of visual diver surveys and real-time PCR assays (targeting DNA and RNA) for detecting two marine invasive species whose infestation levels varied between species and location: Sabella spallanzanii and Styela clava. Filtered water samples (n = 171) were collected in parallel with dive surveys at two locations as part of the New Zealand Marine High Risk Site Surveillance programme: Nelson Harbour (27 sites) and Waitemata Harbour (30 sites). Diver surveys resulted in a greater number of detections compared to real-time PCR: S. clava - 21 versus 5 sites in Nelson, 6 versus 1 in Auckland; S. spallanzanii - 18 versus 10 in Auckland, no detections in Nelson. Occupancy modelling derived detection probabilities for the real-time PCR for S. clava were low (14%), compared to S. spallanzanii (66%). This could be related to abundances, or species-specific differences in DNA shedding. Only one RNA sample was positive, suggesting that most detections were from extracellular DNA or non-viable fragments. While molecular methods cannot yet replace visual observations, this study shows they provide useful complementary information.
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Affiliation(s)
- Susanna A Wood
- a Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- a Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,c Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Witold Ming
- a Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Ulla von Ammon
- a Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,b School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Chris Woods
- d National Institute of Water & Atmospheric Research Ltd., New Zealand
| | - Megan Carter
- d National Institute of Water & Atmospheric Research Ltd., New Zealand
| | - Matt Smith
- d National Institute of Water & Atmospheric Research Ltd., New Zealand
| | - Graeme Inglis
- d National Institute of Water & Atmospheric Research Ltd., New Zealand
| | - Anastasija Zaiko
- a Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,b School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Lauterbach SE, Nelson SN, Nolting JM, Trujillo JD, Richt JA, Bowman AS. Evaluation of a Field-Deployable Insulated Isothermal Polymerase Chain Reaction Nucleic Acid Analyzer for Influenza A Virus Detection at Swine Exhibitions. Vector Borne Zoonotic Dis 2018; 19:212-216. [PMID: 30183529 DOI: 10.1089/vbz.2018.2345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Rapid detection of influenza A virus (IAV) at swine exhibitions, where zoonotic transmission has occurred, can allow exhibition officials to quickly implement mitigation strategies and reduce public health risk. While laboratory diagnostic methods using PCR exist, pen-side detection of IAV can reduce lag time between sample collection and results. Portable insulated isothermal PCR (RT-iiPCR) has been used for point-of-care pathogen detection in veterinary medicine. This study compared laboratory methods of real-time reverse transcription PCR (rRT-PCR) to RT-iiPCR to determine the potential effectiveness of RT-iiPCR for detection of IAV in swine in the field. Two methods of extraction (magnetic bead and spin-column) and the two PCR platforms were used in a crossover study design to detect IAV in nasal wipes of 150 individual swine from one exhibition. Magnetic bead extraction is considered the laboratory gold standard while spin-column purification is considered the field-deployable method. IAV RNA was detected in 17 samples using Mag/rRT-PCR (reference assay) and 16 samples using Mag/RT-iiPCR (Sensitivity-S 76.5%), whereas only 14 samples using Spin/rRT-PCR (S 88.2%) and 12 samples using Spin/RT-iiPCR (field method) (S 58.8%) were positive, demonstrating a reduction in detection of viral RNA using column purification. There is moderate agreement (Cohen's kappa = 0.6575) between Mag/rRT-PCR and Spin/RT-iiPCR. There is good agreement between both PCR assays when using the same method of extraction (Mag: Cohen's kappa = 0.8203, Spin: Cohen's kappa = 0.7642). RT-iiPCR requires testing of 10 more samples than the rRT-PCR to detect disease at the 95% confidence level in a population of 300 animals with a disease prevalence of 20%. In conclusion, although there is some reduction in sensitivity, RT-iiPCR used in conjunction with spin-column purification is an acceptable method of IAV in swine detection at exhibitions where it may help reduce lag time and allow for rapid control of an IAV outbreak.
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Affiliation(s)
- Sarah E Lauterbach
- 1 Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio
| | - Sarah N Nelson
- 1 Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio
| | - Jacqueline M Nolting
- 1 Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio
| | - Jessie D Trujillo
- 2 Diagnostic Medicine Pathobiology, Kansas State University, College of Veterinary Medicine, Manhattan, Kansas
| | - Jürgen A Richt
- 2 Diagnostic Medicine Pathobiology, Kansas State University, College of Veterinary Medicine, Manhattan, Kansas
| | - Andrew S Bowman
- 1 Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio
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Cooke KL, Frenzer P, Tucker SJ, Crawford PC, Kirk SK, Levy JK. Rapid Diagnosis of Babesia gibsoni by Point-of-Need Testing by Insulated Isothermal PCR in Dogs at High Risk of Infection. J Vet Intern Med 2018; 32:232-235. [PMID: 29377357 PMCID: PMC5787167 DOI: 10.1111/jvim.15033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/12/2017] [Accepted: 11/29/2017] [Indexed: 12/26/2022] Open
Abstract
Background Dogs seized by law enforcement agencies during dogfighting investigations are at increased risk of Babesia gibsoni infection. A rapid and cost‐effective diagnostic test would increase the feasibility of mass screening of dogs for infection and monitoring treatment efficacy in B. gibsoni‐infected dogs. Objective To determine the performance of a point‐of‐need insulated isothermal PCR (iiPCR) test for diagnosis of B. gibsoni in dogs rescued in dogfighting investigations. Animals Two hundred and thirty‐three dogs seized in dogfighting investigations. Methods Cross‐sectional study. Whole blood samples were tested for B. gibsoni and Babesia spp. by iiPCR. Results were compared to a reference standard comprised of concordant results from real‐time PCR in a commercial diagnostic laboratory and antibody titers. Results The iiPCR system was quick to learn, portable, and had a short processing time of <2 hours. Sensitivity and specificity of the iiPCR assay for B. gibsoni were 90% (95% confidence interval [CI] 81–95%) and 99% (CI, 95–100%), respectively. Sensitivity and specificity of the iiPCR assay for Babesia spp. were 87% (CI, 78–93%) and 98% (CI, 0.94–99%), respectively. Conclusions and Clinical Importance The iiPCR system produced few false‐positive results, indicating that positive results are likely to represent true infections when used in high‐risk animals. The iiPCR system can fail to identify 10–15% of truly infected dogs. However, the portability, speed, and economy of the iiPCR system compared to testing through a reference laboratory can allow rescue groups to screen and identify infection in more dogs.
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Affiliation(s)
- K L Cooke
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL
| | - P Frenzer
- Maddie's Shelter Medicine Program, Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL
| | - S J Tucker
- Maddie's Shelter Medicine Program, Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL
| | - P C Crawford
- Maddie's Shelter Medicine Program, Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL
| | - S K Kirk
- Maddie's Shelter Medicine Program, Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL
| | - J K Levy
- Maddie's Shelter Medicine Program, Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL
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Abstract
The four serotypes of dengue virus (DENV) cause one of the most important and rapidly emerging mosquito-borne viral diseases in humans. Of the currently available diagnostic tests for dengue, the reverse transcription-PCR (RT-PCR) assay is the most sensitive and specific, and so it is commonly used as the gold standard. However, the requirement of a sophisticated and expensive thermal cycler makes it very difficult to use as a point-of-care diagnostic test in resource-limited regions where dengue is endemic. Tsai et al. (J Clin Microbiol 56:e01865-17, 2018, https://doi.org/10.1128/JCM.01865-17) report the analytical and clinical performances of a reverse transcription-insulated isothermal PCR (RT-iiPCR) assay with a portable nucleic acid analyzer for rapid detection of the four DENV serotypes; its reproducibility and complete agreement on clinical samples with the multiplex RT-PCR assay developed by the Centers for Disease Control and Prevention suggest that the dengue RT-iiPCR is a potential point-of-care test. Compared with other DENV RNA detection methods, the unique isothermal PCR design of RT-iiPCR, together with further improvements, would represent a promising new type of field-deployable diagnostic test for dengue.
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Validation of the Pockit Dengue Virus Reagent Set for Rapid Detection of Dengue Virus in Human Serum on a Field-Deployable PCR System. J Clin Microbiol 2018; 56:JCM.01865-17. [PMID: 29436418 DOI: 10.1128/jcm.01865-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/30/2018] [Indexed: 01/05/2023] Open
Abstract
Dengue virus (DENV) infection, a mosquito-borne disease, is a major public health problem in tropical countries. Point-of-care DENV detection with good sensitivity and specificity enables timely early diagnosis of DENV infection, facilitating effective disease management and control, particularly in regions of low resources. The Pockit dengue virus reagent set (GeneReach Biotech), a reverse transcription insulated isothermal PCR (RT-iiPCR), is available to detect all four serotypes of DENV on the field-deployable Pockit system, which is ready for on-site applications. In this study, analytical and clinical performances of the assay were evaluated. The index assay did not react with 14 non-DENV human viruses, indicating good specificity. Compared to the U.S. CDC DENV-1-4 real-time quantitative RT-PCR (qRT-PCR) assay, testing with serial dilutions of virus-spiked human sera demonstrated that the index assay had detection endpoints that were separately comparable with the 4 serotypes. Excellent reproducibility was observed among repeat tests done by six operators at three sites. In clinical performance, 195 clinical sera collected around Kaohsiung city in 2012 and 21 DENV-4-spiked sera were tested with the RT-iiPCR and qRT-PCR assays in parallel. The 121 (11 DENV-1, 78 DENV-2, 11 DENV-3, and 21 DENV-4) qRT-PCR-positive and 95 qRT-PCR-negative samples were all positive and negative by the RT-iiPCR reagent results, respectively, demonstrating high (100%) interrater agreement (95% confidence interval [CI95%], ∼98.81% to 100%; κ = 1). With analytical and clinical performance equivalent to those of the reference qRT-PCR assay, the index PCR assay on the field-deployable system can serve as a highly sensitive and specific on-site tool for DENV detection.
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Vissani MA, Tordoya MS, Tsai YL, Lee PYA, Shen YH, Lee FC, Wang HTT, Parreño V, Barrandeguy M. On-site detection of equid alphaherpesvirus 3 in perineal and genital swabs of mares and stallions. J Virol Methods 2018; 257:29-32. [PMID: 29627335 DOI: 10.1016/j.jviromet.2018.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/04/2018] [Accepted: 04/04/2018] [Indexed: 01/11/2023]
Abstract
Equine coital exanthema (ECE) is an infectious, venereally transmitted muco-cutaneous disease affecting mares and stallions, caused by equid alphaherpesvirus 3 (EHV3). Diagnostic tools for rapid identification of EHV3 are of primary importance to diminish the risk of EHV3 dissemination at the time of breeding. In the last years, it has been shown that the performance of the insulated-isothermal polymerase chain reaction (iiPCR) is comparable to virus isolation, nested PCR and real-time PCR (qPCR) in detecting pathogens of various animal species. Analytical sensitivity and specificity of the iiPCR were compared with a qPCR, using a plasmid containing the target region of the EHV3 glycoprotein G gene and an Argentinian EHV3 isolate (E/9283/07 C3A). In order to evaluate the diagnostic performance of the iiPCR, nucleic acids of 85 perineal and genital swabs (PGS) of mares and stallions were extracted by tacoTM mini and tested by both techniques. EHV3 was detected in 46 and 45 of the 85 PGS by the iiPCR and qPCR, respectively. There was almost perfect agreement between the two diagnostic methods (98.82%; 95% CI: 95.03-100%; κ = 0.98). The iiPCR had a limit of detection of 95.00% at 6 genome equivalents per reaction and a detection endpoint for viral DNA comparable to that of the qPCR, and did not react with six non-targeted equine pathogens. The iiPCR represents a sensitive and specific method for the rapid on-site diagnosis of EHV3 infection. Its routinely implementation in breeding facilities, and artificial insemination and embryo transfer centers, will contribute to prevent the dissemination of this venereal, highly contagious disease in horses.
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Affiliation(s)
- M A Vissani
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología, Argentina
| | - M S Tordoya
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología, Argentina
| | - Y-L Tsai
- GeneReach USA, Lexington, MA, USA
| | | | - Y-H Shen
- GeneReach USA, Lexington, MA, USA
| | - F-C Lee
- GeneReach USA, Lexington, MA, USA
| | | | - V Parreño
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología, Argentina
| | - M Barrandeguy
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología, Argentina; Cátedra de Enfermedades Infecciosas, Escuela de Veterinaria, Universidad del Salvador, Champagnat 1599, Ruta Panamericana km54.5 (B1630AHU), Pilar, Buenos Aires, Argentina.
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Mendoza-Gallegos RA, Rios A, Garcia-Cordero JL. An Affordable and Portable Thermocycler for Real-Time PCR Made of 3D-Printed Parts and Off-the-Shelf Electronics. Anal Chem 2018; 90:5563-5568. [DOI: 10.1021/acs.analchem.7b04843] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Roberto A. Mendoza-Gallegos
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Parque PIIT, Apodaca, Nuevo León C.P. 66628, Mexico
| | - Amelia Rios
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Parque PIIT, Apodaca, Nuevo León C.P. 66628, Mexico
| | - Jose L. Garcia-Cordero
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Parque PIIT, Apodaca, Nuevo León C.P. 66628, Mexico
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Carossino M, Li Y, Lee PYA, Tsai CF, Chou PH, Williams D, Skillman A, Frank Cook R, Brown G, Chang HFG, Wang HTT, Balasuriya UBR. Evaluation of a field-deployable reverse transcription-insulated isothermal PCR for rapid and sensitive on-site detection of Zika virus. BMC Infect Dis 2017; 17:778. [PMID: 29258444 PMCID: PMC5735522 DOI: 10.1186/s12879-017-2852-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 11/22/2017] [Indexed: 01/13/2023] Open
Abstract
Background The recent emergence of Zika virus (ZIKV) in Brazil and its precipitous expansion throughout the Americas has highlighted the urgent need for a rapid and reliable on-site diagnostic assay suitable for viral detection. Such point-of-need (PON), low-cost diagnostics are essential for ZIKV control in vulnerable areas with limited resources. Methods We developed and evaluated a ZIKV-specific field-deployable RT-iiPCR reagent set targeting the E gene for rapid detection of ZIKV in ZIKV-spiked human and mosquito specimens, and compared its performance to the Center for Disease Control and Prevention (CDC) and Pan American Health Organization (PAHO) RT-qPCR assays targeting the E and NS2B genes, respectively. Results These assays demonstrated exclusive specificity for ZIKV (African and Asian lineages), had limits of detection ranging from 10 to 100 in vitro transcribed RNA copies/μl and detection endpoints at 10 plaque forming units/ml of infectious tissue culture fluid. Analysis of human whole blood, plasma, serum, semen, urine, and mosquito pool samples spiked with ZIKV showed an agreement of 90% (k = 0.80), 92% (k = 0.82), 95% (k = 0.86), 92% (k = 0.81), 90% (k = 0.79), and 100% (k = 1), respectively, between the RT-iiPCR assay and composite results from the reference RT-qPCR assays. Overall, the concurrence between the ZIKV RT-iiPCR and the reference RT-qPCR assays was 92% (k = 0.83). Conclusions The ZIKV RT-iiPCR has a performance comparable to the reference CDC and PAHO RT-qPCR assays but provides much faster results (~1.5 h) with a field-deployable system that can be utilized as a PON diagnostic with the potential to significantly improve the quality of the health care system in vulnerable areas. Electronic supplementary material The online version of this article (10.1186/s12879-017-2852-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mariano Carossino
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Yanqiu Li
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | | | | | | | - Dennis Williams
- University of Kentucky Medical Center, Chandler Hospital, Kentucky Blood Center, University of Kentucky, Lexington, KY, USA
| | - Ashley Skillman
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - R Frank Cook
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Grayson Brown
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | | | | | - Udeni B R Balasuriya
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA.
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Progress and Challenges towards Point-of-Care Diagnostic Development for Dengue. J Clin Microbiol 2017; 55:3339-3349. [PMID: 28904181 DOI: 10.1128/jcm.00707-17] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Dengue detection strategies involve viral RNA, antigen, and/or antibody detection. Each strategy has its advantages and disadvantages. Optimal, user-friendly, rapid diagnostic tests based on immunochromatographic assays are pragmatic point-of-care tests (POCTs) in regions where dengue is endemic where there are limited laboratory capabilities and optimal storage conditions. Increasingly, there is a greater public health significance for a multiplexing assay that differentiates dengue from Zika or pathogens with similar clinical presentations. Although there have been many assay/platform developments toward POCTs, independent validation and implementation remain very limited. This review highlights the current key progress and challenges toward the development of a dengue POCT.
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Sun YL, Yen CH, Tu CF. Immunocapture loop-mediated isothermal amplification assays for the detection of canine parvovirus. J Virol Methods 2017; 249:94-101. [PMID: 28834737 DOI: 10.1016/j.jviromet.2017.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/15/2017] [Accepted: 08/15/2017] [Indexed: 11/17/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) assay was used for rapid canine parvovirus (CPV) diagnosis. To reduce the time required and increase the sensitivity of the assay, an immunocapture (IC) technique was developed in this study to exclude the DNA extraction step in molecular diagnostic procedures for CPV. A polyclonal rabbit anti-CPV serum was produced against VP2-EpC that was cloned via DNA recombination. The polyclonal anti-VP2-EpC serum was used for virus capture to prepare microtubes. IC-LAMP was performed to amplify a specific CPV target gene sequence from the CPV viral particles that were captured on the microtubes, and the amplicons were analyzed using agarose electrophoresis or enzyme-linked immunosorbent assay (IC-LAMP-ELISA) and lateral-flow dipstick (IC-LAMP-LFD). The detection sensitivities of IC-LAMP, IC-LAMP-ELISA, and IC-LAMP-LFD were 10-1, 10-1, and 10-1 TCID50/mL, respectively. Using the IC-LAMP-ELISA and IC-LAMP-LFD assays, the complete CPV diagnostic process can be achieved within 1.5h. Both of the developed IC-LAMP-based assays are simple, direct visual and efficient techniques that are applicable to the detection of CPV.
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Affiliation(s)
- Yu-Ling Sun
- Aquatic Technology Laboratories, Agricultural Technology Research Institute, No. 1, Ln. 51, Dahu Rd., Xiangshan Dist, 300 Hsinchu, Taiwan.
| | - Chon-Ho Yen
- Animal Technology Laboratories, Agricultural Technology Research Institute, Hsinchu, Taiwan
| | - Ching-Fu Tu
- Animal Technology Laboratories, Agricultural Technology Research Institute, Hsinchu, Taiwan
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Evaluation and Clinical Validation of Two Field-Deployable Reverse Transcription-Insulated Isothermal PCR Assays for the Detection of the Middle East Respiratory Syndrome-Coronavirus. J Mol Diagn 2017; 19:817-827. [PMID: 28807812 PMCID: PMC7106309 DOI: 10.1016/j.jmoldx.2017.06.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/19/2017] [Accepted: 06/21/2017] [Indexed: 02/07/2023] Open
Abstract
Middle East respiratory syndrome (MERS) is an emerging zoonotic viral respiratory disease that was first identified in Saudi Arabia in 2012. In 2015, the largest MERS outbreak outside of the Middle East region occurred in the Republic of Korea. The rapid nosocomial transmission of MERS-coronavirus (MERS-CoV) in Korean health care settings highlighted the importance and urgent need for a rapid and reliable on-site diagnostic assay to implement effective control and preventive measures. Here, the evaluation and validation of two newly developed reverse transcription-insulated isothermal PCR (RT-iiPCR) methods targeting the ORF1a and upE genes of MERS-CoV are described. Compared with World Health Organization-recommended singleplex real-time quantitative RT-PCR (RT-qPCR) assays, both RT-iiPCR assays had comparable analytical sensitivity for the detection of MERS-CoV RNA in tissue culture fluid and in sputum samples spiked with infectious virus. Furthermore, clinical evaluation was performed with sputum samples collected from subjects with acute and chronic respiratory illnesses, including patients infected with MERS-CoV. The overall agreement values between the two RT-iiPCR assays and the reference RT-qPCR assays were 98.06% (95% CI, 94.43%-100%; κ = 0.96) and 99.03% (95% CI, 95.88%-100%; κ = 0.99) for ORF1a and upE assays, respectively. The ORF1a and upE MERS-CoV RT-iiPCR assays coupled with a field-deployable system provide a platform for a highly sensitive and specific on-site tool for diagnosis of MERS-CoV infections.
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Wilkes RP, Anis E, Dunbar D, Lee PYA, Tsai YL, Lee FC, Chang HFG, Wang HTT, Graham EM. Rapid and sensitive insulated isothermal PCR for point-of-need feline leukaemia virus detection. J Feline Med Surg 2017; 20:362-369. [PMID: 28589743 PMCID: PMC5871024 DOI: 10.1177/1098612x17712847] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Objectives Feline leukaemia virus (FeLV), a gamma retrovirus, causes diseases of the
feline haematopoietic system that are invariably fatal. Rapid and accurate
testing at the point-of-need (PON) supports prevention of virus spread and
management of clinical disease. This study evaluated the performance of an
insulated isothermal PCR (iiPCR) that detects proviral DNA, and a reverse
transcription (RT)-iiPCR that detects both viral RNA and proviral DNA, for
FeLV detection at the PON. Methods Mycoplasma haemofelis, feline coronavirus, feline
herpesvirus, feline calicivirus and feline immunodeficiency virus were used
to test analytical specificity. In vitro transcribed RNA, artificial
plasmid, FeLV strain American Type Culture Collection VR-719 and a clinical
FeLV isolate were used in the analytical sensitivity assays. A retrospective
study including 116 clinical plasma and serum samples that had been tested
with virus isolation, real-time PCR and ELISA, and a prospective study
including 150 clinical plasma and serum samples were implemented to evaluate
the clinical performances of the iiPCR-based methods for FeLV detection. Results Ninety-five percent assay limit of detection was calculated to be 16 RNA and
five DNA copies for the RT-iiPCR, and six DNA copies for the iiPCR. Both
reactions had analytical sensitivity comparable to a reference real-time PCR
(qPCR) and did not detect five non-target feline pathogens. The clinical
performance of the RT-iiPCR and iiPCR had 98.82% agreement (kappa[κ] = 0.97)
and 100% agreement (κ = 1.0), respectively, with the qPCR (n = 85). The
agreement between an automatic nucleic extraction/RT-iiPCR system and virus
isolation to detect FeLV in plasma or serum was 95.69% (κ = 0.95) and 98.67%
(κ = 0.85) in a retrospective (n = 116) and a prospective (n = 150) study,
respectively. Conclusions and relevance These results suggested that both RT-iiPCR and iiPCR assays can serve as
reliable tools for PON FeLV detection.
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Affiliation(s)
- Rebecca P Wilkes
- 1 Clinical Virology Laboratory, University of Tennessee Veterinary Medical Center, Knoxville, TN, USA.,*Current address: Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, Tifton, GA, USA
| | - Eman Anis
- 1 Clinical Virology Laboratory, University of Tennessee Veterinary Medical Center, Knoxville, TN, USA.,2 Department of Virology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Beheira, Egypt.,*Current address: Veterinary Diagnostic and Investigational Laboratory, College of Veterinary Medicine, University of Georgia, Tifton, GA, USA
| | - Dawn Dunbar
- 3 Veterinary Diagnostic Services, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | | | | | | | - Elizabeth M Graham
- 3 Veterinary Diagnostic Services, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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Chinigarzadeh A, Muniandy S, Salleh N. Combinatorial effect of genistein and female sex-steroids on uterine fluid volume and secretion rate and aquaporin (AQP)-1, 2, 5, and 7 expression in the uterus in rats. ENVIRONMENTAL TOXICOLOGY 2017; 32:832-844. [PMID: 27235753 DOI: 10.1002/tox.22283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 04/29/2016] [Indexed: 06/05/2023]
Abstract
UNLABELLED We hypothesized that genistein can interfere with the regulation of uterine fluid volume, secretion rate and expression of aquaporin in the uterus by female sex-steroids, i.e., estrogen and progesterone. Therefore, the aims of this study were to investigate changes in these parameters in the presence of genistein and female sex-steroids. METHODS Female Sprague-Dawley rats were ovariectomized and received 3-days estradiol-17β benzoate (E2) plus genistein (25, 50, or 100 mg kg-1 day-1 ) or 3-days E2 followed by 3-days E2 plus progesterone with genistein (25, 50, or 100 mg kg-1 day-1 ). A day after last treatment, uterine fluid secretion rate was determined by in vivo uterine perfusion with rats under anesthesia. Animals were sacrificed and uteri were harvested and subjected for histological analyses. Luminal/outer uterine circumference was determined and distribution of AQP-1, 2, 5, and 7 in endometrium was visualized by immunofluorescence. Expression of AQP-1, 2, 5, and 7 proteins and mRNAs were determined by Western blotting and Real-time PCR respectively. RESULTS Combined treatment of E2 with high dose genistein (50 and 100 mg kg-1 day-1 ) resulted in significant decrease in uterine fluid volume, secretion rate and expression of AQP-1, 2, 5, and 7 proteins and mRNAs in uterus (p < 0.05). No significant changes in these parameters were observed when 25 mg kg-1 day-1 genistein was given with E2 or when genistein was given with E2 followed by E2 plus progesterone Conclusions: Decreased in uterine fluid volume, secretion rate and AQP-1, 2, 5, and 7 expression in the uterus by high dose genistein in the presence of E2 could potentially affect female fertility. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 832-844, 2017.
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Affiliation(s)
- Asma Chinigarzadeh
- Department of Physiology, Faculty of Medicine, University of Malaya, 50603, Lembah Pantai, Kuala Lumpur, Malaysia
| | - Sekaran Muniandy
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603, Lembah Pantai, Kuala Lumpur, Malaysia
| | - Naguib Salleh
- Department of Physiology, Faculty of Medicine, University of Malaya, 50603, Lembah Pantai, Kuala Lumpur, Malaysia
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Translation of a laboratory-validated equine herpesvirus-1 specific real-time PCR assay into an insulated isothermal polymerase chain reaction (iiPCR) assay for point-of-need diagnosis using POCKIT™ nucleic acid analyzer. J Virol Methods 2016; 241:58-63. [PMID: 27993615 DOI: 10.1016/j.jviromet.2016.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/13/2016] [Accepted: 12/15/2016] [Indexed: 11/22/2022]
Abstract
Equine herpesvirus myeloencephalopathy (EHM), a major problem for the equine industry in the United States, is caused by equine herpesvirus-1 (EHV-1). In addition, EHV-1 is associated with upper respiratory disease, abortion, and chorioretinal lesions in horses. Here we describe the development and evaluation of an inexpensive, user-friendly insulated isothermal PCR (iiPCR) method targeting open reading 30 (ORF30) to detect both neuropathogenic and non-neuropathogenic strains on the field-deployable POCKIT™ device for point-of-need detection of EHV-1. The analytical sensitivity of the EHV-1 iiPCR assay was 13 genome equivalents per reaction. The assay did not cross react with ten non-target equine viral pathogens. Performance of the EHV-1 iiPCR assay was compared to two previously described real-time PCR (qPCR) assays in two laboratories by using 104 archived clinical samples. All 53 qPCR-positive and 46 of the 51 qPCR-negative samples tested positive and negative, respectively, by the iiPCR. The agreement between the two assays was 95.19% (confidence interval 90.48-99.90%) with a kappa value of 0.90. In conclusion, the newly developed EHV-1 iiPCR assay is robust to provide specificity and sensitivity comparable to qPCR assays for the detection of EHV-1 nucleic acid in clinical specimens.
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Chinigarzadeh A, Muniandy S, Salleh N. Estradiol, progesterone and genistein differentially regulate levels of aquaporin (AQP)-1, 2, 5 and 7 expression in the uteri of ovariectomized, sex-steroid deficient rats. Steroids 2016; 115:47-55. [PMID: 27521800 DOI: 10.1016/j.steroids.2016.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 07/10/2016] [Accepted: 08/07/2016] [Indexed: 02/06/2023]
Abstract
UNLABELLED In this study, effects of estradiol, progesterone and genistein on uterine aquaporin (AQP)-1, 2, 5 and 7 expression were investigated in sex-steroid deficient state which could help to elucidate the mechanisms underlying uterine fluid volume changes that were reported under these hormone and hormone-like compound influences. METHODS Uteri from ovariectomized, female Sprague-Dawley rats receiving seven days estradiol, progesterone or genistein (25, 50 and 100mg/kg/day) were harvested and levels of AQP-1, 2, 5 and 7 proteins and mRNAs were determined by Western blotting and Real-time PCR (qPCR) respectively. Distribution of these proteins in uterus was observed by immunohistochemistry. RESULTS Genistein caused a dose-dependent increase in uterine AQP-1, 2, 5 and 7 protein and mRNA expression, however at the levels lower than following estradiol or progesterone stimulations. Effects of genistein were antagonized by estradiol receptor blocker, ICI 182780. Estradiol caused the highest AQP-2 protein and mRNA expression while progesterone caused the highest AQP-1, 5 and 7 protein and mRNA expression in uterus. AQP-1, 2, 5 and 7 protein were found to be distributed in the myometrium as well as in uterine luminal and glandular epithelia and endometrial blood vessels. In conclusion, the observed effects of estradiol, progesterone and genistein on uterine AQP-1, 2, 5 and 7 expression could help to explain the differences in the amount of fluid accumulated in the uterus under these different conditions.
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Affiliation(s)
- Asma Chinigarzadeh
- Dept of Physiology, Faculty of Medicine, University of Malaya, 50603 Lembah Pantai, Kuala Lumpur, Malaysia
| | - Sekaran Muniandy
- Dept of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Lembah Pantai, Kuala Lumpur, Malaysia
| | - Naguib Salleh
- Dept of Physiology, Faculty of Medicine, University of Malaya, 50603 Lembah Pantai, Kuala Lumpur, Malaysia.
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Ambagala A, Fisher M, Goolia M, Nfon C, Furukawa-Stoffer T, Ortega Polo R, Lung O. Field-Deployable Reverse Transcription-Insulated Isothermal PCR (RT-iiPCR) Assay for Rapid and Sensitive Detection of Foot-and-Mouth Disease Virus. Transbound Emerg Dis 2016; 64:1610-1623. [PMID: 27589902 PMCID: PMC7169878 DOI: 10.1111/tbed.12554] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 12/23/2022]
Abstract
Foot‐and‐mouth disease (FMD) is a highly contagious viral disease of cloven‐hoofed animals, which can decimate the livestock industry and economy of countries previously free of this disease. Rapid detection of foot‐and‐mouth disease virus (FMDV) is critical to containing an FMD outbreak. Availability of a rapid, highly sensitive and specific, yet simple and field‐deployable assay would support local decision‐making during an FMDV outbreak. Here we report validation of a novel reverse transcription‐insulated isothermal PCR (RT‐iiPCR) assay that can be performed on a commercially available, compact and portable POCKIT™ analyser that automatically analyses data and displays ‘+’ or ‘−’ results. The FMDV RT‐iiPCR assay targets the 3D region of the FMDV genome and was capable of detecting 9 copies of in vitro‐transcribed RNA standard with 95% confidence. It accurately identified 63 FMDV strains belonging to all seven serotypes and showed no cross‐reactivity with viruses causing similar clinical diseases in cloven‐hoofed animals. The assay was able to identify FMDV RNA in multiple sample types including oral, nasal and lesion swabs, epithelial tissue suspensions, vesicular and oral fluid samples, even before the appearance of clinical signs. Clinical sensitivity of the assay was comparable or slightly higher than the laboratory‐based real‐time RT‐PCR assay in use. The assay was able to detect FMDV RNA in vesicular fluid samples without nucleic acid extraction. For RNA extraction from more complex sample types, a commercially available taco™ mini transportable magnetic bead‐based, automated extraction system was used. This assay provides a potentially useful field‐deployable diagnostic tool for rapid detection of FMDV in an outbreak in FMD‐free countries or for routine diagnostics in endemic countries with less structured laboratory systems.
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Affiliation(s)
- A Ambagala
- Canadian Food Inspection Agency, National Centres for Animal Disease, Lethbridge Laboratory, Lethbridge, AB, Canada
| | - M Fisher
- Canadian Food Inspection Agency, National Centres for Animal Disease, Lethbridge Laboratory, Lethbridge, AB, Canada
| | - M Goolia
- Canadian Food Inspection Agency, National Centre for Foreign Animal Diseases, Canadian Science Centre for Human and Animal Health, Winnipeg, MB, Canada
| | - C Nfon
- Canadian Food Inspection Agency, National Centre for Foreign Animal Diseases, Canadian Science Centre for Human and Animal Health, Winnipeg, MB, Canada
| | - T Furukawa-Stoffer
- Canadian Food Inspection Agency, National Centres for Animal Disease, Lethbridge Laboratory, Lethbridge, AB, Canada
| | - R Ortega Polo
- Canadian Food Inspection Agency, National Centres for Animal Disease, Lethbridge Laboratory, Lethbridge, AB, Canada
| | - O Lung
- Canadian Food Inspection Agency, National Centres for Animal Disease, Lethbridge Laboratory, Lethbridge, AB, Canada
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Tung HY, Wang SH, Chiang YC, Tsai MS. Rapid screening of roundup ready soybean in food samples by a hand-held PCR device. Food Sci Biotechnol 2016; 25:1101-1107. [PMID: 30263381 DOI: 10.1007/s10068-016-0177-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 04/10/2016] [Accepted: 05/18/2016] [Indexed: 01/06/2023] Open
Abstract
Insulated isothermal PCR (iiPCR) method was recently available for rapid on-site detection of roundup ready soybean (RRS; event GTS40-3-2) in food materials and products. Performance of this method was evaluated in this study. The 100% detection endpoint for the RRS by iiPCR was found in samples containing 0.1% RRS, equivalent to the results of the reference real-time PCR (rtPCR). Analysis of nucleic acids of soybean-based processed food products indicated 95% agreement between the iiPCR and rtPCR for RRS detection. By testing soybean milk and tofu samples using simple pretreatment methods, we found that the agreements between iiPCR and rtPCR methods of the aforementioned samples were 80% and 90%, respectively. Replicated tests of all discrepant samples implied that these samples had trace amounts of RRS, suggesting that the iiPCR system is more sensitive than the rtPCR method. In conclusion, the iiPCR technology can be a useful point-of-need tool to help make a timely decision in the consumption of genetically modified organisms.
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Affiliation(s)
- Hsiang-Yun Tung
- 1College of Biotechnology and Bioresources, Da-Yeh University, Changhua, Taiwan, 51591 China
| | - Sue-Hong Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan, 402 China
| | - Yu-Cheng Chiang
- Department of Food Science and Technology, Hung Kuang University, Taichung, Taiwan, 43302 China
| | - Ming-Shiun Tsai
- 1College of Biotechnology and Bioresources, Da-Yeh University, Changhua, Taiwan, 51591 China
- 4Department of BioIndustry Technology, Da-Yeh University, Changhua, Taiwan, 51591 China
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Dehghan F, Soori R, Dehghan P, Gholami K, Muniandy S, Azarbayjani MA, Yusof A. Changes in Knee Laxity and Relaxin Receptor Isoforms Expression (RXFP1/RXFP2) in the Knee throughout Estrous Cycle Phases in Rodents. PLoS One 2016; 11:e0160984. [PMID: 27513858 PMCID: PMC4981442 DOI: 10.1371/journal.pone.0160984] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 07/28/2016] [Indexed: 12/31/2022] Open
Abstract
The changes in knee laxity and relaxin receptor expression at different phases of rodent estrous cycle are not known. Here, changes in the parameter were investigated in rats at different phases of the estrous cycle. Estrous cycle phases of intact female rats were determined by cytological examination of the vaginal smear. Following phase identification, blood was collected for serum hormone analyses. Knee passive range of motion (ROM) was determined by using a digital miniature goniometer. The animals were then sacrificed and patellar tendon, collateral ligaments and hamstring muscles were harvested for relaxin/insulin-like family peptide receptor 1 and 2 (RXFP1/RXFP2) analyses. Knee passive ROM was the highest at proestrus followed by diestrus and the lowest at estrus. Estrogen level was the highest at proestrus while progesterone and relaxin levels were the highest at diestrus. A strong correlation was observed between relaxin and progesterone levels. At proestrus, expression of RXFP1 and RXFP2 proteins and mRNAs were the highest at proestrus followed by diestrus and estrus. The finding shows that higher level of progesterone and relaxin in diestrus might be responsible for higher laxity of knee joint in rats.
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Affiliation(s)
- Firouzeh Dehghan
- Department of Exercise Physiology, Faculty of Physical Education and Sport Sciences, University of Tehran, Tehran, Iran
- Department of exercise science, Sports Center, University of Malaya, Kuala Lumpur, 50603, Malaysia
- * E-mail:
| | - Rahman Soori
- Department of Exercise Physiology, Faculty of Physical Education and Sport Sciences, University of Tehran, Tehran, Iran
| | - Parvin Dehghan
- Health Deputy, Babol University of Medical Sciences, Babol, Iran
| | - Khadijeh Gholami
- Department of Physiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Sekaran Muniandy
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Mohammad Ali Azarbayjani
- Department of Physical Education and Sports Sciences, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Ashril Yusof
- Department of exercise science, Sports Center, University of Malaya, Kuala Lumpur, 50603, Malaysia
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Lin YH, Lin YJ, Chang TD, Hong LL, Chen TY, Chang PFL. Development of a TaqMan Probe-Based Insulated Isothermal Polymerase Chain Reaction (iiPCR) Assay for Detection of Fusarium oxysporum f. sp. cubense Race 4. PLoS One 2016; 11:e0159681. [PMID: 27448242 PMCID: PMC4957775 DOI: 10.1371/journal.pone.0159681] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/05/2016] [Indexed: 01/08/2023] Open
Abstract
This study developed a novel and inexpensive detection method based on a TaqMan probe-based insulated isothermal polymerase chain reaction (iiPCR) method for the rapid detection of Panama disease caused by Fusarium oxysporum f. sp. cubense (Foc) race 4, which is currently among the most serious fungal vascular diseases worldwide. By using the portable POCKIT™ device with the novel primer set iiFoc-1/iiFoc-2, the Foc race 4 iiPCR assay (including DNA amplification and signal monitoring) could be completed within one hour. The developed Foc race 4 iiPCR assay is thus a user-friendly and efficient platform designed specifically for the detection of Foc race 4. The detection limit of this optimized Foc iiPCR system was estimated to be 1 copy of the target standard DNA as well as 1 fg of the Foc genomic DNA. This approach can serve as a rapid detection method for in planta detection of Foc race 4 in field-infected banana. It was concluded that this molecular detection procedure based on iiPCR has good potential for use as an efficient detection method.
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Affiliation(s)
- Ying-Hong Lin
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Yi-Jia Lin
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Tsai-De Chang
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Li-Ling Hong
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Tzu-Yu Chen
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pi-Fang Linda Chang
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- NCHU-UCD Plant and Food Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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Kuo HC, Lo DY, Chen CL, Tsai YL, Ping JF, Lee CH, Lee PYA, Chang HFG. Rapid and sensitive detection of Mycoplasma synoviae by an insulated isothermal polymerase chain reaction-based assay on a field-deployable device. Poult Sci 2016; 96:35-41. [PMID: 27389062 PMCID: PMC5161023 DOI: 10.3382/ps/pew228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/04/2016] [Accepted: 05/10/2016] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma synoviae (MS), causing respiratory diseases, arthritis, and eggshell apex abnormalities in avian species, is an important pathogen in the poultry industry. Implementation of a biosecurity plan is important in MS infection management. Working on a field-deployable POCKIT™ device, an insulated isothermal polymerase chain reaction (iiPCR) assay has a potential for timely MS detection on the farm. The MS iiPCR assay had limit of detection 95% of about 9 genome equivalents by testing serial dilutions of a standard DNA. The detection endpoint of the assay for detection of MS genomic DNA was comparable to a reference real-time PCR. The assay did not crossreact with other important avian pathogens, including avian reovirus, Mycoplasma gallisepticum, Staphylococcus aureus, Escherichia coli, Pasteurella multocida, and Salmonella Pullorum. When 92 synovial fluid and respiratory tract swab samples collected from chickens, turkeys, and geese suspected of MS infection were tested, the clinical performance of the MS iiPCR had 97.8% agreement (Cohen's kappa value, 0.95) with that of the reference real-time PCR. In conclusion, the MS iiPCR/POCKIT™ system, working with field-deployable manual or automatic nucleic acid extraction methods, has potential to serve as a rapid and sensitive on-site tool to facilitate timely detection of MS.
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Affiliation(s)
- Hung-Chih Kuo
- Yunlin-Chiayi-Tainan of Animal Disease Diagnostic Center, Department of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Dan-Yuan Lo
- Yunlin-Chiayi-Tainan of Animal Disease Diagnostic Center, Department of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
| | - Chiou-Lin Chen
- Yunlin-Chiayi-Tainan of Animal Disease Diagnostic Center, Department of Veterinary Medicine, National Chiayi University, Chiayi, Taiwan
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Porcine deltacoronavirus: Overview of infection dynamics, diagnostic methods, prevalence and genetic evolution. Virus Res 2016; 226:71-84. [PMID: 27270129 PMCID: PMC7114555 DOI: 10.1016/j.virusres.2016.05.028] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 05/27/2016] [Accepted: 05/30/2016] [Indexed: 12/25/2022]
Abstract
Porcine deltacoronavirus (PDCoV) was first reported in Hong Kong, China in 2012 and reported in United States swine in February 2014. PDCoV has subsequently been detected in South Korea, mainland China, and Thailand. PDCoV has been experimentally confirmed to cause diarrhea in inoculated pigs and need to be differentially diagnosed from porcine epidemic diarrhea virus and transmissible gastroenteritis virus in the field. Rapid diagnosis is critical for the implementation of efficient control strategies against PDCoV. Developing high-quality diagnostic methods and understanding PDCoV infection dynamics to collect appropriate specimens at the appropriate time window are important to obtain reliable diagnostic results. Among the virological methods, PDCoV-specific RT-PCR remains the method of choice for the detection of PDCoV; immunohistochemistry combined with hematoxylin and eosin staining has also been commonly used to examine histopathological lesions caused by PDCoV. Serological assays can provide information about previous exposure to PDCoV and also determine antibody responses to infection or vaccination. Prevalence of PDCoV is lower compared to that of PEDV. However, among PDCoV-positive samples, co-infection with other enteric pathogen e.g. PEDV is common. It is also important to understand molecular epidemiology of PDCoV and genetic relationships of global PDCoVs. This review discusses PDCoV infection dynamics and appropriate sample collection for diagnostic testing, the commonly used virological and serological methods for PDCoV diagnosis, prevalence and genetic evolution of PDCoVs.
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Zhang J, Tsai YL, Lee PYA, Chen Q, Zhang Y, Chiang CJ, Shen YH, Li FC, Chang HFG, Gauger PC, Harmon KM, Wang HTT. Evaluation of two singleplex reverse transcription-Insulated isothermal PCR tests and a duplex real-time RT-PCR test for the detection of porcine epidemic diarrhea virus and porcine deltacoronavirus. J Virol Methods 2016; 234:34-42. [PMID: 27060624 PMCID: PMC7113669 DOI: 10.1016/j.jviromet.2016.03.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 03/02/2016] [Accepted: 03/28/2016] [Indexed: 11/30/2022]
Abstract
A new PEDV RT-iiPCR method could detect PEDV sensitively and specifically. A new PDCoV RT-iiPCR method could detect PDCoV sensitively and specifically. A new duplex rRT-PCR could detect and differentiate PEDV and PDCoV simultaneously. A portable automatic extraction method worked well with PEDV and PDCoV RT-iiPCRs. The RT-iiPCRs are potentially useful tools for on-site PEDV and PDCoV detection.
Recent outbreaks of porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV) in multiple countries have caused significant economic losses and remain a serious challenge to the swine industry. Rapid diagnosis is critical for the implementation of efficient control strategies before and during PEDV and PDCoV outbreaks. Insulated isothermal PCR (iiPCR) on the portable POCKIT™ device is user friendly for on-site pathogen detection. In the present study, a singleplex PEDV RT-iiPCR, a singleplex PDCoV RT-iiPCR, and a duplex PEDV/PDCoV real-time RT-PCR (rRT-PCR) commercial reagents targeting the M gene were compared to an N gene-based PEDV rRT-PCR and an M gene-based PDCoV rRT-PCR that were previously published and used as reference PCRs. All PCR assays were highly specific and did not cross react with other porcine enteric pathogens. Analytical sensitivities of the PEDV RT-iiPCR, PDCoV RT-iiPCR and duplex PEDV/PDCoV rRT-PCR were determined using in vitro transcribed RNA as well as viral RNA extracted from ten-fold serial dilutions of PEDV and PDCoV cell culture isolates. Performance of each PCR assay was further evaluated using 170 clinical samples (86 fecal swabs, 24 feces, 19 intestines, and 41 oral fluids). Compared to the reference PEDV rRT-PCR, the sensitivity, specificity and accuracy of the PEDV RT-iiPCR were 97.73%, 98.78%, and 98.24%, respectively, and those of the duplex PEDV/PDCoV rRT-PCR were 98.86%, 96.34%, and 97.65%, respectively. Compared to the reference PDCoV rRT-PCR, the sensitivity, specificity and accuracy of the PDCoV RT-iiPCR were 100%, 100%, and 100%, respectively, and those of the PEDV/PDCoV duplex rRT-PCR were 96.34%, 100%, and 98.24%, respectively. Overall, all three new PCR assays were comparable to the reference rRT-PCRs for detection of PEDV and/or PDCoV. The PEDV and PDCoV RT-iiPCRs are potentially useful tools for on-site detection and the duplex PEDV/PDCoV rRT-PCR provides a convenient method to simultaneously detect the two viruses and differentiate PEDV from PDCoV.
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Affiliation(s)
- Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA.
| | | | | | - Qi Chen
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA
| | - Yan Zhang
- Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, OH, USA
| | | | | | | | | | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA
| | - Karen M Harmon
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA
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