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Suther C, Stoufer S, Zhou Y, Moore MD. Recent Developments in Isothermal Amplification Methods for the Detection of Foodborne Viruses. Front Microbiol 2022; 13:841875. [PMID: 35308332 PMCID: PMC8930189 DOI: 10.3389/fmicb.2022.841875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 11/15/2022] Open
Abstract
Foodborne and enteric viruses continue to impose a significant public health and economic burden globally. As many of these viruses are highly transmissible, the ability to detect them portably, sensitively, and rapidly is critical to reduce their spread. Although still considered a gold standard for detection of these viruses, real time polymerase chain reaction (PCR)-based technologies have limitations such as limited portability, need for extensive sample processing/extraction, and long time to result. In particular, the limitations related to the susceptibility of real time PCR methods to potential inhibitory substances present in food and environmental samples is a continuing challenge, as the need for extensive nucleic acid purification prior to their use compromises the portability and rapidity of such methods. Isothermal amplification methods have been the subject of much investigation for these viruses, as these techniques have been found to be comparable to or better than established PCR-based methods in portability, sensitivity, specificity, rapidity, and simplicity of sample processing. The purpose of this review is to survey and compare reports of these isothermal amplification methods developed for foodborne and enteric viruses, with a special focus on the performance of these methods in the presence of complex matrices.
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Affiliation(s)
- Cassandra Suther
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA, United States
- Department of Medicine, University of Connecticut Health, Farmington, CT, United States
| | - Sloane Stoufer
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA, United States
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut Health, Farmington, CT, United States
| | - Matthew D. Moore
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA, United States
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2
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Qian XF, Duan AL, Huang RX, Li NX, Li YP, Guo XG. Pooled analysis of LAMP assay for the diagnosis of norovirus infection. J Clin Lab Anal 2021; 35:e23919. [PMID: 34331319 PMCID: PMC8418469 DOI: 10.1002/jcla.23919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/19/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022] Open
Abstract
Background Rapid laboratory detection is essential to diagnose norovirus infection. LAMP has many advantages compared with RT‐PCR for detecting norovirus, including high sensitivity, high specificity, rapidity, low cost, and intuitive results, which can be easily read with the naked eye with the help of color‐based reporters. In this study, we intend to analyze the accuracy of LAMP methods for the diagnosis of norovirus infection. Methods Two researchers independently retrieved relevant literature up to January 2021 (PubMed, Web of Science, Cochrane Library, Embase, CNKI, Wan Fang, and VIP). The researchers screened all articles and extracted their research data for meta‐analysis. QUADAS‐2 tool was used to evaluate the quality of the included studies by Review Manager 5.3. Forest plots were performed by Meta‐DiSc 1.4 to evaluate the accuracy of the test. Deeks’ funnel plot symmetry tests were conducted by Stata 15.0 to check the potential publication bias. Results Eleven sets of data extracted from the eight included studies were included for meta‐analysis. For the detection of norovirus, the pooled sensitivity, specificity, positive LR, negative LR, diagnostic OR, and their 95% CI were 0.96 (0.95–0.97), 0.99 (0.99–1.00), 91.14 (31.88–260.56), 0.06 (0.04–0.09), and 1473.68 (562.96–3857.70), respectively. Besides, AUC in the SROC curve was 0.9920. Conclusion LAMP had high sensitivity and specificity in terms of the diagnosis of norovirus infection. However, further extension of this approach should be researched to ensure the accuracy and practicability of this hopeful test in the future.
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Affiliation(s)
- Xi-Feng Qian
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Sixth Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Ai-Ling Duan
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Sixth Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Rong-Xian Huang
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Sixth Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Nan-Xi Li
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Mental Medicine, The Mental Health School of Guangzhou Medical University, Guangzhou, China
| | - Ya-Ping Li
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, China
| | - Xu-Guang Guo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Wan J, Guo J, Lu Z, Bie X, Lv F, Zhao H. Development of a test kit for visual loop-mediated isothermal amplification of Salmonella in spiked ready-to-eat fruits and vegetables. J Microbiol Methods 2019; 169:105830. [PMID: 31891738 DOI: 10.1016/j.mimet.2019.105830] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 12/25/2019] [Accepted: 12/27/2019] [Indexed: 02/02/2023]
Abstract
The purpose of this study was to assemble two types of loop-mediated isothermal amplification (LAMP) kit that have the ability to visually detect Salmonella in ready-to-eat fruits and vegetables. The reaction results were obtained within 20-40 min after addition of DNA and can be discerned by the naked eye or an amplification plot. The stability of the LAMP wet kit was evident after multiple freezing and thawing cycles, and the one-step LAMP lyophilized kit was further evolved to allow ambient temperature transport for deployment in resource-limited settings. The cost-effective wet kit had the ability to detect minimum amounts of 1.8 CFU/ml Salmonella DNA without enrichment, while the sensitivity of the one-step LAMP lyophilized kit was only 9.8 × 103 CFU/ml. They both have good anti-interference, as they were both able to detect 2.1 × 102 CFU/ml Salmonella mixed with 106 CFU/ml four non-Salmonella strain mixture. Moreover, cucumber and lettuce that were contaminated with an initial inoculation of 1.7 CFU of Salmonella/10 g showed detection within a reaction time of 30 min after 10 h enrichment. The present research setup is a convenient and practical kit for Salmonella rapid detection that has good application prospects in food safety monitoring.
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Affiliation(s)
- Jiajia Wan
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Jianping Guo
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
| | - Fengxia Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Haizhen Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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4
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Ma D, Shen L, Wu K, Diehnelt CW, Green AA. Low-cost detection of norovirus using paper-based cell-free systems and synbody-based viral enrichment. Synth Biol (Oxf) 2018; 3:ysy018. [PMID: 30370338 PMCID: PMC6195790 DOI: 10.1093/synbio/ysy018] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 08/18/2018] [Accepted: 09/14/2018] [Indexed: 11/14/2022] Open
Abstract
Noroviruses are a primary cause of gastroenteritis and foodborne illness with cases that affect millions of people worldwide each year. Inexpensive tests for norovirus that do not require sophisticated laboratory equipment are important tools for ensuring that patients receive timely treatment and for containing outbreaks. Herein, we demonstrate a low-cost colorimetric assay that detects norovirus from clinical samples by combining paper-based cell-free transcription-translation systems, isothermal amplification and virus enrichment by synbodies. Using isothermal amplification and cell-free RNA sensing with toehold switches, we demonstrate that the assay enables detection of norovirus GII.4 Sydney from stool down to concentrations of 270 aM in reactions that can be directly read by eye. Furthermore, norovirus-binding synbodies and magnetic beads are used to concentrate the virus and provide a 1000-fold increase in assay sensitivity extending its detection limit to 270 zM. These results demonstrate the utility of paper-based cell-free diagnostic systems for identification of foodborne pathogens and provide a versatile diagnostic assay that can be applied to the concentration, amplification and detection of a broad range of infectious agents.
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Affiliation(s)
- Duo Ma
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and School of Molecular Sciences, Arizona State University, AZ, USA
| | - Luhui Shen
- Biodesign Center for Innovations in Medicine, The Biodesign Institute and School of Molecular Sciences, Arizona State University, AZ, USA
| | - Kaiyue Wu
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and School of Molecular Sciences, Arizona State University, AZ, USA
| | - Chris W Diehnelt
- Biodesign Center for Innovations in Medicine, The Biodesign Institute and School of Molecular Sciences, Arizona State University, AZ, USA
| | - Alexander A Green
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and School of Molecular Sciences, Arizona State University, AZ, USA
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Development of a Recombinase Polymerase Amplification Assay for Detection of Epidemic Human Noroviruses. Sci Rep 2017; 7:40244. [PMID: 28067278 PMCID: PMC5220337 DOI: 10.1038/srep40244] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/05/2016] [Indexed: 12/16/2022] Open
Abstract
Human norovirus is a leading cause of viral gastroenteritis worldwide. Rapid detection could facilitate control, however widespread point-of-care testing is infrequently done due to the lack of robust and portable methods. Recombinase polymerase amplification (RPA) is a novel isothermal method which rapidly amplifies and detects nucleic acids using a simple device in near real-time. An RT-RPA assay targeting a recent epidemic human norovirus strain (GII.4 New Orleans) was developed and evaluated in this study. The assay successfully detected purified norovirus RNA from multiple patient outbreak isolates and had a limit of detection of 3.40 ± 0.20 log10 genomic copies (LGC), which is comparable to most other reported isothermal norovirus amplification methods. The assay also detected norovirus in directly boiled stool, and displayed better resistance to inhibitors than a commonly used RT-qPCR assay. The assay was specific, as it did not amplify genomes from 9 non-related enteric viruses and bacteria. The assay detected norovirus in some samples in as little as 6 min, and the entire detection process can be performed in less than 30 min. The reported RT-RPA method shows promise for sensitive point-of-care detection of epidemic human norovirus, and is the fastest human norovirus amplification method to date.
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Response to the Questions Posed by the Food Safety and Inspection Service, the Centers for Disease Control and Prevention, the National Marine Fisheries Service, and the Defense Health Agency, Veterinary Services Activity Regarding Control Strategies for Reducing Foodborne Norovirus Infections. J Food Prot 2016; 79:843-89. [PMID: 27296435 DOI: 10.4315/0362-028x.jfp-15-215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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7
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Chen H, Hu Y. Molecular Diagnostic Methods for Detection and Characterization of Human Noroviruses. Open Microbiol J 2016; 10:78-89. [PMID: 27335620 PMCID: PMC4899541 DOI: 10.2174/1874285801610010078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 02/04/2023] Open
Abstract
Human noroviruses are a group of viral agents that afflict people of all age groups. The viruses are now recognized as the most common causative agent of nonbacterial acute gastroenteritis and foodborne viral illness worldwide. However, they have been considered to play insignificant roles in the disease burden of acute gastroenteritis for the past decades until the recent advent of new and more sensitive molecular diagnostic methods. The availability and application of the molecular diagnostic methods have led to enhanced detection of noroviruses in clinical, food and environmental samples, significantly increasing the recognition of noroviruses as an etiologic agent of epidemic and sporadic acute gastroenteritis. This article aims to summarize recent efforts made for the development of molecular methods for the detection and characterization of human noroviruses.
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Affiliation(s)
- Haifeng Chen
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Yuan Hu
- Northeast Region Laboratory, Office of Regulatory Affairs, U.S. Food and Drug Administration, Jamaica, NY, USA
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8
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Molecular Diagnosis of Gastrointestinal Infections. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Norovirus is an important cause of gastroenteritis outbreaks globally and the most prevalent cause of sporadic gastroenteritis in many regions. Rapid and accurate identification of causative viral agents is critical for outbreak investigation, disease surveillance, and management. Because norovirus is not cultivable and has a highly diversified and variable genome, it is difficult to develop diagnostic assays. Detection methods have evolved from electron microscopy to conventional end-point reverse transcription polymerase chain reaction (RT-PCR), immunoassay, real-time RT-PCR, other molecular technologies, and nanotechnology array-based assays. The status and features of various testing methods are summarized in this review.
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Affiliation(s)
- Xiaoli Pang
- Provincial Laboratory for Public Health, Walter Mackenzie Health Sciences Centre, University of Alberta Hospital, 8440 - 112 Street, Edmonton, Alberta T6G 2J2, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, 8440-112 Street, Edmonton, Alberta T6G 2B7, Canada.
| | - Bonita E Lee
- Department of Pediatrics, University of Alberta, 11405, 87 Avenue, Edmonton, Alberta T6G 1C9, Canada
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10
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Abstract
Norovirus, an RNA virus of the family Caliciviridae, is a human enteric pathogen that causes substantial morbidity across both health care and community settings. Several factors enhance the transmissibility of norovirus, including the small inoculum required to produce infection (<100 viral particles), prolonged viral shedding, and its ability to survive in the environment. In this review, we describe the basic virology and immunology of noroviruses, the clinical disease resulting from infection and its diagnosis and management, as well as host and pathogen factors that complicate vaccine development. Additionally, we discuss overall epidemiology, infection control strategies, and global reporting efforts aimed at controlling this worldwide cause of acute gastroenteritis. Prompt implementation of infection control measures remains the mainstay of norovirus outbreak management.
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Affiliation(s)
- Elizabeth Robilotti
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Stan Deresinski
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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11
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Luo J, Xu Z, Nie K, Ding X, Guan L, Wang J, Xian Y, Wu X, Ma X. Visual detection of norovirus genogroup II by reverse transcription loop-mediated isothermal amplification with hydroxynaphthol blue dye. FOOD AND ENVIRONMENTAL VIROLOGY 2014; 6:196-201. [PMID: 24752892 DOI: 10.1007/s12560-014-9142-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 04/04/2014] [Indexed: 06/03/2023]
Abstract
A simple, rapid, specific, and sensitive colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay with hydroxynaphthol blue dye (HNB) was established, targeting RNA-dependent RNA polymerase and capsid protein gene for the detection of the dominant norovirus genogroup in China-NoV GII. The assay was carried out at 65 °C for 60 min with no cross-reactivity with other common gastroenteritis viruses. The sensitivity of this assay was 10(3) copies per reaction which is equivalent to the conventional RT-PCR test. The clinical test showed 94.83% coincidence rate for NoV genogroup II detection compared with the results, confirmed by the Department of Viral Diarrhea of Chinese Center for Disease Control and Prevention via conventional RT-PCR. The HNB dye-based RT-LAMP could be a novel rapid screening method for prevalent norovirus genogroup II in China, especially in those resource-limited hospitals and rural local clinics.
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Affiliation(s)
- Jianming Luo
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing, 102206, China
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12
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Evaluation of the TRCRtest NV-W for norovirus detection in stools by the Transcription-Reverse Transcription Concerted method. J Virol Methods 2013; 193:620-6. [DOI: 10.1016/j.jviromet.2013.07.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 07/11/2013] [Accepted: 07/18/2013] [Indexed: 11/20/2022]
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Dicaprio E, Ma Y, Hughes J, Li J. Epidemiology, prevention, and control of the number one foodborne illness: human norovirus. Infect Dis Clin North Am 2013; 27:651-74. [PMID: 24011835 PMCID: PMC7126578 DOI: 10.1016/j.idc.2013.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Erin Dicaprio
- Department of Food Science and Technology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, 110 Parker Food Science and Technology Building, 2015 Fyffe Road, Columbus, OH 43210, USA
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Kirby A, Iturriza-Gómara M. Norovirus diagnostics: options, applications and interpretations. Expert Rev Anti Infect Ther 2012; 10:423-33. [PMID: 22512752 DOI: 10.1586/eri.12.21] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Noroviruses are a frequent cause of both acute gastroenteritis and outbreaks of gastroenteritis. Infection is usually self-limiting although it has been associated with mortality in children in the developing world and in vulnerable groups such as immunodeficient or immunosuppressed and elderly patients elsewhere. Diagnostic tests may be useful in preventing or limiting the spread and duration of outbreaks, and are needed to define norovirus-associated morbidity and mortality. However, the interpretation of test results should take account of the limitations of the different tests currently available. Therefore, the clinical, immunological and molecular tests available for norovirus detection have been reviewed. Early recognition of cases (clinical diagnoses) together with confirmation by sensitive and specific laboratory tests may contribute to reducing the spread of norovirus within hospitals. Syndromic testing that includes multiple or multiplex assays for the detection of viral, bacterial and parasitic pathogens with the inclusion of control groups are likely to better define norovirus-associated morbidity and mortality in low- and middle-income countries.
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Affiliation(s)
- Andrew Kirby
- Department of Clinical Infection, Microbiology & Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
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Medici MC, Tummolo F, Albonetti V, Abelli LA, Chezzi C, Calderaro A. Molecular detection and epidemiology of astrovirus, bocavirus, and sapovirus in Italian children admitted to hospital with acute gastroenteritis, 2008-2009. J Med Virol 2012; 84:643-50. [PMID: 22337304 DOI: 10.1002/jmv.23231] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Although a number of enteric viruses have been identified in children with acute gastroenteritis, the majority of cases of gastroenteritis remain undiagnosed. In order to provide more insights into the epidemiology of enteric viruses that are not included usually in routine diagnostic tests, cases of childhood sporadic gastroenteritis of unknown etiology requiring hospital admission in Parma, Italy, during 2008-2009, were screened for astrovirus (AstV), sapovirus (SaV), and bocavirus (BoV). The stools of 712 children, negative for rotavirus, norovirus, adenovirus, enterovirus, and reovirus, were examined by PCR or RT-PCR for AstV, BoV, and SaV. The prevalence of AstV, BoV, and SaV in the patients examined was 2.1%, 3.2%, 2.4%, respectively, with the viruses being detected mostly in children <3 years of age. AstV strains were characterized by sequencing as types 1, 2, and 4, with a AstV-1 peak occurring in the 2008 fall-winter season. BoV strains were characterized as types 1, 2, and 3, with BoV-3 circulating more frequently in the 2008 autumn and winter season and BoV-2 during March-April 2009. The most common SaVs were GI.2 and GII.1 while GIV and GV SaVs were detected sporadically. Overall, AstV, BoV, and SaV infections accounted for 7.7% of the sporadic cases of acute gastroenteritis with unknown etiology selected for the study. Different virus types and lineages were found to circulate and temporal peaks of virus activity were also demonstrated, suggesting either small clusters of infections or small outbreaks or epidemics in local population.
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Affiliation(s)
- Maria Cristina Medici
- Section of Microbiology, Department of Pathology and Laboratory Medicine, University Medical School, Parma, Italy.
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Yu ACH, Vatcher G, Yue X, Dong Y, Li MH, Tam PHK, Tsang PYL, Wong AKY, Hui MHK, Yang B, Tang H, Lau LT. Nucleic acid-based diagnostics for infectious diseases in public health affairs. Front Med 2012; 6:173-86. [PMID: 22660977 PMCID: PMC7088663 DOI: 10.1007/s11684-012-0195-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 03/03/2012] [Indexed: 11/29/2022]
Abstract
Infectious diseases, mostly caused by bacteria and viruses but also a result of fungal and parasitic infection, have been one of the most important public health concerns throughout human history. The first step in combating these pathogens is to get a timely and accurate diagnosis at an affordable cost. Many kinds of diagnostics have been developed, such as pathogen culture, biochemical tests and serological tests, to help detect and fight against the causative agents of diseases. However, these diagnostic tests are generally unsatisfactory because they are not particularly sensitive and specific and are unable to deliver speedy results. Nucleic acid-based diagnostics, detecting pathogens through the identification of their genomic sequences, have shown promise to overcome the above limitations and become more widely adopted in clinical tests. Here we review some of the most popular nucleic acid-based diagnostics and focus on their adaptability and applicability to routine clinical usage. We also compare and contrast the characteristics of different types of nucleic acid-based diagnostics.
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Affiliation(s)
- Albert Cheung-Hoi Yu
- Neuroscience Research Institute, Department of Neurobiology, School of Basic Medical Sciences, Key Laboratory for Neuroscience, Peking University, Beijing, 100191, China.
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Huang J, Sun Y, Liu Y, Xiao H, Zhuang S. Development of a loop-mediated isothermal amplification method for rapid detection of caprine arthritis-encephalitis virus proviral DNA. Arch Virol 2012; 157:1463-9. [PMID: 22566005 DOI: 10.1007/s00705-012-1322-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/22/2012] [Indexed: 11/26/2022]
Abstract
A rapid detection assay based on loop-mediated isothermal amplification (LAMP) has been developed for detecting caprine arthritis-encephalitis (CAEV) proviral DNA. The LAMP assay utilized a set of five primers designed against highly conserved sequences located within the p25 gene region. The assay successfully detected CAEV proviral DNA in total DNA extracts originating from cell culture, whole blood samples and separated PBMCs. There was no cross-reaction with the negative control. Amplification was monitored using a Loopamp real-time turbidimeter; turbidity and the corresponding time were recorded. Amplification from CAEV-Shanxi DNA was detected as early as 17 min, with a maximum sensitivity of 0.0001 TCID(50), reached at 32 min. Sixty-eight animal blood samples were tested using AGID, PCR and LAMP assay, and the positive rates were 30.9 %, 33.8 % and 47.1 %, respectively. Whole blood can be used directly, eliminating the need for separation of PBMCs and nucleic acid extraction, reducing the overall procedure time to approximately 80 min. Therefore, the LAMP assay provides a specific and sensitive means for detecting CAEV proviral DNA in a simple, fast, and cost-effective manner and should be useful in eradication programs and epidemiological studies. Furthermore, the LAMP assay can be performed in less-well-equipped laboratories as well as in the field.
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Affiliation(s)
- Jinhai Huang
- School of Chemical engineering & Technology, Tianjin University, Nankai District, Tianjin 300072, China.
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Wang X, Zhu JP, Zhang Q, Xu ZG, Zhang F, Zhao ZH, Zheng WZ, Zheng LS. Detection of enterovirus 71 using reverse transcription loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 2012; 179:330-4. [DOI: 10.1016/j.jviromet.2011.11.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 11/15/2011] [Accepted: 11/22/2011] [Indexed: 11/28/2022]
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19
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Xia JF, Yan XF, Yu H, Qu D, Long JE. Simple and rapid detection of human enterovirus 71 by reverse-transcription and loop-mediated isothermal amplification: cryopreservation affected the detection ability. Diagn Microbiol Infect Dis 2011; 71:244-51. [PMID: 21899976 PMCID: PMC7127202 DOI: 10.1016/j.diagmicrobio.2011.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 07/16/2011] [Accepted: 07/26/2011] [Indexed: 11/25/2022]
Abstract
Human enterovirus 71 (EV71) is the primary pathogen of hand, foot, and mouth disease (HFMD). EV71 infection may lead to neurologic damage, with higher incidence of fatality compared with other HFMD pathogens. An effective drug or vaccine against EV71 infection is currently unavailable. It is desirable to determine the pathogen of HFMD accurately and quickly for early treatment. In the current study, reverse-transcription and loop-mediated isothermal amplification (RT-LAMP) technology were developed to detect EV71. The efficacy of detecting EV71 was compared with regular nested reverse-transcription polymerase chain reaction (RT-PCR). After detecting 108 clinical specimens, results showed that RT-LAMP can specifically detect EV71, but not Coxsackie virus A16, and exhibited a specificity of 100% and a sensitivity of 97.1%, which was higher than regular RT-PCR. The findings indicate that RT-LAMP is a practical method for EV71 diagnostic applications, particularly in small county institutes of medical service. The detection ability of RT-LAMP was significantly affected by cryopreservation as the clinical specimens were repeatedly subject to freezing and thawing treatments.
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Affiliation(s)
- Ju-Feng Xia
- Department of Medical Microbiology and Parasitology, Laboratory of Medical Microbiology, Shang Medical College of Fudan University, Shanghai 200032, PR China
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Paschke C, Apelt N, Fleischmann E, Perona P, Walentiny C, Löscher T, Herbinger KH. Controlled study on enteropathogens in travellers returning from the tropics with and without diarrhoea. Clin Microbiol Infect 2011; 17:1194-200. [DOI: 10.1111/j.1469-0691.2010.03414.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Molecular Diagnosis of Gastrointestinal Infections. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Tonelli A, Tedeschi T, Germini A, Sforza S, Corradini R, Medici MC, Chezzi C, Marchelli R. Real time RNA transcription monitoring by Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes: norovirus detection. MOLECULAR BIOSYSTEMS 2011; 7:1684-92. [PMID: 21399831 DOI: 10.1039/c0mb00353k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes have been reported as a valuable strategy for DNA analysis; however, no investigations targeting RNA molecules and no comparisons between different derivatization approaches have been reported so far. In this work, two TO-conjugated PNAs for genogroup II noroviruses (NoV GII) detection were designed and synthesized. Both the probes target the most conserved stretch of nucleotides identified in the open reading frame 1-2 (ORF1-ORF2) junction region and differ for the dye conjugation strategy: one PNA is end-labelled with the TO molecule tethered by a linker; the other probe bears the TO molecule directly linked to the PNA backbone, replacing a conventional nucleobase. The spectroscopic properties of the two PNA probes were studied and their applicability to NoVs detection, using an isothermal assay, was investigated. Both probes showed good specificity and high fluorescence enhancement upon hybridization, especially targeting RNA molecules. Moreover, the two probes were successfully employed for NoVs detection from stool specimens in an isothermal-based amplification assay targeting RNA 'amplicons'. The probes showed to be specific even in the presence of high concentrations of non-target RNA.
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Affiliation(s)
- Alessandro Tonelli
- Department of Organic and Industrial Chemistry, University of Parma, Vle GP Usberti 17/A, 43124 Parma, Italy
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Butot S, Le Guyader FS, Krol J, Putallaz T, Amoroso R, Sánchez G. Evaluation of various real-time RT-PCR assays for the detection and quantitation of human norovirus. J Virol Methods 2010; 167:90-4. [DOI: 10.1016/j.jviromet.2010.03.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 03/12/2010] [Accepted: 03/22/2010] [Indexed: 10/19/2022]
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Yoda T, Suzuki Y, Yamazaki K, Sakon N, Kanki M, Kase T, Takahashi K, Inoue K. Application of a modified loop-mediated isothermal amplification kit for detecting Norovirus genogroups I and II. J Med Virol 2010; 81:2072-8. [PMID: 19856470 PMCID: PMC7166440 DOI: 10.1002/jmv.21626] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Norovirus is a major etiologic agent in worldwide outbreaks of gastroenteritis associated with food as well as person‐to‐person transmission. The ubiquitous nature of Norovirus necessitates simple and rapid detection methods with high accuracy and sensitivity. To this end, several investigators have evaluated the usefulness of commercial reverse‐transcription loop‐mediated isothermal amplification (RT‐LAMP) kits for detecting Norovirus genogroups I (GI) and II (GII). In previous studies, the conventional Loopamp kit for Norovirus GII showed a relatively high detection rate, while that for Norovirus GI showed a relatively low detection rate. In the present study, clinical Norovirus specimens were used to compare the detection rate of a modified Loopamp kit for Norovirus GI with the rates of the conventional Loopamp kit for Norovirus GI and an “in‐house” RT‐LAMP GI primer set, methods which had a high detection rate. Results from the present study showed that the modified Loopamp kit for Norovirus GI had a higher detection rate for two viral genotypes (GI.3, GI.11). On comparison with an “in‐house” GII primer set using genotype GII.4 viruses circulating recently, the detection rate by the Loopamp kit for Norovirus GII was found to be higher, with a 98% detection rate. These results indicate the applicability of the modified LAMP kit for GI and the conventional LAMP kit for GII for detection of Noroviruses in clinical samples. J. Med. Virol. 81:2072–2078, 2009. © 2009 Wiley‐Liss, Inc.
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Affiliation(s)
- Tomoko Yoda
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka, Japan.
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Abstract
Noroviruses are a major cause of epidemic gastroenteritis in children and adults, and GII.4 has been the predominant genotype since its first documented occurrence in 1987. This study examined the evolutionary dynamics of GII.4 noroviruses over more than three decades to investigate possible mechanisms by which these viruses have emerged to become predominant. Stool samples (n = 5,424) from children hospitalized at the Children's Hospital in Washington, DC, between 1974 and 1991 were screened for the presence of noroviruses by a custom multiplex real-time reverse transcription-PCR. The complete genome sequences of five GII.4 noroviruses (three of which predate 1987 by more than a decade) in this archival collection were determined and compared to the sequences of contemporary strains. Evolutionary analysis determined that the GII.4 VP1 capsid gene evolved at a rate of 4.3 x 10(-3) nucleotide substitutions/site/year. Only six sites in the VP1 capsid protein were found to evolve under positive selection, most of them located in the shell domain. No unique mutations were observed in or around the two histoblood group antigen (HBGA) binding sites in the P region, indicating that this site has been conserved since the 1970s. The VP1 proteins from the 1974 to 1977 noroviruses contained a unique sequence of four consecutive amino acids in the P2 region, which formed an exposed protrusion on the modeled capsid structure. This protrusion and other observed sequence variations did not affect the HBGA binding profiles of recombinant virus-like particles derived from representative 1974 and 1977 noroviruses compared with more recent noroviruses. Our analysis of archival GII.4 norovirus strains suggests that this genotype has been circulating for more than three decades and provides new ancestral strain sequences for the analysis of GII.4 evolution.
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Mori Y, Notomi T. Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases. J Infect Chemother 2009; 15:62-9. [PMID: 19396514 PMCID: PMC7087713 DOI: 10.1007/s10156-009-0669-9] [Citation(s) in RCA: 689] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Indexed: 11/27/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an established nucleic acid amplification method offering rapid, accurate, and cost-effective diagnosis of infectious diseases. This technology has been developed into commercially available detection kits for a variety of pathogens including bacteria and viruses. The current focus on LAMP methodology is as a diagnostic system to be employed in resource-limited laboratories in developing countries, where many fatal tropical diseases are endemic. The combination of LAMP and novel microfluidic technologies such as Lab-on-a-chip may facilitate the realization of genetic point-of-care testing systems to be used by both developed and developing countries in the near future. This review will describe the historical, current, and future developments of such technologies.
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Affiliation(s)
- Yasuyoshi Mori
- Biochemical Research Laboratory, Research and Development Division, Eiken Chemical Co., Ltd., 1381-3 Shimoishigami, Ohtawara, Tochigi, 324-0036, Japan.
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