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Fischer TK, Rasmussen LD, Fonager J. Taking gastro-surveillance into the 21st century. J Clin Virol 2019; 117:43-48. [PMID: 31176211 DOI: 10.1016/j.jcv.2019.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/20/2019] [Accepted: 05/30/2019] [Indexed: 01/04/2023]
Abstract
Enteric viruses, particularly rotaviruses and noroviruses, are leading causes of gastroenteritis worldwide. Human rotaviruses are ubiquitous and globally almost every child has been infected by 3-5 years of age. Noroviruses affect people of all ages and is the leading cause of foodborne outbreaks. Rota- and noroviruses account for ˜40% and ˜17% of diarrhea-associated hospitalizations, and ˜200,000 deaths annually respectively, with most deaths occurring in developing countries. Two rotavirus vaccines have currently been implemented in ˜95 countries and several norovirus vaccine candidates are currently in development and/or clinical testing. Surveillance of enteric viruses is an important part of outbreak investigations as well as pre- and post-vaccine impact studies but is even in developed countries often limited to investigation of sporadic cases or comprehensive outbreaks. Conventional methods for enteric virus detection and subtyping relies on standard RT-PCR methods, supplemented with Sanger-sequencing. However, for viruses with even moderate mutationrates, PCR-based-typing of only limited parts of the virus genome is challenging and requires regular update of primers. Full-genomecharacterization technologies based on sequence independent methods based on next generation sequencing (NGS), have demonstrated great potential for enteric virus detection and/or typing in both clinical and environmental samples. However, cost-benefits must balance for such methods to be widely accepted for public health purposes. In Europe as also globally, routine use of NGS-methods for surveillance of enteric viruses is currently limited to few national public health laboratories. What important lessons can be learned from these and what is the future of NGS-based surveillance?
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Affiliation(s)
- Thea K Fischer
- Department of Clinical Research, Nordsjaellands Hospital, Hilleroed, Denmark; Departments of Infectious Diseases and Global Health, Clinical Institute, University of Southern Denmark, Denmark; National Virus Surveillance and WHO Reference Laboratories, Dept of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark.
| | - Lasse D Rasmussen
- National Virus Surveillance and WHO Reference Laboratories, Dept of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus Research & Development Laboratory, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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2
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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: 79] [Impact Index Per Article: 13.2] [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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Yaren O, Bradley KM, Moussatche P, Hoshika S, Yang Z, Zhu S, Karst SM, Benner SA. A norovirus detection architecture based on isothermal amplification and expanded genetic systems. J Virol Methods 2016; 237:64-71. [PMID: 27546345 DOI: 10.1016/j.jviromet.2016.08.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/17/2016] [Accepted: 08/18/2016] [Indexed: 01/15/2023]
Abstract
Noroviruses are the major cause of global viral gastroenteritis with short incubation times and small inoculums required for infection. This creates a need for a rapid molecular test for norovirus for early diagnosis, in the hope of preventing the spread of the disease. Non-chemists generally use off-the shelf reagents and natural DNA to create such tests, suffering from background noise that comes from adventitious DNA and RNA (collectively xNA) that is abundant in real biological samples, especially feces, a common location for norovirus. Here, we create an assay that combines artificially expanded genetic information systems (AEGIS, which adds nucleotides to the four in standard xNA, pairing orthogonally to A:T and G:C) with loop-mediated isothermal amplification (LAMP) to amplify norovirus RNA at constant temperatures, without the power or instrument requirements of PCR cycling. This assay was then validated using feces contaminated with murine norovirus (MNV). Treating stool samples with ammonia extracts the MNV RNA, which is then amplified in an AEGIS-RT-LAMP where AEGIS segments are incorporated both into an internal LAMP primer and into a molecular beacon stem, the second lowering background signaling noise. This is coupled with RNase H nicking during sample amplification, allowing detection of as few as 10 copies of noroviral RNA in a stool sample, generating a fluorescent signal visible to human eye, all in a closed reaction vessel.
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Affiliation(s)
- Ozlem Yaren
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, # 7, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, # 7, Alachua, FL 32615, USA
| | - Patricia Moussatche
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, # 17, Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, # 7, Alachua, FL 32615, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, # 7, Alachua, FL 32615, USA
| | - Shu Zhu
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville FL 32611, USA; The Emerging Pathogens Institute, University of Florida, Gainesville FL 32611, USA
| | - Stephanie M Karst
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville FL 32611, USA; The Emerging Pathogens Institute, University of Florida, Gainesville FL 32611, USA
| | - Steven A Benner
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, # 17, Alachua, FL 32615, USA.
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4
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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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Yoda T, Suzuki Y, Aoyama I, Yamazaki K, Nakata S, Takahashi K. No crucial amino acid changes in the predicted histo blood group antigen-binding sites of norovirus genotype GII.4 capsid between non-secretors and secretors origin might suggest an alternative route of infection or existence of coincidental molecules. J Med Microbiol 2015; 64:1544-1547. [PMID: 26432289 DOI: 10.1099/jmm.0.000178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tomoko Yoda
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka City, Japan
| | - Yasuhiko Suzuki
- Hokkaido University Research Center for Zoononsis Control and Hokkaido University, Global Station for Zoonosis, Sapporo, Japan
| | - Ikuko Aoyama
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka City, Japan
| | - Kenji Yamazaki
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka City, Japan
| | - Shuji Nakata
- Nakata Pediatric Clinic, Shiraishi medical building 2F, Nangoudoori 1-1-1, Shiraishi-ku, Sapporo, Japan 003-0023
| | - Kazuo Takahashi
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Nakamichi 1-3-69, Higashinari-ku, Osaka City, Japan
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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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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: 15] [Impact Index Per Article: 1.5] [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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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: 23] [Impact Index Per Article: 2.1] [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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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: 13] [Impact Index Per Article: 1.0] [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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