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König KMK, Jahun AS, Nayak K, Drumright LN, Zilbauer M, Goodfellow I, Hosmillo M. Design, development, and validation of a strand-specific RT-qPCR assay for GI and GII human Noroviruses. Wellcome Open Res 2021; 6:245. [PMID: 34708158 PMCID: PMC8506223 DOI: 10.12688/wellcomeopenres.17078.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2021] [Indexed: 11/20/2022] Open
Abstract
Human noroviruses (HuNoV) are the major cause of viral gastroenteritis worldwide. Similar to other positive-sense single-stranded RNA viruses, norovirus RNA replication requires the formation of a negative strand RNA intermediate. Methods for detecting and quantifying the viral positive or negative sense RNA in infected cells and tissues can be used as important tools in dissecting virus replication. In this study, we have established a sensitive and strand-specific Taqman-based quantitative polymerase chain reaction (qPCR) assay for both genogroups GI and GII HuNoV. This assay shows good reproducibility, has a broad dynamic range and is able to detect a diverse range of isolates. We used tagged primers containing a non-viral sequence for the reverse transcription (RT) reaction and targeted this tag in the succeeding qPCR reaction to achieve strand specificity. The specificity of the assay was confirmed by the detection of specific viral RNA strands in the presence of high levels of the opposing strands, in both RT and qPCR reactions. Finally, we further validated the assay in norovirus replicon-bearing cell lines and norovirus-infected human small intestinal organoids, in the presence or absence of small-molecule inhibitors. Overall, we have established a strand-specific qPCR assay that can be used as a reliable method to understand the molecular details of the human norovirus life cycle.
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Affiliation(s)
- Katja Marie Kjara König
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- Insitute of Chemistry and Metabolomics, Center for Structural and Cell Biology in Medicine (CSCM), University of Lübeck, Lübeck, Germany
| | - Aminu S. Jahun
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Komal Nayak
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Lydia N. Drumright
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
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Larivé O, Brandani J, Dubey M, Kohn T. An integrated cell culture reverse transcriptase quantitative PCR (ICC-RTqPCR) method to simultaneously quantify the infectious concentrations of eight environmentally relevant enterovirus serotypes. J Virol Methods 2021; 296:114225. [PMID: 34216645 DOI: 10.1016/j.jviromet.2021.114225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/27/2022]
Abstract
Enterovirus (EV) infectivity is typically measured as a bulk parameter, yet EV serotypes vary in their susceptibility to natural and engineered stressors. Here we developed an integrated cell culture reverse transcriptase quantitative PCR (ICC-RTqPCR) method to simultaneously and specifically quantify the infectious concentrations of eight EV serotypes commonly encountered in sewage (coxsackieviruses A9, B1, B2, B3, B4 and B5, and echoviruses 25 and 30). The method uses two cell lines for virus replication and serotype-specific qPCR primers for quantification. Primers were designed to target multiple environmental strains of a given serotype and displayed high specificity. The ICC-RTqPCR method exhibited a linear calibration range between 50 and 1000 (echoviruses) or 5000 (coxsackieviruses) infectious units per mL. Over this range, measurements were not influenced by the presence of non-target serotypes, and calibration slopes were reproducible for different virus batches and cell ages. The ICC-RTqPCR method was able to accurately quantify the infectious concentration of a virus after inactivation by heat, and the concentration of a virus within a wastewater matrix. This method will be valuable to assess the differing fates of EV serotypes in natural or engineered systems, and to portray the associated changes in EV population composition.
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Affiliation(s)
- Odile Larivé
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Jade Brandani
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Manupriyam Dubey
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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Sano D, Watanabe R, Oishi W, Amarasiri M, Kitajima M, Okabe S. Viral Interference as a Factor of False-Negative in the Infectious Adenovirus Detection Using Integrated Cell Culture-PCR with a BGM Cell Line. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:84-92. [PMID: 33392927 DOI: 10.1007/s12560-020-09453-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
This study investigated the influence of viral interference on the detection of enteric viruses using the integrated cell culture (ICC)-PCR with a BGM cell line. It was possible to detect 102 plaque-forming units (PFU)/flask of enterovirus 71 (EV71) in spite of the presence of 104 PFU/flask of adenovirus 40 (AdV40). Meanwhile, 104 PFU/flask of AdV40 was not detected in the presence of 102 PFU/flask of EV71. This inhibition of AdV40 detection using ICC-PCR was attributable to the growth of EV71, because the addition of a growth inhibitor of EV71 (rupintrivir) neutralized the detection inhibition of AdV40. The growth inhibition of AdV40 under co-infection with EV71 is probably caused by the immune responses of EV71-infected cells. AdV is frequently used as a fecal contamination indicator of environmental water, but this study demonstrated that false-negative detection of infectious AdV using ICC-PCR could be caused by the co-existence of infectious EV in a water sample. The addition of rupintrivir could prevent false-negative detection of AdV using ICC-PCR. This study, therefore, emphasizes the importance of confirming the presence of multiple enteric viruses in a sample derived from environmental water prior to the application of ICC-PCR because the viral interference phenomenon may lead to the false-negative detection of target viruses.
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Affiliation(s)
- Daisuke Sano
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
| | - Ryosuke Watanabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Wakana Oishi
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Mohan Amarasiri
- Department of Health Science, School of Allied Health Sciences, Kitasato University, A1-505, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa, 252-0373, Japan
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
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Di Cola G, Fantilli AC, Pisano MB, Ré VE. Foodborne transmission of hepatitis A and hepatitis E viruses: A literature review. Int J Food Microbiol 2021; 338:108986. [PMID: 33257099 DOI: 10.1016/j.ijfoodmicro.2020.108986] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022]
Abstract
Foodborne viruses have been recognized as a growing concern to the food industry and a serious public health problem. Hepatitis A virus (HAV) is responsible for the majority of viral outbreaks of food origin worldwide, while hepatitis E virus (HEV) has also been gaining prominence as a foodborne viral agent in the last years, due to its zoonotic transmission through the consumption of uncooked or undercooked infected meat or derivatives. However, there is a lack of scientific reports that gather all the updated information about HAV and HEV as foodborne viruses. A search of all scientific articles about HAV and HEV in food until March 2020 was carried out, using the keywords "HAV", "HEV", "foodborne", "outbreak" and "detection in food". Foodborne outbreaks due to HAV have been reported since 1956, mainly in the USA, and in Europe in recent years, where the number of outbreaks has been increasing throughout time, and nowadays it has become the continent with the highest foodborne HAV outbreak report. Investigation and detection of HAV in food is more recent, and the first detections were performed in the 1990s decade, most of them carried out on seafood, first, and frozen food, later. On the other hand, HEV has been mainly looked for and detected in food derived from reservoir animals, such as meat, sausages and pate of pigs and wild boars. For this virus, only isolated cases and small outbreaks of foodborne transmission have been recorded, most of them in industrialized countries, due to HEV genotype 3 or 4. Virus detection in food matrices requires special processing of the food matrix, followed by RNA detection by molecular techniques. For HAV, a real-time PCR has been agreed as the standard method for virus detection in food; in the case of HEV, a consensus assay for its detection in food has not been reached yet. Our investigation shows that there is still little data about HAV and HEV prevalence and frequency of contamination in food, prevalent viral strains, and sources of contamination, mainly in developing countries, where there is no research and legislation in this regard. Studies on these issues are needed to get a better understanding of foodborne viruses, their maintenance and their potential to cause diseases.
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Affiliation(s)
- Guadalupe Di Cola
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gomez s/n, CP: 5016 Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - Anabella C Fantilli
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gomez s/n, CP: 5016 Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - María Belén Pisano
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gomez s/n, CP: 5016 Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Viviana E Ré
- Instituto de Virología "Dr. J. M. Vanella", Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Enfermera Gordillo Gomez s/n, CP: 5016 Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
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Zhang Y, Qu S, Xu L. Progress in the study of virus detection methods: The possibility of alternative methods to validate virus inactivation. Biotechnol Bioeng 2019; 116:2095-2102. [PMID: 31038205 DOI: 10.1002/bit.27003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/21/2019] [Accepted: 04/25/2019] [Indexed: 11/09/2022]
Abstract
Virus inactivation validation studies have been widely applied in the risk assessment of biogenic material-based medical products, such as biological products, animal tissue-derived biomaterials, and allogeneic biomaterials, to decrease the risk of virus transmission. Traditional virus detection methods in an inactivation validation study utilize cell culture as a tool to quantify the infectious virus by observing cytopathic effects (CPEs) after virus inactivation. However, this is susceptible to subjective factors because CPEs must be observed by experts under a microscope during virus titration. In addition, this method is costly and time- and labor-consuming. Molecular biological technologies such as quantitative polymerase chain reaction (qPCR) have been widely used for virus detection but cannot distinguish infectious and noninfectious viruses. Therefore, qPCR cannot be directly applied to virus inactivation validation studies. In this paper, methods to detect viruses and progress in the challenge of differentiating infectious and noninfectious viruses with the combination of pretreatment and qPCR techniques such as the integrated cell culture-qPCR (ICC-qPCR) method are reviewed. In addition, the advantages and disadvantages of each new method, as well as its prospect in virus inactivation validation studies, are discussed.
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Affiliation(s)
- Yu Zhang
- Institute for Medical Devices Control, National Institutes for Food and Drug Control, Beijing, China.,School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Shuxin Qu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Liming Xu
- Institute for Medical Devices Control, National Institutes for Food and Drug Control, Beijing, China
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Hamza IA, Bibby K. Critical issues in application of molecular methods to environmental virology. J Virol Methods 2019; 266:11-24. [PMID: 30659861 DOI: 10.1016/j.jviromet.2019.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
Abstract
Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines. Real-time polymerase chain reaction (qPCR) screening of viral nucleic acid is routinely used to investigate virus contamination in water due to the high sensitivity and specificity. Additionally, the introduction of metagenomic approaches into environmental virology has facilitated the discovery of viruses that cannot be grown in cell culture. This review (i) highlights the applications of molecular techniques in environmental virology such as PCR and its modifications to overcome the critical issues associated with the inability to discriminate between infectious viruses and nonviable viruses, (ii) outlines the strengths and weaknesses of Nucleic Acid Sequence Based Amplification (NASBA) and microarray, (iii) discusses the role of digital PCR as an emerging water quality monitoring assay and its advantages over qPCR, (iv) addresses the viral metagenomics in terms of detecting emerging viral pathogens and diversity in aquatic environment. Indeed, there are many challenges for selecting methods to detect classic and emerging viruses in environmental samples. While the existing techniques have revealed the importance and diversity of viruses in the water environment, further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Water Pollution Research, National Research Centre, Cairo, Egypt.
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, USA
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7
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Yu JM, Li LL, Xie GC, Zhang CY, Ao YY, Duan ZJ. Experimental infection of Marmota monax with a novel hepatitis A virus. Arch Virol 2018; 163:1187-1193. [PMID: 29387970 DOI: 10.1007/s00705-018-3715-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/11/2017] [Indexed: 11/25/2022]
Abstract
To establish an animal model for the newly identified Marmota Himalayana hepatovirus, MHHAV, so as to develop a better understanding of the infection of hepatitis A viruses. Five experimental woodchucks (Marmota monax) were inoculated intravenously with the purified MHHAV from wild woodchuck feces. One animal injected with PBS was defined as a control. Feces and blood were routinely collected. After the animals were subjected to necropsy, different tissues were collected. The presence of viral RNA and negative sense viral RNA was analyzed in all the samples and histopathological and in situ hybridization analysis was performed for the tissues. MHHAV infection caused fever but no severe symptoms or death. Virus was shed in feces beginning at 2 dpi, and MHHAV RNA persisted in feces for ~2 months, with a biphasic increase, and in blood for ~30 days. Viral RNA was detected in all the tissues, with high levels in the liver and spleen. Negative-strand viral RNA was detected only in the liver. Furthermore, the animals showed histological signs of hepatitis at 45 dpi. MHHAV can infect M. monax and is associated with hepatic disease. Therefore, this animal can be used as a model of HAV pathogenesis and to evaluate antiviral and anticancer therapeutics.
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Affiliation(s)
- Jie-Mei Yu
- National Institute for Viral Disease Control and Prevention, CDC China, Beijing, 100052, China
| | - Li-Li Li
- National Institute for Viral Disease Control and Prevention, CDC China, Beijing, 100052, China
| | - Guang-Cheng Xie
- National Institute for Viral Disease Control and Prevention, CDC China, Beijing, 100052, China
| | - Cui-Yuan Zhang
- National Institute for Viral Disease Control and Prevention, CDC China, Beijing, 100052, China
| | - Yuan-Yun Ao
- National Institute for Viral Disease Control and Prevention, CDC China, Beijing, 100052, China
| | - Zhao-Jun Duan
- National Institute for Viral Disease Control and Prevention, CDC China, Beijing, 100052, China.
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Fikatas A, Dimitriou TG, Kyriakopoulou Z, Moschonas GD, Amoutzias GD, Mossialos D, Gartzonika C, Levidiotou-Stefanou S, Markoulatos P. Detection of negative and positive RNA strand of poliovirus Sabin 1 and echovirus E19 by a stem-loop reverse transcription PCR. Lett Appl Microbiol 2017. [PMID: 28631392 DOI: 10.1111/lam.12766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this report a strand specific RT-PCR was established for the detection of the replicative negative RNA strand of poliovirus sabin 1 (Sabin1) and Echovirus 19 (E19) strains. The key for the successful conduction of the assay was the use of a specific reverse transcription primer targeting the 5'-UTR of enteroviruses that consisted of a stem-loop structure at the 5'-end and an enteroviral-specific sequence at the 3'-end. The stem loop RT-PCR was found to be an accurate and sensitive method, detecting even 10-2 CCID50 of poliovirus sabin 1 (Sabin1) and E19 strains 6 h postinfection (p.i.), while CPE appeared 3 days later. This assay was also validated in SiHa and Caski cell lines that are not used for the detection of enteroviruses. The negative RNA strand was detected 6 h and 12 h p.i. in SiHa and Caski cells, when these cell lines were inoculated with 105 and 1 CCID50 respectively, whereas CPE was observed 5 days p.i for SiHa cells and 8 days p.i for Caski cells and that only at 105 CCID50 . The results show that this approach may be used for replacing the time-consuming cell cultures in order to detect the active replication of enteroviruses. SIGNIFICANCE AND IMPACT OF THE STUDY Enteroviruses are positive stranded RNA viruses that may cause severe diseases. The conventional method for detection of active viral replication involves virus isolation in sensitive cell cultures followed by titration and seroneutralization. In this report, we describe the use of a stem-loop secondary structured oligonucleotide in RT-PCR assay for the detection of the replicative negative strand of the positive-stranded RNA of poliovirus sabin 1 and E19 strains. This approach proved to be a useful tool that may be used for replacing the time-consuming cell culture assays in order to detect the active replication of enteroviruses.
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Affiliation(s)
- A Fikatas
- Microbiology - Virology Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - T G Dimitriou
- Microbiology - Virology Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Z Kyriakopoulou
- Microbiology - Virology Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - G D Moschonas
- Microbiology - Virology Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - G D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - D Mossialos
- Microbiology - Virology Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - C Gartzonika
- Department of Microbiology, Medical School, University of Ioannina, Ioannina, Greece
| | - S Levidiotou-Stefanou
- Department of Microbiology, Medical School, University of Ioannina, Ioannina, Greece
| | - P Markoulatos
- Microbiology - Virology Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
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Lin J, Singh A. Detection of human enteric viruses in Umgeni River, Durban, South Africa. JOURNAL OF WATER AND HEALTH 2015; 13:1098-112. [PMID: 26608771 DOI: 10.2166/wh.2015.238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The prevalence of adenovirus (AdV), rotaviruses (RV) and enteroviruses (EV) in Umgeni River waters of Durban, South Africa was assessed qualitatively and quantitatively during April 2011 to January 2012 using polymerase chain reaction (PCR)/reverse transcription-polymerase chain reaction (RT-PCR), nested PCR and quantitative PCR (qPCR), as well as nested integrated cell culture PCR (nested ICC-PCR). The phylogenetic analysis of the adenovirus and enterovirus amplicons was also performed. The nested PCR results effectively detected the presence of AdV and EV in all water samples. The results of qPCR demonstrated that higher populations of EV and of AdV were widely found in the Umgeni River. Rotavirus could only be detected in the upper Umgeni River, mainly during drier seasons. Nested ICC-PCR further confirmed the presence of infectious AdV and EV particles in 100% of water samples using various cell lines. The present study identifies potential viral hazards of Umgeni River water for domestic water supply and recreational activities.
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Affiliation(s)
- Johnson Lin
- Discipline of Microbiology, School of Life Sciences, University of KwaZulu-Natal (Westville), Private Bag X54001, Durban, South Africa E-mail:
| | - Atheesha Singh
- Discipline of Microbiology, School of Life Sciences, University of KwaZulu-Natal (Westville), Private Bag X54001, Durban, South Africa E-mail:
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Lim SM, Koraka P, Osterhaus ADME, Martina BEE. Development of a strand-specific real-time qRT-PCR for the accurate detection and quantitation of West Nile virus RNA. J Virol Methods 2013; 194:146-53. [PMID: 23965252 DOI: 10.1016/j.jviromet.2013.07.050] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 07/17/2013] [Accepted: 07/22/2013] [Indexed: 01/12/2023]
Abstract
Studying the tropism and replication kinetics of West Nile virus (WNV) in different cell types in vitro and in tissues in animal models is important for understanding its pathogenesis. As detection of the negative strand viral RNA is a more reliable indicator of active replication for single-stranded positive-sense RNA viruses, the specificity of qRT-PCR assays currently used for the detection of WNV positive and negative strand RNA was reassessed. It was shown that self- and falsely-primed cDNA was generated during the reverse transcription step in an assay employing unmodified primers and several reverse transcriptases. As a result, a qRT-PCR assay using the thermostable rTth in combination with tagged primers was developed, which greatly improved strand specificity by circumventing the events of self- and false-priming. The reliability of the assay was then addressed in vitro using BV-2 microglia cells as well as in C57/BL6 mice. It was possible to follow the kinetics of positive and negative-strand RNA synthesis both in vitro and in vivo; however, the sensitivity of the assay will need to be optimized in order to detect and quantify negative-strand RNA synthesis in the very early stages of infection. Overall, the strand-specific qRT-PCR assay developed in this study is an effective tool to quantify WNV RNA, reassess viral replication, and study tropism of WNV in the context of WNV pathogenesis.
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Affiliation(s)
- Stephanie M Lim
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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Rodríguez-Lázaro D, Cook N, Ruggeri FM, Sellwood J, Nasser A, Nascimento MSJ, D'Agostino M, Santos R, Saiz JC, Rzeżutka A, Bosch A, Gironés R, Carducci A, Muscillo M, Kovač K, Diez-Valcarce M, Vantarakis A, von Bonsdorff CH, de Roda Husman AM, Hernández M, van der Poel WHM. Virus hazards from food, water and other contaminated environments. FEMS Microbiol Rev 2011; 36:786-814. [PMID: 22091646 PMCID: PMC7114518 DOI: 10.1111/j.1574-6976.2011.00306.x] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 08/30/2011] [Indexed: 12/11/2022] Open
Abstract
Numerous viruses of human or animal origin can spread in the environment and infect people via water and food, mostly through ingestion and occasionally through skin contact. These viruses are released into the environment by various routes including water run‐offs and aerosols. Furthermore, zoonotic viruses may infect humans exposed to contaminated surface waters. Foodstuffs of animal origin can be contaminated, and their consumption may cause human infection if the viruses are not inactivated during food processing. Molecular epidemiology and surveillance of environmental samples are necessary to elucidate the public health hazards associated with exposure to environmental viruses. Whereas monitoring of viral nucleic acids by PCR methods is relatively straightforward and well documented, detection of infectious virus particles is technically more demanding and not always possible (e.g. human norovirus or hepatitis E virus). The human pathogenic viruses that are most relevant in this context are nonenveloped and belong to the families of the Caliciviridae, Adenoviridae, Hepeviridae, Picornaviridae and Reoviridae. Sampling methods and strategies, first‐choice detection methods and evaluation criteria are reviewed. Virus hazards from food, water and the environment, their reservoirs and routes of transmission; Sampling methods and sampling strategies thereof, including the first choice test methods, and criteria for data evaluation are described.
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Hyeon JY, Chon JW, Park C, Lee JB, Choi IS, Kim MS, Seo KH. Rapid detection method for hepatitis A virus from lettuce by a combination of filtration and integrated cell culture-real-time reverse transcription PCR. J Food Prot 2011; 74:1756-61. [PMID: 22004827 DOI: 10.4315/0362-028x.jfp-11-155] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have developed a rapid and simple method for filtration using a positively charged membrane to concentrate hepatitis A virus (HAV) from lettuce and an integrated cell culture-real-time reverse transcription PCR (ICC-real-time RT-PCR) to detect infectious HAV. The most suitable buffer for HAV concentration by filtration was 100 mM Tris-HCl, 50 mM glycine (pH 9.5). Filtration using the NanoCeram matrix was compared with polyethylene glycol precipitation for viral concentration from lettuce inoculated with 6 log RNA copies of HAV. The recovery rate of filtration was statistically higher than that of polyethylene glycol precipitation (47.3 versus 24.9%, respectively). The sensitivity of ICC-real-time RT-PCR for detection of infectious HAV was determined by inoculation of FRhK-4 cells with HAV (4 log to 0 log RNA copies). ICC-real-time RT-PCR detected infectious HAV on average 5 days earlier than cytopathic effects at all inoculation levels. HAV recovered from lettuce (approximately 3 log RNA copies) was also analyzed with ICC-real-time RT-PCR. Infectious HAV was detected within 2 days postinfection by ICC-real-time RT-PCR, whereas cytopathic effects were not observed until 7 days postinfection. Coupled with a virus concentration and purification system using a positively charged membrane, ICC-real-time RT-PCR has the potential to become a novel and rapid method for the detection of infectious HAV in vegetables.
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Affiliation(s)
- Ji-Yeon Hyeon
- Department of Public Health, College of Veterinary Medicine, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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Hamza IA, Jurzik L, Überla K, Wilhelm M. Methods to detect infectious human enteric viruses in environmental water samples. Int J Hyg Environ Health 2011; 214:424-36. [PMID: 21920815 PMCID: PMC7106513 DOI: 10.1016/j.ijheh.2011.07.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 07/24/2011] [Accepted: 07/28/2011] [Indexed: 02/06/2023]
Abstract
Currently, a wide range of analytical methods is available for virus detection in environmental water samples. Molecular methods such as polymerase chain reaction (PCR) and quantitative real time PCR (qPCR) have the highest sensitivity and specificity to investigate virus contamination in water, so they are the most commonly used in environmental virology. Despite great sensitivity of PCR, the main limitation is the lack of the correlation between the detected viral genome and viral infectivity, which limits conclusions regarding the significance for public health. To provide information about the infectivity of the detected viruses, cultivation on animal cell culture is the gold standard. However, cell culture infectivity assays are laborious, time consuming and costly. Also, not all viruses are able to produce cytopathic effect and viruses such as human noroviruses have no available cell line for propagation. In this brief review, we present a summary and critical evaluation of different approaches that have been recently proposed to overcome limitations of the traditional cell culture assay and PCR assay such as integrated cell culture-PCR, detection of genome integrity, detection of capsid integrity, and measurement of oxidative damages on viral capsid protein. Techniques for rapid detection of infectious viruses such as fluorescence microscopy and automated flow cytometry have also been suggested to assess virus infectivity in water samples.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Hygiene, Social and Environmental Medicine, Ruhr-University Bochum, Germany.
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14
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Pecson BM, Ackermann M, Kohn T. Framework for using quantitative PCR as a nonculture based method to estimate virus infectivity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:2257-63. [PMID: 21322644 DOI: 10.1021/es103488e] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Measuring the efficiency of virus disinfection with quantitative PCR (qPCR) has been criticized as inadequate due to the production of false-positive signals. Such a claim, however, presupposes an understanding of the theoretical qPCR response. Many studies have assumed that the loss in qPCR signal upon disinfection should equal the loss in infectivity, without accounting for the fact that qPCR typically assays only a fraction of the viral genome. This study aimed to develop a theoretical framework to relate viral infectivity with genome damage measured by qPCR. The framework quantified damage to the entire genome based on the qPCR amplification of smaller sections, assuming single-hit inactivation and a Poissonian distribution of damage. The framework was tested and modified using UV(254) inactivation studies with bacteriophage MS2 (culturing and qPCR of approximately half the genome). Genome regions showed heterogeneous sensitivities to UV(254) treatment, thus deviating from the assumption of Poissonian damage. We offered two modifications to account for these deviations and confirmed that the qPCR-based framework accurately estimated virus infectivity. This framework offers the potential to monitor the infectivity of viruses that remain nonculturable (norovirus). While developed for UV(254)-inactivated virus, the framework should apply to any disinfection technique that causes inactivation via single genomic lesions.
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Affiliation(s)
- Brian M Pecson
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Station 2, 1015 Lausanne, Switzerland
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15
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Use of propidium monoazide in reverse transcriptase PCR to distinguish between infectious and noninfectious enteric viruses in water samples. Appl Environ Microbiol 2010; 76:4318-26. [PMID: 20472736 DOI: 10.1128/aem.02800-09] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Human enteric viruses can be present in untreated and inadequately treated drinking water. Molecular methods, such as the reverse transcriptase PCR (RT-PCR), can detect viral genomes in a few hours, but they cannot distinguish between infectious and noninfectious viruses. Since only infectious viruses are a public health concern, methods that not only are rapid but also provide information on the infectivity of viruses are of interest. The intercalating dye propidium monoazide (PMA) has been used for distinguishing between viable and nonviable bacteria with DNA genomes, but it has not been used to distinguish between infectious and noninfectious enteric viruses with RNA genomes. In this study, PMA in conjunction with RT-PCR (PMA-RT-PCR) was used to determine the infectivity of enteric RNA viruses in water. Coxsackievirus, poliovirus, echovirus, and Norwalk virus were rendered noninfectious or inactivated by treatment with heat (72 degrees C, 37 degrees C, and 19 degrees C) or hypochlorite. Infectious or native and noninfectious or inactivated viruses were treated with PMA. This was followed by RNA extraction and RT-PCR or quantitative RT-PCR (qRT-PCR) analysis. The PMA-RT-PCR results indicated that PMA treatment did not interfere with detection of infectious or native viruses but prevented detection of noninfectious or inactivated viruses that were rendered noninfectious or inactivated by treatment at 72 degrees C and 37 degrees C and by hypochlorite treatment. However, PMA-RT-PCR was unable to prevent detection of enteroviruses that were rendered noninfectious by treatment at 19 degrees C. After PMA treatment poliovirus that was rendered noninfectious by treatment at 37 degrees C was undetectable by qRT-PCR, but PMA treatment did not affect detection of Norwalk virus. PMA-RT-PCR was also shown to be effective for detecting infectious poliovirus in the presence of noninfectious virus and in an environmental matrix. We concluded that PMA can be used to differentiate between potentially infectious and noninfectious viruses under the conditions defined above.
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Amado LA, Marchevsky RS, de Paula VS, Hooper C, Freire MDS, Gaspar AMC, Pinto MA. Experimental hepatitis A virus (HAV) infection in cynomolgus monkeys (Macaca fascicularis): evidence of active extrahepatic site of HAV replication. Int J Exp Pathol 2010; 91:87-97. [PMID: 20096073 DOI: 10.1111/j.1365-2613.2009.00699.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
This work studied the replication sites of hepatitis A virus (HAV) in cynomolgus monkeys (Macaca fascicularis) after intravenous inoculation. The cynomolgus monkeys were inoculated with the Brazilian hepatitis A virus strain (HAF-203). Monkeys were euthanized on days 15, 30, 45 and 60 postinoculation (pi). Liver samples, submandibular salivary gland, mesenteric lymph node and tonsils were removed for virological and pathological evaluation. Immunofluorescence analyses on liver and salivary gland sections using confocal laser scanning microscopy revealed the presence of HAV antigen (HAV Ag). The presence of HAV genome was monitored by real-time PCR. The HAV RNA was detected at 7 days postinoculation (dpi), concomitantly in serum, saliva and faeces. The highest HAV viral load was observed in faeces at 15 dpi (10(5) copies/ml), followed by serum viral load of 10(4) copies/ml at 20 dpi and saliva viral load of 10(3 )copies/ml at 7 dpi. The animals showed first histological and biochemical signs of hepatitis at 15 dpi. The HAV antigen (Ag) was present from day 7 until day 60 pi in the liver and salivary glands. The HAV replicative intermediate was also detected in the liver (4.5 x 10(4) copies/mg), salivary glands (1.9 x 10(3) copies/mg), tonsils (4.2 x 10(1) copies/mg) and lymph nodes (3.4 x 10(1) copies/mg). Our data demonstrated that the salivary gland as an extrahepatic site of early HAV replication could create a potential risk of saliva transmitted infection. In addition, the cynomolgus monkey was confirmed as a suitable model to study the pathogenesis of HAV human infection.
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Affiliation(s)
- Luciane A Amado
- Laboratório de Desenvolvimento Tecnológico em Virologia, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil.
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Lambertini E, Spencer SK, Bertz PD, Loge FJ, Borchardt MA. New mathematical approaches to quantify human infectious viruses from environmental media using integrated cell culture-qPCR. J Virol Methods 2009; 163:244-52. [PMID: 19835913 DOI: 10.1016/j.jviromet.2009.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 09/28/2009] [Accepted: 10/06/2009] [Indexed: 10/20/2022]
Abstract
Quantifying infectious viruses by cell culture depends on visualizing cytopathic effect, or for integrated cell culture-PCR, attaining confidence a PCR-positive signal is the result of virus growth and not inoculum carryover. This study developed mathematical methods to calculate infectious virus numbers based on viral growth kinetics in cell culture. Poliovirus was inoculated into BGM cell monolayers at 10 concentrations from 0.001 to 1000 PFU/ml. Copy numbers of negative-strand RNA, a marker of infectivity for single-stranded positive RNA viruses, were measured over time by qRT-PCR. Growth data were analyzed by two approaches. First, data were fit with a continuous function to estimate directly the initial virus number, expressed as genomic copies. Such estimates correlated with actual inoculum numbers across all concentrations (R(2)=0.62, n=17). Second, the length of lag phase appeared to vary inversely with inoculum titers; hence, standard curves to predict inoculum virus numbers were derived based on three definitions of lag time: (1) time of first detection of (-)RNA, (2) second derivative maximum of the fitted continuous function, and (3) time when the fitted curve crossed a threshold (-)RNA concentration. All three proxies yielded standard curves with R(2)=0.69-0.90 (n=17). The primary advantage of these growth kinetics approaches is being able to quantify virions that are unambiguously infectious, a particular advantage for viruses that do not produce CPE.
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Affiliation(s)
- E Lambertini
- Department of Civil and Environmental Engineering, University of California-Davis, 1 Shields Avenue, Davis, CA 95616, United States.
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18
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Boncristiani HF, Rossi RD, Criado MF, Furtado FM, Arruda E. Magnetic purification of biotinylated cDNA removes false priming and ensures strand-specificity of RT-PCR for enteroviral RNAs. J Virol Methods 2009; 161:147-53. [DOI: 10.1016/j.jviromet.2009.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 06/01/2009] [Accepted: 06/04/2009] [Indexed: 10/20/2022]
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Quantitative PCR for determining the infectivity of bacteriophage MS2 upon inactivation by heat, UV-B radiation, and singlet oxygen: advantages and limitations of an enzymatic treatment to reduce false-positive results. Appl Environ Microbiol 2009; 75:5544-54. [PMID: 19592538 DOI: 10.1128/aem.00425-09] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Health risks posed by waterborne viruses are difficult to assess because it is tedious or impossible to determine the infectivity of many viruses. Recent studies hypothesized that quantitative PCR (qPCR) could selectively quantify infective viruses if preceded by an enzymatic treatment (ET) to reduce confounding false-positive signals. The goal of this study was to determine if ET with qPCR (ET-qPCR) can be used to accurately quantify the infectivity of the human viral surrogate bacteriophage MS2 upon partial inactivation by three treatments (heating at 72 degrees C, singlet oxygen, and UV radiation). Viruses were inactivated in buffered solutions and a lake water sample and assayed with culturing, qPCR, and ET-qPCR. To ensure that inactivating genome damage was fully captured, primer sets that covered the entire coding region were used. The susceptibility of different genome regions and the maximum genomic damage after each inactivating treatment were compared. We found that (i) qPCR alone caused false-positive results for all treatments, (ii) ET-qPCR significantly reduced (up to >5.2 log units) but did not eliminate the false-positive signals, and (iii) the elimination of false-positive signals differed between inactivating treatments. By assaying the whole coding region, we demonstrated that genome damage only partially accounts for virus inactivation. The possibility of achieving complete accordance between culture- and PCR-based assays is therefore called into doubt. Despite these differences, we postulate that ET-qPCR can track infectivity, given that decreases in infectivity were always accompanied by dose-dependent decreases in ET-qPCR signal. By decreasing false-positive signals, ET-qPCR improved the detection of infectivity loss relative to qPCR.
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20
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Paula VS, Perse AS, Amado LA, Morais LM, Lima SMB, Tourinho RS, Gaspar AMC, Pinto MA. Kinetics of hepatitis A virus replication in vivo and in vitro using negative-strand quantitative PCR. Eur J Clin Microbiol Infect Dis 2009; 28:1167-76. [DOI: 10.1007/s10096-009-0759-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 05/10/2009] [Indexed: 11/28/2022]
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Application of PCR-based methods to assess the infectivity of enteric viruses in environmental samples. Appl Environ Microbiol 2008; 75:297-307. [PMID: 19011062 DOI: 10.1128/aem.01150-08] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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22
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Bessaud M, Autret A, Jegouic S, Balanant J, Joffret ML, Delpeyroux F. Development of a Taqman RT-PCR assay for the detection and quantification of negatively stranded RNA of human enteroviruses: evidence for false-priming and improvement by tagged RT-PCR. J Virol Methods 2008; 153:182-9. [PMID: 18706930 DOI: 10.1016/j.jviromet.2008.07.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 07/09/2008] [Accepted: 07/17/2008] [Indexed: 11/28/2022]
Abstract
Human enteroviruses are among the most common viruses infecting humans. These viruses are known to be able to infect a wide range of tissues and are believed to establish persistent infections. Enteroviruses are positive-sense single-stranded RNA viruses whose replication involves the synthesis of negative strand intermediates. Therefore, the specific detection of negatively stranded viral RNA in tissues or cells is a reliable marker of active enteroviral replication. The present report presents the development of a real-time RT-PCR allowing the specific detection and quantification of negatively stranded viral RNA. Since it was known that specific amplification of single-stranded RNA can be made difficult by false-priming events leading to false-positive or overestimated results, the assay was developed by using a tagged RT primer. This tagged RT-PCR was shown to be able to amplify specifically negative RNA of enteroviruses grown in cell cultures by preventing the amplification of cDNAs generated by false-priming.
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Affiliation(s)
- Maël Bessaud
- Unité postulante de biologie des virus entériques, Institut Pasteur, 25 rue du Dr Roux, 75 015 Paris, France.
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23
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Croci L, Dubois E, Cook N, de Medici D, Schultz AC, China B, Rutjes SA, Hoorfar J, Van der Poel WHM. Current Methods for Extraction and Concentration of Enteric Viruses from Fresh Fruit and Vegetables: Towards International Standards. FOOD ANAL METHOD 2008. [DOI: 10.1007/s12161-008-9025-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Viruses in water are usually present in concentrations too low for detection by direct analysis. Virological investigation of water samples is always a multi-stage process involving concentration of viruses present followed by an appropriate detection procedure. There are several approaches to detection of viruses. Part or all of the concentrate may be inoculated into cell cultures to detect infectious cytopathogenic virus, and if this is done in a quantitative fashion the virus can be enumerated, the count being reported as plaque-forming units, the tissue culture infectious dose, or most probable number units. The virus may be isolated and identified from the cell cultures. Viruses that multiply without producing an identifiable cytopathic effect in culture may sometimes be detected by immunoperoxidase or immunofluorescence staining. The concentrate may also be analyzed by molecular biological procedures (usually polymerase chain reaction (PCR) or real-time-PCR). The problem then is that such techniques do not usually detect the infectious virus, and novel approaches have been made recently to meet this challenge.
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Affiliation(s)
- Peter Wyn-Jones
- Institute of Geography and Earth Sciences, University of Wales, Aberystwyth, UK
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25
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Horsington J, Zhang Z. Analysis of foot-and-mouth disease virus replication using strand-specific quantitative RT-PCR. J Virol Methods 2007; 144:149-55. [PMID: 17561277 DOI: 10.1016/j.jviromet.2007.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 04/23/2007] [Accepted: 05/01/2007] [Indexed: 11/29/2022]
Abstract
Foot-and-mouth disease virus (FMDV) is a positive-sense, single stranded RNA virus and its replication involves the synthesis of a negative strand intermediate. In the present study, a strand-specific quantitative RT-PCR assay was developed for analysis of FMDV replication. Strand-specific detection of viral positive and negative strand RNA was achieved using a high reverse transcription (RT) temperature (62 degrees C) and a tagged RT primer. In both the positive and negative strand assays, the lowest reliably detectable concentration was 1 x 10(2) copies/microl. The assays developed were successfully used to analyse viral replication in tissues collected from experimentally infected sheep during both acute and persistent infection. The results showed that while replication was observed in all tissues examined during acute infection, active viral replication during persistent infection was only detected in the tonsil. These results are consistent with the current opinion that the tonsil in sheep is the main predilection site for virus persistence. This assay will be used in the future to look further at replication in experimentally infected animals, including the study of individual cell types, and will improve our understanding of FMDV pathogenesis.
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Affiliation(s)
- Jacquelyn Horsington
- Institute for Animal Health, Pirbright Laboratory, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
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26
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Gallagher EM, Margolin AB. Development of an integrated cell culture—Real-time RT-PCR assay for detection of reovirus in biosolids. J Virol Methods 2007; 139:195-202. [PMID: 17161876 DOI: 10.1016/j.jviromet.2006.10.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Revised: 10/02/2006] [Accepted: 10/19/2006] [Indexed: 11/19/2022]
Abstract
The current method for viral detection in biosolids is a plaque assay, as specified by the EPA in the 40 CFR Part 503 rule. Development of an integrated cell culture-polymerase chain reaction (ICC-PCR) assay has allowed detection of viruses that are under-detected and undetected by the plaque assay. This study examined the efficiency of the ICC-PCR method to detect mammalian orthoreovirus, a virus typically under-detected in biosolids. Biosolid samples seeded with mammalian orthoreovirus type 1 (Lang) detected to 3 x 10(5) plaque forming units (pfu) with a plaque assay, 10(2)pfu equivalents with real-time RT-PCR and no incubation, and 10(8)pfu equivalents with real-time RT-PCR after 7 days incubation. More infectious virus was detected using ICC-real-time RT-PCR than a plaque assay. Twenty-four environmental samples from three locations around the United States did not plaque with the EPA method; however the ICC-PCR detected infectious reovirus in 13 of the samples. Raw biosolids samples accounted for 12 of the positive samples, and 1 positive was from an aerobically digested sample.
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Affiliation(s)
- Elizabeth M Gallagher
- Department of Microbiology, University of New Hampshire, 46 College Road, Rm. 235, Durham, NH 03824, USA
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Anwar A, August JT, Too HP. A stem-loop-mediated reverse transcription real-time PCR for the selective detection and quantification of the replicative strand of an RNA virus. Anal Biochem 2006; 352:120-8. [PMID: 16527238 DOI: 10.1016/j.ab.2006.01.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2005] [Revised: 01/27/2006] [Accepted: 01/30/2006] [Indexed: 11/30/2022]
Abstract
A stem-loop-based method to quantify the replicative strand of a model system, dengue virus, with high specificity and sensitivity is described. The high specificity of this approach is achieved at two levels: the use of a reverse transcription primer folded into a stem-loop structure with optimal energetics and the use of specific PCR primers to the loop structure. This approach has exceptional specificity to the replicative RNA as compared with the genomic sequence (>10(5)-fold difference), with a detection sensitivity of 10 copies. The high correlation to the biological "gold standard" plaque assay, used to quantify infectious virus, renders this method a useful quantitative tool that can replace the time-consuming, labor-intensive, and low-throughput plaque-based assays. The method has been extended to the detection of replicative strands of other RNA viruses (West Nile virus and human respiratory syncytial virus) with similar results. This real-time PCR method is reliable, simple to perform, and easily adaptable to different targets. The ability to detect and rapidly quantify replicating viruses is an important step in the elucidation of pathogenesis and is also useful for the evaluation of drugs designed to inhibit viral replication.
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Affiliation(s)
- Azlinda Anwar
- Division of Biomedical Sciences, Johns Hopkins in Singapore, Singapore 138669, Singapore.
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