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Yao L, Li F, Qu M, Guo Y, Jiang Y, Wang L, Zhai Y. Development and Evaluation of a Novel Armored RNA Technology Using Bacteriophage Qβ. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:383-392. [PMID: 31435846 DOI: 10.1007/s12560-019-09400-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/31/2019] [Indexed: 05/23/2023]
Abstract
Foodborne viruses are a global threat to food safety. Real-time reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used method to detect viral RNA in food. Armored RNA (AR) prepared using the MS2 phage system is a successful positive control for detecting foodborne viruses and is an important quality control process when using real-time RT-PCR. In this study, we report a novel technology for preparing AR using bacteriophage Qβ and compare its stability with AR prepared using the MS2 phage system for packaging norovirus detection target RNA. AR could be successfully and efficiently produced using the developed bacteriophage Qβ system. Two types of AR-AR-QNoV prepared using the Qβ system and AR-MNoV prepared using the MS2 system-were stored at different temperatures for different durations. After incubating at - 20 °C for 360 days, the copy numbers of AR-QNoV and AR-MNoV decreased by 8.9% and 35.9%, respectively. After incubating at 4 °C for 60 days, the copy numbers of AR-QNoV and AR-MNoV decreased by 12.0% and 38.9%, respectively. After incubating at 45 °C, the copy numbers of AR-QNoV decreased by 71.8% after 5 days, whereas those of AR-MNoV decreased by 92.9% after only 4 days. After 5 days, AR-MNoV could not be detected using real-time RT-PCR. There was a significant difference in copy numbers decrease rate between AR-QNoV and AR-MNoV at three different temperatures (P < 0.05 ). Therefore, AR prepared using the new bacteriophage Qβ system is more stable than the traditional AR, making the developed strategy a good candidate for AR preparation and quality control.
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Affiliation(s)
- Lin Yao
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Fengling Li
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Meng Qu
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Yingying Guo
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Yanhua Jiang
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China.
| | - Lianzhu Wang
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
| | - Yuxiu Zhai
- Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, People's Republic of China
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Gholami M, Ravanshad M, Baesi K, Samiee SM, Hosseini Rozbahani N, Mohraz M. Preparation and Evaluation of Ribonuclease-Resistant Viral HIV RNA Standards Based on Armored RNA Technology. IRANIAN BIOMEDICAL JOURNAL 2018. [PMID: 29776310 PMCID: PMC6305816 DOI: 10.29252/.22.6.394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Background: The human immunodeficiency virus type 1 (HIV-1) is an infectious viral agent that gradually extinguishes the immune system, resulting in acquired immune deficiency syndrome (AIDS). The aim of this study was to construct an RNA-positive control based on armored (AR) RNA technology, using HIV-1 RNA as a model. Methods: The MS2 maturase, a coat protein gene (at positions 1765 to 1787) and HIV-1 pol gene were cloned into pET-32a plasmid. The prepared plasmid was transformed into Escherichia coli strain BL2 (DE3), and the expression of the construct was induced by 1 mM of isopropyl-L-thio-D-galactopyranoside (IPTG) at 37 °C for 16 h to obtain the fabricated AR RNA. The AR RNA was precipitated and purified using polyethylene glycol and Sephacryl S-200 chromatography. Results: The stability of AR RNA was evaluated by treatment with DNase I and RNase A and confirmed by transmission electron microscopy and gel agarose electrophoresis. Tenfold serial dilution of AR RNA from 101 to 105 was prepared. Real-time PCR assays had a range of detection between 101 and 105. In addition, R2 value was 0.998, and the slope of the standard curve was -3.33. Conclusion: Prepared AR RNA, as a positive control, could be used as a basis for launching an in-house HIV-1 virus assay and other infectious agents. It can be readily available to laboratories and HIV research centers. The AR RNA is non-infectious and highly resistant to ribonuclease enzyme and can reduce the risk of infection in the clinical laboratory.
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Affiliation(s)
- Mohammad Gholami
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehrdad Ravanshad
- Department of Medical Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Kazem Baesi
- Hepatitis and AIDS Department, Pasteur Institute of Iran, Tehran, Iran
| | - Siamak M. Samiee
- Food and Drug Laboratory Research Center, Ministry of Health and Medical Education, Tehran, Iran
| | - Negin Hosseini Rozbahani
- Department of Immunology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Minoo Mohraz
- Iranian Research Center for HIV AIDS (IRCHA), Iranian Institute for Reduction of High-Risk Behaviors, Tehran University of Medical Science, Tehran, Iran
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Zambenedetti MR, Pavoni DP, Dallabona AC, Dominguez AC, Poersch CDO, Fragoso SP, Krieger MA. Internal control for real-time polymerase chain reaction based on MS2 bacteriophage for RNA viruses diagnostics. Mem Inst Oswaldo Cruz 2017; 112:339-347. [PMID: 28403327 PMCID: PMC5398160 DOI: 10.1590/0074-02760160380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 01/17/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Real-time reverse transcription polymerase chain reaction (RT-PCR) is routinely used to detect viral infections. In Brazil, it is mandatory the use of nucleic acid tests to detect hepatitis C virus (HCV), hepatitis B virus and human immunodeficiency virus in blood banks because of the immunological window. The use of an internal control (IC) is necessary to differentiate the true negative results from those consequent from a failure in some step of the nucleic acid test. OBJECTIVES The aim of this study was the construction of virus-modified particles, based on MS2 bacteriophage, to be used as IC for the diagnosis of RNA viruses. METHODS The MS2 genome was cloned into the pET47b(+) plasmid, generating pET47b(+)-MS2. MS2-like particles were produced through the synthesis of MS2 RNA genome by T7 RNA polymerase. These particles were used as non-competitive IC in assays for RNA virus diagnostics. In addition, a competitive control for HCV diagnosis was developed by cloning a mutated HCV sequence into the MS2 replicase gene of pET47b(+)-MS2, which produces a non-propagating MS2 particle. The utility of MS2-like particles as IC was evaluated in a one-step format multiplex real-time RT-PCR for HCV detection. FINDINGS We demonstrated that both competitive and non-competitive IC could be successfully used to monitor the HCV amplification performance, including the extraction, reverse transcription, amplification and detection steps, without compromising the detection of samples with low target concentrations. In conclusion, MS2-like particles generated by this strategy proved to be useful IC for RNA virus diagnosis, with advantage that they are produced by a low cost protocol. An attractive feature of this system is that it allows the construction of a multicontrol by the insertion of sequences from more than one pathogen, increasing its applicability for diagnosing different RNA viruses.
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Affiliation(s)
- Miriam Ribas Zambenedetti
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil.,Universidade Federal do Paraná, Departamento de Bioprocessos e Biotecnologia, Curitiba, PR, Brasil
| | - Daniela Parada Pavoni
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil
| | | | | | | | - Stenio Perdigão Fragoso
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil
| | - Marco Aurélio Krieger
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica, Curitiba, PR, Brasil.,Fundação Oswaldo Cruz-Fiocruz, Instituto de Biologia Molecular do Paraná, Curitiba, PR, Brasil
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Zhao L, Li R, Liu A, Zhao S. A novel duplex real time quantitative reverse transcription polymerase chain reaction for rubella virus with armored RNA as a noncompetitive internal positive control. J Virol Methods 2015; 219:84-89. [PMID: 25862104 DOI: 10.1016/j.jviromet.2015.03.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/31/2015] [Accepted: 03/31/2015] [Indexed: 11/28/2022]
Abstract
The objective of this study was to build and apply a duplex real time quantitative reverse transcription-polymerase chain reaction (RT-PCR) for rubella virus. Firstly, a 60-bp-long armored RV RNA was constructed in the laboratory. Secondly, a duplex real time RT-PCR assay was established. Thirdly, the 60-bp-long armored RV RNA was used as an internal positive control (IPC) for the duplex real time RT-PCR. And finally the duplex real time RT-PCR assay was applied to detect RV RNA in clinical specimens. The in-house assay has a high amplification efficiency (0.99), a high analytical sensitivity (200 copies/mL), and a good reproducibility. The diagnostic specificity and sensitivity of the in-house assay were both 100%, due to the monitoring of the armored RV RNA IPC. Therefore, the in-house duplex real time quantitative RT-PCR assay is a specific, sensitive, reproducible and accurate assay for quantitation of RV RNA in clinical specimens. And noncompetitive armored RV RNA IPC can monitor RT-PCR inhibition and prevent false-negative and inaccurate results in the real time detection system.
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Affiliation(s)
- Lihong Zhao
- Department of Laboratory, Tai'an Central Hospital, Tai'an 271000, China
| | - Ruiying Li
- Department of Reproductive Genetics, Tai'an Central Hospital, Tai'an 271000, China
| | - Aihua Liu
- Central Laboratory, Tai'an Central Hospital, Tai'an 271000, China
| | - Shuping Zhao
- Department of Laboratory, Tai'an Central Hospital, Tai'an 271000, China.
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Monjure CJ, Tatum CD, Panganiban AT, Arainga M, Traina-Dorge V, Marx PA, Didier ES. Optimization of PCR for quantification of simian immunodeficiency virus genomic RNA in plasma of rhesus macaques (Macaca mulatta) using armored RNA. J Med Primatol 2013; 43:31-43. [PMID: 24266615 DOI: 10.1111/jmp.12088] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2013] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Quantification of plasma viral load (PVL) is used to monitor disease progression in SIV-infected macaques. This study was aimed at optimizing of performance characteristics of the quantitative PCR (qPCR) PVL assay. METHODS The PVL quantification procedure was optimized by inclusion of an exogenous control hepatitis C virus armored RNA (aRNA), a plasma concentration step, extended digestion with proteinase K, and a second RNA elution step. Efficiency of viral RNA (vRNA) extraction was compared using several commercial vRNA extraction kits. Various parameters of qPCR targeting the gag region of SIVmac239, SIVsmE660, and the LTR region of SIVagmSAB were also optimized. RESULTS Modifications of the SIV PVL qPCR procedure increased vRNA recovery, reduced inhibition and improved analytical sensitivity. The PVL values determined by this SIV PVL qPCR correlated with quantification results of SIV RNA in the same samples using the 'industry standard' method of branched-DNA (bDNA) signal amplification. CONCLUSIONS Quantification of SIV genomic RNA in plasma of rhesus macaques using this optimized SIV PVL qPCR is equivalent to the bDNA signal amplification method, less costly and more versatile. Use of heterologous aRNA as an internal control is useful for optimizing performance characteristics of PVL qPCRs.
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Affiliation(s)
- C J Monjure
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA, USA
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