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Sluimer J, van den Akker WMR, Goderski G, Swart A, van der Veer B, Cremer J, Chung NH, Molenkamp R, Voermans J, Guldemeester J, Eggink D, Presser LD, Meijer A. High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment. Sci Rep 2024; 14:1378. [PMID: 38228693 DOI: 10.1038/s41598-023-50912-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 12/27/2023] [Indexed: 01/18/2024] Open
Abstract
A two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.
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Grants
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
- V/190028/22/PR Ministerie van Volksgezondheid, Welzijn en Sport
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Affiliation(s)
- John Sluimer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Willem M R van den Akker
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Gabriel Goderski
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Arno Swart
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Bas van der Veer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jeroen Cremer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ngoc Hoa Chung
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jolanda Voermans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Judith Guldemeester
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dirk Eggink
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Lance D Presser
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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2
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Maiti B, Anupama KP, Rai P, Karunasagar I, Karunasagar I. Isothermal amplification-based assays for rapid and sensitive detection of severe acute respiratory syndrome coronavirus 2: Opportunities and recent developments. Rev Med Virol 2021; 32:e2274. [PMID: 34216498 PMCID: PMC8420443 DOI: 10.1002/rmv.2274] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 06/27/2021] [Indexed: 12/21/2022]
Abstract
The coronavirus disease 2019 (COVID‐19) is a global pandemic caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). To date, the virus has been detected in 219 countries of the world. Therefore, managing the disease becomes the priority, in which detecting the presence of the virus is a crucial step. Presently, real‐time RT polymerase chain reaction (RT‐qPCR) is considered a gold standard nucleic acid amplification test (NAAT). The test protocol of RT‐qPCR is complicated, places high demands on equipment, testing reagents, research personnel skills and is expensive. Therefore, simpler point‐of‐care (POC) tests are needed to accelerate clinical decision‐making and take some of the workload from centralized test laboratories. Various isothermal amplification‐based assays have been developed for the sensitive detection of different microorganisms, and recently some of them have been applied for detection of SARS‐CoV‐2. These do not require any programable thermocycler, can produce the results in a single temperature, and therefore, are considered simple. Unlike RT‐qPCR, these methods are highly sensitive, specific, less time‐consuming, simple and affordable, and can be used as POC diagnostic kit for COVID‐19. In this review, we have discussed the potential of isothermal amplification‐based assays as an alternative to RT‐qPCR for the detection of SARS‐CoV‐2.
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Affiliation(s)
- Biswajit Maiti
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Mangaluru, Karnataka, India
| | - Karanth Padyana Anupama
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Mangaluru, Karnataka, India
| | - Praveen Rai
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Paneer Campus, Mangaluru, Karnataka, India
| | - Indrani Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Mangaluru, Karnataka, India
| | - Iddya Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Mangaluru, Karnataka, India
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3
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Chen B, Liu M, Huang C. Current diagnostic and therapeutic strategies for COVID-19. J Pharm Anal 2021; 11:129-137. [PMID: 33520327 PMCID: PMC7832669 DOI: 10.1016/j.jpha.2020.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 01/18/2023] Open
Abstract
The outbreak and spread of novel coronavirus disease 2019 (COVID-19) with pandemic features, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have greatly threatened global public health. Given the perniciousness of COVID-19 pandemic, acquiring a deeper understanding of this viral illness is critical for the development of new vaccines and therapeutic options. In this review, we introduce the systematic evolution of coronaviruses and the structural characteristics of SARS-CoV-2. We also summarize the current diagnostic tools and therapeutic strategies for COVID-19.
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Affiliation(s)
- Binbin Chen
- College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
- School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Mengli Liu
- College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Chengzhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, Southwest University, Chongqing, 400715, China
- Key Laboratory of Luminescence and Real-Time Analytical System, Chongqing Science and Technology Bureau, College of Pharmaceutical Science, Southwest University, Chongqing, 400715, China
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4
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Schneider J, Engler M, Hofmann J, Selinka HC, Jones TC, Drosten C, Diedrich S, Corman VM, Böttcher S. Molecular detection of cosaviruses in a patient with acute flaccid paralysis and in sewage samples in Germany. Virus Res 2021; 297:198285. [PMID: 33548413 DOI: 10.1016/j.virusres.2020.198285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/02/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022]
Abstract
Cosaviruses (CoSV) were first identified in stool samples collected from non-polio acute flaccid paralysis (AFP) cases and their healthy contacts in Pakistan in 2003. The clinical importance of CoSV remains unclear as data on epidemiology are scarce and no routine diagnostic testing is done. In this study, we characterized human CoSV (HCoSV) in a child with non-polio AFP and in sewage samples collected in Berlin, Germany. Using unbiased high-throughput sequencing and specific PCR, we characterized a HCoSV-D in stool samples of a three-year-old child hospitalized in Germany with non-polio AFP and travel history to Pakistan. The shedding pattern and absence of other relevant pathogens suggests that HCoSV-D may have been involved in the genesis of AFP. The HCoSV-RNA concentration was high, with 2.57 × 106 copies per mL fecal/suspension, decreasing in follow-up samples. To investigate the possibility of local circulation of HCoSV, we screened Berlin sewage samples collected between 2013 and 2018. Molecular testing of sewage samples has shown the presence of CoSV in several parts of the world, but until now not in Germany. Of our sewage samples, 54.3 % were positive for CoSV, with up to three viral species identified in samples. Phylogenetically, the German sequences clustered intermixed with sequences obtained globally. Together, these findings emphasize the need for further clinical, epidemiological, environmental, pathogenicity and phylogenetic studies of HCoSV.
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Affiliation(s)
- J Schneider
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany
| | - M Engler
- Department of Paediatrics, Sana Klinikum Offenbach GmbH, Starkenburgring 66, 63069, Offenbach am Main, Germany
| | - J Hofmann
- Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany
| | - H C Selinka
- German Environment Agency, Microbiological Risks, Corrensplatz 1, 14195, Berlin, Germany
| | - T C Jones
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - C Drosten
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Site Berlin, Berlin, Germany
| | - S Diedrich
- National Reference Center for Poliomyelitis and Enteroviruses, Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany
| | - V M Corman
- Institute of Virology, Charité-Universitätsmedizin, Charitéplatz 1, 10117, Berlin, Germany; Labor Berlin, Charité-Vivantes GmbH, Sylter Straße 2, 13353, Berlin, Germany; German Centre for Infection Research (DZIF), Associated Partner Site Berlin, Berlin, Germany.
| | - S Böttcher
- National Reference Center for Poliomyelitis and Enteroviruses, Robert Koch-Institute, Nordufer 20, 13353, Berlin, Germany.
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5
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Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK, Bleicker T, Brünink S, Schneider J, Schmidt ML, Mulders DG, Haagmans BL, van der Veer B, van den Brink S, Wijsman L, Goderski G, Romette JL, Ellis J, Zambon M, Peiris M, Goossens H, Reusken C, Koopmans MP, Drosten C. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. ACTA ACUST UNITED AC 2020; 25. [PMID: 31992387 PMCID: PMC6988269 DOI: 10.2807/1560-7917.es.2020.25.3.2000045] [Citation(s) in RCA: 4642] [Impact Index Per Article: 1160.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through travellers does already occur. Aim We aimed to develop and deploy robust diagnostic methodology for use in public health laboratory settings without having virus material available. Methods Here we present a validated diagnostic workflow for 2019-nCoV, its design relying on close genetic relatedness of 2019-nCoV with SARS coronavirus, making use of synthetic nucleic acid technology. Results The workflow reliably detects 2019-nCoV, and further discriminates 2019-nCoV from SARS-CoV. Through coordination between academic and public laboratories, we confirmed assay exclusivity based on 297 original clinical specimens containing a full spectrum of human respiratory viruses. Control material is made available through European Virus Archive – Global (EVAg), a European Union infrastructure project. Conclusion The present study demonstrates the enormous response capacity achieved through coordination of academic and public laboratories in national and European research networks.
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Affiliation(s)
- Victor M Corman
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | | | | | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Tobias Bleicker
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Sebastian Brünink
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Julia Schneider
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Marie Luisa Schmidt
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Bas van der Veer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sharon van den Brink
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Lisa Wijsman
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Gabriel Goderski
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | | | | | | | - Herman Goossens
- Department of Medical Microbiology, Vaccine and Infectious Diseases Institute, University of Antwerp, Antwerp, Belgium
| | - Chantal Reusken
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Christian Drosten
- Charité - Universitätsmedizin Berlin Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
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6
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Development and evaluation of a real-time RT-PCR assay for detection of a novel avian influenza A (H5N6) virus. J Virol Methods 2018; 257:79-84. [PMID: 29729298 DOI: 10.1016/j.jviromet.2018.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/22/2018] [Accepted: 05/02/2018] [Indexed: 12/19/2022]
Abstract
As of Aug 25, 2017, 17 incidences of human infection and 6 deaths due to the novel H5N6 virus have been reported in China. Genetic analysis of the viral genome revealed that this reassortant virus is highly pathogenic to poultry, and that the virus has a risk of transmission to humans. Accordingly, the development of a rapid, sensitive, and specific molecular diagnostic assay is critical for public health. In this study, a real-time reverse-transcription PCR (RT-PCR) assay was developed to specifically detect the novel H5N6 virus, with primer pairs targeting the hemagglutinin and neuraminidase gene sequences of this virus. RNA was extracted from throat swab specimens from patients with influenza-like illness (ILIs), and environmental samples were collected from live poultry markets (LPMs) for H5N6 virus detection by real-time RT-PCR. The method was demonstrated to enable specific detection of the avian H5N6 virus, with no cross-reactivity with seasonal influenza viruses (H1N1, H1N1 pdm09, H3N2 or B); H5N1, H7N9, H9N2 viruses; or other human respiratory viruses. The detection limit of the assay was 1.0 × 101 copies per reaction for N6 and 1.0 × 102 copies per reaction for H5 assays. The assay is a powerful tool for rapid, sensitive, and specific detection of H5N6 virus infection in specimens derived from humans, animals, and the environment.
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7
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Banakar A, Sadeghi M, Shushtari A. An intelligent device for diagnosing avian diseases: Newcastle, infectious bronchitis, avian influenza. COMPUTERS AND ELECTRONICS IN AGRICULTURE 2016; 127:744-753. [PMID: 32287574 PMCID: PMC7125684 DOI: 10.1016/j.compag.2016.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/13/2016] [Accepted: 08/08/2016] [Indexed: 06/11/2023]
Abstract
In commercial poultry production there are a number of diseases which are of particular importance due to the heavy economic losses that can arise if a flock becomes infected. The development of an automated and rapid disease detection system would therefore be of considerable benefit to both production and animal welfare. This study represents an intelligence device for diagnosing avian diseases by using Data-mining methods and Dempster-Shafer evidence theory (D-S). 14-day-old chickens were divided into four groups. Each group was deliberately infected with a disease: Newcastle Disease (ND), Bronchitis Virus (BV), Avian Influenenza (AI), and the last group was considered as control samples. Fast Fourier Transform (FFT) and Discrete Wavelet Transform (DWT) were used to process the chicken's sound signals in frequency and time-frequency domains, respectively. In order to achieve information, 25 statistical features from frequency domains, and 75 statistical features from time-frequency domains were extracted. During dimensionality reduction stage, the best features of the sound signals were selected, using improved distance evaluation (IDE) method. The chicken's sound signals were analyzed in two consecutive days after virus infection. Support vector machine (SVM) was used as the classifier in this study. The first classification was done with SVM and based on sound features in frequency and time-frequency domains with accuracy of 41.35 and 83.33%, respectively. The accuracy of the method based on D-S infusion of sound data reached 91.15%. The developed model based on achievement result could diagnose Newcastle Disease, Bronchitis Virus and Avian Influenza from sound signals.
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Affiliation(s)
- Ahmad Banakar
- Department of Biosystems Engineering, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Sadeghi
- Department of Biosystems Engineering, Tarbiat Modares University, Tehran, Iran
| | - Abdolhamid Shushtari
- Department of Poultry Disease, Razi Vaccine and Serum Research Institute, Karaj, Iran
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8
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Abstract
Here we report one of the smallest real-time polymerase chain reaction (PCR) systems to date with an approximate size of 100 mm × 60 mm × 33 mm. The system is an autonomous unit requiring an external 12 V power supply. Four simultaneous reactions are performed in the form of virtual reaction chambers (VRCs) where a ≈200 nL sample is covered with mineral oil and placed on a glass cover slip. Fast, 40 cycle amplification of an amplicon from the H7N9 gene was used to demonstrate the PCR performance. The standard curve slope was -3.02 ± 0.16 cycles at threshold per decade (mean ± standard deviation) corresponding to an amplification efficiency of 0.91 ± 0.05 per cycle (mean ± standard deviation). The PCR device was capable of detecting a single deoxyribonucleic acid (DNA) copy. These results further suggest that our handheld PCR device may have broad, technologically-relevant applications extending to rapid detection of infectious diseases in small clinics.
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Affiliation(s)
| | - Bojan Robert Ilic
- National Institute of Standard and Technology (NIST), Center for Nanoscale Science and Technology, 100 Bureau Drive, MS 6201, Gaithersburg, MD 20899-6201, USA
| | - Andreas Manz
- KIST-Europe, Microfluidics Group, Campus E7.1, 66111 Saarbrücken, Germany.
| | - Pavel Neužil
- KIST-Europe, Microfluidics Group, Campus E7.1, 66111 Saarbrücken, Germany. and Brno University of Technology (BUT), Central European Institute of Technology (CEITEC), Technická 3058/10, CZ-616 00 Brno, Czech Republic
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9
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Shi D, Shen S, Fan X, Chen S, Wang D, Li C, Wu X, Li L, Bai D, Zhang C, Wang J. Evaluation of Commercial Diagnostic Assays for the Specific Detection of Avian Influenza A (H7N9) Virus RNA Using a Quality-Control Panel and Clinical Specimens in China. PLoS One 2015; 10:e0137862. [PMID: 26361351 PMCID: PMC4567293 DOI: 10.1371/journal.pone.0137862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 08/23/2015] [Indexed: 11/18/2022] Open
Abstract
A novel avian influenza A H7N9-subtype virus emerged in China in 2013 and threatened global public health. Commercial kits that specifically detect avian influenza A (H7N9) virus RNA are urgently required to prepare for the emergence and potential pandemic of this novel influenza virus. The safety and effectiveness of three commercial molecular diagnostic assays were evaluated using a quality-control panel and clinical specimens collected from over 90 patients with confirmed avian influenza A (H7N9) virus infections. The analytical performance evaluation showed that diverse influenza H7N9 viruses can be detected with high within- and between-lot reproducibility and without cross-reactivity to other influenza viruses (H1N1 pdm09, seasonal H1N1, H3N2, H5N1 and influenza B). The detection limit of all the commercial assays was 2.83 Log10 copies/μl [0.7 Log10TCID50/mL of avian influenza A (H7N9) virus strain A/Zhejiang/DTID-ZJU01/2013], which is comparable to the method recommended by the World Health Organization (WHO). In addition, using a WHO-Chinese National Influenza Center (CNIC) method as a reference for clinical evaluation, positive agreement of more than 98% was determined for all of the commercial kits, while negative agreement of more than 99% was observed. In conclusion, our findings provide comprehensive evidence for the high performance of three commercial diagnostic assays and suggest the application of these assays as rapid and effective diagnostic tools for avian influenza A (H7N9) virus in the routine clinical practice of medical laboratories.
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Affiliation(s)
- Dawei Shi
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, People’s Republic of China
| | - Shu Shen
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, People’s Republic of China
| | - Xingliang Fan
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, People’s Republic of China
- WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
| | - Suhong Chen
- Beijing Institute of Radiation Medicine, Beijing, People’s Republic of China
| | - Dayan Wang
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- WHO Collaborating Center for Reference and Research on Influenza, Beijing, People’s Republic of China
| | - Changgui Li
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, People’s Republic of China
- WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
| | - Xing Wu
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, People’s Republic of China
- WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
| | - Lili Li
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, People’s Republic of China
| | - Dongting Bai
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, People’s Republic of China
| | - Chuntao Zhang
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, People’s Republic of China
- * E-mail: (CTZ); (JZW)
| | - Junzhi Wang
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing, People’s Republic of China
- WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
- * E-mail: (CTZ); (JZW)
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10
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Evaluation and application of a one-step duplex real-time reverse transcription polymerase chain reaction assay for the rapid detection of influenza A (H7N9) virus from poultry samples. Arch Virol 2015; 160:2471-7. [PMID: 26179621 DOI: 10.1007/s00705-015-2511-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Abstract
In China, a novel reassortant influenza A (H7N9) virus, which has caused 435 cases of human infection, has recently emerged. Most cases of human infections with the H7N9 virus are known to be associated with a poultry farm and live-poultry markets. In this study, a one-step duplex real-time reverse transcription polymerase chain reaction (RRT-PCR) assay was developed for the simultaneous detection of the hemagglutinin (HA) and neuraminidase (NA) genes of the H7N9 virus for effective surveillance and early diagnosis of cases from clinical samples collected from live-poultry markets or poultry farms. The detection limit of this assay was as low as 0.1 EID50 of H7N9 viruses, which is similar to the detection limit of the real-time RT-PCR assay released by the Word Health Organization. The coefficients of variation (CVs) of both inter-assay and intra-assay reproducibility were less than 1.55 %, showing good reproducibility. No cross-reactivity was observed with RNA of other subtypes of influenza virus or other avian respiratory viruses. The assay can effectively detect H7N9 influenza virus RNA from multiple sources, including chickens, pigeons, ducks, humans, and the environment. Furthermore, the RRT-PCR assay was evaluated with more than 700 clinical samples collected from live-poultry markets and 120 experimentally infected chicken samples. Together, these results indicate that the duplex RRT-PCR assay is a specific, sensitive, and efficient diagnostic method for the epidemiological surveillance and diagnosis of H7N9 virus from different sources, particularly poultry samples.
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11
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Single Fluorescence Channel-based Multiplex Detection of Avian Influenza Virus by Quantitative PCR with Intercalating Dye. Sci Rep 2015; 5:11479. [PMID: 26088868 PMCID: PMC5155576 DOI: 10.1038/srep11479] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/30/2015] [Indexed: 12/03/2022] Open
Abstract
Since its invention in 1985 the polymerase chain reaction (PCR) has become a well-established method for amplification and detection of segments of double-stranded DNA. Incorporation of fluorogenic probe or DNA intercalating dyes (such as SYBR Green) into the PCR mixture allowed real-time reaction monitoring and extraction of quantitative information (qPCR). Probes with different excitation spectra enable multiplex qPCR of several DNA segments using multi-channel optical detection systems. Here we show multiplex qPCR using an economical EvaGreen-based system with single optical channel detection. Previously reported non quantitative multiplex real-time PCR techniques based on intercalating dyes were conducted once the PCR is completed by performing melting curve analysis (MCA). The technique presented in this paper is both qualitative and quantitative as it provides information about the presence of multiple DNA strands as well as the number of starting copies in the tested sample. Besides important internal control, multiplex qPCR also allows detecting concentrations of more than one DNA strand within the same sample. Detection of the avian influenza virus H7N9 by PCR is a well established method. Multiplex qPCR greatly enhances its specificity as it is capable of distinguishing both haemagglutinin (HA) and neuraminidase (NA) genes as well as their ratio.
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Xu X, Bao H, Ma Y, Sun J, Zhao Y, Wang Y, Shi J, Zeng X, Li Y, Wang X, Chen H. Simultaneous detection of novel H7N9 and other influenza A viruses in poultry by multiplex real-time RT-PCR. Virol J 2015; 12:69. [PMID: 25925390 PMCID: PMC4424497 DOI: 10.1186/s12985-015-0300-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 04/17/2015] [Indexed: 11/10/2022] Open
Abstract
Background A novel reassortant H7N9 influenza A virus has crossed the species barrier from poultry to cause human infections in China in 2013 and 2014. Rapid detection of the novel H7N9 virus is important to detect this virus in poultry and reduce the risk of an epidemic in birds or humans. Findings In this study, a multiplex real-time RT-PCR (rRT-PCR) assay for rapid detection of H7N9 and other influenza A viruses was developed. To evaluate the assay, various influenza A viruses, other avian respiratory viruses, and 1,070 samples from poultry were tested. Fluorescence signals corresponding to H7 and N9 subtypes were detected only when H7 and N9 subtypes were present, while the fluorescence signal for the influenza A M gene was detected in all specimens with influenza A strains. The fluorescent signal can be detected in dilutions as low as 56 copies per reaction for the H7, N9 and M genes. Intra- and inter-assay variability tests showed a reliable assay. In poultry samples, a comparison of rRT-PCR with virus isolation showed a high level of agreement. Conclusions The multiplex rRT-PCR assay in this study has good specificity, sensitivity and reproducibility, and will be useful for laboratory surveillance and rapid diagnosis of H7N9 and other influenza A viruses.
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Affiliation(s)
- Xiaolong Xu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, People's Republic of China.
| | - Hongmei Bao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, People's Republic of China.
| | - Yong Ma
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, People's Republic of China.
| | - Jiashan Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, People's Republic of China.
| | - Yuhui Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, People's Republic of China.
| | - Yunhe Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, People's Republic of China.
| | - Jianzhong Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, People's Republic of China.
| | - Xianying Zeng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, People's Republic of China.
| | - Yanbing Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, People's Republic of China.
| | - Xiurong Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, People's Republic of China.
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, People's Republic of China.
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Case-control study of risk factors for human infection with avian influenza A(H7N9) virus in Shanghai, China, 2013. Epidemiol Infect 2014; 143:1826-32. [PMID: 25471822 DOI: 10.1017/s0950268814003264] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The first human infection with avian influenza A(H7N9) virus was reported in Shanghai, China in March 2013. An additional 32 cases of human H7N9 infection were identified in the following months from March to April 2013 in Shanghai. Here we conducted a case-control study of the patients with H7N9 infection (n = 25) using controls matched by age, sex, and residence to determine risk factors for H7N9 infection. Our findings suggest that chronic disease and frequency of visiting a live poultry market (>10 times, or 1-9 times during the 2 weeks before illness onset) were likely to be significantly associated with H7N9 infection, with the odds ratios being 4.07 [95% confidence interval (CI) 1.32-12.56], 10.61 (95% CI 1.85-60.74), and 3.76 (95% CI 1.31-10.79), respectively. Effective strategies for live poultry market control should be reinforced and ongoing education of the public is warranted to promote behavioural changes that can help to eliminate direct or indirect contact with influenza A(H7N9) virus.
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Cao RY, Xiao JH, Cao B, Li S, Kumaki Y, Zhong W. Inhibition of Novel Reassortant Avian Influenza H7N9 Virus Infection in vitro with Three Antiviral Drugs, Oseltamivir, Peramivir and Favipiravir. ACTA ACUST UNITED AC 2014; 23:237-40. [DOI: 10.3851/imp2672] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2013] [Indexed: 10/26/2022]
Abstract
Background: A novel reassortant avian-origin influenza A (H7N9) virus was isolated from respiratory specimens obtained from three patients and was identified as H7N9 in China. Antiviral agents are required to treat patients with avian influenza H7N9 virus infection. Methods: In this study, we assessed the antiviral potential of oseltamivir, peramivir, favipiravir (T-705), amantadine and rimantadine against novel reassortant avian-origin influenza H7N9 virus in vitro. Results: All three avian influenza H7N9 virus strains were sensitive to oseltamivir, peramivir and favipiravir (T-705), but resistant to amantadine and rimantadine. Conclusions: Our data show a pattern of antiviral sensitivity for this novel H7N9 strain of influenza that suggests the compounds oseltamivir, peramivir and favipiravir should be useful for therapy.
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Affiliation(s)
- Rui-Yuan Cao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, PR China
| | - Jun-Hai Xiao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, PR China
| | - Bin Cao
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Beijing Institute of Respiratory Medicine, Capital Medical University, Beijing, PR China
| | - Song Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, PR China
| | - Yohichi Kumaki
- Institute for Antiviral Research, Department of Animal, Dairy and Veterinary Science, Utah State University, Logan, UT, USA
| | - Wu Zhong
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, PR China
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Fan J, Cui D, Lau S, Xie G, Guo X, Zheng S, Huang X, Yang S, Yang X, Huo Z, Yu F, Lou J, Tian L, Li X, Dong Y, Zhu Q, Chen Y. Detection of a novel avian influenza A (H7N9) virus in humans by multiplex one-step real-time RT-PCR assay. BMC Infect Dis 2014; 14:541. [PMID: 25298249 PMCID: PMC4286936 DOI: 10.1186/1471-2334-14-541] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 09/29/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND A novel avian influenza A (H7N9) virus emerged in eastern China in February 2013. 413 confirmed human cases, including 157 deaths, have been recorded as of July 31, 2014. METHODS Clinical specimens, including throat swabs, sputum or tracheal aspirates, etc., were obtained from patients exhibiting influenza-like illness (ILIs), especially from those having pneumonia and a history of occupational exposure to poultry and wild birds. RNA was extracted from these samples and a multiplex one-step real-time RT-PCR assay was developed to specifically detect the influenza A virus (FluA). PCR primers targeted the conserved M and Rnase P (RP) genes, as well as the hemagglutinin and neuraminidase genes of the H7N9 virus. RESULTS The multiplex assay specifically detected the avian H7N9 virus, and no cross-reaction with other common respiratory pathogens was observed. The detection limit of the assay was approximately 0.05 50% tissue culture infective doses (TCID50), or 100 copies per reaction. Positive detection of the H7N9 virus in sputum/tracheal aspirates was higher than in throat swabs during the surveillance of patients with ILIs. Additionally, detection of the matrix (M) and Rnase P genes aided in the determination of the novel avian H7N9 virus and ensured the quality of the clinical samples. CONCLUSIONS These results demonstrate that the multiplex assay detected the novel avian H7N9 virus with high specificity and sensitivity, which is essential for the early diagnosis and treatment of infected patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yu Chen
- Department of Clinical Laboratory, the First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China.
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16
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Pinsent A, Blake IM, White MT, Riley S. Surveillance of low pathogenic novel H7N9 avian influenza in commercial poultry barns: detection of outbreaks and estimation of virus introduction time. BMC Infect Dis 2014; 14:427. [PMID: 25085078 PMCID: PMC4129106 DOI: 10.1186/1471-2334-14-427] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/18/2014] [Indexed: 12/02/2022] Open
Abstract
Background Both high and low pathogenic subtype A avian influenza remain ongoing threats to the commercial poultry industry globally. The emergence of a novel low pathogenic H7N9 lineage in China presents itself as a new concern to both human and animal health and may necessitate additional surveillance in commercial poultry operations in affected regions. Methods Sampling data was simulated using a mechanistic model of H7N9 influenza transmission within commercial poultry barns together with a stochastic observation process. Parameters were estimated using maximum likelihood. We assessed the probability of detecting an outbreak at time of slaughter using both real-time polymerase chain reaction (rt-PCR) and a hemagglutinin inhibition assay (HI assay) before considering more intense sampling prior to slaughter. The day of virus introduction and R0 were estimated jointly from weekly flock sampling data. For scenarios where R0 was known, we estimated the day of virus introduction into a barn under different sampling frequencies. Results If birds were tested at time of slaughter, there was a higher probability of detecting evidence of an outbreak using an HI assay compared to rt-PCR, except when the virus was introduced <2 weeks before time of slaughter. Prior to the initial detection of infection Nsample = 50 (1%) of birds were sampled on a weekly basis once, but after infection was detected, Nsample = 2000 birds (40%) were sampled to estimate both parameters. We accurately estimated the day of virus introduction in isolation with weekly and 2-weekly sampling. Conclusions A strong sampling effort would be required to infer both the day of virus introduction and R0. Such a sampling effort would not be required to estimate the day of virus introduction alone once R0 was known, and sampling Nsample = 50 of birds in the flock on a weekly or 2 weekly basis would be sufficient. Electronic supplementary material The online version of this article (doi:10.1186/1471-2334-14-427) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amy Pinsent
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, UK.
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Nakauchi M, Takayama I, Takahashi H, Tashiro M, Kageyama T. Development of a reverse transcription loop-mediated isothermal amplification assay for the rapid diagnosis of avian influenza A (H7N9) virus infection. J Virol Methods 2014; 204:101-4. [PMID: 24747008 DOI: 10.1016/j.jviromet.2014.03.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/04/2014] [Accepted: 03/07/2014] [Indexed: 02/05/2023]
Abstract
A genetic diagnosis system for detecting avian influenza A (H7N9) virus infection using reverse transcription-loop-mediated isothermal amplification (RT-LAMP) technology was developed. The RT-LAMP assay showed no cross-reactivity with seasonal influenza A (H3N2 and H1N1pdm09) or influenza B viruses circulating in humans or with avian influenza A (H5N1) viruses. The sensitivity of the RT-LAMP assay was 42.47 copies/reaction. Considering the high specificity and sensitivity of the assay for detecting the avian influenza A (H7N9) virus and that the reaction was completed within 30 min, the RT-LAMP assay developed in this study is a promising rapid diagnostic tool for avian influenza A (H7N9) virus infection.
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Affiliation(s)
- Mina Nakauchi
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Ikuyo Takayama
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Hitoshi Takahashi
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Masato Tashiro
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Tsutomu Kageyama
- Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan.
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18
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Kalthoff D, Bogs J, Harder T, Grund C, Pohlmann A, Beer M, Hoffmann B. Nucleic acid-based detection of influenza A virus subtypes H7 and N9 with a special emphasis on the avian H7N9 virus. ACTA ACUST UNITED AC 2014; 19. [PMID: 24650867 DOI: 10.2807/1560-7917.es2014.19.10.20731] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In 2013, a novel influenza A virus of subtype H7N9 was transmitted from avian sources to humans in China, causing severe illness and substantial mortality. Rapid and sensitive diagnostic approaches are the basis of epidemiological studies and of utmost importance for the detection of infected humans and animals. We developed various quantitative reverse transcriptase PCR (RT-qPCR) assays for (i) the generic detection of the haemagglutinin (HA) gene of H7 viruses or the neuraminidase (NA) gene of N9 viruses, and (ii) the specific detection of HA and NA of the novel avian H7N9/2013 virus. The sensitivity of the newly developed assays was compared with previously published PCRs, and the specificity of all RT-qPCRs was examined using a panel of 42 different H7 and 16 different N9 isolates. Furthermore, we analysed the performance of the RT-qPCR assays with dilution series and diagnostic samples obtained from animal experiments. Our study provides a comprehensive set of RT-qPCR assays for the reliable detection of the novel avian H7N9 virus, with high sensitivity and improved and tailored specificity values compared with published assays. Finally, we also present data about the robustness of a duplex assay for the simultaneous detection of HA and NA of the avian influenza H7N9/2013 virus.
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Affiliation(s)
- D Kalthoff
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
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Development of novel AllGlo-probe-based one-step multiplex qRT-PCR assay for rapid identification of avian influenza virus H7N9. Arch Virol 2014; 159:1707-13. [DOI: 10.1007/s00705-014-1979-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 01/06/2014] [Indexed: 11/26/2022]
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20
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H7N9 influenza-the laboratory presentations: a letter to editor. Asian Pac J Trop Biomed 2013; 3:584-5. [PMID: 23835531 PMCID: PMC3695587 DOI: 10.1016/s2221-1691(13)60118-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 06/13/2013] [Indexed: 10/26/2022] Open
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Computational assay of H7N9 influenza neuraminidase reveals R292K mutation reduces drug binding affinity. Sci Rep 2013; 3:3561. [PMID: 24356381 PMCID: PMC3868970 DOI: 10.1038/srep03561] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 11/25/2013] [Indexed: 12/17/2022] Open
Abstract
The emergence of a novel H7N9 avian influenza that infects humans is a serious cause for concern. Of the genome sequences of H7N9 neuraminidase available, one contains a substitution of arginine to lysine at position 292, suggesting a potential for reduced drug binding efficacy. We have performed molecular dynamics simulations of oseltamivir, zanamivir and peramivir bound to H7N9, H7N9-R292K, and a structurally related H11N9 neuraminidase. They show that H7N9 neuraminidase is structurally homologous to H11N9, binding the drugs in identical modes. The simulations reveal that the R292K mutation disrupts drug binding in H7N9 in a comparable manner to that observed experimentally for H11N9-R292K. Absolute binding free energy calculations with the WaterSwap method confirm a reduction in binding affinity. This indicates that the efficacy of antiviral drugs against H7N9-R292K will be reduced. Simulations can assist in predicting disruption of binding caused by mutations in neuraminidase, thereby providing a computational ‘assay.'
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Zhu Z, Fan H, Qi X, Qi Y, Shi Z, Wang H, Cui L, Zhou M. Development and evaluation of a SYBR green-based real time RT-PCR assay for detection of the emerging avian influenza A (H7N9) virus. PLoS One 2013; 8:e80028. [PMID: 24278234 PMCID: PMC3835827 DOI: 10.1371/journal.pone.0080028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/27/2013] [Indexed: 11/19/2022] Open
Abstract
Most recently a novel avian-origin influenza A (H7N9) virus emerged in China and has been associated with lots of human infection and fatal cases. Genetic analysis of the viral genome revealed that this reassortant virus might be better adapted to humans than other avian influenza viruses. Molecular diagnostic methods are thus urgently needed in public health laboratories. In this study, a SYBR green-based one-step real time reverse transcription-PCR (RT-PCR) was developed to detect the novel H7N9 virus. The primer pairs on the basis of the hemagglutinin and neuraminidase gene sequences of H7N9 viruses amplified subtype-specific fragments with Tm values of 80.77±0.06°C for H7 and 81.20±0.17°C for N9 respectively. The standard curves showed a dynamic linear range across 6 log units of RNA copy number (106 to 101 copies/ µl) with a detection limit of 10 copies per reaction for both H7 and N9 assays by using serial ten-fold diluted in-vitro transcribed viral RNA. In addition, no cross-reactivity was observed with seasonal H1N1, H1N1 pdm09, H3N2, H5N1 and H9N2 viruses as well as other human respiratory viruses. When the assay was further evaluated in H7N9 virus infected clinical samples, positive amplification signals were obtained in all of the specimens with the accordance between H7 and N9 assays. Therefore, the established SYBR green-based real time RT-PCR assay could provide a rapid, sensitive, specific and reliable alternative approach with lower costs for high throughput screening of suspected samples from humans, animals and environments in first line public health laboratories.
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Affiliation(s)
- Zheng Zhu
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Huan Fan
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Xian Qi
- Department of Acute Infectious Diseases Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yuhua Qi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Zhiyang Shi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Hua Wang
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Lunbiao Cui
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
- * E-mail: (LC); (MZ)
| | - Minghao Zhou
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
- * E-mail: (LC); (MZ)
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Tran-To Su C, Ouyang X, Zheng J, Kwoh CK. Structural analysis of the novel influenza A (H7N9) viral Neuraminidase interactions with current approved neuraminidase inhibitors Oseltamivir, Zanamivir, and Peramivir in the presence of mutation R289K. BMC Bioinformatics 2013; 14 Suppl 16:S7. [PMID: 24564719 PMCID: PMC3853198 DOI: 10.1186/1471-2105-14-s16-s7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Since late March 2013, there has been another global health concern with a sudden wave of flu infections by a novel strain of avian influenza A (H7N9) virus in China. To-date, there have been more than 100 infections with 23 deaths. It is more worrying as this viral strain has never been detected in humans and only been found to be of low-pathogenicity. Currently, there are 3 effective neuraminidase inhibitors for this H7N9 virus strain, i.e. oseltamivir, zanamivir, and peramivir. These drugs have been used for treatment of the H7N9 influenza in China. However, how these inhibitors work and affect the binding cavity of the novel H7N9 neuraminidase in the presence of potential mutations has not been disclosed. In our study, we investigate steric effects and subsequently show the conformational restraints of the inhibitor-binding site of the non-mutated and mutated H7N9 neuraminidase structures to different drug compounds. Results Combination of molecular docking and Molecular Dynamics simulation reveal that zanamivir forms more favorable and stable complex than oseltamivir and peramivir when binding to the active site of the H7N9 neuraminidase. And it is likely that the novel influenza A (H7N9) virus adopts a higher probability to acquire resistance to peramivir than the other two inhibitors. Conformational changes induced by the mutation R289K causes loss of number of hydrogen bonds between the inhibitors and the H7N9 viral neuraminidase in 2 out of 3 complexes. In addition, our results of binding-affinity relationships of the 3 inhibitors with the viral neuraminidase proteins of previous pandemics (H1N1, H5N1) and the current novel H7N9 reflected the extent of binding effectiveness of the 3 inhibitors to the novel H7N9 neuraminidase. Conclusions The results are novel and specific for the A/Hangzhou/1/2013(H7N9) influenza strain. Furthermore, the protocol could be useful for further drug-binding analysis and prediction of future viral mutations to which the virus evolves through adaptation and acquires resistance to the current available drugs.
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Development of dual-function ELISA for effective antigen and antibody detection against H7 avian influenza virus. BMC Microbiol 2013; 13:219. [PMID: 24083616 PMCID: PMC4015598 DOI: 10.1186/1471-2180-13-219] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/26/2013] [Indexed: 11/10/2022] Open
Abstract
Background Outbreaks in poultry involving influenza virus from H7 subtype have resulted in human infections, thus causing a major concern for public health, as well as for the poultry industry. Currently, no efficient rapid test is available for large-scale detection of either antigen or antibody of H7 avian influenza viruses. Results In the present study, a dual function ELISA was developed for the effective detection of antigen and antibody against H7 AIVs. The test was established based on antigen-capture-ELISA and epitope blocking ELISA. The two Mabs 62 and 98 which were exploited in the assay were identified to recognize two conformational neutralizing epitopes on H7 HA1. Both of the epitopes exist in all of the human H7 strains, including the recent H7N9 strain from China and > 96.6% of avian H7 strains. The dual ELISA was able to detect all of the five H7 antigens tested without any cross reaction to other influenza subtypes. The antigen detection limit was less than 1 HA unit of H7. For antibody detection, the sensitivity and specificity of the dual ELISA was evaluated and compared to HI and microneutralization using immunized animal sera to different H7 strains and different subtypes of AIVs. Results indicated that antibodies to H7 were readily detected in immunized animal sera by the dual ELISA whereas specimens with antibodies to other AIVs yielded negative results. Conclusions This is the first dual-function ELISA reported for either antigen or antibody detection against H7 AIVs. The assay was highly sensitive and 100% specific in both functions rendering it effective for H7 diagnosis.
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Rapid and sensitive detection of H7N9 avian influenza virus by use of reverse transcription-loop-mediated isothermal amplification. J Clin Microbiol 2013; 51:3760-4. [PMID: 24006004 DOI: 10.1128/jcm.01907-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An epidemic of human H7N9 influenza virus infection recently emerged in China whose clinical features include high mortality and which has also resulted in serious economic loss. The novel reassortant avian-origin influenza A (H7N9) virus which was the causative agent of this epidemic raised the possibility of triggering a large-scale influenza pandemic worldwide. It seemed likely that fast molecular detection assays specific for this virus would be in great demand. Here, we report a one-step reverse transcription-loop-mediated isothermal amplification (RT-LAMP) method for rapid detection of the hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 virus, the minimum detection limit of which was evaluated using in vitro RNA transcription templates. In total, 135 samples from clinical specimens (from either patients or poultry) were tested using this method in comparison with the real-time PCR recommended by the World Health Organization (WHO). Our results showed that (i) RT-LAMP-based trials can be completed in approximately 12 to 23 min and (ii) the detection limit for the H7 gene is around 10 copies per reaction, similar to that of the real-time PCR, whereas the detection limit for its counterpart the N9 gene is 5 copies per reaction, a 100-fold-higher sensitivity than the WHO-recommended method. Indeed, this excellent performance of our method was also validated by the results for a series of clinical specimens. Therefore, we believe that the simple, fast, and sensitive method of RT-LAMP might be widely applied for detection of H7N9 infections and may play a role in prevention of an influenza pandemic.
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Li Y, Wu T, Qi X, Ge Y, Guo X, Wu B, Yu H, Zhu Y, Shi Z, Wang H, Cui L, Zhou M. Simultaneous detection of hemagglutinin and neuraminidase genes of novel influenza A (H7N9) by duplex real-time reverse transcription polymerase chain reaction. J Virol Methods 2013; 194:194-6. [PMID: 24001700 PMCID: PMC7113656 DOI: 10.1016/j.jviromet.2013.08.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/26/2013] [Accepted: 08/21/2013] [Indexed: 12/01/2022]
Abstract
A novel avian influenza A H7N9 virus has recently emerged in humans. We present a duplex rRT-PCR assay for the low-cost detection of this virus. The assay performed on a par with the WHO-recommended detection assay. Assay sensitivity, specificity and reproducibility make it suitable for scaling-up.
A novel reassortant influenza A (H7N9) virus emerged recently in China. In this study, a duplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay was developed for the simultaneous detection of hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 influenza viruses. The sensitivity of the assay was determined to be 10 RNA copies per reaction for both HA and NA genes. No cross-reactivity was observed with other influenza virus subtypes or respiratory tract viruses. One hundred and forty-six clinical and environmental specimens were tested and compared with reference methods and were found to be consistent. The assay is suitable for large-scale screening due to short turnaround times and high specificity, sensitivity, and reproducibility.
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Affiliation(s)
- Yan Li
- Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
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Abstract
The recent emergence of influenza A virus (H7N9) emphasizes the need for its rapid detection. While commercial nucleic acid amplification tests (NAATs) are commonly used to detect seasonal influenza virus, this study demonstrated that the analytical sensitivity of commercial assays is highly variable compared to that of CDC-based in-house NAATs for the detection of H7N9.
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Zhu Z, Yang Y, Feng Y, Shi B, Chen L, Zheng Y, Tian D, Song Z, Xu C, Qin B, Zhang X, Guan W, Liu F, Yang T, Yang H, Zeng D, Zhou W, Hu Y, Zhou X. Infection of inbred BALB/c and C57BL/6 and outbred Institute of Cancer Research mice with the emerging H7N9 avian influenza virus. Emerg Microbes Infect 2013; 2:e50. [PMID: 26038485 PMCID: PMC3821289 DOI: 10.1038/emi.2013.50] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/03/2013] [Accepted: 07/07/2013] [Indexed: 01/21/2023]
Abstract
A new avian-origin influenza virus A (H7N9) recently crossed the species barrier and infected humans; therefore, there is an urgent need to establish mammalian animal models for studying the pathogenic mechanism of this strain and the immunological response. In this study, we attempted to develop mouse models of H7N9 infection because mice are traditionally the most convenient models for studying influenza viruses. We showed that the novel A (H7N9) virus isolated from a patient could infect inbred BALB/c and C57BL/6 mice as well as outbred Institute of Cancer Research (ICR) mice. The amount of bodyweight lost showed differences at 7 days post infection (d.p.i.) (BALB/c mice 30%, C57BL/6 and ICR mice approximately 20%), and the lung indexes were increased both at 3 d.p.i. and at 7 d.p.i.. Immunohistochemistry demonstrated the existence of the H7N9 viruses in the lungs of the infected mice, and these findings were verified by quantitative real-time polymerase chain reaction (RT-PCR) and 50% tissue culture infectious dose (TCID50) detection at 3 d.p.i. and 7 d.p.i.. Histopathological changes occurred in the infected lungs, including pulmonary interstitial inflammatory lesions, pulmonary oedema and haemorrhages. Furthermore, because the most clinically severe cases were in elderly patients, we analysed the H7N9 infections in both young and old ICR mice. The old ICR mice showed more severe infections with more bodyweight lost and a higher lung index than the young ICR mice. Compared with the young ICR mice, the old mice showed a delayed clearance of the H7N9 virus and higher inflammation in the lungs. Thus, old ICR mice could partially mimic the more severe illness in elderly patients.
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Affiliation(s)
- Zhaoqin Zhu
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Yuqin Yang
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Yanling Feng
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Bisheng Shi
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Lixiang Chen
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Ye Zheng
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Di Tian
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Zhigang Song
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Chunhua Xu
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Boyin Qin
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Xiaonan Zhang
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Wencai Guan
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Fang Liu
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Tao Yang
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Hua Yang
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Dong Zeng
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Wenjiang Zhou
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China
| | - Yunwen Hu
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China ; Key laboratory of Medical Molecular Virology of the Ministries of Education, School of Basic Medical Science, Fudan Univeristy, Shanghai 200032, China
| | - Xiaohui Zhou
- Shanghai Public Health Clinical Center, Fudan University , Shanghai 201508, China ; Key laboratory of Medical Molecular Virology of the Ministries of Education, School of Basic Medical Science, Fudan Univeristy, Shanghai 200032, China
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Rapid and sensitive detection of novel avian-origin influenza A (H7N9) virus by reverse transcription loop-mediated isothermal amplification combined with a lateral-flow device. PLoS One 2013; 8:e69941. [PMID: 23936359 PMCID: PMC3731295 DOI: 10.1371/journal.pone.0069941] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/18/2013] [Indexed: 11/19/2022] Open
Abstract
A severe disease in humans caused by a novel avian-origin influenza A (H7N9) virus emerged in China recently, which has caused at least 128 cases and 26 deaths. Rapid detection of the novel H7N9 virus is urgently needed to differentiate the disease from other infections, and to facilitate infection control as well as epidemiologic investigations. In this study, a reverse transcription loop-mediated isothermal amplification combined with a lateral flow device (RT-LAMP-LFD) assay to rapidly detect H7N9 virus was developed and evaluated. The RT-LAMP primers were designed to target the haemagglutinin (HA) and neuraminidase (NA) genes of H7N9 virus. Results of 10-fold dilution series assays showed that analysis of RT-LAMP products by the LFD method was as sensitive as real-time turbidity detection, and that the analytic sensitivities of the HA and NA RT-LAMP assays were both 10 copies of synthetic RNA. Furthermore, both the assays showed 100% clinical specificity for identification of H7N9 virus. The performance characteristics of the RT-LAMP-LFD assay were evaluated with 80 clinical specimens collected from suspected H7N9 patients. The NA RT-LAMP-LFD assay was more sensitive than real time RT-PCR assay. Compared with a combination of virus culture and real-time RT-PCR, the sensitivity, specificity, positive predictive value, and negative predictive value of the RT-LAMP-LFD assay were all 100%. Overall, The RT-LAMP-LFD assay established in this study can be used as a reliable method for early diagnosis of the avian-origin influenza A (H7N9) virus infection.
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