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Kufner V, Frey AC, Burkhard SH, Schmutz S, Ziltener G, Zaheri M, Wiedmer CV, Plate A, Trkola A, Huber M, Mueller NJ. Exploring viral aetiology in upper respiratory tract infections: insights from metagenomic next-generation sequencing in Swiss outpatients before and during the SARS-CoV-2 pandemic. Swiss Med Wkly 2024; 154:3797. [PMID: 38587784 DOI: 10.57187/s.3797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
AIMS OF THE STUDY Upper respiratory tract infections are among the most common reasons for primary care consultations. They are diagnosed predominantly based on clinical assessment. Here, we investigated the benefit of viral metagenomic next-generation sequencing (mNGS) in an outpatient setting. METHODS This prospective cross-sectional study included immunocompetent patients with acute upper respiratory tract infections. General practitioners collected pharyngeal swabs and demographic and clinical data. Specimens were analysed using viral mNGS and conventional tests. RESULTS Two hundred seventy-seven patients were recruited by 21 general practitioners between 10/2019 and 12/2020, of which 91% had a suspected viral aetiology. For 138 patients (49.8%), mNGS identified one or more respiratory viruses. The mNGS showed a high overall agreement with conventional routine diagnostic tests. Rhinoviruses were the most frequently detected respiratory viruses (20.2% of patients). Viral mNGS reflected the influenza wave in early 2020 and the SARS-CoV-2 pandemic outbreak in Switzerland in March 2020. Notably, rhinoviruses continued to circulate despite non-pharmaceutical hygiene measures. CONCLUSIONS Viral mNGS allowed the initial diagnosis to be retrospectively re-evaluated. Assuming reduced turnaround times, mNGS has the potential to directly guide the treatment of upper respiratory tract infections. On an epidemiological level, our study highlights the utility of mNGS in respiratory infection surveillance, allowing early detection of epidemics and providing information crucial for prevention.
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Affiliation(s)
- Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Andrea C Frey
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Sara H Burkhard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Gabriela Ziltener
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Caroline V Wiedmer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Andreas Plate
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nicolas J Mueller
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
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Epidemiology of Community-Acquired Respiratory Tract Infections in Patients Admitted at the Emergency Departments. Trop Med Infect Dis 2022; 7:tropicalmed7090233. [PMID: 36136644 PMCID: PMC9501977 DOI: 10.3390/tropicalmed7090233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
Objectives: Community-acquired respiratory infections (CARTIs) are responsible for serious morbidities worldwide. Identifying the aetiology can decrease the use of unnecessary antimicrobial therapy. In this study, we intend to determine the pathogenic agents responsible for respiratory infections in patients presenting to the emergency department of several Lebanese hospitals. Methods: A total of 100 patients presenting to the emergency departments of four Lebanese hospitals and identified as having CARTIs between September 2017 and September 2018 were recruited. Specimens of upper and lower respiratory tract samples were collected. Pathogens were detected by a multiplex polymerase chain reaction respiratory panel. Results: Of 100 specimens, 84 contained at least one pathogen. Many patients were detected with ≥2 pathogens. The total number of pathogens from these 84 patients was 163. Of these pathogens, 36 (22%) were human rhinovirus, 28 (17%) were Streptococcus pneumoniae, 16 (10%) were metapneumovirus, 16 (10%) were influenza A virus, and other pathogens were detected with lower percentages. As expected, the highest occurrence of pathogens was observed between December and March. Respiratory syncytial virus accounted for 2% of the cases and only correlated to paediatric patients. Conclusion: CARTI epidemiology is important and understudied in Lebanon. This study offers the first Lebanese data about CARTI pathogens. Viruses were the most common aetiologies of CARTIs. Thus, a different approach must be used for the empirical management of CARTI. Rapid testing might be useful in identifying patients who need antibiotic therapy.
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Butler D, Ebrahimi A. Rapid and sensitive detection of viral particles by coupling redox cycling and electrophoretic enrichment. Biosens Bioelectron 2022; 208:114198. [PMID: 35395617 PMCID: PMC8931995 DOI: 10.1016/j.bios.2022.114198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/24/2022] [Accepted: 03/16/2022] [Indexed: 12/27/2022]
Abstract
The COVID-19 pandemic has highlighted the need for rapid, low-cost, and sensitive virus detection platforms to monitor and mitigate widespread outbreaks. Electrochemical sensors are a viable choice to fill this role but still require improvements to the signal magnitude, especially for early detection and low viral loads. Herein, finite element analysis of a novel biosensor concept for single virion counting using a generator-collector microelectrode design is presented. The proposed design combines a redox-cycling amplified electrochemical current with electrophoresis-driven electrode-particle collision for rapid virus detection. The effects of experimental (e.g. scan rate, collector bias) and geometric factors are studied to optimize the sensor design. Two generator-collector configurations are explored: a ring-disk configuration to analyze sessile droplets and an interdigitated electrode (IDE) design housed in a microchannel. For the ring-disk configuration, we calculate an amplification factor of ∼5 and collector efficiency of ∼0.8 for a generator-collector spacing of 600 nm. For the IDE, the collector efficiency is even larger, approaching unity. The dual-electrode mode is critical for increasing the current and electric field strength. As a result, the current steps upon virus capture are more than an order of magnitude larger compared to single-mode. Additionally, single virus capture times are reduced from over 700 s down to ∼20 s. Overall, the frequency of virus capture and magnitude of the electrochemical current steps depend on the virus properties and electrode configuration, with the IDE capable of single virus detection within seconds owing to better particle confinement in the microchannel.
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Affiliation(s)
- Derrick Butler
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA; Materials Research Institute, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Aida Ebrahimi
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA; Materials Research Institute, The Pennsylvania State University, University Park, PA, 16802, USA; Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA; Center for Biodevices, The Pennsylvania State University, University Park, PA, 16802, USA.
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Liu WK, Chen DH, Tan WP, Qiu SY, Xu D, Zhang L, Gu SJ, Zhou R, Liu Q. Paramyxoviruses respiratory syncytial virus, parainfluenza virus, and human metapneumovirus infection in pediatric hospitalized patients and climate correlation in a subtropical region of southern China: a 7-year survey. Eur J Clin Microbiol Infect Dis 2019; 38:2355-2364. [PMID: 31489496 PMCID: PMC6858468 DOI: 10.1007/s10096-019-03693-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/26/2019] [Indexed: 11/11/2022]
Abstract
To investigate the features of paramyxovirus respiratory syncytial virus (RSV), parainfluenza virus (PIV), and human metapneumovirus (HMPV) infection and determine the effect of meteorological conditions in Guangzhou, a subtropical region of southern China. We collected 11,398 respiratory samples from hospitalized pediatric patients with acute respiratory illness between July 2009 and June 2016 in Guangzhou. The samples were tested simultaneously for 18 respiratory pathogens using real-time PCR. Local meteorological data were also collected for correlation analysis. Of 11,398 patients tested, 5606 (49.2%) patients tested positive for one or more pathogens; RSV, PIV, and HMPV were the first, sixth, and ninth most frequently detected pathogens, in 1690 (14.8%), 502 (4.4%), and 321 (2.8%) patients, respectively. A total 17.9% (4605/5606) of patients with positive results had coinfection with other pathogens. Significant differences were found in the prevalence of RSV, PIV, and HMPV among all age groups (p < 0.001). RSV and HMPV had similar seasonal patterns, with two prevalence peaks every year. PIV appeared alternatively with RSV and HMPV. Multiple linear regression models were established for RSV, PIV, and HMPV prevalence and meteorological factors (p < 0.05). RSV and PIV incidence was negatively correlated with monthly mean relative humidity; RSV and HMPV incidence was negatively correlated with sunshine duration; PIV incidence was positively correlated with mean temperature. We described the features of paramyxovirus infection in a subtropical region of China and highlighted the correlation with meteorological factors. These findings will assist public health authorities and clinicians in improving strategies for controlling paramyxovirus infection.
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Affiliation(s)
- Wen-Kuan Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - De-Hui Chen
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei-Ping Tan
- Department of Pediatrics, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shu-Yan Qiu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Duo Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Li Zhang
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Shu-Jun Gu
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rong Zhou
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Qian Liu
- Scientific Research Center, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- Department of Pediatrics, Dongguan Eighth People’s Hospital, Dongguan, China
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Liu WK, Liu Q, Chen DH, Tan WP, Cai Y, Qiu SY, Xu D, Li C, Li X, Lin ZS, Zhou R. Epidemiology of HBoV1 infection and relationship with meteorological conditions in hospitalized pediatric patients with acute respiratory illness: a 7-year study in a subtropical region. BMC Infect Dis 2018; 18:329. [PMID: 30012099 PMCID: PMC6048719 DOI: 10.1186/s12879-018-3225-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 06/29/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Human bocavirus 1 (HBoV1) is an important cause of acute respiratory illness (ARI), yet the epidemiology and effect of meteorological conditions on infection is not fully understood. To investigate the distribution of HBoV1 and determine the effect of meteorological conditions, hospitalized pediatric patients were studied in a subtropical region of China. METHODS Samples from 11,399 hospitalized pediatric patients (≤14 years old), with ARI were tested for HBoV1 and other common respiratory pathogens using real-time PCR, between July 2009 and June 2016. In addition, local meteorological data were collected. RESULTS Of the 11,399 patients tested, 5606 (49.2%) were positive for at least one respiratory pathogen. Two hundred forty-eight of 11,399 (2.2%) were positive for HBoV1 infection. Co-infection was common in HBoV1-positive patients (45.2%, 112/248). A significant difference in the prevalence of HBoV1 was found in patients in different age groups (p < 0.001), and the peak prevalence was found in patients aged 7-12 months (4.7%, 56/1203). Two HBoV1 prevalence peaks were found in summer (between June and September) and winter (between November and December). The prevalence of HBoV1 was significantly positively correlated with mean temperature and negatively correlated with mean relative humidity, and the mean temperature in the preceding month had better explanatory power than the current monthly temperature. CONCLUSIONS This study provides a better understanding of the characteristics of HBoV1 infection in children in subtropical regions. Data from this study provide useful information for the future control and prevention of HBoV1 infections.
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Affiliation(s)
- Wen-Kuan Liu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Qian Liu
- Central Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - De-Hui Chen
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Wei-Ping Tan
- Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yong Cai
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Shu-Yan Qiu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Duo Xu
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Chi Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Xiao Li
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Zheng-Shi Lin
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Rong Zhou
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
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Chan M, Koo SH, Jiang B, Lim PQ, Tan TY. Comparison of the Biofire FilmArray Respiratory Panel, Seegene AnyplexII RV16, and Argene for the detection of respiratory viruses. J Clin Virol 2018; 106:13-17. [PMID: 30007137 PMCID: PMC7185839 DOI: 10.1016/j.jcv.2018.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/18/2018] [Accepted: 07/05/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Respiratory infections are common reasons for hospital admission, and are associated with enormous economic burden due to significant morbidity and mortality. The wide spectrum of microbial agents underlying the pathology renders the diagnosis of respiratory infections challenging. Molecular diagnostics offer an advantage to the current serological and culture-based methods in terms of sensitivity, coverage, hands-on time, and time to results. OBJECTIVES This study aimed to compare the clinical performance of three commercial kits for respiratory viral detection. STUDY DESIGN The performance of FilmArray Respiratory Panel, AnyplexII RV16, and Argene was compared using clinical respiratory samples (n = 224, comprising 189 nasopharyngeal swabs in Universal Transport Medium (UTM) and 35 endotracheal aspirates), based on common overlapping targets across the platforms. Influenza A "equivocal" and "no-subtype" samples by FilmArray were further compared to a laboratory-developed Influenza A/B test. RESULTS AND CONCLUSIONS The overall performance of all three platforms appeared to be comparable with regards to sensitivities (95.8-97.9%) and specificities (96.1-98.0%), detection of coinfections, and distinguishment of influenza from non-influenza cases. "Equivocal" and "no-subtype" samples by FilmArray mostly represented weak Influenza A by laboratory-developed test. Lower respiratory tract samples had comparable final-run success-rates and discordant-rates as compared to UTM. Coronavirus HKU1, which was not targeted by AnyplexII RV16, were detected as OC43. The expected test volume would be the main determinant for the selection of platform. Among the platforms, the FilmArray is the most automated but is of the lowest-throughput and has the highest reagent cost.
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Affiliation(s)
- Maurice Chan
- Department of Laboratory Medicine, Changi General Hospital, Singapore
| | - Seok Hwee Koo
- Clinical Trials & Research Unit, Changi General Hospital, Singapore
| | - Boran Jiang
- Department of Laboratory Medicine, Changi General Hospital, Singapore
| | - Pei Qi Lim
- Clinical Trials & Research Unit, Changi General Hospital, Singapore
| | - Thean Yen Tan
- Department of Laboratory Medicine, Changi General Hospital, Singapore.
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Hastings AK, Amato KR, Wen SC, Peterson LS, Williams JV. Human metapneumovirus small hydrophobic (SH) protein downregulates type I IFN pathway signaling by affecting STAT1 expression and phosphorylation. Virology 2016; 494:248-56. [PMID: 27131212 DOI: 10.1016/j.virol.2016.04.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 12/17/2022]
Abstract
Type I interferon (IFN) is a key mediator of antiviral immunity. Human metapneumovirus (HMPV) inhibits IFN signaling, but does not encode homologues of known IFN antagonists. We tested the hypothesis that a specific viral protein prevents type I IFN signaling by targeting signal transducer and activator of transcription-1 (STAT1). We found that human airway epithelial cells (capable of expressing IFNs) became impaired for STAT1 phosphorylation even without direct infection due to intrinsic negative feedback. HMPV-infected Vero cells (incapable of expressing IFN) displayed lower STAT1 expression and impaired STAT1 phosphorylation in response to type I IFN treatment compared to mock-infected cells. Transient overexpression of HMPV small hydrophobic (SH) protein significantly inhibited STAT1 phosphorylation and signaling, and recombinant virus lacking SH protein was unable to inhibit STAT1 phosphorylation. Our results indicate a role for the SH protein of HMPV in the downregulation of type I IFN signaling through the targeting of STAT1.
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Affiliation(s)
- Andrew K Hastings
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
| | - Katherine R Amato
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
| | - Sherry C Wen
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
| | - Laura S Peterson
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
| | - John V Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, United States.
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Salez N, Vabret A, Leruez-Ville M, Andreoletti L, Carrat F, Renois F, de Lamballerie X. Evaluation of Four Commercial Multiplex Molecular Tests for the Diagnosis of Acute Respiratory Infections. PLoS One 2015; 10:e0130378. [PMID: 26107509 PMCID: PMC4481272 DOI: 10.1371/journal.pone.0130378] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 05/20/2015] [Indexed: 11/19/2022] Open
Abstract
Acute Respiratory Infections (ARIs) are responsible for considerable morbidity and mortality worldwide. Documentation of respiratory specimens can help for an appropriate clinical management with a significant effect on the disease progress in patient, the antimicrobial therapy used and the risk of secondary spread of infection. Here, we compared the performances of four commercial multiplex kits used in French University Hospital diagnostic microbiology laboratories for the detection of ARI pathogens (i.e., the xTAG Respiratory Viral Panel Fast, RespiFinder SMART 22, CLART PneumoVir and Fast Track Diagnostics Respiratory Pathogen 33 kits). We used a standardised nucleic acids extraction protocol and a comprehensive comparative approach that mixed reference to well established real-time PCR detection techniques and analysis of convergent positive results. We tested 166 respiratory clinical samples and identified a global high degree of correlation for at least three of the techniques (xTAG, RespiFinder and FTD33). For these techniques, the highest Youden's index (YI), positive predictive (PPV) and specificity (Sp) values were observed for Core tests (e.g., influenza A [YI:0.86-1.00; PPV:78.95-100.00; Sp:97.32-100.00] & B [YI:0.44-1.00; PPV:100.00; Sp:100.00], hRSV [YI:0.50-0.99; PPV:85.71-100.00; Sp:99.38-100.00], hMPV [YI:0.71-1.00; PPV:83.33-100.00; Sp:99.37-100.00], EV/hRV [YI:0.62-0.82; PPV:93.33-100.00; Sp:94.48-100.00], AdV [YI:1.00; PPV:100.00; Sp:100.00] and hBoV [YI:0.20-0.80; PPV:57.14-100.00; Sp:98.14-100.00]). The present study completed an overview of the multiplex techniques available for the diagnosis of acute respiratory infections.
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Affiliation(s)
- Nicolas Salez
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", Marseille, France
- * E-mail:
| | - Astrid Vabret
- Laboratory of Human and Molecular Virology, IFR146 ICORE, University Hospital, Caen, France
| | - Marianne Leruez-Ville
- Virology Laboratory, Hôpital Necker Enfants malades, APHP, Université Paris Descartes, Sorbonne Paris Cité-EA 36–20, Paris, France
| | - Laurent Andreoletti
- Unité de Virologie Médicale et Moléculaire, Centre Hospitalier Universitaire, and IFR 53/EA-4303 (DAT/PPCIDH), Faculté de Médecine, Reims, France
| | - Fabrice Carrat
- UMR-S 707 INSERM, Pierre et Marie Curie University, Paris, France
- Public Assistance Hospital of Paris, Department of Internal Medicine, Hôpital Saint Antoine, Unité de Santé Publique, Paris, France
| | - Fanny Renois
- Unité de Virologie Médicale et Moléculaire, Centre Hospitalier Universitaire, and IFR 53/EA-4303 (DAT/PPCIDH), Faculté de Médecine, Reims, France
| | - Xavier de Lamballerie
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", Marseille, France
- IHU Institute hospitalo-universitaire Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France
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Fowlkes A, Giorgi A, Erdman D, Temte J, Goodin K, Di Lonardo S, Sun Y, Martin K, Feist M, Linz R, Boulton R, Bancroft E, McHugh L, Lojo J, Filbert K, Finelli L. Viruses associated with acute respiratory infections and influenza-like illness among outpatients from the Influenza Incidence Surveillance Project, 2010-2011. J Infect Dis 2013; 209:1715-25. [PMID: 24338352 PMCID: PMC5749912 DOI: 10.1093/infdis/jit806] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background. The Influenza Incidence Surveillance Project (IISP) monitored outpatient acute respiratory infection (ARI; defined as the presence of ≥2 respiratory symptoms not meeting ILI criteria) and influenza-like illness (ILI) to determine the incidence and contribution of associated viral etiologies. Methods. From August 2010 through July 2011, 57 outpatient healthcare providers in 12 US sites reported weekly the number of visits for ILI and ARI and collected respiratory specimens on a subset for viral testing. The incidence was estimated using the number of patients in the practice as the denominator, and the virus-specific incidence of clinic visits was extrapolated from the proportion of patients testing positive. Results. The age-adjusted cumulative incidence of outpatient visits for ARI and ILI combined was 95/1000 persons, with a viral etiology identified in 58% of specimens. Most frequently detected were rhinoviruses/enteroviruses (RV/EV) (21%) and influenza viruses (21%); the resulting extrapolated incidence of outpatient visits was 20 and 19/1000 persons respectively. The incidence of influenza virus-associated clinic visits was highest among patients aged 2–17 years, whereas other viruses had varied patterns among age groups. Conclusions. The IISP provides a unique opportunity to estimate the outpatient respiratory illness burden by etiology. Influenza virus infection and RV/EV infection(s) represent a substantial burden of respiratory disease in the US outpatient setting, particularly among children.
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Respiratory virus identification by interval polymerase chain reaction testing in the southeastern United States. Am J Infect Control 2013; 41:769-72. [PMID: 23507154 DOI: 10.1016/j.ajic.2012.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 11/21/2012] [Accepted: 11/26/2012] [Indexed: 11/20/2022]
Abstract
BACKGROUND This study was designed to determine if testing the first ~40 nasal washings (interval) each month for 1 year, could be used as an epidemiologic tool for seasonality and prevalence of respiratory viruses such as human metapneumovirus in an adult and pediatric population in the southeastern United States. MATERIALS AND METHODS Results of interval polymerase chain reaction (PCR) testing of 469 specimens for 8 viruses were compared with our current procedures using PCR, culture, or respiratory synctial virus antigen for all 7435 specimens (routine). RESULTS One hundred thirty-six viruses out of 469 specimens (29.0%) and 1,495 viruses out of 7,435 specimens (20.1%) were identified by interval and routine testing, respectively. Seasonal detection varied among viruses and to some degree between interval and routine testing. A higher percent of positives and dual infections were detected by interval testing of pediatric specimens, likely due to the use of PCR for viruses commonly seen in this population. Human metapneumovirus was detected in both pediatric and adult specimens between January and August. CONCLUSIONS Interval testing can be used to provide a snapshot of prevalence and seasonality of respiratory viruses, although as currently designed they may not be sensitive enough to identify the beginning of a specific virus season. Exclusive use of interval PCR testing identified several dual infections, including human metapneumovirus, throughout most of the year in Florida. A rapid turnaround time to results translates into improved infection control and improved patient care.
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Vallières E, Renaud C. Clinical and economical impact of multiplex respiratory virus assays. Diagn Microbiol Infect Dis 2013; 76:255-61. [PMID: 23601453 PMCID: PMC7132665 DOI: 10.1016/j.diagmicrobio.2013.03.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/21/2013] [Accepted: 03/05/2013] [Indexed: 01/15/2023]
Abstract
During the last decade, a variety of molecular assays targeting respiratory viruses have been developed and commercialized. Therefore, multiplex PCR are increasingly used in everyday clinical practice. This improves our understanding of respiratory virus epidemiology and enhances our concerns about their clinical impact in specific patient populations. However, questions remain regarding cost-effectiveness of performing these diagnostic tests in routine and their real impact on patient care. This article will review available data and highlight unresolved questions about cost-effectiveness, infection control, clinical utility and public health impact of multiplex respiratory virus assays.
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Affiliation(s)
- Emilie Vallières
- Département de Microbiologie et Immunologie, CHU Sainte-Justine, Université de Montréal, Montréal, Québec H3T 1C5, Canada
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Comparison of the Biofire FilmArray RP, Genmark eSensor RVP, Luminex xTAG RVPv1, and Luminex xTAG RVP fast multiplex assays for detection of respiratory viruses. J Clin Microbiol 2013; 51:1528-33. [PMID: 23486707 DOI: 10.1128/jcm.03368-12] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There are several U.S. FDA-cleared molecular respiratory virus panels available today, each with advantages and disadvantages. This study compares four multiplex panels, the BioFire Diagnostics FilmArray RP (respiratory panel), the GenMark Dx eSensor RVP (respiratory viral panel), the Luminex xTAG RVPv1, and the Luminex xTAG RVP fast. Three hundred specimens (200 retrospective and 100 consecutive) were tested using all four platforms to determine performance characteristics. The overall sensitivity and specificity, respectively, and 95% confidence interval (CI; in parentheses) for each panel were as follows: FilmArray RP, 84.5% (79.2, 88.6) and 100% (96.2, 100); eSensor RVP, 98.3% (95.5, 99.5) and 99.2% (95.4, 100); xTAG RVPv1, 92.7% (88.5, 95.4) and 99.8% (96.0, 100); and xTAG RVP fast, 84.4% (78.5, 88.9) and 99.9% (96.1, 100). The sensitivity of each assay fluctuated by viral target, with the greatest discrepancies noted for adenovirus and influenza virus B detection. Hands-on time and time to result were recorded and ease of use was assessed to generate a complete profile of each assay.
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Comparison of three multiplex PCR assays for the detection of respiratory viral infections: evaluation of xTAG respiratory virus panel fast assay, RespiFinder 19 assay and RespiFinder SMART 22 assay. BMC Infect Dis 2012; 12:163. [PMID: 22828244 PMCID: PMC3519643 DOI: 10.1186/1471-2334-12-163] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 06/28/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A broad spectrum of pathogens is causative for respiratory tract infections, but symptoms are mostly similar. Therefore, the identification of the causative viruses and bacteria is only feasible using multiplex PCR or several monoplex PCR tests in parallel. METHODS The analytical sensitivity of three multiplex PCR assays, RespiFinder-19, RespiFinder-SMART-22 and xTAG-Respiratory-Virus-Panel-Fast-Assay (RVP), were compared to monoplex real-time PCR with quantified standardized control material. All assays include the most common respiratory pathogens. RESULTS To compare the analytical sensitivity of the multiplex assays, samples were inoculated with 13 different quantified viruses in the range of 10(1) to 10(5) copies/ml. Concordant results were received for rhinovirus, whereas the RVP detected influenzavirus, RSV and hMPV more frequently in low concentrations. The RespiFinder-19 and the RespiFinder-SMART-22 showed a higher analytical sensitivity for adenoviruses and coronaviruses, whereas the RVP was incapable to detect adenovirus and coronavirus in concentrations of 10(4) copies/ml. The RespiFinder-19 and RespiFinder-SMART-22A did not detect influenzaviruses (104 copies/ml) and RSV (10(3) copies/ml). The detection of all 13 viruses in one sample was only achieved using monoplex PCR. To analyze possible competitive amplification reactions between the different viruses, samples were further inoculated with only 4 different viruses in one sample. Compared to the detection of 13 viruses in parallel, only a few differences were found.The incidence of respiratory viruses was compared in tracheal secretion (TS) samples (n = 100) of mechanically ventilated patients in winter (n = 50) and summer (n = 50). In winter, respiratory viruses were detected in 32 TS samples (64%) by RespiFinder-19, whereas the detection rate with RVP was only 22%. The most frequent viruses were adenovirus (32%) and PIV-2 (20%). Multiple infections were detected in 16 TS samples (32%) by RespiFinder-19. Fewer infections were found in summer (RespiFinder-19: 20%; RVP: 6%). All positive results were verified using monoplex PCR. CONCLUSIONS Multiplex PCR tests have a broad spectrum of pathogens to test at a time. Analysis of multiple inoculated samples revealed a different focus of the detected virus types by the three assays. Analysis of clinical samples showed a high concordance of detected viruses by the RespiFinder-19 compared to monoplex tests.
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Poritz MA, Blaschke AJ, Byington CL, Allen L, Nilsson K, Jones DE, Thatcher SA, Robbins T, Lingenfelter B, Amiott E, Herbener A, Daly J, Dobrowolski SF, Teng DHF, Ririe KM. FilmArray, an automated nested multiplex PCR system for multi-pathogen detection: development and application to respiratory tract infection. PLoS One 2011; 6:e26047. [PMID: 22039434 PMCID: PMC3198457 DOI: 10.1371/journal.pone.0026047] [Citation(s) in RCA: 262] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 09/16/2011] [Indexed: 12/19/2022] Open
Abstract
The ideal clinical diagnostic system should deliver rapid, sensitive, specific and reproducible results while minimizing the requirements for specialized laboratory facilities and skilled technicians. We describe an integrated diagnostic platform, the "FilmArray", which fully automates the detection and identification of multiple organisms from a single sample in about one hour. An unprocessed biologic/clinical sample is subjected to nucleic acid purification, reverse transcription, a high-order nested multiplex polymerase chain reaction and amplicon melt curve analysis. Biochemical reactions are enclosed in a disposable pouch, minimizing the PCR contamination risk. FilmArray has the potential to detect greater than 100 different nucleic acid targets at one time. These features make the system well-suited for molecular detection of infectious agents. Validation of the FilmArray technology was achieved through development of a panel of assays capable of identifying 21 common viral and bacterial respiratory pathogens. Initial testing of the system using both cultured organisms and clinical nasal aspirates obtained from children demonstrated an analytical and clinical sensitivity and specificity comparable to existing diagnostic platforms. We demonstrate that automated identification of pathogens from their corresponding target amplicon(s) can be accomplished by analysis of the DNA melting curve of the amplicon.
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Affiliation(s)
- Mark A Poritz
- Idaho Technology, Inc., Salt Lake City, Utah, United States of America.
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Olofsson S, Brittain-Long R, Andersson LM, Westin J, Lindh M. PCR for detection of respiratory viruses: seasonal variations of virus infections. Expert Rev Anti Infect Ther 2011; 9:615-26. [PMID: 21819328 PMCID: PMC7103711 DOI: 10.1586/eri.11.75] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Real-time PCR and related methods have revolutionized the laboratory diagnosis of viral respiratory infections because of their high detection sensitivity, rapidness and potential for simultaneous detection of 15 or more respiratory agents. Results from studies with this diagnostic modality have significantly expanded our knowledge about the seasonality of viral respiratory diseases, pinpointed the difficulties to make a reliable etiologic diagnosis without the aid of an unbiased multiplex molecular assay for respiratory viruses, and revealed previously unknown details as to possible infections with multiple agents as aggravating factors. The scope of this article is to review and discuss this new knowledge and its implications for diagnostic strategies and other measures essential for the clinical management of respiratory viral infections and for epidemiological surveillance of seasonal respiratory infections.
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Affiliation(s)
- Sigvard Olofsson
- Department of Clinical Virology, University of Gothenburg, Guldhedsgatan 10B, S-413 46 Gothenburg, Sweden.
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16
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Abstract
Respiratory tract infection is a leading cause of morbidity and mortality worldwide, especially among young children. Human coronaviruses (HCoVs) have only recently been shown to cause both lower and upper respiratory tract infections. To date, five coronaviruses (HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63 and HCoV HKU-1) that infect humans have been identified, four of which (HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU-1) circulate continuously in the human population. Human coronavirus NL63 (HCoV-NL63) was first isolated from the aspirate from a 7-month-old baby in early 2004. Infection with HCoV-NL63 has since been shown to be a common worldwide occurrence and has been associated with many clinical symptoms and diagnoses, including severe lower respiratory tract infection, croup and bronchiolitis. HCoV-NL63 causes disease in children, the elderly and the immunocompromised, and has been detected in 1.0-9.3% of respiratory tract infections in children. In this article, the current knowledge of human coronavirus HCoV-NL63, with special reference to the clinical features, prevalence and seasonal incidence, and coinfection with other respiratory viruses, will be discussed.
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Affiliation(s)
- Burtram C Fielding
- Molecular Virology Research Laboratory, Medical Microbiology Cluster, Department of Medical Biosciences, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Modderdam Road, Bellville, Western Cape, 7535, South Africa.
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Lee BE, Mukhi SN, May-Hadford J, Plitt S, Louie M, Drews SJ. Determination of the relative economic impact of different molecular-based laboratory algorithms for respiratory viral pathogen detection, including Pandemic (H1N1), using a secure web based platform. Virol J 2011; 8:277. [PMID: 21645365 PMCID: PMC3123288 DOI: 10.1186/1743-422x-8-277] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 06/06/2011] [Indexed: 11/10/2022] Open
Abstract
Background During period of crisis, laboratory planners may be faced with a need to make operational and clinical decisions in the face of limited information. To avoid this dilemma, our laboratory utilizes a secure web based platform, Data Integration for Alberta Laboratories (DIAL) to make near real-time decisions. This manuscript utilizes the data collected by DIAL as well as laboratory test cost modeling to identify the relative economic impact of four proposed scenarios of testing for Pandemic H1N1 (2009) and other respiratory viral pathogens. Methods Historical data was collected from the two waves of the pandemic using DIAL. Four proposed molecular testing scenarios were generated: A) Luminex respiratory virus panel (RVP) first with/without US centers for Disease Control Influenza A Matrix gene assay (CDC-M), B) CDC-M first with/without RVP, C) RVP only, and D) CDC-M only. Relative cost estimates of different testing algorithm were generated from a review of historical costs in the lab and were based on 2009 Canadian dollars. Results Scenarios A and B had similar costs when the rate of influenza A was low (< 10%) with higher relative cost in Scenario A with increasing incidence. Scenario A provided more information about mixed respiratory virus infection as compared with Scenario B. Conclusions No one approach is applicable to all conditions. Testing costs will vary depending on the test volume, prevalence of influenza A strains, as well as other circulating viruses and a more costly algorithm involving a combination of different tests may be chosen to ensure that tests results are returned to the clinician in a quicker manner. Costing should not be the only consideration for determination of laboratory algorithms.
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Molecular diagnostic assays for detection of viral respiratory pathogens in institutional outbreaks. Mol Diagn Ther 2011; 14:283-93. [PMID: 21053994 PMCID: PMC7099217 DOI: 10.1007/bf03256384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Outbreaks of viral respiratory disease in institutions may be associated with high morbidity and mortality, depending upon the viral etiology and the age and immune status of the affected patients. Control of outbreaks may include isolation and/or cohorting, and prohylaxis or treatment with specific antiviral agents may be indicated, all dependent upon the specific cause of the outbreak. Conventional methods of viral diagnosis detect only a limited number of the viruses that are known to cause outbreaks. The availability of sensitive and specific molecular assays has facilitated rapid diagnosis of a wider range of viruses from respiratory outbreaks. Molecular methods have distinct advantages over conventional methods, including the ability to rapidly develop assays for emerging viruses and new variants of existing viruses. In addition, molecular testing allows rapid detection of resistance to antiviral agents or mutations leading to increased virulence. However, high-throughput molecular testing requires batch processes that may compromise the ability to respond quickly to urgent testing demands.
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19
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Kumar D, Humar A. Respiratory viral infections in transplant and oncology patients. Infect Dis Clin North Am 2010; 24:395-412. [PMID: 20466276 PMCID: PMC7135290 DOI: 10.1016/j.idc.2010.01.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Deepali Kumar
- Department of Medicine, Transplant Infectious Diseases, University of Alberta, 6-030 Katz-Rexall Center for Health Research, Edmonton, Alberta T6G 2E1, Canada.
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Abdul-Rasool S, Fielding BC. Understanding Human Coronavirus HCoV-NL63. Open Virol J 2010; 4:76-84. [PMID: 20700397 PMCID: PMC2918871 DOI: 10.2174/1874357901004010076] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 01/25/2010] [Accepted: 04/09/2010] [Indexed: 12/15/2022] Open
Abstract
Even though coronavirus infection of humans is not normally associated with severe diseases, the identification of the coronavirus responsible for the outbreak of severe acute respiratory syndrome showed that highly pathogenic coronaviruses can enter the human population. Shortly thereafter, in Holland in 2004, another novel human coronavirus (HCoV-NL63) was isolated from a seven-month old infant suffering from respiratory symptoms. This virus has subsequently been identified in various countries, indicating a worldwide distribution. HCoV-NL63 has been shown to infect mainly children and the immunocommpromised, who presented with either mild upper respiratory symptoms (cough, fever and rhinorrhoea) or more serious lower respiratory tract involvement such as bronchiolitis and croup, which was observed mainly in younger children. In fact, HCoV-NL63 is the aetiological agent for up to 10% of all respiratory diseases. This review summarizes recent findings of human coronavirus HCoV-NL63 infections, including isolation and identification, phylogeny and taxonomy, genome structure and transcriptional regulation, transmission and pathogenesis, and detection and diagnosis.
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Affiliation(s)
- Sahar Abdul-Rasool
- Anatomy Cluster, Department of Medical Biosciences, Faculty of Natural Sciences, University of the Western Cape, Western Cape, South Africa
| | - Burtram C Fielding
- Molecular Virology Research Laboratory, Medical Microbiology Cluster, Department of Medical Biosciences, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Modderdam Road, Bellville, Western Cape 7535, South Africa
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Enhanced viral etiological diagnosis of respiratory system infection outbreaks by use of a multitarget nucleic acid amplification assay. J Clin Microbiol 2009; 47:3839-45. [PMID: 19828744 DOI: 10.1128/jcm.01469-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A study was undertaken to assess the utility of the xTAG respiratory viral panel (RVP) for enhanced laboratory investigation of respiratory outbreaks. Specimens (n = 1,108) from 244 suspected respiratory virus outbreaks in 2006 and 2007 in Alberta, Canada, were included in the study. Testing by direct fluorescent antigen detection (DFA) and various in-house nucleic acid amplification tests (NATs) for common respiratory viruses provided an etiological diagnosis in 177 outbreaks (72.5%), with 524 samples testing positive (47.3%) for a respiratory virus. Two hundred samples from 51 unresolved outbreaks were further tested by RVP retrospectively. Fifty-eight samples from 30 unresolved outbreaks had a respiratory virus detected by RVP (47 picornavirus-positive, 9 coronavirus-positive, and 2 influenza virus A-positive samples). Overall, detection of a viral etiological agent was achieved in 90.8% of outbreaks using a combination of DFA, NATs, and RVP. Use of RVP enhances the laboratory investigation of respiratory virus outbreaks and facilitates appropriate patient and outbreak management.
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De Vos N, Vankeerberghen A, Vaeyens F, Van Vaerenbergh K, Boel A, De Beenhouwer H. Simultaneous detection of human bocavirus and adenovirus by multiplex real-time PCR in a Belgian paediatric population. Eur J Clin Microbiol Infect Dis 2009; 28:1305-10. [PMID: 19705175 PMCID: PMC7087762 DOI: 10.1007/s10096-009-0780-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2009] [Accepted: 07/10/2009] [Indexed: 12/31/2022]
Abstract
Since the discovery of human bocavirus (hBoV), the virus has been detected worldwide in respiratory tract samples from young children by various polymerase chain reaction (PCR) assays and real-time PCRs (Q-PCR). Until now, no data have been reported on the presence of hBoV in Belgium and the detection of hBoV in a multiplex Q-PCR setting has not been described. The aim of this study was to develop a fast and reliable multiplex Q-PCR for the simultaneous detection of hBoV DNA and adenovirus (AdV) DNA. During the winter of 2004–2005, 445 nasopharyngeal aspirates (NPAs) were analysed from 404 Belgian children up to 5 years old with acute respiratory tract infections (ARTIs). (Co)infections with hBoV, AdV, respiratory syncytial virus (RSV), human metapneumovirus (hMPV) and influenza A virus were investigated. A viral agent was detected in 61% (n = 272/445) of the NPAs. Multiplex Q-PCR found a prevalence of 11% (n = 51/445) hBoV and 13% (n = 58/445) AdV. Coinfections were more frequently found with AdV (62%; n = 36/58) than with hBoV (49%; n = 25/51). Follow-up samples were available from 22 patients with ARTIs. In three patients, hBoV DNA persisted for one month. Multiplex Q-PCR may help in closing the diagnostic gap by addressing a broader range of potential respiratory pathogens.
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Affiliation(s)
- N De Vos
- Laboratory of Clinical Biology, Department of Microbiology and Molecular Biology, Onze Lieve Vrouw (OLV) Hospital, Moorselbaan 164, 9300, Aalst, Belgium
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Al-Assam A, Langley JM, Sarwal S. Respiratory Watch: Development of a provincial system for respiratory syncytial virus surveillance in Nova Scotia, 2005-2008. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2009; 20:e153-6. [PMID: 21119793 PMCID: PMC2807260 DOI: 10.1155/2009/361948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
OBJECTIVE Respiratory syncytial virus (RSV) is the most common cause of severe lower respiratory tract infection in young children and is increasingly recognized as a cause of influenza-like illness in those older than 65 years of age. A surveillance system to provide timely local information about RSV activity in Nova Scotia (NS) is described. METHODS A case report form was developed for weekly reporting of all laboratory isolates of RSV at diagnostic laboratories around the province. Laboratories were asked to send the forms by fax each Friday to the Nova Scotia Department of Health Promotion and Protection. Data were entered in Excel (Microsoft, USA) and aggregate results summarized by age, sex, health district and date of laboratory confirmation for 2005 to 2008. RESULTS During three winter seasons (2005-2006, 2006-2007 and 2007-2008), there were 207, 350 and 186 isolates of RSV reported in NS, respectively. The average incidences of RSV in NS varied greatly by age, with the highest rates in infants younger than 24 months of age, and approaching 4000 cases per 100,000 population in infants up to five months of age. The duration of the RSV outbreak was approximately five to six months each year, but the month of onset varied. CONCLUSIONS A RSV surveillance system was successfully established in NS that provides weekly data to the public health system, clinicians and infection control practitioners. The time of onset and severity of the RSV season varied over time. These data can be used to plan anti-RSV passive prophylaxis programs and infection control education, and distinguish RSV outbreaks from other viruses in acute care and long-term care settings.
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Affiliation(s)
- Assaad Al-Assam
- Formerly with the Department of Health Promotion and Protection, Government of Nova Scotia
- Departments of Community Health and Epidemiology and
- Canadian Center for Vaccinology, IWK Health Centre and Dalhousie University
| | - Joanne M Langley
- Departments of Community Health and Epidemiology and
- Pediatrics
- Canadian Center for Vaccinology, IWK Health Centre and Dalhousie University
| | - Shelly Sarwal
- Formerly with the Department of Health Promotion and Protection, Government of Nova Scotia
- Departments of Community Health and Epidemiology and
- Canadian Center for Vaccinology, IWK Health Centre and Dalhousie University
- Department of Health Promotion and Protection, Government of Nova Scotia, Halifax, Nova Scotia
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Abstract
SUMMARY Clinical laboratories historically diagnose seven or eight respiratory virus infections using a combination of techniques including enzyme immunoassay, direct fluorescent antibody staining, cell culture, and nucleic acid amplification tests. With the discovery of six new respiratory viruses since 2000, laboratories are faced with the challenge of detecting up to 19 different viruses that cause acute respiratory disease of both the upper and lower respiratory tracts. The application of nucleic acid amplification technology, particularly multiplex PCR coupled with fluidic or fixed microarrays, provides an important new approach for the detection of multiple respiratory viruses in a single test. These multiplex amplification tests provide a sensitive and comprehensive approach for the diagnosis of respiratory tract infections in individual hospitalized patients and the identification of the etiological agent in outbreaks of respiratory tract infection in the community. This review describes the molecular methods used to detect respiratory viruses and discusses the contribution that molecular testing, especially multiplex PCR, has made to our ability to detect respiratory viruses and to increase our understanding of the roles of various viral agents in acute respiratory disease.
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