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Wang Y, Huang Y, Peng Y, Cao Q, Liu W, Zhou Z, Xu G, Li L, Zhou R. Development and validation of a rapid five-minute nucleic acid extraction method for respiratory viruses. Virol J 2024; 21:189. [PMID: 39155366 PMCID: PMC11331601 DOI: 10.1186/s12985-024-02381-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/02/2024] [Indexed: 08/20/2024] Open
Abstract
BACKGROUND The rapid transmission and high pathogenicity of respiratory viruses significantly impact the health of both children and adults. Extracting and detecting their nucleic acid is crucial for disease prevention and treatment strategies. However, current extraction methods are laborious and time-consuming and show significant variations in nucleic acid content and purity among different kits, affecting detection sensitivity and efficiency. Our aim is to develop a novel method that reduces extraction time, simplifies operational steps, and ensures high-quality acquisition of respiratory viral nucleic acid. METHODS We extracted respiratory syncytial virus (RSV) nucleic acid using reagents with different components and analyzed cycle threshold (Ct) values via quantitative real-time polymerase chain reaction (qRT-PCR) to optimize and validate the novel lysis and washing solution. The performance of this method was compared against magnetic bead, spin column, and precipitation methods for extracting nucleic acid from various respiratory viruses. The clinical utility of this method was confirmed by comparing it to the standard magnetic bead method for extracting clinical specimens of influenza A virus (IAV). RESULTS The solution, composed of equal parts glycerin and ethanol (50% each), offers an innovative washing approach that achieved comparable efficacy to conventional methods in a single abbreviated cycle. When combined with our A Plus lysis solution, our novel five-minute nucleic acid extraction (FME) method for respiratory viruses yielded superior RNA concentrations and purity compared to traditional methods. FME, when used with a universal automatic nucleic acid extractor, demonstrated similar efficiency as various conventional methods in analyzing diverse concentrations of respiratory viruses. In detecting respiratory specimens from 525 patients suspected of IAV infection, the FME method showed an equivalent detection rate to the standard magnetic bead method, with a total coincidence rate of 95.43% and a kappa statistic of 0.901 (P < 0.001). CONCLUSIONS The FME developed in this study enables the rapid and efficient extraction of nucleic acid from respiratory samples, laying a crucial foundation for the implementation of expedited molecular diagnosis.
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Affiliation(s)
- Yu Wang
- Guangzhou National Laboratory, Guangzhou, China
| | | | - Yuqing Peng
- Guangzhou National Laboratory, Guangzhou, China
| | - Qinglin Cao
- Guangzhou National Laboratory, Guangzhou, China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Guangxin Xu
- Guangzhou National Laboratory, Guangzhou, China
| | - Lei Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science of Technology, Wuhan, China.
- GIRM Biosafety (Guangzhou) Co., Ltd, Guangzhou, China.
| | - Rong Zhou
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
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Altawalah H, Alfouzan W, Al-Fadalah T, Zalzala MA, Ezzikouri S. Viral etiology of severe lower respiratory tract infections in SARS-CoV-2 negative hospitalized patients during the COVID-19 pandemic in Kuwait. Heliyon 2024; 10:e29855. [PMID: 38681623 PMCID: PMC11046192 DOI: 10.1016/j.heliyon.2024.e29855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Background The prevalence of respiratory infections is largely underexplored in Kuwait. The aim of our study is to determine the etiology of infections from patients who are SARS-CoV-2 negative hospitalized with severe lower respiratory tract infections (LRTIs) in Kuwait during the coronavirus disease 2019 (COVID-19) pandemic. Methods We conducted an observational cross-sectional study among severe LRTI patients between September 2021 and March 2022. Respiratory samples from 545 non-COVID-19 severe LRTIs patients were prospectively evaluated with FTD Respiratory 21 Plus® real-time PCR, targeting 20 different viruses and 1 atypical bacterial pathogen. Results Among all 545 hospitalized cases, 411 (75.4 %) tested positive for at least one respiratory pathogen. The most common were rhinovirus (HRV) (32.7 %), respiratory syncytial virus (RSV) (20.9 %), metapneumovirus (HMPV) (14.1 %), bocavirus (13.2 %), and influenza A (12.7 %). The proportion of pathogens detected was highest in the under-5 age group, while HKU1 (44.4 %) predominated in the elderly (>50 years). Conclusion Our study reveals a high prevalence of respiratory viruses in severe acute lower respiratory tract infections among non-COVID-19 hospitalized patients in Kuwait. HRV remains the main etiology affecting the country, particularly in infants. These results underscore the necessity of employing multiplex PCR for accurate diagnosis and describing the epidemiology of infections among severe lower respiratory tract infections. This will facilitate the use of specific antiviral therapy and help avoid excessive or inappropriate antibiotic therapy.
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Affiliation(s)
- Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
- Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait, Kuwait
| | - Wadha Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
- Laboratory Medicine, Farwania Hospital, Ministry of Health, Farwania, Kuwait
| | - Talal Al-Fadalah
- Qualities and Accreditation Directorate, Ministry of Health, Kuwait, Kuwait
| | - Mariam Ali Zalzala
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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3
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Pavord ID, Hoyte FCL, Lindsley AW, Ambrose CS, Spahn JD, Roseti SL, Cook B, Griffiths JM, Hellqvist Å, Martin N, Llanos JP, Martin N, Colice G, Corren J. Tezepelumab reduces exacerbations across all seasons in patients with severe, uncontrolled asthma (NAVIGATOR). Ann Allergy Asthma Immunol 2023; 131:587-597.e3. [PMID: 37619779 DOI: 10.1016/j.anai.2023.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/27/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Asthma exacerbation frequencies vary throughout the year owing to seasonal triggers. Tezepelumab is a human monoclonal antibody that targets thymic stromal lymphopoietin. In the phase 3 NAVIGATOR study (NCT03347279), tezepelumab significantly reduced the annualized asthma exacerbation rate (AAER) vs placebo in patients with severe, uncontrolled asthma. OBJECTIVE To evaluate the effect of tezepelumab on asthma exacerbations across all seasons in NAVIGATOR patients (post hoc). METHODS NAVIGATOR was a multicenter, randomized, double-blind, placebo-controlled study. Patients (12-80 years old) were randomized 1:1 to tezepelumab 210 mg or placebo subcutaneously every 4 weeks for 52 weeks. AAER over 52 weeks was assessed by season. Data from patients in the Southern Hemisphere were transformed to align with Northern Hemisphere seasons. RESULTS Tezepelumab reduced the AAER vs placebo by 63% (95% confidence interval [CI], 52-72) in winter, 46% (95% CI, 26-61) in spring, 62% (95% CI, 48-73) in summer, and 54% (95% CI, 41-64) in fall. In matched climates, during the spring allergy season (March 1 to June 15) and ragweed allergy season (September), tezepelumab reduced the AAER vs placebo in patients with seasonal allergy by 59% (95% CI, 29-77) and 70% (95% CI, 33-87), respectively. In patients with perennial allergy and in those with seasonal allergy, tezepelumab reduced the AAER vs placebo across all seasons. CONCLUSION Tezepelumab reduced exacerbations across all seasons vs placebo in patients with severe, uncontrolled asthma, including patients with seasonal and perennial allergies. These data further support the efficacy of tezepelumab in a broad population of patients with severe, uncontrolled asthma. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT03347279 (https://clinicaltrials.gov/ct2/show/NCT03347279).
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Affiliation(s)
- Ian D Pavord
- Respiratory Medicine, NIHR Oxford Biomedical Research Centre, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Flavia C L Hoyte
- Division of Allergy and Immunology, National Jewish Health, Denver, Colorado
| | | | - Christopher S Ambrose
- Respiratory and Immunology, BioPharmaceuticals Medical, AstraZeneca, Gaithersburg, Maryland
| | - Joseph D Spahn
- Respiratory and Immunology, BioPharmaceuticals Medical, AstraZeneca, Wilmington, Delaware
| | - Stephanie L Roseti
- Late-Stage Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Bill Cook
- Respiratory and Immunology, BioPharmaceuticals Medical, AstraZeneca, Gaithersburg, Maryland
| | - Janet M Griffiths
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Åsa Hellqvist
- Biometrics, Late-stage Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Nicole Martin
- Biometrics, Late-stage Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Waltham, Massachusetts; Cytel Inc., Waltham, Massachusetts
| | | | - Neil Martin
- Respiratory and Immunology, BioPharmaceuticals Medical, AstraZeneca, Cambridge, United Kingdom; NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, United Kingdom
| | - Gene Colice
- Late-Stage Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland
| | - Jonathan Corren
- David Geffen School of Medicine, University of California, Los Angeles, California
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4
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Recent updates on liposomal formulations for detection, prevention and treatment of coronavirus disease (COVID-19). Int J Pharm 2023; 630:122421. [PMID: 36410670 PMCID: PMC9674400 DOI: 10.1016/j.ijpharm.2022.122421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/12/2022] [Accepted: 11/17/2022] [Indexed: 11/20/2022]
Abstract
The unprecedented outbreak of severe acute respiratory syndrome-2 (SARS-CoV-2) worldwide has rendered it one of the most notorious pandemics ever documented in human history. As of November 2022, nearly 626 million cases of infection and over 6.6 million deaths have been reported globally. The scientific community has made significant progress in therapeutics and prevention for the management of coronavirus disease (COVID-19), including the development of vaccines and antiviral agents such as monoclonal antibodies and antiviral drugs. Although many advancements and a plethora of positive results have been obtained and global restrictions are being uplifted, obstacles in efficiently delivering these therapies, such as their rapid clearance, suboptimal biodistribution, and toxicity to organs, have yet to be addressed. To address these drawbacks, researchers have attempted applying nanotechnology-based formulations. Here, we summarized the recent data about COVID-19, its emergence, pathophysiology and life cycle, diagnosis, and currently-available medications. Subsequently, we discussed the progress in lipid nanocarriers, such as liposomes in infection detection and control. This review provides critical insights into the design of the latest liposomal-based formulations for tackling the barriers to detecting, preventing, and treating SARS-CoV-2.
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Wittkowski KM. The First Three Months of COVID-19: Epidemiological Evidence for Two SARS-CoV-2 Strains Spreading and Implications for Prevention Strategies. Cureus 2022; 14:e29146. [PMID: 36259001 PMCID: PMC9572891 DOI: 10.7759/cureus.29146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2022] [Indexed: 11/21/2022] Open
Abstract
About a month after the COVID-19 epidemic peaked in Mainland China and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) migrated to Europe and then the USA, the epidemiological data began to provide important insights into the risks associated with the disease and the effectiveness of intervention strategies such as travel restrictions and lockdowns ("social distancing"). Respiratory diseases, including the 2003 severe acute respiratory syndrome (SARS) epidemic, remain only about two months in any given population, although peak incidence and lethality can vary. The epidemiological data suggested that at least two strains of SARS-CoV-2 had evolved during the first months of the epidemic while the virus migrated from Mainland China to Europe. South Korea (SK), Iran, Italy (IT), and Italy's neighbors were then hit by the more dangerous "SKII" variant. While the first epidemic in continental Asia was about to end and in Europe about to level off, the more recent epidemic in the younger US population was still increasing, albeit not exponentially anymore. The same models that help us to understand the epidemic also help us to choose prevention strategies. The containment of high-risk people, such as the elderly with comorbidities, and reducing disease severity, by either vaccination, reduction of comorbidities (seen as risk factors already in Italy), or early treatment of complications, are the best strategies against a respiratory virus disease (RVD). Lockdowns can be effective during the month following the peak incidence of infections when the exponential increase of cases ends (the window of opportunity). From the standard susceptible-infectious-resistant (SIR) model used, containing low-risk people too early, instead, merely prolongs the time the virus needs to circulate until the incidence is high enough to reach "herd immunity." Containing low-risk people too late is also not helpful, unless to prevent a rebound if containment started too early.
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Affiliation(s)
- Knut M Wittkowski
- Research and Development, Advanced Statistics for Drug Exploration, Repurposing, and Approval (ASDERA) LLC, New York, USA
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6
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Heredia-Rodríguez M, Balbás-Álvarez S, Lorenzo-López M, Gómez-Pequera E, Jorge-Monjas P, Rojo-Rello S, Sánchez-De Prada L, Sanz-Muñoz I, Eiros JM, Martínez-Paz P, Gonzalo-Benito H, Tamayo-Velasco Á, Martín-Fernández M, Sánchez-Conde P, Tamayo E, Gómez-Sánchez E. PCR-based diagnosis of respiratory virus in postsurgical septic patients: A preliminary study before SARS-CoV-2 pandemic. Medicine (Baltimore) 2022; 101:e29902. [PMID: 35960076 PMCID: PMC9370242 DOI: 10.1097/md.0000000000029902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/05/2022] [Accepted: 06/06/2022] [Indexed: 01/04/2023] Open
Abstract
Respiratory viruses are part of the normal microbiota of the respiratory tract, which sometimes cause infection with/without respiratory insufficiency and the need for hospital or ICU admission. The aim of this study is to determine the prevalence of respiratory viruses in nontransplanted postoperative septic patients as well as lymphocyte count influence in their presence and its relationship to mortality. 223 nontransplanted postsurgical septic patients were recruited on the Intensive Care Unit (ICU) at Hospital Clínico Universitario de Valladolid prior to the SARS-COV-2 pandemic. Patients were split into 2 groups according to the presence/absence of respiratory viruses. Multivariate logistic regression analysis was used to identify independent factors related to positive respiratory virus PCR test. Respiratory viruses were isolated in 28.7% of patients. 28-day mortality was not significantly different between virus-positive and virus-negative groups. Logistic regression analysis revealed that lymphocyte count ≤ 928/µl is independently associated with a positive PCR result [OR 3.76, 95% CI (1.71-8.26), P = .001] adjusted by platelet count over 128,500/µL [OR 4.27, 95% CI (1.92-9.50) P < .001] and the presence of hypertension [OR 2.69, 95% CI (1.13-6.36) P = .025] as confounding variables. Respiratory viruses' detection by using PCR in respiratory samples of nontransplanted postoperative septic patients is frequent. These preliminary results revealed that the presence of lymphopenia on sepsis diagnosis is independently associated to a positive virus result, which is not related to a higher 28-day mortality.
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Affiliation(s)
- María Heredia-Rodríguez
- Department of Anaesthesiology and Critical Care, Complejo Asistencial Universitario de Salamanca, Gerencia Regional de Salud de Castilla y León (SACYL), Salamanca, Spain
- Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Group for Biomedical Research in Critical Care Medicine (BioCritic), Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
| | - Sara Balbás-Álvarez
- Department of Anaesthesiology and Critical Care, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Mario Lorenzo-López
- Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Group for Biomedical Research in Critical Care Medicine (BioCritic), Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Department of Anaesthesiology and Critical Care, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Estefanía Gómez-Pequera
- Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Group for Biomedical Research in Critical Care Medicine (BioCritic), Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Department of Anaesthesiology and Critical Care, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Pablo Jorge-Monjas
- Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Group for Biomedical Research in Critical Care Medicine (BioCritic), Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Department of Anaesthesiology and Critical Care, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Silvia Rojo-Rello
- Department of Microbiology, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Laura Sánchez-De Prada
- Department of Microbiology, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Ivan Sanz-Muñoz
- Department of Microbiology, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - José María Eiros
- Department of Microbiology, Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Pedro Martínez-Paz
- Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Group for Biomedical Research in Critical Care Medicine (BioCritic), Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
| | - Hugo Gonzalo-Benito
- Group for Biomedical Research in Critical Care Medicine (BioCritic), Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Research Unit, Hospital Clínico Universitario de Valladolid, Instituto de Estudios en Ciencias de la Salud de Castilla y León (ICSCyL), Valladolid, Spain
| | - Álvaro Tamayo-Velasco
- Group for Biomedical Research in Critical Care Medicine (BioCritic), Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Department of Hematology, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Marta Martín-Fernández
- Group for Biomedical Research in Critical Care Medicine (BioCritic), Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Department of Medicine, Dermatology and Toxicology, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
| | - Pilar Sánchez-Conde
- Department of Anaesthesiology and Critical Care, Complejo Asistencial Universitario de Salamanca, Gerencia Regional de Salud de Castilla y León (SACYL), Salamanca, Spain
- Department of Surgery, Faculty of Medicine, Universidad de Salamanca, Salamanca, Spain
| | - Eduardo Tamayo
- Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Group for Biomedical Research in Critical Care Medicine (BioCritic), Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Department of Anaesthesiology and Critical Care, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Esther Gómez-Sánchez
- Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Group for Biomedical Research in Critical Care Medicine (BioCritic), Department of Surgery, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
- Department of Anaesthesiology and Critical Care, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
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Gupta P, Siddiqui MK, Huang X, Morales-Menendez R, Panwar H, Terashima-Marin H, Wajid MS. COVID-WideNet-A capsule network for COVID-19 detection. Appl Soft Comput 2022; 122:108780. [PMID: 35369122 PMCID: PMC8962064 DOI: 10.1016/j.asoc.2022.108780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 02/08/2022] [Accepted: 03/22/2022] [Indexed: 02/03/2023]
Abstract
Ever since the outbreak of COVID-19, the entire world is grappling with panic over its rapid spread. Consequently, it is of utmost importance to detect its presence. Timely diagnostic testing leads to the quick identification, treatment and isolation of infected people. A number of deep learning classifiers have been proved to provide encouraging results with higher accuracy as compared to the conventional method of RT-PCR testing. Chest radiography, particularly using X-ray images, is a prime imaging modality for detecting the suspected COVID-19 patients. However, the performance of these approaches still needs to be improved. In this paper, we propose a capsule network called COVID-WideNet for diagnosing COVID-19 cases using Chest X-ray (CXR) images. Experimental results have demonstrated that a discriminative trained, multi-layer capsule network achieves state-of-the-art performance on the COVIDx dataset. In particular, COVID-WideNet performs better than any other CNN based approaches for diagnosis of COVID-19 infected patients. Further, the proposed COVID-WideNet has the number of trainable parameters that is 20 times less than that of other CNN based models. This results in fast and efficient diagnosing COVID-19 symptoms and with achieving the 0.95 of Area Under Curve (AUC), 91% of accuracy, sensitivity and specificity respectively. This may also assist radiologists to detect COVID and its variant like delta.
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Affiliation(s)
- P.K. Gupta
- Department of Computer Science and Engineering, Jaypee University of Information Technology, Waknaghat, Solan, HP, 173 234, India
| | - Mohammad Khubeb Siddiqui
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, N.L, Mexico,Corresponding author
| | - Xiaodi Huang
- School of Computing Mathematics and Engineering, Charles Sturt University, Albury, NSW, Australia
| | | | - Harsh Panwar
- Queen Mary University of London, Mile End Rd, Bethnal Green, London, United Kingdom
| | - Hugo Terashima-Marin
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, N.L, Mexico
| | - Mohammad Saif Wajid
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, N.L, Mexico
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Abstract
In the last few decades, plasmonic colorimetric biosensors raised increasing interest in bioanalytics thanks to their cost-effectiveness, responsiveness, and simplicity as compared to conventional laboratory techniques. Potential high-throughput screening and easy-to-use assay procedures make them also suitable for realizing point of care devices. Nevertheless, several challenges such as fabrication complexity, laborious biofunctionalization, and poor sensitivity compromise their technological transfer from research laboratories to industry and, hence, still hamper their adoption on large-scale. However, newly-developing plasmonic colorimetric biosensors boast impressive sensing performance in terms of sensitivity, dynamic range, limit of detection, reliability, and specificity thereby continuously encouraging further researches. In this review, recently reported plasmonic colorimetric biosensors are discussed with a focus on the following categories: (i) on-platform-based (localized surface plasmon resonance, coupled plasmon resonance and surface lattice resonance); (ii) colloid aggregation-based (label-based and label free); (iii) colloid non-aggregation-based (nanozyme, etching-based and growth-based).
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Vázquez M, Anfossi L, Ben-Yoav H, Diéguez L, Karopka T, Della Ventura B, Abalde-Cela S, Minopoli A, Di Nardo F, Shukla VK, Teixeira A, Tvarijonaviciute A, Franco-Martínez L. Use of some cost-effective technologies for a routine clinical pathology laboratory. LAB ON A CHIP 2021; 21:4330-4351. [PMID: 34664599 DOI: 10.1039/d1lc00658d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Classically, the need for highly sophisticated instruments with important economic costs has been a major limiting factor for clinical pathology laboratories, especially in developing countries. With the aim of making clinical pathology more accessible, a wide variety of free or economical technologies have been developed worldwide in the last few years. 3D printing and Arduino approaches can provide up to 94% economical savings in hardware and instrumentation in comparison to commercial alternatives. The vast selection of point-of-care-tests (POCT) currently available also limits the need for specific instruments or personnel, as they can be used almost anywhere and by anyone. Lastly, there are dozens of free and libre digital tools available in health informatics. This review provides an overview of the state-of-the-art on cost-effective alternatives with applications in routine clinical pathology laboratories. In this context, a variety of technologies including 3D printing and Arduino, lateral flow assays, plasmonic biosensors, and microfluidics, as well as laboratory information systems, are discussed. This review aims to serve as an introduction to different technologies that can make clinical pathology more accessible and, therefore, contribute to achieve universal health coverage.
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Affiliation(s)
- Mercedes Vázquez
- National Centre For Sensor Research, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Laura Anfossi
- Department of Chemistry, University of Turin, Via Giuria, 5, I-10125 Turin, Italy
| | - Hadar Ben-Yoav
- Nanobioelectronics Laboratory (NBEL), Department of Biomedical Engineering, Ilse Katz Institute of Nanoscale Science and Technology, Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Lorena Diéguez
- Medical Devices Research Group, International Iberian Nanotechnology Laboratory - INL, 4715-330 Braga, Portugal
| | | | - Bartolomeo Della Ventura
- Department of Physics "E. Pancini", University of Naples Federico II, Via Cintia 26, I-80126 Napoli, Italy
| | - Sara Abalde-Cela
- Medical Devices Research Group, International Iberian Nanotechnology Laboratory - INL, 4715-330 Braga, Portugal
| | - Antonio Minopoli
- Department of Physics "E. Pancini", University of Naples Federico II, Via Cintia 26, I-80126 Napoli, Italy
| | - Fabio Di Nardo
- Department of Chemistry, University of Turin, Via Giuria, 5, I-10125 Turin, Italy
| | - Vikas Kumar Shukla
- Nanobioelectronics Laboratory (NBEL), Department of Biomedical Engineering, Ilse Katz Institute of Nanoscale Science and Technology, Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Alexandra Teixeira
- Medical Devices Research Group, International Iberian Nanotechnology Laboratory - INL, 4715-330 Braga, Portugal
| | - Asta Tvarijonaviciute
- Interdisciplinary Laboratory of Clinical Pathology, Interlab-UMU, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, 30100 Murcia, Spain.
| | - Lorena Franco-Martínez
- Interdisciplinary Laboratory of Clinical Pathology, Interlab-UMU, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, 30100 Murcia, Spain.
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Klement RJ, Bandyopadhyay PS. The Epistemology of a Positive SARS-CoV-2 Test. Acta Biotheor 2021; 69:359-375. [PMID: 32888175 PMCID: PMC7473592 DOI: 10.1007/s10441-020-09393-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/19/2020] [Indexed: 12/21/2022]
Abstract
We investigate the epistemological consequences of a positive polymerase chain reaction SARS-CoV test for two relevant hypotheses: (i) V is the hypothesis that an individual has been infected with SARS-CoV-2; (ii) C is the hypothesis that SARS-CoV-2 is the cause of flu-like symptoms in a given patient. We ask two fundamental epistemological questions regarding each hypothesis: First, how much confirmation does a positive test lend to each hypothesis? Second, how much evidence does a positive test provide for each hypothesis against its negation? We respond to each question within a formal Bayesian framework. We construe degree of confirmation as the difference between the posterior probability of the hypothesis and its prior, and the strength of evidence for a hypothesis against its alternative in terms of their likelihood ratio. We find that test specificity-and coinfection probabilities when making inferences about C-were key determinants of confirmation and evidence. Tests with < 87% specificity could not provide strong evidence (likelihood ratio > 8) for V against ¬V regardless of sensitivity. Accordingly, low specificity tests could not provide strong evidence in favor of C in all plausible scenarios modeled. We also show how a positive influenza A test disconfirms C and provides weak evidence against C in dependence on the probability that the patient is influenza A infected given that his/her symptoms are not caused by SARS-CoV-2. Our analysis points out some caveats that should be considered when attributing symptoms or death of a positively tested patient to SARS-CoV-2.
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Affiliation(s)
- Rainer Johannes Klement
- Department of Radiotherapy and Radiation Oncology, Leopoldina Hospital Schweinfurt, Robert-Koch-Straße 10, 97422, Schweinfurt, Germany.
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11
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Lyu S, Li J, Wu M, He D, Fu T, Ni F, Tan X, Wu G, Pan B, Li L, Wang H, Zeng G, Ni Z, Tan W, Zong Y, Chen L, Liu P, Qin H, He P, Zhang L, An Y, Liang Z. The Use of Aerosolized Medications in Adult Intensive Care Unit Patients: A Prospective, Multicenter, Observational, Cohort Study. J Aerosol Med Pulm Drug Deliv 2021; 34:383-391. [PMID: 34129389 DOI: 10.1089/jamp.2021.0004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Background: Only limited data are available on the real-life clinical utilization of aerosolized medications in intensive care unit (ICU) patients. Exploring the utilization of aerosolized medications in the ICU may contribute to develop appropriate education and improve the quality of aerosol therapy. Methods: A 2-week, prospective, multicenter, observational, cohort study was conducted to record how the aerosolized medications were utilized in the Chinese ICUs, including indications, medications used in solo or combination, dosage, and side-effects in adult patients. Results: A total of 1006 patients from 28 ICUs were enrolled, of which 389 (38.7%) received aerosol therapy. The most common indications for aerosol therapy were difficulty in secretion management (23.1%) and chronic obstructive pulmonary disease exacerbation (18.5%). The combination of inhaled corticosteroids and short-acting muscarinic antagonist was the most commonly used medication (19.5%, 76/389). Ninety-two percent (358/389) of the patients did not have any side effects during aerosol therapy. More patients in the group with mechanical ventilation received bronchodilators than spontaneous breathing patients (81.3% vs. 55.5%, p < 0.001), and more patients who breathed spontaneously through a tracheostomy received mucus-regulating agents than other patients (70% vs. 37.9%, p = 0.004). Conclusion: In mainland China, more than one-third of adult ICU patients received aerosol therapy. Medications utilized during aerosol therapy were variable in patients with different respiratory support. To promote appropriate use of aerosolized medications, high-quality randomized, controlled trials and clinical guidance on aerosolized medication indications and dosing are needed to improve clinical outcomes.
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Affiliation(s)
- Shan Lyu
- Department of Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Jie Li
- Division of Respiratory Care, Department of Cardiopulmonary Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Mengmeng Wu
- Department of Critical Care Medicine, Binzhou People's Hospital, Binzhou, China
| | - Dehua He
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tinggan Fu
- Department of Surgical Intensive Care Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fang Ni
- Department of Respiratory and Critical Care Medicine, The Central Hospital of Wuhan, Wuhan, China
| | - Xu Tan
- Department of Respiratory and Critical Care Medicine, Union Hospital Affiliated with Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Guanghan Wu
- Department of Critical Care Medicine, People's Hospital of Jianghua Yao Autonomous County, Yongzhou, China
| | - Binhai Pan
- Department of Respiratory and Critical Care Medicine, Jinling Hospital, Nanjing, China
| | - Liucun Li
- Department of Respiratory and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Haiyan Wang
- Department of Emergency Critical Care Medicine, West China Hospital Sichuan University-Ziyang Hospital, Ziyang, China
| | - Guilan Zeng
- Department of Critical Care Medicine, Zhangzhou Hospital Traditional Chinese Medicine, Zhangzhou, China
| | - Zhong Ni
- Department of Respiratory and Critical Care Medicine, West China Medical Center, Sichuan University, Chengdu, China
| | - Wei Tan
- Department of Respiratory and Critical Care Medicine, The First Hospital of China Medical University, Shenyang, China
| | - Yajuan Zong
- Department of Critical Care Medicine, Yixing No.2 People's Hospital, Yixing, China
| | - Lihua Chen
- Department of Critical Care Medicine, Gansu Second Provincial People's Hospital, Lanzhou, China
| | - Ping Liu
- Department of Critical Care Medicine, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hao Qin
- Department of Respiratory and Critical Care Medicine, Shanghai Changhai Hospital, Shanghai, China
| | - Ping He
- Department of Cardiac Surgery, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, China
| | - Liu Zhang
- Department of Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Youzhong An
- Department of Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Zongan Liang
- Department of Respiratory and Critical Care Medicine, West China Medical Center, Sichuan University, Chengdu, China
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12
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Choi WI, Kim IB, Park SJ, Ha EH, Lee CW. Comparison of the clinical characteristics and mortality of adults infected with human coronaviruses 229E and OC43. Sci Rep 2021; 11:4499. [PMID: 33627764 PMCID: PMC7904943 DOI: 10.1038/s41598-021-83987-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022] Open
Abstract
The purpose of the study was to compare clinical characteristics and mortality among adults infected with human coronaviruses (HCoV) 229E and OC43. We conducted a retrospective cohort study of adults (≥ 18 years) admitted to the ward of a university teaching hospital for suspected viral infection from October 2012 to December 2017. Multiplex real-time polymerase chain reaction (PCR) was used to test for respiratory viruses. Multivariate logistic regression was used to compare mortality among patients with HCoV 229E and HCoV OC43 infections. The main outcome was 30-day all-cause mortality. Of 8071 patients tested, 1689 were found to have a respiratory virus infection. Of these patients, 133 had HCoV infection, including 12 mixed infections, 44 HCoV 229E infections, and 77 HCoV OC43 infections. HCoV 229E infections peaked in January and February, while HCoV OC43 infections occurred throughout the year. The 30-day all-cause mortality was 25.0% among patients with HCoV 229E infection, and 9.1% among patients with HCoV OC43 infection (adjusted odds ratio: 3.58, 95% confidence interval: 1.19–10.75). Infections with HCoVs 229E and OC43 appear to have different seasonal patterns, and HCoV 229E might be more virulent than HCoV OC43.
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Affiliation(s)
- Won-Il Choi
- Department of Internal Medicine, Myongji Hospital, Hanyang University College of Medicine, 55 Hwasu-ro, 14 beon-gil, Deogyang-gu, Goyang-si, Gyeongji-do, 10475, Republic of Korea.
| | - In Byung Kim
- Department of Emergency Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang, Republic of Korea
| | - Sang Joon Park
- Department of Internal Medicine, Myongji Hospital, Hanyang University College of Medicine, 55 Hwasu-ro, 14 beon-gil, Deogyang-gu, Goyang-si, Gyeongji-do, 10475, Republic of Korea
| | - Eun-Hye Ha
- Department of Internal Medicine, Myongji Hospital, Hanyang University College of Medicine, 55 Hwasu-ro, 14 beon-gil, Deogyang-gu, Goyang-si, Gyeongji-do, 10475, Republic of Korea
| | - Choong Won Lee
- Department of Occupational and Environmental Medicine, Sungso Hospital, Andong, Republic of Korea
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13
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Saadi S, Kallala O, Fodha I, Jerbi A, BenHamida-Rebai M, Ben Hadj Fredj M, Ben Hamouda H, Mathlouthi J, Khlifa M, Boussofara R, Boussetta K, Abroug S, Trabelsi A. Correlation between Children Respiratory Virus Infections and Climate Factors. J PEDIAT INF DIS-GER 2021. [DOI: 10.1055/s-0040-1722569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
Objective Respiratory viruses are the most important cause of lower respiratory tract infections (LRTI) in children. Meteorological factors can influence viral outbreaks. The objective of this study was to determine the association between climate variables and respiratory virus detection.
Methods Multicenter prospective 1-year surveillance was conducted among children hospitalized for LRTI in Tunisia. Nasopharyngeal aspirates were tested by direct immunofluorescence assay (DIFA) for the detection of respiratory syncytial virus (RSV); adenovirus (AdV); influenza virus (IFV) A and B; and parainfluenza virus 1, 2, and 3 (PIV1/2/3). Samples were further analyzed by reverse-transcription polymerase chain reaction for the detection of human metapneumovirus (hMPV). Monthly meteorological data were determined by consulting the National Institute of Meteorology and the World Weather Online Meteorological Company websites. Pearson's correlation tests were used to determine the statistical association between the detection of respiratory viruses and climatic characteristics.
Results Among 572 patients, 243 (42.5%) were positive for at least one virus. The most frequently detected viruses by DIFA were RSV (30.0%), followed by IFVA (3.8%), IFVB (3.5%), PIV (0.9%), and AdV (0.9%). HMPV was detected in 13 RSV-negative samples (3.3%). Dual infections were detected in seven cases (1.2%). Monthly global respiratory viruses and RSV detections correlated significantly with temperature, rainfall, cloud cover, wind speed, wind temperature, and duration of sunshine. Monthly IFV detection significantly correlated with rainfall, wind speed, wind temperature, and duration of sunshine. HMPV detection significantly correlated with temperature and wind temperature.
Conclusion Respiratory viral outbreaks are clearly related to meteorological factors in Tunisia.
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Affiliation(s)
- Souhir Saadi
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Ouafa Kallala
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Imene Fodha
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Amira Jerbi
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Meriem BenHamida-Rebai
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Mouna Ben Hadj Fredj
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Sciences and Techniques, University of Kairouan, Kairouan, Tunisia
| | | | - Jihen Mathlouthi
- Neonatology Ward, Farhat Hached University Hospital, Sousse, Tunisia
| | - Monia Khlifa
- Pediatric Ward, Regional Hospital of Msaken, Sousse, Tunisia
| | | | | | - Saoussen Abroug
- Pediatric Ward, Sahloul University Hospital, Sousse, Tunisia
| | - Abdelhalim Trabelsi
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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14
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Ranjan P, Singhal A, Yadav S, Kumar N, Murali S, Sanghi SK, Khan R. Rapid diagnosis of SARS-CoV-2 using potential point-of-care electrochemical immunosensor: Toward the future prospects. Int Rev Immunol 2021; 40:126-142. [PMID: 33448909 DOI: 10.1080/08830185.2021.1872566] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Coronavirus disease (COVID-19) is an emerging and highly infectious disease making global public health concern and socio-economic burden. It is caused due to Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2). It has the tendency to spread rapidly through person-to-person. Currently, several molecular diagnostic platforms such as PCR, qRT-PCR, reverse transcription loop-mediated isothermal amplification (RT-LAMP), CRISPR are utilized for the diagnosis of SARS-CoV-2. These conventional techniques are costly, time consuming and require sophisticated instrumentation facility with well trained personnel for testing. Hence, it is tough to provide testing en-masse to the people in developing countries. On the other hand, several serological biosensors such as lateral flow immunosensor, optical, electrochemical, microfluidics integrated electrochemical/fluorescence is currently utilized for the diagnosis of SARS-CoV-2. In current pandemic situation, there is an urgent need of rapid and efficient diagnosis on mass scale of SARS-CoV-2 for early stage detection. Early monitoring of viral infections can help to control and prevent the spreading of infections in large chunk of population. In this review, the SARS-CoV-2 and their biomarkers in biological samples, collection of samples and recently reported potential electrochemical immunosensors for the rapid diagnosis of SARS-CoV-2 are discussed.
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Affiliation(s)
- Pushpesh Ranjan
- Microfluidics and MEMS Centre, CSIR - Advanced Materials and Processes Research Institute (AMPRI), Bhopal, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ayushi Singhal
- Microfluidics and MEMS Centre, CSIR - Advanced Materials and Processes Research Institute (AMPRI), Bhopal, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shalu Yadav
- Microfluidics and MEMS Centre, CSIR - Advanced Materials and Processes Research Institute (AMPRI), Bhopal, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Neeraj Kumar
- Microfluidics and MEMS Centre, CSIR - Advanced Materials and Processes Research Institute (AMPRI), Bhopal, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - S Murali
- Microfluidics and MEMS Centre, CSIR - Advanced Materials and Processes Research Institute (AMPRI), Bhopal, India
| | - Sunil K Sanghi
- Microfluidics and MEMS Centre, CSIR - Advanced Materials and Processes Research Institute (AMPRI), Bhopal, India
| | - Raju Khan
- Microfluidics and MEMS Centre, CSIR - Advanced Materials and Processes Research Institute (AMPRI), Bhopal, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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15
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Ribeiro BV, Cordeiro TAR, Oliveira E Freitas GR, Ferreira LF, Franco DL. Biosensors for the detection of respiratory viruses: A review. TALANTA OPEN 2020; 2:100007. [PMID: 34913046 PMCID: PMC7428963 DOI: 10.1016/j.talo.2020.100007] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 12/26/2022] Open
Abstract
The recent events of outbreaks related to different respiratory viruses in the past few years, exponentiated by the pandemic caused by the coronavirus disease 2019 (COVID-19), reported worldwide caused by SARS-CoV-2, raised a concern and increased the search for more information on viruses-based diseases. The detection of the virus with high specificity and sensitivity plays an important role for an accurate diagnosis. Despite the many efforts to identify the SARS-CoV-2, the diagnosis still relays on expensive and time-consuming analysis. A fast and reliable alternative is the use of low-cost biosensor for in loco detection. This review gathers important contributions in the biosensor area regarding the most current respiratory viruses, presents the advances in the assembly of the devices and figures of merit. All information is useful for further biosensor development for the detection of respiratory viruses, such as for the new coronavirus.
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Affiliation(s)
- Brayan Viana Ribeiro
- Group of Electrochemistry Applied to Polymers and Sensors - Multidisciplinary Group of Research, Science and Technology (RMPCT), Laboratory of Electroanlytical Applied to Biotechnology and Food Engineering (LEABE) - Chemistry Institute, Federal University of Uberlândia - campus Patos de Minas, Av. Getúlio Vargas, 230, 38.700-128, Patos de Minas, Minas Gerais 38700-128, Brazil
| | - Taís Aparecida Reis Cordeiro
- Institute of Science and Technology, Laboratory of Electrochemistry and Applied Nanotechnology, Federal University of the Jequitinhonha and Mucuri Valleys, Diamantina, Minas Gerais, Brazil
| | - Guilherme Ramos Oliveira E Freitas
- Laboratory of Microbiology (MICRO), Biotechnology Institute, Federal University of Uberlândia - campus Patos de Minas - Av. Getúlio Vargas, 230, 38.700-128, Patos de Minas, Minas Gerais, Brazil
| | - Lucas Franco Ferreira
- Institute of Science and Technology, Laboratory of Electrochemistry and Applied Nanotechnology, Federal University of the Jequitinhonha and Mucuri Valleys, Diamantina, Minas Gerais, Brazil
| | - Diego Leoni Franco
- Group of Electrochemistry Applied to Polymers and Sensors - Multidisciplinary Group of Research, Science and Technology (RMPCT), Laboratory of Electroanlytical Applied to Biotechnology and Food Engineering (LEABE) - Chemistry Institute, Federal University of Uberlândia - campus Patos de Minas, Av. Getúlio Vargas, 230, 38.700-128, Patos de Minas, Minas Gerais 38700-128, Brazil
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16
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Ventura BD, Cennamo M, Minopoli A, Campanile R, Censi SB, Terracciano D, Portella G, Velotta R. Colorimetric Test for Fast Detection of SARS-CoV-2 in Nasal and Throat Swabs. ACS Sens 2020; 5:3043-3048. [PMID: 32989986 PMCID: PMC7534800 DOI: 10.1021/acssensors.0c01742] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mass testing is fundamental to face the pandemic caused by the coronavirus SARS-CoV-2 discovered at the end of 2019. To this aim, it is necessary to establish reliable, fast, and cheap tools to detect viral particles in biological material so to identify the people capable of spreading the infection. We demonstrate that a colorimetric biosensor based on gold nanoparticle (AuNP) interaction induced by SARS-CoV-2 lends itself as an outstanding tool for detecting viral particles in nasal and throat swabs. The extinction spectrum of a colloidal solution of multiple viral-target gold nanoparticles-AuNPs functionalized with antibodies targeting three surface proteins of SARS-CoV-2 (spike, envelope, and membrane)-is red-shifted in few minutes when mixed with a solution containing the viral particle. The optical density of the mixed solution measured at 560 nm was compared to the threshold cycle (Ct) of a real-time PCR (gold standard for detecting the presence of viruses) finding that the colorimetric method is able to detect very low viral load with a detection limit approaching that of the real-time PCR. Since the method is sensitive to the infecting viral particle rather than to its RNA, the achievements reported here open a new perspective not only in the context of the current and possible future pandemics, but also in microbiology, as the biosensor proves itself to be a powerful though simple tool for measuring the viral particle concentration.
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Affiliation(s)
- Bartolomeo Della Ventura
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Via Cintia, 26 Ed. 6, 80126 Napoli, Italy
| | - Michele Cennamo
- Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Via Pansini, 5, 80131 Napoli, Italy
| | - Antonio Minopoli
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Via Cintia, 26 Ed. 6, 80126 Napoli, Italy
| | - Raffaele Campanile
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Via Cintia, 26 Ed. 6, 80126 Napoli, Italy
| | | | - Daniela Terracciano
- Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Via Pansini, 5, 80131 Napoli, Italy
| | - Giuseppe Portella
- Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Via Pansini, 5, 80131 Napoli, Italy
| | - Raffaele Velotta
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Via Cintia, 26 Ed. 6, 80126 Napoli, Italy
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17
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Ventura BD, Cennamo M, Minopoli A, Campanile R, Censi SB, Terracciano D, Portella G, Velotta R. Colorimetric Test for Fast Detection of SARS-CoV-2 in Nasal and Throat Swabs. ACS Sens 2020. [PMID: 32989986 DOI: 10.1021/acssensors.0c0174210.1021/acssensors.0c01742.s001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Mass testing is fundamental to face the pandemic caused by the coronavirus SARS-CoV-2 discovered at the end of 2019. To this aim, it is necessary to establish reliable, fast, and cheap tools to detect viral particles in biological material so to identify the people capable of spreading the infection. We demonstrate that a colorimetric biosensor based on gold nanoparticle (AuNP) interaction induced by SARS-CoV-2 lends itself as an outstanding tool for detecting viral particles in nasal and throat swabs. The extinction spectrum of a colloidal solution of multiple viral-target gold nanoparticles-AuNPs functionalized with antibodies targeting three surface proteins of SARS-CoV-2 (spike, envelope, and membrane)-is red-shifted in few minutes when mixed with a solution containing the viral particle. The optical density of the mixed solution measured at 560 nm was compared to the threshold cycle (Ct) of a real-time PCR (gold standard for detecting the presence of viruses) finding that the colorimetric method is able to detect very low viral load with a detection limit approaching that of the real-time PCR. Since the method is sensitive to the infecting viral particle rather than to its RNA, the achievements reported here open a new perspective not only in the context of the current and possible future pandemics, but also in microbiology, as the biosensor proves itself to be a powerful though simple tool for measuring the viral particle concentration.
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Affiliation(s)
- Bartolomeo Della Ventura
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Via Cintia, 26 Ed. 6, 80126 Napoli, Italy
| | - Michele Cennamo
- Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Via Pansini, 5, 80131 Napoli, Italy
| | - Antonio Minopoli
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Via Cintia, 26 Ed. 6, 80126 Napoli, Italy
| | - Raffaele Campanile
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Via Cintia, 26 Ed. 6, 80126 Napoli, Italy
| | | | - Daniela Terracciano
- Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Via Pansini, 5, 80131 Napoli, Italy
| | - Giuseppe Portella
- Dipartimento di Scienze Mediche Traslazionali, Università di Napoli Federico II, Via Pansini, 5, 80131 Napoli, Italy
| | - Raffaele Velotta
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Via Cintia, 26 Ed. 6, 80126 Napoli, Italy
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18
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Rahmani AR, Leili M, Azarian G, Poormohammadi A. Sampling and detection of corona viruses in air: A mini review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:140207. [PMID: 32554029 PMCID: PMC7295527 DOI: 10.1016/j.scitotenv.2020.140207] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 05/19/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a strain of coronaviruses that causes coronavirus disease 2019 (COVID-19). In these days, the spread of the SARS-CoV-2 virus through the air has become a controversial topic among scientists. Various organizations provide standard methods for monitoring biological agents in the air. Nevertheless, there has been no standard recommended method for sampling and determination of viruses in air. This manuscript aimed at reviewing published papers for sampling and detection of corona viruses, especially SARS-Cov-2 as a global health concern. It was found that SARS-Cov 2 was present in some air samples that were collected from patient's rooms in hospitals. This result warrants its airborne transmission potential. However, due to the fact that in the most reviewed studies, sampling was performed in the patient's room, it seems difficult to discriminate whether it is airborne or is transmitted through respiratory droplets. Moreover, some other disrupting factors such as patient distance from the sampler, using protective or oxygen masks by patients, patient activities, coughing and sneezing during sampling time, air movement, air conditioning, sampler type, sampling conditions, storage and transferring conditions, can affect the results. About the sampling methods, most of the used samplers such as PTFE filters, gelatin filers and cyclones showed suitable performance for trapping SARS-Co and MERS-Cov viruses followed by PCR analysis.
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Affiliation(s)
- Ali Reza Rahmani
- Department of Environmental Health Engineering, Faculty of Health and Research Center for Health Sciences, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mostafa Leili
- Department of Environmental Health Engineering, Faculty of Health and Research Center for Health Sciences, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ghasem Azarian
- Department of Environmental Health Engineering, Faculty of Health and Research Center for Health Sciences, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ali Poormohammadi
- Center of Excellence for Occupational Health, Research Center for Health Sciences, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran.
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19
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Lyu S, Li J, Yang L, Du X, Liu X, Chuan L, Jing G, Wang Z, Shu W, Ye C, Dong Q, Duan J, Fink JB, Gao Z, Liang Z. The utilization of aerosol therapy in mechanical ventilation patients: a prospective multicenter observational cohort study and a review of the current evidence. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1071. [PMID: 33145290 PMCID: PMC7575997 DOI: 10.21037/atm-20-1313] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Background Aerosol delivery via mechanical ventilation has been reported to vary significantly among different intensive care units (ICU). The optimal technique for using each aerosol generator may need to be updated with the available evidence. Methods A 2-week prospective multicenter observational cohort study was implemented to record aerosol delivery for mechanically ventilated adult patients in Chinese ICUs. Our data included the type of aerosol device and its placement, ventilator type, humidification, and aerosolized medication administered. A guide for the optimal technique for aerosol delivery during mechanical ventilation was summarized after a thorough literature review. Results A total of 160 patients (105 males) from 28 ICUs were enrolled, of whom 125 (78.1%) received aerosol therapy via invasive ventilation. Among these 125 patients, 53 received ventilator-integrated jet nebulizer, with 64% (34/53) of them placed the nebulizer close to Y piece in the inspiratory limb. Further, 56 patients used continuous nebulizers, with 84% (47/56) of them placed the nebulizer close to the Y piece in the inspiratory limb. Of the 35 patients who received aerosol therapy via noninvasive ventilation, 30 received single limb ventilators and continuous nebulizers, with 70% (21/30) of them placed between the mask and exhalation port. Only 36% (58/160) of the patients received aerosol treatments consistent with optimal practice. Conclusions Aerosol delivery via mechanical ventilation varied between ICUs, and only 36% of the patients received aerosol treatments consistent with optimal practice. ICU clinicians should be educated on the best practices for aerosol therapy, and quality improvement projects aim to improve the quality and outcome of patients with the optimal technique for aerosol delivery during mechanical ventilation are warranted.
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Affiliation(s)
- Shan Lyu
- Department of Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Jie Li
- Department of Cardiopulmonary Sciences, Division of Respiratory Care, Rush University Medical Center, Chicago, IL, USA
| | - Limin Yang
- Department of Respiratory Care, Zhejiang University School of Medical Sir Run Run Shaw Hospital, Hangzhou, China
| | - Xiaoliang Du
- Department of Neurosurgical, Tongji Medical College of Huazhong University of Science and Technology Tongji Hospital, Wuhan, China
| | - Xiaoyi Liu
- Department of Critical Care Medicine, Dazhou Central Hospital, Dazhou, China
| | - Libo Chuan
- Intensive Care Unit, the First People's Hospital of Yunnan Province, Kunming, China
| | - Guoqiang Jing
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou, China
| | - Zhenyan Wang
- Department of Critical Care Medicine, Peking University International Hospital, Beijing, China
| | - Weiwei Shu
- Department of Critical Care Medicine, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Chunjuan Ye
- Department of Surgical Intensive Care Unit, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qionglan Dong
- Department of Critical Care Medicine, the Third People's Hospital of Mianyang, Mianyang, China
| | - Jun Duan
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - James B Fink
- Department of Cardiopulmonary Sciences, Division of Respiratory Care, Rush University Medical Center, Chicago, IL, USA.,Aerogen Pharma Corp, San Mateo, CA, USA
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Zongan Liang
- Department of Respiratory and Critical Care Medicine, West China Medical Center, Sichuan University, Chengdu, China
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20
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Adenovirus load correlates with respiratory disease severity among hospitalized pediatric patients. Int J Infect Dis 2020; 97:145-150. [PMID: 32531431 DOI: 10.1016/j.ijid.2020.06.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES Human adenoviruses (HAdVs) are common pathogens that can cause respiratory, gastrointestinal and other infections. We investigated the correlation between adenovirus viral load in clinical respiratory samples and the respiratory disease severity in pediatric patients. METHODS Medical records of patients hospitalized in the Sheba Medical Center (SMC) with confirmed adenovirus infection were retrospectively analyzed. The possible correlation between disease severity score and Real time PCR 'cycle threshold' (Ct), a proxy of viral load, was assessed in patients aged 9 years and under. In addition, Ct values of hospitalized versus community-care patient samples, positive for various respiratory viruses including adenovirus, were compared. RESULTS Adenovirus load in respiratory samples, as measured by Ct values, was found to be negatively correlated with respiratory disease severity in hospitalized pediatric patients aged under 9 years. Moreover, hospitalized patients presented with significantly higher Ct levels for various respiratory viruses as compared to community-care patients. CONCLUSION In this study we found a correlation between Ct values obtained from adenovirus q-PCR analysis of respiratory clinical samples and disease severity in patients aged 9 years and under. Such finding may serve as a predictor of respiratory disease course in pediatric patients and will be beneficial for the differential diagnosis and treatment of pediatric patients.
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21
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Molecular Diagnosis of Pneumonia Using Multiplex Real-Time PCR Assay RespiFinder® SMART 22 FAST in a Group of Moroccan Infants. Adv Virol 2020; 2020:6212643. [PMID: 32148499 PMCID: PMC7049438 DOI: 10.1155/2020/6212643] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 01/25/2020] [Indexed: 01/18/2023] Open
Abstract
Background In Morocco, pediatric pneumonia remains a serious public health problem, as it constitutes the first cause of mortality due to infectious diseases. The etiological diagnosis of acute respiratory tract infections is difficult. Therefore, it is necessary to use Multiplex real-time polymerase chain reaction assay tests in a routine setting for exact and fast identification. Objectives In this paper, we present the clinical results of pediatric pneumonia and describe their etiology by using molecular diagnosis. Study design: Tracheal secretion was collected from infants presenting respiratory distress isolated or associated with systemic signs, attending the unit of Neonatology between December 1, 2016, and Mai 31, 2018. Samples were tested with the multiplex RespiFinder® SMART 22 FAST which potentially detects 18 viruses and 4 bacteria. Results Of the 86 infants considered in this study (mean age 31 ± 19 days) suspected of acute respiratory tract infections, 71 (83%) were positive for one or multiple viruses or/and bacteria. The majority of acute respiratory tract infections had a viral origin (95%): respiratory syncytial viruses (A and B) (49%), rhinovirus (21%), coronaviruses 229E (11%), humain metapneumovirus (5%), influenza A (3%), influenza H1N1 (1%), adenovirus (2%), and parainfluenza virus type 4 (2%). Among our patients, 6% had Mycoplasma pneumoniae. Coinfections were not associated with severe respiratory symptoms. Conclusion The clinical spectrum of respiratory infections is complex and often nonspecific. Thus, the early and fast detection of related causative agents is crucial. The use of multiplex real time polymerase chain reaction may help choose an accurate treatment, reduce the overall use of unnecessary antibiotics, preserve intestinal flora, and decrease nosocomial infection by reducing the length of hospitalization.
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22
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Study of Infectious Agents in Respiratory Diseases. PEDIATRIC RESPIRATORY DISEASES 2020. [PMCID: PMC7121745 DOI: 10.1007/978-3-030-26961-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Kelly-Cirino C, Mazzola LT, Chua A, Oxenford CJ, Van Kerkhove MD. An updated roadmap for MERS-CoV research and product development: focus on diagnostics. BMJ Glob Health 2019; 4:e001105. [PMID: 30815285 PMCID: PMC6361340 DOI: 10.1136/bmjgh-2018-001105] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/13/2018] [Accepted: 10/23/2018] [Indexed: 01/12/2023] Open
Abstract
Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. In this review we identified sources for molecular and serological diagnostic tests used in MERS-CoV detection, case management and outbreak investigations, as well as surveillance for humans and animals (camels), and summarised the performance of currently available tests, diagnostic needs, and associated challenges for diagnostic test development and implementation. A more detailed understanding of the kinetics of infection of MERS-CoV is needed in order to optimise the use of existing assays. Notably, MERS-CoV point-of-care tests are needed in order to optimise supportive care and to minimise transmission risk. However, for new test development, sourcing clinical material continues to be a major challenge to achieving assay validation. Harmonisation and standardisation of laboratory methods are essential for surveillance and for a rapid and effective international response to emerging diseases. Routine external quality assessment, along with well-characterised and up-to-date proficiency panels, would provide insight into MERS-CoV diagnostic performance worldwide. A defined set of Target Product Profiles for diagnostic technologies will be developed by WHO to address these gaps in MERS-CoV outbreak management.
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Affiliation(s)
| | | | - Arlene Chua
- Department of Information, Evidence and Research, WHO, Geneva, Switzerland.,Medecins Sans Frontières, Geneva, Switzerland
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24
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Nybond S, Réu P, Rhedin S, Svedberg G, Alfvén T, Gantelius J, Svahn HA. Adenoviral detection by recombinase polymerase amplification and vertical flow paper microarray. Anal Bioanal Chem 2018; 411:813-822. [PMID: 30498984 PMCID: PMC6338793 DOI: 10.1007/s00216-018-1503-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/30/2018] [Accepted: 11/16/2018] [Indexed: 12/15/2022]
Abstract
Respiratory viral infections often mimic the symptoms of infections caused by bacteria; however, restricted and targeted administration of antibiotics is needed to combat growing antimicrobial resistance. This is particularly relevant in low-income settings. In this work, we describe the use of isothermal amplification of viral DNA at 37 °C coupled to a paper-based vertical flow microarray (VFM) setup that utilizes a colorimetric detection of amplicons using functionalized gold nanoparticles. Two oligonucleotide probes, one in-house designed and one known adenoviral probe were tested and validated for microarray detection down to 50 nM using a synthetic target template. Furthermore, primers were shown to function in a recombinase polymerase amplification reaction using both synthetic template and viral DNA. As a proof-of-concept, we demonstrate adenoviral detection with four different adenoviral species associated with respiratory infections using the paper-based VFM format. The presented assay was validated with selected adenoviral species using the in-house probe, enabling detection at 1 ng of starting material with intra- and inter-assay %CV of ≤ 9% and ≤ 13%. Finally, we validate our overall method using clinical samples. Based on the results, the combination of recombinase polymerase amplification, paper microarray analysis, and nanoparticle-based colorimetric detection could thus be a useful strategy towards rapid and affordable multiplexed viral diagnostics.
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Affiliation(s)
- Susanna Nybond
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Protein Science, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
| | - Pedro Réu
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Protein Science, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
| | - Samuel Rhedin
- Department of Medicine, Solna, Unit of Infectious Diseases, Karolinska Institutet and Karolinska University Hospital, 17176, Stockholm, Sweden
| | - Gustav Svedberg
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Protein Science, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
| | - Tobias Alfvén
- Sachs' Children & Youth Hospital, South General Hospital, 11883, Stockholm, Sweden.,Department of Public Health Sciences, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Jesper Gantelius
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Protein Science, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden.,Department of Public Health Sciences, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Helene Andersson Svahn
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Protein Science, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden.
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Li J, Tao Y, Tang M, Du B, Xia Y, Mo X, Cao Q. Rapid detection of respiratory organisms with the FilmArray respiratory panel in a large children's hospital in China. BMC Infect Dis 2018; 18:510. [PMID: 30305033 PMCID: PMC6180626 DOI: 10.1186/s12879-018-3429-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/01/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Respiratory tract infections (RTIs) are the most common illness in children, and rapid diagnosis is required for the optimal management of RTIs, especially severe infections. METHODS Nasopharyngeal swab or sputum specimens were collected from children aged 19 days to 15 years who were admitted to a hospital in Shanghai and diagnosed with RTIs. The specimens were tested with the FilmArray Respiratory Panel, a multiplex PCR assay that detects 16 viruses, Mycoplasma pneumoniae (M. pneumoniae), Bordetella pertussis (B. pertussis) and Chlamydophila pneumoniae (C. pneumoniae). RESULTS Among the 775 children studied, 626 (80.8%, 626/775) tested positive for at least one organism, and multiple organisms were detected in 198 (25.5%). Rhinoviruses/enteroviruses (25.5%, 198/775) were detected most often, followed by respiratory syncytial virus (19.5%, 151/775), parainfluenza virus 3 (14.8%, 115/775), influenza A or B (10.9%), adenovirus (10.8%), M. pneumoniae (10.6%) and B. pertussis (6.3%). The prevalence of organisms differed by age, and most of the viruses were more common in winter. Of the 140 children suspected of having pertussis, 35.0% (49/140) tested positive for B. pertussis. CONCLUSIONS FilmArray RP allows the rapid simultaneous detection of a wide number of respiratory organisms, with limited hands-on time, in Chinese pediatric patients with RTIs.
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Affiliation(s)
- Jin Li
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yue Tao
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Mingyu Tang
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Bailu Du
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yijun Xia
- Medical Affairs, Great China
- bioMérieux (Shanghai) Company, Limited, Shanghai, China
| | - Xi Mo
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Qing Cao
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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26
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Sansone M, Wiman Å, Karlberg ML, Brytting M, Bohlin L, Andersson LM, Westin J, Nordén R. Molecular characterization of a nosocomial outbreak of influenza B virus in an acute care hospital setting. J Hosp Infect 2018; 101:30-37. [PMID: 29909095 PMCID: PMC7114871 DOI: 10.1016/j.jhin.2018.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/04/2018] [Indexed: 01/21/2023]
Abstract
Aim To describe a hospital outbreak of influenza B virus (InfB) infection during season 2015/2016 by combining clinical and epidemiological data with molecular methods. Methods Twenty patients diagnosed with InfB from a hospital outbreak over a four-week-period were included. Nasopharyngeal samples (NPS) positive for InfB by multiplex real-time polymerase chain reaction were sent for lineage typing and whole genome sequencing (WGS). Medical records were reviewed retrospectively for data regarding patient characteristics, localization, exposure and outcome, and assembled into a timeline. In order to find possible connections to the hospital outbreak, all patients with a positive NPS for influenza from the region over an extended time period were also reviewed. Findings All 20 cases of InfB were of subtype B/Yamagata, and 17 of 20 patients could be linked to each other by either shared room or shared ward. WGS was successful or partially successful for 15 of the 17 viral isolates, and corroborated the epidemiological link supporting a close relationship. In the main affected ward, 19 of 75 inpatients were infected with InfB during the outbreak period, resulting in an attack rate of 25%. One probable case of influenza-related death was identified. Conclusion InfB may spread within an acute care hospital, and advanced molecular methods may facilitate assessment of the source and extent of the outbreak. A multi-faceted approach, including rapid diagnosis, early recognition of outbreak situations, simple rules for patient management and the use of regular infection control measures, may prevent nosocomial transmission of influenza virus.
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Affiliation(s)
- M Sansone
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Å Wiman
- Public Health Agency of Sweden, Solna, Sweden
| | | | - M Brytting
- Public Health Agency of Sweden, Solna, Sweden
| | - L Bohlin
- Department of Internal Medicine, Kungalv Hospital, Kungalv, Sweden
| | - L-M Andersson
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - J Westin
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - R Nordén
- Institute of Biomedicine, Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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27
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Meyers L, Ginocchio CC, Faucett AN, Nolte FS, Gesteland PH, Leber A, Janowiak D, Donovan V, Dien Bard J, Spitzer S, Stellrecht KA, Salimnia H, Selvarangan R, Juretschko S, Daly JA, Wallentine JC, Lindsey K, Moore F, Reed SL, Aguero-Rosenfeld M, Fey PD, Storch GA, Melnick SJ, Robinson CC, Meredith JF, Cook CV, Nelson RK, Jones JD, Scarpino SV, Althouse BM, Ririe KM, Malin BA, Poritz MA. Automated Real-Time Collection of Pathogen-Specific Diagnostic Data: Syndromic Infectious Disease Epidemiology. JMIR Public Health Surveill 2018; 4:e59. [PMID: 29980501 PMCID: PMC6054708 DOI: 10.2196/publichealth.9876] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/29/2018] [Accepted: 04/12/2018] [Indexed: 12/22/2022] Open
Abstract
Background Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy. Objective The aim of this study was to demonstrate the automated export, aggregation, and analysis of infectious disease diagnostic test results from clinical laboratories across the United States in a manner that protects patient confidentiality. We hypothesized that such a system could aid in monitoring the seasonal occurrence of respiratory pathogens and may have advantages with regard to scope and ease of reporting compared with existing surveillance systems. Methods We describe a system, BioFire Syndromic Trends, for rapid disease reporting that is syndrome-based but pathogen-specific. Deidentified patient test results from the BioFire FilmArray multiplex molecular diagnostic system are sent directly to a cloud database. Summaries of these data are displayed in near real time on the Syndromic Trends public website. We studied this dataset for the prevalence, seasonality, and coinfections of the 20 respiratory pathogens detected in over 362,000 patient samples acquired as a standard-of-care testing over the last 4 years from 20 clinical laboratories in the United States. Results The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks, and adenovirus and the bacterial pathogens show constant detection over the year. The dataset can also be considered in an ecological framework; the viruses and bacteria detected by this test are parasites of a host (the human patient). Interestingly, the rate of pathogen codetections, on average 7.94% (28,741/362,101), matches predictions based on the relative abundance of organisms present. Conclusions Syndromic Trends preserves patient privacy by removing or obfuscating patient identifiers while still collecting much useful information about the bacterial and viral pathogens that they harbor. Test results are uploaded to the database within a few hours of completion compared with delays of up to 10 days for other diagnostic-based reporting systems. This work shows that the barriers to establishing epidemiology systems are no longer scientific and technical but rather administrative, involving questions of patient privacy and data ownership. We have demonstrated here that these barriers can be overcome. This first look at the resulting data stream suggests that Syndromic Trends will be able to provide high-resolution analysis of circulating respiratory pathogens and may aid in the detection of new outbreaks.
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Affiliation(s)
| | - Christine C Ginocchio
- BioFire Diagnostics, Salt Lake City, UT, United States.,bioMérieux USA, Durham, NC, United States.,Hofstra Northwell School of Medicine, Hempstead, NY, United States
| | | | - Frederick S Nolte
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Per H Gesteland
- Departments of Pediatrics and Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Amy Leber
- Laboratory of Microbiology and Immunoserology, Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, United States
| | - Diane Janowiak
- Department of Lab Operations, South Bend Medical Foundation, South Bend, IN, United States
| | - Virginia Donovan
- Department of Pathology, New York University Winthrop Hospital, Mineola, NY, United States
| | - Jennifer Dien Bard
- Clinical Microbiology and Virology Laboratory, Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, United States.,Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Silvia Spitzer
- Molecular Genetics Laboratory, Stony Brook University Medical Center, Stony Brook, NY, United States
| | - Kathleen A Stellrecht
- Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, NY, United States
| | - Hossein Salimnia
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Rangaraj Selvarangan
- Clinical Microbiology, Virology and Molecular Infectious Diseases Laboratory, Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, United States
| | - Stefan Juretschko
- Department of Pathology and Laboratory Medicine, Division of Infectious Disease Diagnostics, Northwell Health, Lake Success, NY, United States
| | - Judy A Daly
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Jeremy C Wallentine
- Department of Pathology, Intermountain Medical Center, Murray, UT, United States
| | - Kristy Lindsey
- Laboratory of Microbiology, University of Massachusetts Medical School-Baystate, Springfield, MA, United States
| | - Franklin Moore
- Laboratory of Microbiology, University of Massachusetts Medical School-Baystate, Springfield, MA, United States
| | - Sharon L Reed
- Department of Pathology and Medicine, Divisions of Clinical Pathology and Infectious Diseases, UC San Diego, San Diego, CA, United States
| | - Maria Aguero-Rosenfeld
- Department of Clinical Laboratories, New York University Langone Health, New York, NY, United States
| | - Paul D Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Gregory A Storch
- Department of Pediatrics, Washington University, St. Louis, MO, United States
| | - Steve J Melnick
- Department of Pathology and Clinical Laboratories, Nicklaus Children's Hospital, Miami, FL, United States
| | - Christine C Robinson
- Department of Pathology and Laboratory Medicine, Microbiology/Virology Laboratory Section, Children's Hospital Colorado, Aurora, CO, United States
| | - Jennifer F Meredith
- Department of Laboratory Services, Microbiology Section, Greenville Health System, Greenville, SC, United States
| | | | | | - Jay D Jones
- BioFire Diagnostics, Salt Lake City, UT, United States
| | | | - Benjamin M Althouse
- University of Washington, Seattle, WA, United States.,New Mexico State University, Las Cruces, NM, United States
| | | | - Bradley A Malin
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN, United States
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Mummidi PS, Tripathy R, Dwibedi B, Mahapatra A, Baraha S. Viral aetiology of wheezing in children under five. Indian J Med Res 2018. [PMID: 28639594 PMCID: PMC5501050 DOI: 10.4103/ijmr.ijmr_840_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background & objectives: Wheezing is a common problem in children under five with acute respiratory infections (ARIs). Viruses are known to be responsible for a considerable proportion of ARIs in children. This study was undertaken to know the viral aetiology of wheezing among the children less than five years of age, admitted to a tertiary care hospital in eastern India. Methods: Seventy five children, under the age of five years admitted with wheezing, were included in the study. Throat and nasal swabs were collected, and real-time multiplex polymerase chain reaction (PCR) assay was used to screen for influenza 1 and 2, respiratory syncytial virus (RSV), parainfluenza virus (PIV) 1, 2, 3 and 4, rhinovirus, human meta-pneumovirus, bocavirus (HBoV), Coronavirus, adenovirus, Enterovirus and Parechovirus. Results: The total viral detection rate was 28.57 per cent. Viral RNA markers were detected from children diagnosed to be having pneumonia (3 cases), bronchiolitis (9 cases), episodic wheeze (2 cases) and multitrigger wheeze (6 cases). RSV was the most common virus (35%) followed by PIV1, 2 and 3 (20%), HBoV (10%) and rhinovirus (5%). However, mixed infection was observed in 30 per cent of cases. Interpretation & conclusions: The study reported the presence of respiratory viral agents in 28.57 per cent of children with wheezing; RSV and PIV were most common, accounting to 55 per cent of the total cases. Mixed infection was reported in 30 per cent of cases. Seasonal variation in the occurrence of these viruses was also noted. Further studies need to be done with a large sample and longer follow up period to verify these findings.
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Affiliation(s)
| | - Radha Tripathy
- Department of Paediatrics, Hitech Medical College & Hospital, Bhubaneswar, India
| | - Bhagirathi Dwibedi
- Regional Medical Research Centre, Indian Council of Medical Research (ICMR), Bhubaneswar, India
| | - Amarendra Mahapatra
- Regional Medical Research Centre, Indian Council of Medical Research (ICMR), Bhubaneswar, India
| | - Suryakanta Baraha
- Department of Paediatrics, Hitech Medical College & Hospital, Bhubaneswar, India
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Abstract
OBJECTIVES The aim of the study was to assess whether bone mass and metabolism are impaired in genetically at-risk children with screening-detected celiac disease. METHODS Included were 71 children with screening-detected celiac disease diagnosed at 10.0 ± 0.7 (mean ± standard deviation) years and 142 matched controls and 30 children with screening-detected celiac disease diagnosed at 3.3 ± 0.4 years of age presently on a gluten-free diet for 6.9 ± 1.1 years and 60 matched controls. All participants were assessed for bone mineral density (BMD) of total body and spine by dual x-ray absorptiometry, serum 25(OH) vitamin D3, parathyroid hormone (PTH), interleukin (IL)-1β, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12p70, IL-13, IL-15, interferon gamma, and tumor necrosis factor alpha. RESULTS At diagnosis, screening-detected celiac disease children as compared to controls had a mean -0.03 g/cm reduced BMD of both total body and spine (P = 0.009 and P = 0.005, respectively), a mean -11.4 nmol/L lower level of 25(OH) vitamin D3 (P < 0.001), and a mean +1.0 pmol/L higher PTH level (P < 0.001). Systemic levels of the cytokines IL-1β, IL-6, IL-8, IL-10, IL-12p70, IL-13, and tumor necrosis factor alpha were all increased in screening-detected celiac disease as compared to controls (P < 0.001). No difference in BMD, 25(OH) vitamin D3, PTH, and cytokine levels were detected in children on a gluten-free diet compared with controls. CONCLUSIONS Children with screening-detected celiac disease have reduced BMD, lower levels of vitamin D3, higher levels of PTH, and signs of systemic inflammation compared with controls. These differences were not found in celiac disease children on a gluten-free diet, indicating that children with screening-detected celiac disease benefit from an early diagnosis and treatment.
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Koo B, Jin CE, Lee TY, Lee JH, Park MK, Sung H, Park SY, Lee HJ, Kim SM, Kim JY, Kim SH, Shin Y. An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections. Biosens Bioelectron 2017; 90:187-194. [PMID: 27894035 PMCID: PMC7127409 DOI: 10.1016/j.bios.2016.11.051] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/31/2016] [Accepted: 11/22/2016] [Indexed: 11/19/2022]
Abstract
Recently, RNA viral infections caused by respiratory viruses, such as influenza, parainfluenza, respiratory syncytial virus, coronavirus, and Middle East respiratory syndrome-coronavirus (MERS-CoV), and Zika virus, are a major public health threats in the world. Although myriads of diagnostic methods based on RNA amplification have been developed in the last decades, they continue to lack speed, sensitivity, and specificity for clinical use. A rapid and accurate diagnostic method is needed for appropriate control, including isolation and treatment of the patients. Here, we report an isothermal, label-free, one-step RNA amplification and detection system, termed as iROAD, for the diagnosis of respiratory diseases. It couples a one-step isothermal RNA amplification method and a bio-optical sensor for simultaneous viral RNA amplification/detection in a label-free and real-time manner. The iROAD assay offers a one-step viral RNA amplification/detection example to rapid analysis (<20min). The detection limit of iROAD assay was found to be 10-times more sensitive than that of real-time reverse transcription-PCR method. We confirmed the clinical utility of the iROAD assay by detecting viral RNAs obtained from 63 human respiratory samples. We envision that the iROAD assay will be useful and potentially adaptable for better diagnosis of emerging infectious diseases including respiratory diseases.
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Affiliation(s)
- Bonhan Koo
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Choong Eun Jin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Tae Yoon Lee
- Department of Technology Education, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeong Hoon Lee
- Department of Electrical Engineering, Kwangwoon University, 447-1 Wolgye, Nowon, Seoul 136-791, Republic of Korea
| | - Mi Kyoung Park
- One BioMed Pte Ltd, 60 Biopolis street, Genome #02-01, Singapore 138672, Singapore
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Se Yoon Park
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea; Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Hyun Jung Lee
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Sun Mi Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea.
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Biomedical Engineering Research Center, Asan Institute of Life Sciences, Asan Medical Center, 88 Olympicro-43gil, Songpa-gu, Seoul, Republic of Korea.
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Steensels D, Reynders M, Descheemaeker P, Curran MD, Jacobs F, Denis O, Delforge ML, Montesinos I. Performance evaluation of direct fluorescent antibody, Focus Diagnostics Simplexa™ Flu A/B & RSV and multi-parameter customized respiratory Taqman® array card in immunocompromised patients. J Virol Methods 2017; 245:61-65. [PMID: 28365410 PMCID: PMC7119654 DOI: 10.1016/j.jviromet.2017.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 03/25/2017] [Accepted: 03/26/2017] [Indexed: 11/29/2022]
Abstract
Limited sensitivity of direct fluorescent antibody testing in comparison to molecular methods. Simplexa™ direct assay is sensitive and specific for the detection of Flu A, B and RSV. Performing the TAC would increase the diagnostic yield and detection of co-infections significantly. Immunocompromised patient population with overall positivity rate of 62%. Co-infection rate of 15.3% found by TAC.
Background Molecular assays for diagnosis of Flu A, Flu B, and RSV with short turn-around-time (TAT) are of considerable clinical importance. In addition, rapid and accurate diagnosis of a large panel of viral and atypical pathogens can be crucial in immunocompromised patients. Objectives First, to evaluate the performance of the Simplexa™ Direct assay system in comparison with direct fluorescent antibody (DFA) and customized Taqman® Array Card (TAC) testing for RSV, Flu A, and Flu B in immunocompromised patients. Second, to evaluate different algorithms for the detection of respiratory pathogens in terms of cost, turn-around-time (TAT) and diagnostic yield. Study design We collected 125 nasopharyngeal swabs (NTS) and 25 BAL samples from symptomatic immunocompromised patients. Samples for which Simplexa™ and TAC results were discordant underwent verification testing. The TAC assay is based on singleplex RT-PCR, targeting 24 viruses, 8 bacteria and 2 fungi simultaneously. Results The overall sensitivity was significantly lower for DFA testing than for the two molecular methods (p < 0.05). Performance characteristics of Simplexa™ testing were not significantly different compared to TAC testing (p > 0.1). For BAL samples only, the sensitivity and specificity of the Simplexa™ assay was 100%. In total, 6.7, 16 and 18% of samples were positive for Flu A, Flu B or RSV by DFA, Simplexa™ and TAC testing, respectively. When considering not only these pathogens but also all results for TAC, the method identified 93 samples with one or more respiratory pathogens (62%). A co-infection rate of 15.3% was found by TAC. The estimated costs and TAT were 8.2€ and 2 h for DFA, 31.8€ and 1.5 h for Simplexa™ and 55€ and 3 h for TAC testing. Conclusions Performing the Simplexa™ test 24 h a day/7 days a week instead of DFA would considerably improve the overall sensitivity and time-to-result, albeit at a higher cost generated in the laboratory. Performing the TAC would increase the diagnostic yield and detection of co-infections significantly.
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Affiliation(s)
- Deborah Steensels
- Department of Clinical Microbiology, CUB-Erasme, Université Libre de Bruxelles, Brussels, Belgium.
| | - Marijke Reynders
- Department of Clinical Microbiology, AZ St-Jan Brugge-Oostende Hospital, Brugge, Belgium
| | - Patrick Descheemaeker
- Department of Clinical Microbiology, AZ St-Jan Brugge-Oostende Hospital, Brugge, Belgium
| | - Martin D Curran
- Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Cambridge, UK
| | - Frédérique Jacobs
- Department of Infectious Diseases, CUB-Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Olivier Denis
- Department of Clinical Microbiology, CUB-Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie-Luce Delforge
- Department of Clinical Microbiology, CUB-Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Isabel Montesinos
- Department of Clinical Microbiology, CUB-Erasme, Université Libre de Bruxelles, Brussels, Belgium
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Distribution and Molecular Characterization of Human Adenovirus and Epstein-Barr Virus Infections in Tonsillar Lymphocytes Isolated from Patients Diagnosed with Tonsillar Diseases. PLoS One 2016; 11:e0154814. [PMID: 27136093 PMCID: PMC4852932 DOI: 10.1371/journal.pone.0154814] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/19/2016] [Indexed: 11/19/2022] Open
Abstract
Surgically removed palatine tonsils provide a conveniently accessible source of T and B lymphocytes to study the interplay between foreign pathogens and the host immune system. In this study we have characterised the distribution of human adenovirus (HAdV), Epstein-Barr virus (EBV) and human cytomegalovirus (HCMV) in purified tonsillar T and B cell-enriched fractions isolated from three patient age groups diagnosed with tonsillar hypertrophy and chronic/recurrent tonsillitis. HAdV DNA was detected in 93 out of 111 patients (84%), while EBV DNA was detected in 58 patients (52%). The most abundant adenovirus type was HAdV-5 (68%). None of the patients were positive for HCMV. Furthermore, 43 patients (39%) showed a co-infection of HAdV and EBV. The majority of young patients diagnosed with tonsillar hypertrophy were positive for HAdV, whereas all adult patients diagnosed with chronic/recurrent tonsillitis were positive for either HAdV or EBV. Most of the tonsils from patients diagnosed with either tonsillar hypertrophy or chronic/recurrent tonsillitis showed a higher HAdV DNA copy number in T compared to B cell-enriched fraction. Interestingly, in the majority of the tonsils from patients with chronic/recurrent tonsillitis HAdV DNA was detected in T cells only, whereas hypertrophic tonsils demonstrated HAdV DNA in both T and B cell-enriched fractions. In contrast, the majority of EBV positive tonsils revealed a preference for EBV DNA accumulation in the B cell-enriched fraction compared to T cell fraction irrespective of the patients' age.
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Kabir MS, Clements MO, Atkins M, Kimmitt PT. Application of RT-Bst to enhance detection of pathogenic viruses of the respiratory tract. Br J Biomed Sci 2015; 72:128-34. [PMID: 26510269 DOI: 10.1080/09674845.2015.11666809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Inefficiency of RT-PCR can be associated with the suboptimal process of reverse transcription as only 40-80% of RNA is converted to cDNA. We employed a novel method, RT-Bst, to enrich the concentration of cDNA for subsequent multiplex PCR detection of selected RNA viruses. The RT-Bst method amplifies cDNA through reverse transcription of viral RNA using reverse transcriptase and amplification of cDNA using Bst DNA polymerase. Viral RNA was extracted from 25 nasopharyngeal samples for detection of influenza A, B and C; parainfluenza 1-4; human coronaviruses 229E and OC43; respiratory syncytial virus (RSV) and rhinovirus. Both multiplex one-step RT-PCR and RT-Bst PCR were used to compare their performances for detection of virus sequences. These findings were compared with routine laboratory detection. When using RT-Bst PCR, 28% of samples yielded a viral pathogen compared to 20% with RT-PCR and 12% using routine diagnostic tests. RT-Bst PCR was shown to have particular utility in the detection of RSV RNA as this was present in 20% of the samples studied compared to 8% when using RT-PCR. For one patient, RT-Bst PCR was able to detect RSV five days earlier than conventional hospital diagnostic testing. RT-Bst and RT-Bst PCR can be used as alternative approaches to reverse transcription and one-step RT-PCR, respectively, for sequence-independent amplification of RNA virus sequences and a larger scale analysis of this new diagnostic approach is warranted.
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Hosseini SS, Ghasemian E, Jamaati H, Tabaraie B, Amini Z, Cox K. Association between respiratory viruses and exacerbation of COPD: a case-control study. Infect Dis (Lond) 2015; 47:523-9. [DOI: 10.3109/23744235.2015.1022873] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Schwartz PJ. Can the season of birth risk factor for schizophrenia be prevented by bright light treatment for the second trimester mother around the winter solstice? Med Hypotheses 2014; 83:809-15. [DOI: 10.1016/j.mehy.2014.10.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 12/22/2022]
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Andersson ME, Olofsson S, Lindh M. Comparison of the FilmArray assay and in-house real-time PCR for detection of respiratory infection. ACTA ACUST UNITED AC 2014; 46:897-901. [PMID: 25288382 DOI: 10.3109/00365548.2014.951681] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Recently, molecular methods capable of detecting almost all microbial agents that may cause acute respiratory infection have been introduced. The FilmArray Respiratory Panel assay, which integrates nucleic acid extraction, nested amplification and detection in a reaction pouch preloaded with all reagents required for detection of 17 viruses and 3 bacteria, was compared with an in-house real-time PCR that detects these agents in 8 parallel amplifications. When 128 clinical samples representing 18 of these agents were analysed by both assays the agreement was excellent, with kappa values ranging between 0.54 and 1.0. Discordances were mainly observed for adenovirus, but not when version 1.7 of FilmArray was used. The results show that these assays detect a wide range of pathogens with similar performance. FilmArray provides results after approximately 1 h, including ≈ 5 min hands-on time, and does not require advanced equipment or expertise in molecular diagnostics, making it a useful point-of-care-test for acute respiratory infections.
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Affiliation(s)
- Maria E Andersson
- Department of Infectious Diseases, University of Gothenburg , Gothenburg , Sweden
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de-Paris F, Beck C, Pires MR, dos Santos RP, Kuchenbecker RDS, Barth AL. Viral epidemiology of respiratory infections among children at a tertiary hospital in Southern Brazil. Rev Soc Bras Med Trop 2014; 47:223-6. [PMID: 24861298 DOI: 10.1590/0037-8682-0080-2013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 08/27/2013] [Indexed: 05/28/2023] Open
Abstract
INTRODUCTION This study reports the pediatric epidemiology of respiratory syncytial virus (RSV), influenza (IF), parainfluenza (PIV), and adenovirus (ADV) at Hospital de Clínicas de Porto Alegre. METHODS Cases of infection, hospitalizations in intensive care units (ICUs), nosocomial infections, and lethality rates were collected from 2007 to 2010. RESULTS RSV accounted for most nosocomial infections. Intensive care units admission rates for ADV and RSV infections were highest in 2007 and 2010. During 2008-2009, H1N1 and ADV had the highest ICU admission rates. ADV had the highest fatality rate during 2007-2009. CONCLUSIONS Each virus exhibited distinct behavior, causing hospitalization, outbreaks, or lethality.
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Affiliation(s)
- Fernanda de-Paris
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade de Pesquisa Biomédica, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Caroline Beck
- Programa de Pós-Graduação em Epidemiologia, Instituto de Avaliação de Tecnologia em Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Márcia Rosane Pires
- Comissão de Controle de Infecção Hospitalar, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Rodrigo Pires dos Santos
- Comissão de Controle de Infecção Hospitalar, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Ricardo de Souza Kuchenbecker
- Programa de Pós-Graduação em Epidemiologia, Instituto de Avaliação de Tecnologia em Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Afonso Luis Barth
- Laboratório de Biologia Molecular, Serviço de Patologia Clínica, Unidade de Pesquisa Biomédica, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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The Epidemiology of Upper Respiratory Infections at a Tertiary Care Center: Prevalence, Seasonality, and Clinical Symptoms. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/469393] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Improved multiplex PCR detection methods are facilitating the correlation of the etiology of respiratory tract infections with specific symptoms or clinical manifestations. We conducted a retrospective analysis of the incidence of respiratory pathogens and initial symptoms in 1,286 patients at a tertiary care center tested by multiplex respiratory pathogen PCR from July 1, 2012, to June 30, 2013. Rhinovirus/enterovirus (Rhino/Entero) infections were the most prevalent (25.4%) followed by respiratory syncytial virus (RSV) (13.6%) and influenza A (6.2%). Eleven percent of patients were positive for multiple analytes with Rhino/Entero and RSV being the most common combination. Asthma or asthma exacerbation was the most common presenting symptom in patients positive for Rhino/Entero (38.4%) or positive for Rhino/Entero along with RSV or hMPV (34.8%). Of the patients positive for Rhino/Entero and presenting with asthma, 97% were ≤17 years of age. RSV positive patients most commonly presented with respiratory distress (40.3%) followed by asthma (18%) or pneumonia (18%). The most prevalent initial clinical manifestation for influenza was fever (27.4%) followed by respiratory distress (13%) or pneumonia (11.9%). The significant percentage of patients positive for Rhino/Entero virus presenting with asthma supports the role of rhinovirus as an important trigger for asthma exacerbation.
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Crump C, Sundquist J, Sieh W, Winkleby MA, Sundquist K. Season of birth and risk of Hodgkin and non-Hodgkin lymphoma. Int J Cancer 2014; 135:2735-9. [PMID: 24752499 DOI: 10.1002/ijc.28909] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 04/09/2014] [Indexed: 11/11/2022]
Abstract
Infectious etiologies have been hypothesized for Hodgkin and non-Hodgkin lymphoma (HL and NHL) in early life, but findings to date for specific lymphomas and periods of susceptibility are conflicting. We conducted the first national cohort study to examine whether season of birth, a proxy for infectious exposures in the first few months of life, is associated with HL or NHL in childhood through young adulthood. A total of 3,571,574 persons born in Sweden in 1973-2008 were followed up through 2009 to examine the association between season of birth and incidence of HL (943 cases) or NHL (936 cases). We found a sinusoidal pattern in NHL risk by season of birth (p = 0.04), with peak risk occurring among birthdates in April. Relative to persons born in fall (September-November), odds ratios for NHL by season of birth were 1.25 [95% confidence interval (CI), 1.04-1.50; p = 0.02] for spring (March-May), 1.22 (95% CI, 1.01-1.48; p = 0.04) for summer (June-August) and 1.11 (95% CI, 0.91-1.35; p = 0.29) for winter (December-February). These findings did not vary by sex, age at diagnosis or major subtypes. In contrast, there was no seasonal association between birthdate and risk of HL (p = 0.78). In this large cohort study, birth in spring or summer was associated with increased risk of NHL (but not HL) in childhood through young adulthood, possibly related to immunologic effects of delayed infectious exposures compared with fall or winter birth. These findings suggest that immunologic responses in early infancy may play an important role in the development of NHL.
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Affiliation(s)
- Casey Crump
- Department of Medicine, Stanford University, Stanford, CA
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Cho CH, Lee CK, Nam MH, Yoon SY, Lim CS, Cho Y, Kim YK. Evaluation of the AdvanSure™ real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses. Diagn Microbiol Infect Dis 2014; 79:14-8. [PMID: 24582583 PMCID: PMC7132754 DOI: 10.1016/j.diagmicrobio.2014.01.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/19/2014] [Accepted: 01/23/2014] [Indexed: 11/29/2022]
Abstract
Recently, AdvanSure™ kit based on multiplex real-time PCR was developed for simultaneous detection of 14 respiratory viruses (RVs). We compared the performance of AdvanSure with those of Seeplex® RV 15 ACE and culture by determining their sensitivities and specificities against a composite reference standard. Four hundred thirty-seven respiratory samples were tested by modified shell vial culture method, RV 15 ACE, and AdvanSure. One hundred fourteen samples (26.2%) out of 437 samples were positive by culture, while additional 91 (20.8%) were positive by AdvanSure or RV15. One hundred twelve of 114 culture-positive samples were positive by AdvanSure except 2 samples (1 adenovirus, 1 respiratory syncytial virus [RSV]). Overall, the sensitivities of culture, RV15, and AdvanSure were 74.5%, 89.8%, and 95.1%, respectively. Sensitivities of culture, RV15, and AdvanSure for each virus tested were as follows: 91/100/96% for influenza A, 60/0/100% for influenza B, 63/95/97% for RSV, 69/81/89% for adenovirus, and 87/93/93% for parainfluenza virus. For viruses not covered by culture, sensitivities of RV15 and AdvanSure were as follows: 77/88% for rhinovirus, 100/100% for coronavirus OC43, 40/100% for coronavirus 229E/NL63, 13/100% for metapneumovirus, and 44/100% for bocavirus. The overall specificities of culture, RV15, and AdvanSure were 100/98.9/99.5%, respectively. Of 45 coinfected specimens, AdvanSure detected 41 specimens (91.1%) as coinfected, while RV15 detected 27 specimens (60.0%) as coinfected. AdvanSure assay demonstrated exquisite performance for the detection of RVs and will be a valuable tool for the management of RV infection.
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Affiliation(s)
- Chi Hyun Cho
- Department of laboratory medicine, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Chang Kyu Lee
- Department of laboratory medicine, College of Medicine, Korea University, Seoul, Republic of Korea.
| | - Myung-Hyun Nam
- Department of laboratory medicine, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Soo-Young Yoon
- Department of laboratory medicine, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Chae Seung Lim
- Department of laboratory medicine, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Yunjung Cho
- Department of laboratory medicine, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Young Kee Kim
- Department of laboratory medicine, College of Medicine, Korea University, Seoul, Republic of Korea
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Drieghe S, Ryckaert I, Beuselinck K, Lagrou K, Padalko E. Epidemiology of respiratory viruses in bronchoalveolar lavage samples in a tertiary hospital. J Clin Virol 2014; 59:208-11. [PMID: 24447853 PMCID: PMC7172540 DOI: 10.1016/j.jcv.2013.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 10/28/2013] [Accepted: 12/23/2013] [Indexed: 01/26/2023]
Abstract
Background The prevalence of respiratory viruses in adults is largely underexplored, as most studies focus on children. Additionally, in severely ill or immunocompromised adults, where respiratory infections are mostly attributed to bacteria and fungi; respiratory viruses can lead to severe complications. Objectives To evaluate the epidemiology of respiratory viruses in bronchoalveolar lavage fluid (BAL) specimens from patients with lower respiratory tract disease. The study population consisted of different groups including immunocompetent patients (control patients), solid organ transplant recipients, patients with haematological malignancies and other immunocompromised adults. Study design A total of 134 BAL fluid specimens collected during 2009–2011 were retrospectively assessed with the new commercial multiplex real-time PCR FTD Respiratory 21 Plus®, targeting 18 different viruses and 2 atypical bacterial pathogens. Results Viral or atypical bacterial pathogens were detected in 29.1% of BAL fluid specimens. Coronaviruses were most prevalent (13.4%), followed by rhinoviruses (5.2%), RSV (4.5%) and bocaviruses (3.7%). Comparing the total number of viruses detected, a statistically significant difference was observed between the control group and patients with haematological malignancies (27.5% vs. 57.1%, p < 0.05). Conclusion In conclusion, our study highlights the high prevalence of respiratory viruses in BAL fluid specimens from adult patients with lower respiratory tract disease. The methods to be used should be sensitive and cover a wide range of potential pathogens. The specific patient population can also influence the detection rates of respiratory viruses.
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Affiliation(s)
- Stefanie Drieghe
- Department of Clinical Chemistry, Microbiology and Immunology, University Hospital Ghent, De Pintelaan 185, 9000 Ghent, Belgium
| | - Inge Ryckaert
- Department of Clinical Chemistry, Microbiology and Immunology, University Hospital Ghent, De Pintelaan 185, 9000 Ghent, Belgium
| | - Kurt Beuselinck
- Department of Microbiology & Immunology, KU Leuven and Clinical Department Laboratory Medicine University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Katrien Lagrou
- Department of Microbiology & Immunology, KU Leuven and Clinical Department Laboratory Medicine University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Elizaveta Padalko
- Department of Clinical Chemistry, Microbiology and Immunology, University Hospital Ghent, De Pintelaan 185, 9000 Ghent, Belgium; School of Life Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
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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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Litwin CM, Bosley JG. Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center. Arch Virol 2013; 159:65-72. [PMID: 23881085 PMCID: PMC7086932 DOI: 10.1007/s00705-013-1794-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/11/2013] [Indexed: 12/25/2022]
Abstract
Respiratory tract infections (RTIs) are a leading cause of mortality and morbidity. Seasonality has been reported for many viruses, including influenza virus, respiratory syncytial virus (RSV), and the recently described human metapneumovirus (hMPV). We hypothesize that the availability of rapid, multiplex PCR diagnostics will provide better clinical care and new insights into the etiology and clinical spectrum of RTIs. We conducted a retrospective analysis of the incidence of respiratory pathogens at a 500-bed adult and 154-bed pediatric hospital tertiary care center. A total of 939 specimens from patients with an age range of 5 days to 91 years (median, 2 years) were tested by a multiplex respiratory pathogen PCR from November 14, 2011 to November 13, 2012. Sixty-five percent of specimens were positive for at least one pathogen. As the age of the patient increased, the positivity rate for the PCR decreased proportionately. Rhinoviruses/enteroviruses (Rhino/Entero) were the most prevalent (34.3 %) followed by RSV (19.2 %) and hMPV (6.2 %). Twelve percent of the positive samples were positive for multiple analytes, with Rhino/Entero and RSV being the most common combination. The peak months were September and May for Rhino/Entero infections, January for RSV and February for coronavirus. hMPV peaked 2 months after RSV, as has been observed recently in other studies. Multiplex PCR provides rapid diagnostic information that can be used to make knowledgeable clinical decisions and potentially reduce the use of antibiotics. Active respiratory PCR surveillance could also predict seasonal respiratory epidemics to allow for adequate planning of additional infection control measures.
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Affiliation(s)
- Christine M Litwin
- Department of Pathology, Medical College of Georgia, Georgia Regents University, 1120 15th St., Augusta, GA, 30912, USA,
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Sansone M, Andersson M, Brittain-Long R, Andersson LM, Olofsson S, Westin J, Lindh M. Rhinovirus infections in western Sweden: a four-year molecular epidemiology study comparing local and globally appearing types. Eur J Clin Microbiol Infect Dis 2013; 32:947-54. [PMID: 23435753 PMCID: PMC7087832 DOI: 10.1007/s10096-013-1832-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/24/2013] [Indexed: 11/07/2022]
Abstract
Human rhinovirus (HRV) is a highly prevalent pathogen and a major cause of acute respiratory tract infection (ARTI). HRV express less seasonality than other viral ARTIs, which typically appear as seasonal epidemics lasting for 1–2 months. The aim of this study was to investigate the seasonal patterns of HRV types over four consecutive years in one geographic region. HRV identified in respiratory samples from 114 patients over a four-year period were analysed by VP4/VP2 sequencing. HRV-A was found in 64, HRV-B in 11 and HRV-C in 37 cases. Overall, 33 different HRV-A types, nine B types and 21 C types were found. As many as 21 of the HRV types appeared during several seasons, with a maximum time-span of four years. Some types appeared during successive seasons and, in some cases, phylogenetic analysis indicated extended periods of circulation locally. Most of the strains were closely related to HRV identified in other parts of the world during the same time period. HRV strains that circulate locally represent many types and seem to reflect that HRV infections are highly globalised. The existence of simultaneous or successive epidemics with different HRV types in combination with the ability of each type to remain in the local population over extended periods of time may contribute to explaining the high rate of HRV infections.
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Affiliation(s)
- M Sansone
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10B, 413 36 Gothenburg, Sweden
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Cheng MS, Toh CS. Novel biosensing methodologies for ultrasensitive detection of viruses. Analyst 2013; 138:6219-29. [DOI: 10.1039/c3an01394d] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Optimization of one-step duplex real-time RT-PCR for detection of influenza and respiratory syncytial virus in nasopharyngeal aspirates. J Virol Methods 2012; 186:189-92. [PMID: 22796284 DOI: 10.1016/j.jviromet.2012.07.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/28/2012] [Accepted: 07/04/2012] [Indexed: 11/20/2022]
Abstract
Viruses are major contributors to acute respiratory infection-related morbidity and mortality worldwide. The influenza (IF) viruses and human respiratory syncytial virus (RSV) play a particularly important role in the etiology of acute respiratory infections. This study sought to standardize a one-step duplex real-time RT-PCR technique to optimize diagnosis of IFA/IFB and RSVA/RSVB infection. Viral RNA was extracted with the commercially available QIAamp Mini Kit according to manufacturer instructions. RT-PCR was performed with primers to the matrix protein gene of IFA, the hemagglutinin gene of IFB and the N gene of RSVA and RSVB. The limits of detection were 1 copy/μL for IFA, 10 copies/μL for IFB, 5 copies/μL for RSVA, and 250 copies/μL for RSVB. The specificity of RT-PCR was determined by comparison against a panel of several respiratory pathogens. RT-PCR and indirect immunofluorescence (IIF) were compared in a sample of 250 nasopharyngeal aspirates (NPAs) collected during the year 2010. RT-PCR was more sensitive than IIF and able to detect viral co-infections. In summary, RT-PCR optimized for IFA/IFB and RSVA/RSVB is sensitive and specific for these viral agents and is therefore useful for assessment of the etiology of respiratory infections, whether for clinical or epidemiological purposes.
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Hussell T, Godlee A, Salek-Ardakani S, Snelgrove RJ. Respiratory viral infections: knowledge based therapeutics. Curr Opin Immunol 2012; 24:438-43. [PMID: 22770666 DOI: 10.1016/j.coi.2012.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 05/15/2012] [Accepted: 06/06/2012] [Indexed: 12/13/2022]
Abstract
Lung viral infections continue to kill millions of people worldwide. Virus-specific properties, replication kinetics and longevity affect the subsequent vigour of innate and adaptive immunity, which contribute to clinical manifestations. The point at which lung innate immunity activates is different between individuals and is determined by age, genetics, underlying conditions and infection history. On resolution of virus-induced lung disease an 'altered state of homeostasis' exists that in turn affects the next antigenic challenge. The last two years has produced a plethora of studies on the resolution of inflammatory lung disease; highlighting potential for immune modulation. In the future a more precise etiological diagnosis, combined with a knowledge of co-morbidities and an immune signature will lead to the development of more specifically targeted therapeutics.
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Affiliation(s)
- Tracy Hussell
- Imperial College London, Leukocyte Biology Section, National Heart and Lung Institute, London SW7 2AZ, UK.
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