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Wang Z, Liu YL, Chen Y, Siegel L, Cappelleri JC, Chu H. Double-Negative Results Matter: A Reevaluation of Sensitivities for Detecting SARS-CoV-2 Infection Using Saliva Versus Nasopharyngeal Swabs. Am J Epidemiol 2024; 193:548-560. [PMID: 37939113 DOI: 10.1093/aje/kwad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/27/2023] [Indexed: 11/10/2023] Open
Abstract
In a recent systematic review, Bastos et al. (Ann Intern Med. 2021;174(4):501-510) compared the sensitivities of saliva sampling and nasopharyngeal swabs in the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by assuming a composite reference standard defined as positive if either test is positive and negative if both tests are negative (double negative). Even under a perfect specificity assumption, this approach ignores the double-negative results and risks overestimating the sensitivities due to residual misclassification. In this article, we first illustrate the impact of double-negative results in the estimation of the sensitivities in a single study, and then propose a 2-step latent class meta-analysis method for reevaluating both sensitivities using the same published data set as that used in Bastos et al. by properly including the observed double-negative results. We also conduct extensive simulation studies to compare the performance of the proposed method with Bastos et al.'s method for varied levels of prevalence and between-study heterogeneity. The results demonstrate that the sensitivities are overestimated noticeably using Bastos et al.'s method, and the proposed method provides a more accurate evaluation with nearly no bias and close-to-nominal coverage probability. In conclusion, double-negative results can significantly impact the estimated sensitivities when a gold standard is absent, and thus they should be properly incorporated.
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2
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Dimopoulou D, Vourli S, Douros K, Pournaras S, Papaevangelou V. Use of point-of-care molecular tests reduces hospitalization and oseltamivir administration in children presenting with influenza-like illness. J Med Virol 2021; 93:3944-3948. [PMID: 32965697 DOI: 10.1002/jmv.26538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 01/15/2023]
Abstract
Influenza is associated with increased morbidity, healthcare costs, hospitalization rates, and mortality in children. Rapid immunochromatography assay (ICA), a test with low sensitivity, is often used as point-of-care (POC) test. Recently, the rapid syndromic molecular test FilmArray has become available. This observational study aims to evaluate whether the use of FilmArray would decrease the use of antivirals and hospitalization rates among children presenting to the emergency room (ER) with influenza-like illness (ILI) symptoms. Nasopharyngeal swabs were prospectively collected from children, aged 0-16 years, presenting with ILI at the ER of a tertiary hospital during the peak endemic period. Patients were allocated to be tested by either FilmArray or ICA. The use of antivirals and hospitalization rates were noted. Logistic regression models were used to investigate the impact of testing methods on decision-making. Overall, 80 children were included (mean age: 5 years). Admissions were more likely to occur if an ICA test was performed (OR, 3.16; 95% CI, 1.01-9.82; p = .046). Oseltamivir administration was more likely among children who had undergone the ICA test (OR, 4.67; 95% CI, 1.06-20.43; p = .041). The implementation of rapid molecular test had no impact on complementary diagnostic testing or antibacterial prescription. The use of FilmArray significantly reduced both hospitalization and oseltamivir administration in children. Further knowledge on the use of POC tests is required to improve current management of children presenting with ILI and decrease associated healthcare costs.
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Affiliation(s)
- Dimitra Dimopoulou
- Third Department of Pediatrics, ATTIKON University General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Sophia Vourli
- Laboratory of Microbiology, ATTIKON University General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Douros
- Third Department of Pediatrics, ATTIKON University General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Spyridon Pournaras
- Laboratory of Microbiology, ATTIKON University General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Vassiliki Papaevangelou
- Third Department of Pediatrics, ATTIKON University General Hospital, National and Kapodistrian University of Athens, Athens, Greece
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3
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Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, Meyer-Franke A, Joehnk B, Walcott K, Sil A, Langelier C, Pollard KS, Crawford ED, Puschnik AS, Phelps M, Kistler A, DeRisi JL, Doudna JA, Fletcher DA, Ott M. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell 2021; 184:323-333.e9. [PMID: 33306959 DOI: 10.1016/j.cell.2020.12.00] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/03/2020] [Accepted: 11/25/2020] [Indexed: 05/28/2023]
Abstract
The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic, and pre-symptomatic carriers of the virus. CRISPR diagnostics can augment gold-standard PCR-based testing if they can be made rapid, portable, and accurate. Here, we report the development of an amplification-free CRISPR-Cas13a assay for direct detection of SARS-CoV-2 from nasal swab RNA that can be read with a mobile phone microscope. The assay achieved ∼100 copies/μL sensitivity in under 30 min of measurement time and accurately detected pre-extracted RNA from a set of positive clinical samples in under 5 min. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity and directly quantified viral load using enzyme kinetics. Integrated with a reader device based on a mobile phone, this assay has the potential to enable rapid, low-cost, point-of-care screening for SARS-CoV-2.
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Affiliation(s)
- Parinaz Fozouni
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, VIC 3800, Australia
| | - Carley N Gray
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael V D'Ambrosio
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chunyu Zhao
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San Jose, CA 95192, USA
| | - G Renuka Kumar
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie I Stephens
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniela Boehm
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chia-Lin Tsou
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey Shu
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Pei-Yi Chen
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Bastian Joehnk
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles Langelier
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katherine S Pollard
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Epidemiology and Biostatistics and Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily D Crawford
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Joseph L DeRisi
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Division of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jennifer A Doudna
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel A Fletcher
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Biophysics Program, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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Abstract
Viral myocarditis is not uncommon but the role of the influenza virus in causing myocarditis is less studied. It is difficult to diagnose influenza myocarditis. Due to bacterial and viral co-infection during influenza outbreaks, it becomes more difficult to distinguish influenza myocarditis from other causes. Our article provides current information on influenza myocarditis. We did a literature search using appropriate terms and reviewed articles published by November 2020. Our study highlights the incidence of influenza myocarditis and the need to become aware of this condition, especially during epidemics and pandemics. Our study highlights that although influenza myocarditis is a rare condition, it can be fatal. There should be increased awareness about the condition. By the early diagnosis and treatment of influenza myocarditis, we can prevent fatal complications.
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Affiliation(s)
- Nischit Baral
- Internal Medicine, McLaren Flint/Michigan State University College of Human Medicine, Flint, USA
| | - Prakash Adhikari
- Internal Medicine, Piedmont Athens Regional Medical Center, Athens, USA
| | - Govinda Adhikari
- Internal Medicine, McLaren Flint/Michigan State University, Flint, USA
| | - Sandip Karki
- Internal Medicine, McLaren Flint/Michigan State University, Flint, USA
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5
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Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, Meyer-Franke A, Joehnk B, Walcott K, Sil A, Langelier C, Pollard KS, Crawford ED, Puschnik AS, Phelps M, Kistler A, DeRisi JL, Doudna JA, Fletcher DA, Ott M. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell 2020; 184:323-333.e9. [PMID: 33306959 PMCID: PMC7834310 DOI: 10.1016/j.cell.2020.12.001] [Citation(s) in RCA: 477] [Impact Index Per Article: 119.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/03/2020] [Accepted: 11/25/2020] [Indexed: 12/18/2022]
Abstract
The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic, and pre-symptomatic carriers of the virus. CRISPR diagnostics can augment gold-standard PCR-based testing if they can be made rapid, portable, and accurate. Here, we report the development of an amplification-free CRISPR-Cas13a assay for direct detection of SARS-CoV-2 from nasal swab RNA that can be read with a mobile phone microscope. The assay achieved ∼100 copies/μL sensitivity in under 30 min of measurement time and accurately detected pre-extracted RNA from a set of positive clinical samples in under 5 min. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity and directly quantified viral load using enzyme kinetics. Integrated with a reader device based on a mobile phone, this assay has the potential to enable rapid, low-cost, point-of-care screening for SARS-CoV-2.
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Affiliation(s)
- Parinaz Fozouni
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, VIC 3800, Australia
| | - Carley N Gray
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael V D'Ambrosio
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chunyu Zhao
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San Jose, CA 95192, USA
| | - G Renuka Kumar
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie I Stephens
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniela Boehm
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chia-Lin Tsou
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey Shu
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Pei-Yi Chen
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Bastian Joehnk
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Keith Walcott
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anita Sil
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles Langelier
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katherine S Pollard
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Epidemiology and Biostatistics and Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily D Crawford
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Joseph L DeRisi
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Division of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jennifer A Doudna
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel A Fletcher
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Biophysics Program, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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6
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Velasco JM, Shrestha S, Valderama MT, Shrestha J, Shrestha B, Diones PC, Leonardia S, Poolpanichupatam Y, Hussem K, Chua D, Navarro FC, Develos M, Macareo L, Ellison D, Fernandez S, Klungthong C. A multi-country field validation of the FluChip-8G Insight Assay. J Virol Methods 2020; 289:114029. [PMID: 33271255 DOI: 10.1016/j.jviromet.2020.114029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Abstract
INTRODUCTION It is critical to rapidly detect novel and non-seasonal influenza strains. Currently available assays have limited sensitivity in detecting novel influenza subtypes. We performed a multi-country field validation of the FluChip-8G Insight, an assay able to detect and characterize influenza A/B viruses and non-seasonal influenza viruses. MATERIALS AND METHODS We evaluated the performance of the FluChip-8G Insight on nasal and throat swab clinical samples from Thailand, Philippines and Nepal. Influenza PCR positive and negative samples tested using the US CDC Human Influenza Dx Panel reference standard were selected for testing using the FluChip-8G Influenza Insight. RESULTS A total of 909 specimens were included in the analysis. The overall sensitivity and specificity of the FluChip-8G Insight to detect combined influenza A+B was 86 % and 100%, respectively. PPV and NPV were estimated at 100 % (95 % CI 99-100) and 73 % (95 % CI 68-78), respectively. Sensitivity across all influenza subtypes was 100% for specimens with <20 and 20-25 Ct values, respectively, but as Ct values increased, sensitivity across all influenza subtypes decreased significantly (p < 0.001) for specimens with Ct values ≥32. CONCLUSION The FluChip-8G Insight showed good precision and reproducibility among all 3 sites with robust identification of both influenza A and B targets with Ct values <32 and in the absence of co-infection. Positioning this platform in countries considered as hotspots for the emergence of novel/zoonotic influenza strains can increase the lead time in detecting and containing novel influenza strains with pandemic potential.
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Affiliation(s)
- John Mark Velasco
- U.S. Army Medical Directorate - Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand; University of the Philippines Manila, Ermita, Manila, Philippines.
| | - Sanjaya Shrestha
- Walter Reed/AFRIMS Research Unit Nepal (WARUN), Kathmandu, Nepal
| | - Maria Theresa Valderama
- U.S. Army Medical Directorate - Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Jasmin Shrestha
- Walter Reed/AFRIMS Research Unit Nepal (WARUN), Kathmandu, Nepal
| | - Binob Shrestha
- Walter Reed/AFRIMS Research Unit Nepal (WARUN), Kathmandu, Nepal
| | - Paula Corazon Diones
- U.S. Army Medical Directorate - Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Susie Leonardia
- U.S. Army Medical Directorate - Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Yongyuth Poolpanichupatam
- U.S. Army Medical Directorate - Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Kittinun Hussem
- U.S. Army Medical Directorate - Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Domingo Chua
- V Luna Medical Center, Armed Forces of the Philippines Health Service Command, Quezon City, Philippines
| | - Fatima Claire Navarro
- V Luna Medical Center, Armed Forces of the Philippines Health Service Command, Quezon City, Philippines
| | - Maribel Develos
- V Luna Medical Center, Armed Forces of the Philippines Health Service Command, Quezon City, Philippines
| | - Louis Macareo
- U.S. Army Medical Directorate - Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Damon Ellison
- U.S. Army Medical Directorate - Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stefan Fernandez
- U.S. Army Medical Directorate - Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Chonticha Klungthong
- U.S. Army Medical Directorate - Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
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7
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Uyeki TM, Bernstein HH, Bradley JS, Englund JA, File TM, Fry AM, Gravenstein S, Hayden FG, Harper SA, Hirshon JM, Ison MG, Johnston BL, Knight SL, McGeer A, Riley LE, Wolfe CR, Alexander PE, Pavia AT. Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenzaa. Clin Infect Dis 2020; 68:e1-e47. [PMID: 30566567 DOI: 10.1093/cid/ciy866] [Citation(s) in RCA: 329] [Impact Index Per Article: 82.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/05/2018] [Indexed: 12/19/2022] Open
Abstract
These clinical practice guidelines are an update of the guidelines published by the Infectious Diseases Society of America (IDSA) in 2009, prior to the 2009 H1N1 influenza pandemic. This document addresses new information regarding diagnostic testing, treatment and chemoprophylaxis with antiviral medications, and issues related to institutional outbreak management for seasonal influenza. It is intended for use by primary care clinicians, obstetricians, emergency medicine providers, hospitalists, laboratorians, and infectious disease specialists, as well as other clinicians managing patients with suspected or laboratory-confirmed influenza. The guidelines consider the care of children and adults, including special populations such as pregnant and postpartum women and immunocompromised patients.
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Affiliation(s)
- Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Henry H Bernstein
- Division of General Pediatrics, Cohen Children's Medical Center, New Hyde Park, New York
| | - John S Bradley
- Division of Infectious Diseases, Rady Children's Hospital.,University of California, San Diego
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children's Hospital
| | - Thomas M File
- Division of Infectious Diseases Summa Health, Northeast Ohio Medical University, Rootstown
| | - Alicia M Fry
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stefan Gravenstein
- Providence Veterans Affairs Medical Center and Center for Gerontology and Healthcare Research, Brown University, Providence, Rhode Island
| | - Frederick G Hayden
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville
| | - Scott A Harper
- Office of Public Health Preparedness and Response, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jon Mark Hirshon
- Department of Emergency Medicine, Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore
| | - Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - B Lynn Johnston
- Department of Medicine, Dalhousie University, Nova Scotia Health Authority, Halifax, Canada
| | - Shandra L Knight
- Library and Knowledge Services, National Jewish Health, Denver, Colorado
| | - Allison McGeer
- Division of Infection Prevention and Control, Sinai Health System, University of Toronto, Ontario, Canada
| | - Laura E Riley
- Department of Maternal-Fetal Medicine, Massachusetts General Hospital, Boston
| | - Cameron R Wolfe
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Paul E Alexander
- McMaster University, Hamilton, Ontario, Canada.,Infectious Diseases Society of America, Arlington, Virginia
| | - Andrew T Pavia
- Division of Pediatric Infectious Diseases, University of Utah, Salt Lake City
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8
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Abstract
The clinical microbiology laboratory relies on traditional diagnostic methods such as culturing, Gram stains, and biochemical testing. Receipt of a high-quality specimen with an appropriate test order is integral to accurate testing. Recent technological advancements have led to decreased time to results and improved diagnostic accuracy. Examples of advancements discussed in this chapter include automation of bacterial culture processing and incubation, as well as introduction of mass spectrometry for the proteomic identification of microorganisms. In addition, molecular testing is increasingly common in the clinical laboratory. Commercially available multiplex molecular assays simultaneously test for a broad array of syndromic-related pathogens, providing rapid and sensitive diagnostic results. Molecular advancements have also transformed point-of-care (POC) microbiology testing, and molecular POC assays may largely supplant traditional rapid antigen testing in the future. Integration of new technologies with traditional testing methods has led to improved quality and value in the clinical microbiology laboratory. After reviewing this chapter, the reader will be able to:List key considerations for specimen collection for microbiology testing. Discuss the advantages and limitations of automation in the clinical microbiology laboratory. Describe the evolution of microorganism identification methods. Discuss the benefits and limitations of molecular microbiology point-of-care testing. Summarize currently available multiplex molecular microbiology testing options.
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Uyeki TM, Bernstein HH, Bradley JS, Englund JA, File TM, Fry AM, Gravenstein S, Hayden FG, Harper SA, Hirshon JM, Ison MG, Johnston BL, Knight SL, McGeer A, Riley LE, Wolfe CR, Alexander PE, Pavia AT. Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenzaa. Clin Infect Dis 2019; 68. [PMID: 30566567 PMCID: PMC6653685 DOI: 10.1093/cid/ciy866 10.1093/cid/ciz044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
These clinical practice guidelines are an update of the guidelines published by the Infectious Diseases Society of America (IDSA) in 2009, prior to the 2009 H1N1 influenza pandemic. This document addresses new information regarding diagnostic testing, treatment and chemoprophylaxis with antiviral medications, and issues related to institutional outbreak management for seasonal influenza. It is intended for use by primary care clinicians, obstetricians, emergency medicine providers, hospitalists, laboratorians, and infectious disease specialists, as well as other clinicians managing patients with suspected or laboratory-confirmed influenza. The guidelines consider the care of children and adults, including special populations such as pregnant and postpartum women and immunocompromised patients.
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Affiliation(s)
- Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Henry H Bernstein
- Division of General Pediatrics, Cohen Children's Medical Center, New Hyde Park, New York
| | - John S Bradley
- Division of Infectious Diseases, Rady Children's Hospital
- University of California, San Diego
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children's Hospital
| | - Thomas M File
- Division of Infectious Diseases Summa Health, Northeast Ohio Medical University, Rootstown
| | - Alicia M Fry
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stefan Gravenstein
- Providence Veterans Affairs Medical Center and Center for Gerontology and Healthcare Research, Brown University, Providence, Rhode Island
| | - Frederick G Hayden
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville
| | - Scott A Harper
- Office of Public Health Preparedness and Response, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jon Mark Hirshon
- Department of Emergency Medicine, Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore
| | - Michael G Ison
- Divisions of Infectious Diseases and Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - B Lynn Johnston
- Department of Medicine, Dalhousie University, Nova Scotia Health Authority, Halifax, Canada
| | - Shandra L Knight
- Library and Knowledge Services, National Jewish Health, Denver, Colorado
| | - Allison McGeer
- Division of Infection Prevention and Control, Sinai Health System, University of Toronto, Ontario, Canada
| | - Laura E Riley
- Department of Maternal-Fetal Medicine, Massachusetts General Hospital, Boston
| | - Cameron R Wolfe
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Paul E Alexander
- McMaster University, Hamilton, Ontario, Canada
- Infectious Diseases Society of America, Arlington, Virginia
| | - Andrew T Pavia
- Division of Pediatric Infectious Diseases, University of Utah, Salt Lake City
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Rapid Antigen Tests for Influenza: Rationale and Significance of the FDA Reclassification. J Clin Microbiol 2018; 56:JCM.00711-18. [PMID: 29899007 DOI: 10.1128/jcm.00711-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid antigen tests for influenza, here referred to as rapid influenza diagnostic tests (RIDTs), have been widely used for the diagnosis of influenza since their introduction in the 1990s due to their ease of use, rapid results, and suitability for point of care (POC) testing. However, issues related to the diagnostic sensitivity of these assays have been known for decades, and these issues gained greater attention following reports of their poor performance during the 2009 influenza A(H1N1) pandemic. In turn, significant concerns arose about the consequences of false-negative results, which could pose significant risks to both individual patient care and to public health efforts. In response to these concerns, the FDA convened an advisory panel in June 2013 to discuss options to improve the regulation of the performance of RIDTs. A proposed order was published on 22 May 2014, and the final order published on 12 January 2017, reclassifying RIDTs from class I to class II medical devices, with additional requirements to comply with four new special controls. This reclassification is a landmark achievement in the regulation of diagnostic devices for infectious diseases and has important consequences for the future of diagnostic influenza testing with commercial tests, warranting the prompt attention of clinical laboratories, health care systems, and health care providers.
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Abstract
Acute upper and lower respiratory infections are a major public health problem and a leading cause of morbidity and mortality worldwide. At greatest risk are young children, the elderly, the chronically ill, and those with suppressed or compromised immune systems. Viruses are the predominant cause of respiratory tract illnesses and include RNA viruses such as respiratory syncytial virus, influenza virus, parainfluenza virus, metapneumovirus, rhinovirus, and coronavirus. Laboratory testing is required for a reliable diagnosis of viral respiratory infections, as a clinical diagnosis can be difficult since signs and symptoms are often overlapping and not specific for any one virus. Recent advances in technology have resulted in the development of newer diagnostic assays that offer great promise for rapid and accurate detection of respiratory viral infections. This chapter emphasizes the fundamental characteristics and clinical importance of the various RNA viruses that cause upper and lower respiratory tract diseases in the immunocompromised host. It highlights the laboratory methods that can be used to make a rapid and definitive diagnosis for the greatest impact on the care and management of ill patients, and the prevention and control of hospital-acquired infections and community outbreaks.
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Escuyer KL, Waters CL, Gowie DL, Maxted AM, Farrell GM, Fuschino ME, St. George K. The assessment of data sources for influenza virologic surveillance in New York State. Influenza Other Respir Viruses 2017; 11:138-147. [PMID: 27718314 PMCID: PMC5304574 DOI: 10.1111/irv.12433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Following the 2013 USA release of the Influenza Virologic Surveillance Right Size Roadmap, the New York State Department of Health (NYSDOH) embarked on an evaluation of data sources for influenza virologic surveillance. OBJECTIVE To assess NYS data sources, additional to data generated by the state public health laboratory (PHL), which could enhance influenza surveillance at the state and national level. METHODS Potential sources of laboratory test data for influenza were analyzed for quantity and quality. Computer models, designed to assess sample sizes and the confidence of data for statistical representation of influenza activity, were used to compare PHL test data to results from clinical and commercial laboratories, reported between June 8, 2013 and May 31, 2014. RESULTS Sample sizes tested for influenza at the state PHL were sufficient for situational awareness surveillance with optimal confidence levels, only during peak weeks of the influenza season. Influenza data pooled from NYS PHLs and clinical laboratories generated optimal confidence levels for situational awareness throughout the influenza season. For novel influenza virus detection in NYS, combined real-time (rt) RT-PCR data from state and regional PHLs achieved ≥85% confidence during peak influenza activity, and ≥95% confidence for most of low season and all of off-season. CONCLUSIONS In NYS, combined data from clinical, commercial, and public health laboratories generated optimal influenza surveillance for situational awareness throughout the season. Statistical confidence for novel virus detection, which is reliant on only PHL data, was achieved for most of the year.
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Affiliation(s)
- Kay L. Escuyer
- Laboratory of Viral DiseasesWadsworth CenterNew York State Department of HealthAlbanyNYUSA
| | - Christine L. Waters
- Bureau of Communicable Disease ControlNew York State Department of HealthAlbanyNYUSA
| | - Donna L. Gowie
- Bureau of Communicable Disease ControlNew York State Department of HealthAlbanyNYUSA
| | - Angie M. Maxted
- Bureau of Communicable Disease ControlNew York State Department of HealthAlbanyNYUSA
| | - Gregory M. Farrell
- Laboratory of Viral DiseasesWadsworth CenterNew York State Department of HealthAlbanyNYUSA
| | - Meghan E. Fuschino
- Laboratory of Viral DiseasesWadsworth CenterNew York State Department of HealthAlbanyNYUSA
| | - Kirsten St. George
- Laboratory of Viral DiseasesWadsworth CenterNew York State Department of HealthAlbanyNYUSA
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Moghadami M. A Narrative Review of Influenza: A Seasonal and Pandemic Disease. IRANIAN JOURNAL OF MEDICAL SCIENCES 2017; 42:2-13. [PMID: 28293045 PMCID: PMC5337761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Influenza is an acute respiratory disease caused by the influenza A or B virus. It often occurs in outbreaks and epidemics worldwide, mainly during the winter season. Significant numbers of influenza virus particles are present in the respiratory secretions of infected persons, so infection can be transmitted by sneezing and coughing via large particle droplets. The mean duration of influenza virus shedding in immunocompetent adult patients is around 5 days but may continue for up to 10 days or more-particularly in children, elderly adults, patients with chronic illnesses, and immunocompromised hosts. Influenza typically begins with the abrupt onset of high-grade fever, myalgia, headache, and malaise. These manifestations are accompanied by symptoms of respiratory tract illnesses such as nonproductive cough, sore throat, and nasal discharge. After a typical course, influenza can affect other organs such as the lungs, brain, and heart more than it can affect the respiratory tract and cause hospitalization. The best way to prevent influenza is to administer annual vaccinations. Among severely ill patients, an early commencement of antiviral treatment (<2 d from illness onset) is associated with reduced morbidity and mortality, with greater benefits allied to an earlier initiation of treatment. Given the significance of the disease burden, we reviewed the latest findings in the diagnosis and management of influenza.
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Affiliation(s)
- Mohsen Moghadami
- Non-Communicable Diseases Research Center, Shiraz University of Medical Sciences, Shiraz Iran,Correspondence: Mohsen Moghadami, MD; Non-Communicable Diseases Research Center, Shiraz University of Medical Sciences, Shiraz Iran Tel: +98 917 3115262 Fax: +98 71 32308045
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Kammerer PE, Radin JM, Hawksworth AW, Myers CA, Brice GT. Performance of the Quidel Sofia rapid influenza diagnostic test during the 2012-2013 and 2013-2014 influenza seasons. Influenza Other Respir Viruses 2016; 10:220-3. [PMID: 26920652 PMCID: PMC4814867 DOI: 10.1111/irv.12380] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2016] [Indexed: 11/29/2022] Open
Abstract
The Quidel Sofia Influenza A+B Fluorescent Immunoassay was used to test nasal swab specimens from patients with influenza‐like illness at US–Mexico border‐area clinics in the 2012–2013 and 2013–2014 influenza seasons. Compared with real‐time reverse transcription polymerase chain reaction, the overall sensitivities and specificities were 83% and 81%, and 62% and 93%, respectively.
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Affiliation(s)
- Peter E Kammerer
- Operational Infectious Diseases Department, Naval Health Research Center, San Diego, CA, USA
| | - Jennifer M Radin
- Operational Infectious Diseases Department, Naval Health Research Center, San Diego, CA, USA
| | - Anthony W Hawksworth
- Operational Infectious Diseases Department, Naval Health Research Center, San Diego, CA, USA
| | - Chris A Myers
- Operational Infectious Diseases Department, Naval Health Research Center, San Diego, CA, USA
| | - Gary T Brice
- Operational Infectious Diseases Department, Naval Health Research Center, San Diego, CA, USA
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15
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Koul PA, Mir H, Bhat MA, Khan UH, Khan MM, Chadha MS, Lal RB. Performance of rapid influenza diagnostic tests (QuickVue) for influenza A and B Infection in India. Indian J Med Microbiol 2015; 33 Suppl:26-31. [PMID: 25657152 DOI: 10.4103/0255-0857.148831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Rapid point-of-care (POC) tests provide an economical alternative for rapid diagnosis and treatment of influenza, especially in public health emergency situations. OBJECTIVES To test the performance of a rapid influenza diagnostic test, QuickVue (Quidel) as a POC test against a real-time polymerase chain reaction (RT-PCR) assay for detection of influenza A and B in a developing country setting. STUDY DESIGN In a prospective observational design, 600 patients with influenza-like illness (ILI) or with severe acute respiratory illness (SARI) who were referred to the Influenza Clinic of a tertiary care hospital in Srinagar, India from September 2012 to April 2013, were enrolled for diagnostic testing for influenza using QuickVue or RT-PCR. All influenza A-positive patients by RT-PCR were further subtyped using primers and probes for A/H1pdm09 and A/H3. RESULTS Of the 600 patients, 186 tested positive for influenza A or B by RT-PCR (90 A/H1N1pdm09, 7 A/H3 and 89 influenza B), whereas only 43 tested positive for influenza (influenza A=22 and influenza B=21) by QuickVue. Thus, the sensitivity of the QuickVue was only 23% (95% confidence interval, CI: 17.3-29.8) and specificity was 100% (95% CI: 99.1-100) with a positive predictive value (PPV) of 100% (95% CI 91.8-100) and a negative predictive value (NPV) of 74.3% (95% CI: 70.5-77.9) as compared to RT-PCR. CONCLUSIONS The high specificity of QuickVue suggest that this POC test can be a useful tool for patient management or triaging during a public health crisis but a low sensitivity suggests that a negative test result need to be further tested using RT-PCR.
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Affiliation(s)
- P A Koul
- Department of Internal and Pulmonary Medicine and MSM Project for Influenza, Sher I Kashmir Institute of Medical Sciences, Soura, Srinagar, Jammu and Kashmir, India
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Dunn JJ, Ginocchio CC. Can newly developed, rapid immunochromatographic antigen detection tests be reliably used for the laboratory diagnosis of influenza virus infections? J Clin Microbiol 2015; 53:1790-6. [PMID: 25274999 PMCID: PMC4432049 DOI: 10.1128/jcm.02739-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Five years ago, the Point-Counterpoint series was launched. The initial article asked about the role of rapid immunochromatographic antigen testing in the diagnosis of influenza A virus 2009 H1N1 infection (D. F. Welch and C. C. Ginocchio, J Clin Microbiol 48:22-25, 2010, http://dx.doi.org/10.1128/JCM.02268-09). Since that article, not only have major changes been made in immunochromatographic antigen detection (IAD) testing for the influenza viruses, but there has also been rapid development of commercially available nucleic acid amplification tests (NAATs) for influenza virus detection. Further, a novel variant of influenza A, H7N9, has emerged in Asia, and H5N1 is also reemergent. In that initial article, the editor of this series, Peter Gilligan, identified two issues that required further consideration. One was how well IAD tests worked in clinical settings, especially in times of antigen drift and shift. The other was the role of future iterations of influenza NAATs and whether this testing would be available in a community hospital setting. James Dunn, who is Director of Medical Microbiology and Virology at Texas Children's Hospital, has extensive experience using IAD tests for diagnosing influenza. He will discuss the application and value of these tests in influenza diagnosis. Christine Ginocchio, who recently retired as the Senior Medical Director, Division of Infectious Disease Diagnostics, North Shore-LIJ Health System, and now is Vice President for Global Microbiology Affairs at bioMérieux, Durham, NC, wrote the initial counterpoint in this series, where she advocated the use of NAATs for influenza diagnosis. She will update us on the commercially available NAAT systems and explain what their role should be in the diagnosis of influenza infection.
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Affiliation(s)
- James J Dunn
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Christine C Ginocchio
- bioMérieux, Durham, North Carolina, USA Department of Pathology and Laboratory Medicine, Hofstra North Shore-LIJ School of Medicine, Hempstead, New York, USA
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Patel PA, Robicsek A, Grayes A, Schora DM, Peterson KE, Wright MO, Peterson LR. Evaluation of multiple real-time PCR tests on nasal samples in a large MRSA surveillance program. Am J Clin Pathol 2015; 143:652-8. [PMID: 25873498 DOI: 10.1309/ajcpmdy32ztdxpfc] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES We evaluated the LightCycler MRSA Advanced Test (Roche Molecular Diagnostics, Pleasanton, CA), the BD MAX MRSA assay (Becton Dickinson, Franklin Lakes, NJ), and the Xpert MRSA assay (Cepheid, Sunnyvale, CA) on nasal samples using the same population. METHODS Admission and discharge nasal swabs were collected from inpatients using a double-headed swab. One swab was plated onto CHROMagar MRSA (CMA; Becton Dickinson, Sparks, MD) and then broken off into tryptic soy broth (TSB) for enrichment. TSB was incubated for 24 hours and then plated to CMA. The molecular tests were performed on the second swab. We analyzed the cost benefit of testing to evaluate what parameters affect hospital resources. RESULTS A total of 27,647 specimens were enrolled. The sensitivity/specificity was 98.3%/98.9% for the LightCycler MRSA Advanced Test and 95.7%/98.8% for the Xpert MRSA assay, but the difference was not significant. The positive predictive value was 86.7% for the LightCycler MRSA Advanced Test, 82.7% for the Xpert MRSA assay (P > .1), and 72.2% and for the BD MAX MRSA test (P < .001 compared with the LightCycler MRSA Advanced Test). All three assays were cost-effective, with the LightCycler MRSA Advanced Test having the highest economic return. CONCLUSIONS Our results suggest that the performance of the three commercial assays is similar. When assessing economic cost benefit of methicillin-resistant Staphylococcus aureus screening, the two measures with the most impact are the cost of the test and the specificity of the assay results.
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Affiliation(s)
| | - Ari Robicsek
- NorthShore University HealthSystem, Evanston, IL
- NorthShore University of Chicago Pritzker School of Medicine, Chicago, IL
| | | | | | | | | | - Lance R. Peterson
- NorthShore University HealthSystem, Evanston, IL
- NorthShore University of Chicago Pritzker School of Medicine, Chicago, IL
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González-Del Vecchio M, Catalán P, de Egea V, Rodríguez-Borlado A, Martos C, Padilla B, Rodríguez-Sanchez B, Bouza E. An algorithm to diagnose influenza infection: evaluating the clinical importance and impact on hospital costs of screening with rapid antigen detection tests. Eur J Clin Microbiol Infect Dis 2015; 34:1081-5. [PMID: 25620782 DOI: 10.1007/s10096-015-2328-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/13/2015] [Indexed: 10/24/2022]
Abstract
Rapid antigen detection tests (RADTs) are immunoassays that produce results in 15 min or less, have low sensitivity (50 %), but high specificity (95 %). We studied the clinical impact and laboratory savings of a diagnostic algorithm for influenza infection using RADTs as a first-step technique during the influenza season. From January 15th to March 31st 2014, we performed a diagnostic algorithm for influenza infection consisting of an RADT for all respiratory samples received in the laboratory. We studied all the patients with positive results for influenza infection, dividing them into two groups: Group A with a negative RADT but positive reference tests [reverse transcription polymerase chain reaction (RT-PCR) and/or culture] and Group B with an initial positive RADT. During the study period, we had a total of 1,156 patients with suspicion of influenza infection. Of them, 217 (19 %) had a positive result for influenza: 132 (11 %) had an initial negative RADT (Group A) and 85 (7 %) had a positive RADT (Group B). When comparing patients in Group A and Group B, we found significant differences, as follows: prescribed oseltamivir (67 % vs. 82 %; p = 0.02), initiation of oseltamivir before 24 h (89 % vs. 97 %; p = 0.03), antibiotics prescribed (89 % vs. 67 %; p = <0.01), intensive care unit (ICU) admissions after diagnosis (23 % vs. 14 %; p = 0.05), and need for supplementary oxygen (61 % vs. 47 %; p = 0.01). An influenza algorithm including RADTs as the first step improves the time of administration of proper antiviral therapy, reduces the use of antibiotics and ICU admissions, and decreases hospital costs.
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Affiliation(s)
- M González-Del Vecchio
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain,
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Suryaprasad A, Redd JT, Ricks PM, Podewils LJ, Brett M, Oski J, Minenna W, Armao F, Vize BJ, Cheek JE. Effect of rapid influenza diagnostic testing on antiviral treatment decisions for patients with influenza-like illness: southwestern U.S., May-December 2009. Public Health Rep 2014; 129:322-7. [PMID: 24982534 DOI: 10.1177/003335491412900406] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Rapid influenza diagnostic tests (RIDTs) had low test sensitivity for detecting 2009 pandemic influenza A (H1N1pdm09) infection, causing public health authorities to recommend that treatment decisions be based primarily upon risk for influenza complications. We used multivariate Poisson regression analysis to estimate the contribution of RIDT results and risk for H1N1pdm09 complications to receipt of early antiviral (AV) treatment among 290 people with influenza-like illness (ILI) who received an RIDT ≤48 hours after symptom onset from May to December 2009 at four southwestern U.S. facilities. RIDT results had a stronger association with receipt of early AVs (rate ratio [RR] = 3.3, 95% confidence interval [CI] 2.4, 4.6) than did the presence of risk factors for H1N1pdm09 complications (age <5 years or high-risk medical conditions) (RR=1.9, 95% CI 1.3, 2.7). Few at-risk people (28/126, 22%) who had a negative RIDT received early AVs, suggesting the need for sustained efforts by public health to influence clinician practices.
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Affiliation(s)
- Anil Suryaprasad
- Centers for Disease Control and Prevention, Scientific Education and Professional Development Program Office (proposed), Epidemic Intelligence Service, Atlanta, GA
| | - John T Redd
- Indian Health Service, Division of Epidemiology and Disease Prevention, Albuquerque, NM
| | - Philip M Ricks
- Centers for Disease Control and Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Division of Tuberculosis Elimination, Atlanta, GA
| | - Laura Jean Podewils
- Centers for Disease Control and Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Division of Tuberculosis Elimination, Atlanta, GA
| | - Meghan Brett
- University of New Mexico School of Medicine, Albuquerque, NM
| | - Jane Oski
- Tuba City Regional Health Care Corporation, Tuba City, AZ
| | - Wanda Minenna
- Indian Health Service, Whiteriver Service Unit, Whiteriver, AZ
| | - Frank Armao
- Winslow Indian Health Care Center, Winslow, AZ
| | | | - James E Cheek
- Indian Health Service, Division of Epidemiology and Disease Prevention, Albuquerque, NM
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Salez N, Nougairede A, Ninove L, Zandotti C, de Lamballerie X, Charrel RN. Xpert Flu for point-of-care diagnosis of human influenza in industrialized countries. Expert Rev Mol Diagn 2014; 14:411-8. [PMID: 24707995 DOI: 10.1586/14737159.2014.901152] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Respiratory infections, particularly those caused by influenza viruses, represent the third-most important cause of death in the world due to infectious diseases. Nevertheless, despite the enormous publicity attracted by epidemics due to these viruses, laboratory diagnosis, documentation and recording of respiratory diseases is still unsatisfactory. Available diagnostic tests capable of providing results rapidly are either limited and insufficiently sensitive or highly sensitive and specific but insufficiently rapid. Considerable investment and research efforts have been made towards the development of new diagnostics for influenza A and B viruses and the Xpert(®) Flu assay (Cepheid(®), CA, USA) has emerged as one of the most promising. In this article, we review current knowledge of the Xpert Flu test, discuss its potential value as a point-of-care test and outline the potential leads for future development.
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Affiliation(s)
- Nicolas Salez
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", and IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
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Lewandrowski K, Tamerius J, Menegus M, Olivo PD, Lollar R, Lee-Lewandrowski E. Detection of influenza A and B viruses with the Sofia analyzer: a novel, rapid immunofluorescence-based in vitro diagnostic device. Am J Clin Pathol 2013; 139:684-9. [PMID: 23596120 DOI: 10.1309/ajcp7ztljcp3llma] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
This report describes the clinical evaluation of a novel fluorescent immunoassay (FIA), Sofia Influenza A+B FIA (Quidel, San Diego, CA), for the rapid detection and differentiation of influenza A and B viruses. A total of 2,047 subjects provided nasal swabs and nasopharyngeal swabs or aspirates. The overall sensitivity and specificity for influenza A virus vs virus culture were 94% and 95%, respectively, and for influenza B virus were 89% and 96%, respectively. Fourteen hundred and sixty-one specimens were available for testing with reverse transcriptase-polymerase chain reaction (RT-PCR). The sensitivity of the Sofia Influenza A+B FIA for detecting influenza A and B viruses compared with the RT-PCR method was 78% and 86%, respectively. A high percentage of the positive specimens had low cycle threshold values, and almost all of these were positive with the Sofia test. This high level of sensitivity demonstrates that the Sofia influenza A+B FIA could improve the usefulness of rapid influenza virus testing.
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Affiliation(s)
- Kent Lewandrowski
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | | | - Marilyn Menegus
- Department of Clinical Virology, University of Rochester Medical Center, Rochester, NY
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Suzuki M, Yoshimine H, Harada Y, Tsuchiya N, Shimada I, Ariyoshi K, Inoue K. Estimating the influenza vaccine effectiveness against medically attended influenza in clinical settings: a hospital-based case-control study with a rapid diagnostic test in Japan. PLoS One 2013; 8:e52103. [PMID: 23326324 PMCID: PMC3543401 DOI: 10.1371/journal.pone.0052103] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 11/09/2012] [Indexed: 11/19/2022] Open
Abstract
Background Influenza vaccine effectiveness (VE) studies are usually conducted by specialized agencies and require time and resources. The objective of this study was to estimate the influenza VE against medically attended influenza using a test-negative case-control design with rapid influenza diagnostic tests (RIDT) in a clinical setting. Methods A prospective study was conducted at a community hospital in Nagasaki, western Japan during the 2010/11 influenza season. All outpatients aged 15 years and older with influenza-like illnesses (ILI) who had undergone RIDT were enrolled. A test-negative case-control design was applied to estimate the VEs: the cases were ILI patients with positive RIDT results and the controls were ILI patients with negative RIDT results. Information on patient characteristics, including vaccination histories, was collected using questionnaires and medical records. Results Between December 2010 and April 2011, 526 ILI patients were tested with RIDT, and 476 were eligible for the analysis. The overall VE estimate against medically attended influenza was 47.6%, after adjusting for the patients' age groups, presence of chronic conditions, month of visit, and smoking and alcohol use. The seasonal influenza vaccine reduced the risk of medically attended influenza by 60.9% for patients less than 50 years of age, but a significant reduction was not observed for patients 50 years of age and older. A sensitivity analysis provided similar figures. Conclusion The test-negative case-control study using RIDT provided moderate influenza VE consistent with other reports. Utilizing the commonly used RIDT to estimate VE provides rapid assessment of VE; however, it may require validation with more specific endpoint.
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Affiliation(s)
- Motoi Suzuki
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | | | - Yoshitaka Harada
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- Inoue Hospital, Shunkaikai, Nagasaki, Japan
| | - Naho Tsuchiya
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Ikumi Shimada
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Koya Ariyoshi
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- * E-mail:
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Khandaker G, Heron L, Rashid H, Li-Kim-Moy J, Lester-Smith D, Kesson A, McCaskill M, Jones C, Zurynski Y, Elliott EJ, Dwyer DE, Booy R. Comparing the use of, and considering the need for, lumbar puncture in children with influenza or other respiratory virus infections. Influenza Other Respir Viruses 2012; 7:932-7. [PMID: 23122417 PMCID: PMC4634251 DOI: 10.1111/irv.12039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The clinical presentation of influenza in infancy may be similar to serious bacterial infection and be investigated with invasive procedures like lumbar puncture (LP), despite very limited evidence that influenza occurs concomitantly with bacterial meningitis, perhaps because the diagnosis of influenza is very often not established when the decision to perform LP is being considered. METHODS A retrospective medical record review was undertaken in all children presenting to the Children's Hospital at Westmead, Sydney, Australia, in one winter season with laboratory-confirmed influenza or other respiratory virus infections (ORVIs) but excluding respiratory syncytial virus, to compare the use of, and reflect on the need for, the performance of invasive diagnostic procedures, principally LP, but also blood culture, in influenza and non-influenza cases. We also determined the rate of concomitant bacterial meningitis or bacteraemia. FINDINGS Of 294 children, 51% had laboratory-confirmed influenza and 49% had ORVIs such as parainfluenza viruses (34%) and adenoviruses (15%). Of those with influenza, 18% had a LP and 71% had a blood culture performed compared with 6·3% and 55·5% in the ORVI group (for both P<0·01). In multivariate analysis, diagnosis of influenza was a strong independent predictor of both LP (P=0·02) and blood culture (P=0·05) being performed, and, in comparison with ORVIs, influenza cases were almost three times more likely to have a LP performed on presentation to hospital. One child with influenza (0·9%) had bacteraemia and none had meningitis. INTERPRETATION Children with influenza were more likely to undergo LP on presentation to hospital compared with those presenting with ORVIs. If influenza is confirmed on admission by near-patient testing, clinicians may be reassured and less inclined to perform LP, although if meningitis is clinically suspected, the clinician should act accordingly. We found that the risk of bacterial meningitis and bacteraemia was very low in hospitalised children with influenza and ORVIs. A systematic review should be performed to investigate this across a large number of settings.
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Affiliation(s)
- Gulam Khandaker
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases (NCIRS), The Children's Hospital at Westmead and The University of SydneyThe Children's Hospital at Westmead and The University of SydneyThe Sydney Institute for Emerging Infections and Biosecurity (SEIB), Sydney Medical School, The University of SydneyDiscipline of Paediatrics and Child Health, Sydney Medical School, The University of SydneyThe Australian Paediatric Surveillance UnitCentre for Infectious Diseases and Microbiology Laboratory Services (CIDMLS), Institute for Clinical Pathology and Medical Research (ICPMR), Westmead Hospital and The University of Sydney, Sydney, NSW, Australia
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DiMaio MA, Sahoo MK, Waggoner J, Pinsky BA. Comparison of Xpert Flu rapid nucleic acid testing with rapid antigen testing for the diagnosis of influenza A and B. J Virol Methods 2012; 186:137-40. [PMID: 22841669 DOI: 10.1016/j.jviromet.2012.07.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Revised: 07/18/2012] [Accepted: 07/18/2012] [Indexed: 12/26/2022]
Abstract
Influenza infections are associated with thousands of hospital admissions and deaths each year. Rapid detection of influenza is important for prompt initiation of antiviral therapy and appropriate patient triage. In this study the Cepheid Xpert Flu assay was compared with two rapid antigen tests, BinaxNOW Influenza A & B and BD Directigen EZ Flu A+B, as well as direct fluorescent antibody testing for the rapid detection of influenza A and B. Using real-time, hydrolysis probe-based, reverse transcriptase PCR as the reference method, influenza A sensitivity was 97.3% for Xpert Flu, 95.9% for direct fluorescent antibody testing, 62.2% for BinaxNOW, and 71.6% for BD Directigen. Influenza B sensitivity was 100% for Xpert Flu and direct fluorescent antibody testing, 54.5% for BinaxNOW, and 48.5% for BD Directigen. Specificity for influenza A was 100% for Xpert Flu, BinaxNOW, and BD Directigen, and 99.2% for direct fluorescent antibody testing. All methods demonstrated 100% specificity for influenza B. These findings support the use of the Xpert Flu assay in settings requiring urgent diagnosis of influenza A and B.
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Affiliation(s)
- Michael A DiMaio
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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Wiwanitkit S, Wiwanitkit V. Rapid influenza H1N1 diagnostic test: its diagnostic property. Influenza Other Respir Viruses 2011; 6:79. [PMID: 22151132 PMCID: PMC4942077 DOI: 10.1111/j.1750-2659.2011.00320.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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