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Bouzid D, Hingrat QL, Salipante F, Ferré VM, Chevallier T, Tubiana S, Lucet JC, Choquet C, Yazdanpanah Y, Timsit JF, Descamps D, Houhou N, Visseaux B, Loubet P. Agreement of respiratory viruses' detection between nasopharyngeal swab and bronchoalveolar lavage in adults admitted for pneumonia: a retrospective study. Clin Microbiol Infect 2023:S1198-743X(23)00042-3. [PMID: 36708772 PMCID: PMC9873593 DOI: 10.1016/j.cmi.2022.12.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 01/26/2023]
Abstract
OBJECTIVES The COVID-19 pandemic has highlighted the high diagnostic accuracy of the nasopharyngeal swab (including in intensive care unit (ICU) patients). This study aimed to compare nasopharyngeal swab and bronchoalveolar lavage (BAL) results for non-SARS-CoV-2 viruses in patients with suspected pneumonia. METHODS A retrospective analysis was performed in one French academic hospital on consecutive adults from 2012 to 2018 and tested nasopharyngeal swab and BAL within 24 hours by using multiplex PCR. The agreement in pathogen detection between nasopharyngeal swab and BAL was evaluated. RESULTS Patients were primarily men (n = 178/276, 64.5%), with a median age of 60 years (IQR: 51-68 years). Of the 276 patients, 169 (61%) were admitted to the ICU for acute respiratory distress. We detected at least one respiratory virus in 34.4% of the nasopharyngeal swabs (n = 95/276) and 29.0% of BAL (n = 80/276). Two or more viruses were detected in 2.5% of the nasopharyngeal swabs (n = 7/276) and 2.2% of BAL (n = 6/276). Rhinovirus/enteroviruses were the most frequently detected viral group in 10.2% (n = 29/285) of the nasopharyngeal swabs and 9.5% (n = 27/285) of BAL, followed by influenza A, detected in 5.6% (n = 16/285) of the nasopharyngeal swabs and 4.9% (n = 14/285) of BAL. Overall agreement was 83.7% (n = 231/276 (95% CI [78.7%, 87.7%])) (i.e. same pathogen or pathogen combination was identified in the nasopharyngeal swab and BAL for 231 patients). Rhinovirus/enterovirus (n = 29/231) and respiratory syncytial virus (n = 13/231) had the lowest agreement of 62.1% (n = 18/29 (95% CI [42.4%-78.7%])) and 61.5% (n = 8/13 (95% CI [32.3%-84.9%])), respectively). CONCLUSIONS There was a good agreement between nasopharyngeal swabs and BAL in detecting respiratory viruses among adult patients with suspected pneumonia. However, these data still encourage BAL in the case of a negative nasopharyngeal swab.
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Affiliation(s)
- Donia Bouzid
- Université Paris Cité, INSERM UMR1137, IAME, F-75018 Paris, France; Université de Montpellier, VBMI, Inserm U1047, Nîmes, France.
| | - Quentin Le Hingrat
- Université Paris Cité, INSERM UMR1137, IAME, F-75018 Paris, France,AP-HP Nord, Virology Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Florian Salipante
- Department of Biostatistics, Epidemiology, Public Health and Innovation in Methodology, CHU Nîmes, Université de Montpellier, Nîmes, France
| | - Valentine Marie Ferré
- Université Paris Cité, INSERM UMR1137, IAME, F-75018 Paris, France,AP-HP Nord, Virology Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Thierry Chevallier
- Department of Biostatistics, Epidemiology, Public Health and Innovation in Methodology, CHU Nîmes, Université de Montpellier, Nîmes, France
| | - Sarah Tubiana
- Université Paris Cité, INSERM UMR1137, IAME, F-75018 Paris, France,AP-HP Nord, Biostatistics, Epidemiology and Clinical Research Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Jean Christophe Lucet
- Université Paris Cité, INSERM UMR1137, IAME, F-75018 Paris, France,AP-HP Nord, Infectious Disease Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Christophe Choquet
- AP-HP Nord, Emergency Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Yazdan Yazdanpanah
- Université Paris Cité, INSERM UMR1137, IAME, F-75018 Paris, France,AP-HP Nord, Infectious Disease Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Jean François Timsit
- Université Paris Cité, INSERM UMR1137, IAME, F-75018 Paris, France,AP-HP Nord, ICU Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Diane Descamps
- Université Paris Cité, INSERM UMR1137, IAME, F-75018 Paris, France,AP-HP Nord, Virology Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Nadhira Houhou
- Université Paris Cité, INSERM UMR1137, IAME, F-75018 Paris, France,AP-HP Nord, Virology Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Benoit Visseaux
- Université Paris Cité, INSERM UMR1137, IAME, F-75018 Paris, France,AP-HP Nord, Virology Department, Bichat-Claude Bernard University Hospital, Paris, France
| | - Paul Loubet
- Université de Montpellier, VBMI, Inserm U1047, Nîmes, France,Department of Infectious and Tropical Diseases, CHU Nîmes, Université de Montpellier, Nîmes, France
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Cao C, You M, Tong H, Xue Z, Liu C, He W, Peng P, Yao C, Li A, Xu X, Xu F. Similar color analysis based on deep learning (SCAD) for multiplex digital PCR via a single fluorescent channel. LAB ON A CHIP 2022; 22:3837-3847. [PMID: 36073361 DOI: 10.1039/d2lc00637e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Digital PCR (dPCR) has recently attracted great interest due to its high sensitivity and accuracy. However, the existing dPCR depends on multicolor fluorescent dyes and multiple fluorescent channels to achieve multiplex detection, resulting in increased detection cost and limited detection throughput. Here, we developed a deep learning-based similar color analysis method, namely SCAD, to achieve multiplex dPCR in a single fluorescent channel. As a demonstration, we designed a microwell chip-based diplex dPCR system for detecting two genes (blaNDM and blaVIM) with two kinds of green fluorescent probes, whose emission colors are difficult to discriminate by traditional fluorescence intensity-based methods. To verify the possibility of deep learning algorithms to distinguish the similar colors, we first applied t-distributed stochastic neighbor embedding (tSNE) to make a clustering map for the microwells with similar fluorescence. Then, we trained a Vision Transformer (ViT) model on 10 000 microwells with two similar colors and tested it with 262 202 microwells. Lastly, the trained model was proven to have highly accurate classification ability (>98% for both the training set and the test set) and precise quantification ability on both blaNDM and blaVIM (ratio difference <0.10). We envision that the developed SCAD method would significantly expand the detection throughput of dPCR without the need for other auxiliary equipment.
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Affiliation(s)
- Chaoyu Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China.
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Minli You
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China.
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Haoyang Tong
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China.
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Zhenrui Xue
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Chang Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China.
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Wanghong He
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Ping Peng
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Ang Li
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Xiayu Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China.
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China.
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
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Campelo FS, de Aguiar Cordeiro R, Moura FEA. The role of human bocavirus as an agent of community-acquired pneumonia in children under 5 years of age in Fortaleza, Ceará (Northeast Brazil). Braz J Microbiol 2022; 53:1915-1924. [PMID: 35933553 PMCID: PMC9679084 DOI: 10.1007/s42770-022-00806-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/21/2022] [Indexed: 01/13/2023] Open
Abstract
The human bocavirus (HBoV) is an agent of upper and lower respiratory infections, affecting mainly children under 5 years of age. Community-acquired pneumonia (CAP) is an important public health problem in developing countries, representing one of the main causes of hospitalizations and deaths in children. The aim of this study was to describe the prevalence of HBoV and the clinical and epidemiological characteristics in children diagnosed with CAP. For this purpose, nasopharyngeal aspirates were collected from 545 children aged 0 to 60 months diagnosed with CAP between January 2013 and December 2014 in a reference pediatric hospital in Fortaleza, Ceará, Brazil. The samples were subjected to PCR for detection of HBoV and parainfluenza 4 (PIV4) and indirect immunofluorescence for detection of respiratory syncytial virus (RSV), adenovirus (AdV), influenza A and B (FLU A and FLU B), and parainfluenza 1, 2, and 3 (PIV1, PIV2, PIV3). Clinically, most CAP were non-complicated (487/545; 89.3%); however, 10.7% (58/545) of children were treated in the ICU/resuscitation sector. Among the total samples analyzed, 359 (65.8%) were positive for at least one virus surveyed and 105 (19.2%) samples had two or more viruses. HBoV was detected in 87 samples (15.9%), being the second most prevalent virus. RSV, AdV, FLU A, FLU B, and PIV 1-3 were detected in 150 (27.5%), 45 (8.2%), 30 (5.5%), 3 (0.5%), and 131 (24%) samples, respectively. The age average was 12.1 months in children infected with HBoV, and the most frequent symptoms were dyspnea and cough. In addition, 90.6% of HboV-positive children received antibiotics as empirical treatment. HBoV did not show any circulation pattern; however, it seemed to be more frequent in the first half of the year, totaling 68.9% of the cases. HBoV is a frequent agent of pneumonia in the child population studied.
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Affiliation(s)
- Felipe Serra Campelo
- Postgraduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, Brazil
| | - Rossana de Aguiar Cordeiro
- Postgraduate Program in Medical Sciences, Federal University of Ceará, Fortaleza, Brazil ,Postgraduate Program in Medical Microbiology, Federal University of Ceará, Fortaleza, Brazil
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Sawires R, Kuldorff M, Fahey M, Clothier H, Buttery J. Snotwatch: an ecological analysis of the relationship between febrile seizures and respiratory virus activity. BMC Pediatr 2022; 22:359. [PMID: 35733118 PMCID: PMC9215000 DOI: 10.1186/s12887-022-03222-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/15/2022] [Indexed: 11/30/2022] Open
Abstract
Background Febrile seizures are the commonest type of seizure in occurring in the first few years of life, mostly affecting children aged six months to five years old. While largely benign, the incidence of each febrile seizure increases the risk of recurrence, afebrile seizures and epilepsy. Viruses are the most frequent cause of febrile illnesses in which a febrile seizure occurs. Febrile seizure presentation patterns appear to follow a seasonal trend. Aims To identify patterns of febrile seizure incidence across different seasons with specific viral activity, and to establish a framework for analysing virus circulation data with common illnesses within a shared region and population. Setting Our study was a study of febrile seizure presentations in Victoria, Australia and respiratory virus detection. Participants We obtained independent datasets of emergency department febrile seizure presentations at Monash Health and all respiratory multiplex PCR tests performed at Monash Health from January 2010–December 2019 to observe common trends in virus circulation and febrile seizure incidence. Study design Trends were studied temporally through mixed effects Poisson regression analysis of the monthly incidence of febrile seizures and the rate of positive PCR tests. Peak viral seasons (95th centile incidence) were compared to median viral circulation (50th centile incidence) to calculate peak season risk ratios. Results We found a 1.75–2.06 annual risk ratio of febrile seizure incidence in June–September. Temporal analysis of our data showed this peak in febrile seizures was attributable to circulating viruses in this season, and virus modelling showed correlation with increased rates of positive Influenza A (1.48 peak season risk ratio), Influenza B (1.31 peak season risk ratio), Human metapneumovirus (1.19 peak season risk ratio) and Respiratory Syncytial Virus (1.53 peak season risk ratio) on PCR testing. Conclusion Our ecological study statistically demonstrates the recognised winter peak in febrile seizure incidence and ascribes the seasonal relationship to several viral infections which affect the community, including a novel association with Human metapneumovirus. Supplementary Information The online version contains supplementary material available at 10.1186/s12887-022-03222-4.
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Affiliation(s)
- Rana Sawires
- Department of Paediatrics, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia. .,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.
| | - Martin Kuldorff
- Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Michael Fahey
- Department of Neurology, Monash Children's Hospital, Clayton, Victoria, Australia.,Neurogenetics Department, Monash Paediatrics, Monash University, Clayton, Victoria, Australia
| | - Hazel Clothier
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,School of Population & Global health, University of Melbourne, Parkville, Victoria, Australia
| | - Jim Buttery
- Department of Paediatrics, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.,Child Health Informatics, Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
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5
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Treatment of Respiratory Viral Coinfections. EPIDEMIOLGIA (BASEL, SWITZERLAND) 2022; 3:81-96. [PMID: 36417269 PMCID: PMC9620919 DOI: 10.3390/epidemiologia3010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/18/2022] [Accepted: 02/01/2022] [Indexed: 12/14/2022]
Abstract
With the advent of rapid multiplex PCR, physicians have been able to test for multiple viral pathogens when a patient presents with influenza-like illness. This has led to the discovery that many respiratory infections are caused by more than one virus. Antiviral treatment of viral coinfections can be complex because treatment of one virus will affect the time course of the other virus. Since effective antivirals are only available for some respiratory viruses, careful consideration needs to be given on the effect treating one virus will have on the dynamics of the other virus, which might not have available antiviral treatment. In this study, we use mathematical models of viral coinfections to assess the effect of antiviral treatment on coinfections. We examine the effect of the mechanism of action, relative growth rates of the viruses, and the assumptions underlying the interaction of the viruses. We find that high antiviral efficacy is needed to suppress both infections. If high doses of both antivirals are not achieved, then we run the risk of lengthening the duration of coinfection or even of allowing a suppressed virus to replicate to higher viral titers.
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6
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Chung YN, Yoo IY, Yun SA, Kim JY, Lee NY, Huh HJ. Comparison of the AdvanSure RV Plus Real-Time RT-PCR and Real-Q RV II Detection Assays for Respiratory Viruses. Ann Lab Med 2021; 41:506-509. [PMID: 33824243 PMCID: PMC8041588 DOI: 10.3343/alm.2021.41.5.506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/21/2020] [Accepted: 03/15/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Yoo Na Chung
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - In Young Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Ji-Youn Kim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Jacky L, Yurk D, Alvarado J, Belitz P, Fathe K, MacDonald C, Fraser S, Rajagopal A. Robust Multichannel Encoding for Highly Multiplexed Quantitative PCR. Anal Chem 2021; 93:4208-4216. [PMID: 33631072 DOI: 10.1021/acs.analchem.0c04626] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The gold standard of molecular pathogen detection is the quantitative polymerase chain reaction (qPCR). Modern qPCR instruments are capable of detecting 4-6 analytes in a single sample: one per optical detection channel. However, many clinical applications require multiplexing beyond this traditional single-well capacity, including the task of simultaneously testing for SARS-CoV-2 and other respiratory pathogens. This can be addressed by dividing a sample across multiple wells, or using technologies such as genomic sequencing and spatial arrays, but at the expense of significantly higher cost and lower throughput compared with single-well qPCR. These trade-offs represent unacceptable compromises in high-throughput screening scenarios such as SARS-CoV-2 testing. We demonstrate a novel method of detecting up to 20 targets per well with standard qPCR instrumentation: high-definition PCR (HDPCR). HDPCR combines TaqMan chemistry and familiar workflows with robust encoding to enable far higher levels of multiplexing on a traditional qPCR system without an increase in cost or reduction in throughput. We utilize HDPCR with a custom 20-Plex assay, an 8-Plex assay using unmodified predesigned single-plex assays from Integrated DNA Technologies and a 9-Plex pathogen panel inclusive of SARS-CoV-2 and other common respiratory viruses. All three assays were successful when tested on a variety of samples, with overall sample accuracies of 98.8, 98.3, and 100%, respectively. The HDPCR technology enables the large install base of qPCR instrumentation to perform mid-density multiplex diagnostics without modification to instrumentation or workflow, meeting the urgent need for increased diagnostic yield at an affordable price without sacrificing assay performance.
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Affiliation(s)
- Lucien Jacky
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Dominic Yurk
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States.,Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - John Alvarado
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Paul Belitz
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Kristin Fathe
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Chris MacDonald
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Scott Fraser
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, United States
| | - Aditya Rajagopal
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States.,Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, United States.,Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, United States
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8
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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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9
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The prevalence of viral infections in children with cystic fibrosis in a tertiary care center in Saudi Arabia. Int J Pediatr Adolesc Med 2020; 7:83-87. [PMID: 32292813 PMCID: PMC7102630 DOI: 10.1016/j.ijpam.2019.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 07/22/2019] [Accepted: 09/03/2019] [Indexed: 11/23/2022]
Abstract
Introduction Studies have shown that pulmonary exacerbations in cystic fibrosis (CF) patients are associated with respiratory viruses. The most common agent causing viral infections in patients with CF before the age of 3 years is respiratory syncytial virus. Objectives To obtain the prevalence of the different types of viral infection in CF patients and to identify its relation with the type of bacterial infection, (CFTR) mutations and pulmonary function test (PFT). Methodology A retrospective charts review of 387 patients with CF of all age groups who were screened for the detection of viruses during respiratory exacerbation from the period of January 1, 1984 to June 1, 2016. Results A total of 159 CF patients had pulmonary exacerbation and had viral PCR obtained. Fifty-eight patients (36%) had positive viral PCR. Males were more commonly infected in 30/58 patients (52%) compared to females in 28 patients (48%). Forty-five of 58 patients (78%) were alive and 13 patients (22%) died. Rhinovirus was the most frequently reported viral PCR in 33/74 sample (45%). Out of 74 viral PCR, 41 (55.4%) were during the colder seasons (October–February) and 33 (44.5%) during the warmer seasons (March–September). During viral infection and viral recurrence, there was an increase in bacterial colonization specifically of H. influenza and staphylococcus aureus. The most common CFTR mutation for the CF viral infection is: 3120+1G>A in Intron 16 in 11/57 patients (19%). The Eastern Province had the highest viral infection of 24 out of 57 patients (42%). Follow-up PFT post viral infection showed no significant difference in the type and the severity of PFT compared to the initial PFT during the viral illness. Conclusion Viral infections contributed to the increase in morbidity and mortality of CF patients in our population, and rhinovirus was the most common causative agent. Viral infections and viral recurrence increased the prevalence of bacterial infection of specific pathogens such as H. influenza and S. aureus. Physicians should be aware to prevent progressive lung damage in CF patients by treating the concomitant viral and bacterial infections. Viral infection may be associated with some common CFTR mutations.
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10
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Li W, Liu L, Chen L, Shang S. Evaluation of a Commercial Colloidal Gold Assay for Detection of Influenza A and B Virus in Children's Respiratory Specimens. Fetal Pediatr Pathol 2020; 39:93-98. [PMID: 31304835 DOI: 10.1080/15513815.2019.1639088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Objective: To evaluate the clinical diagnostic value of colloidal gold assay for detection of influenza A and B virus. Methods: Results were compared for colloidal gold assay for influenza antigen detection and real-time RT-PCR for RNA detection. Results: By performing the colloidal gold assay, the positive rate was 25.67% (105/409) for influenza A virus and 8.56% (35/409) for influenza B virus. While tested by real-time RT-PCR, 107(26.2%) were positive for influenza A virus and 35(8.6%) for influenza B virus. Using real-time RT-PCR as the gold standard, the sensitivity and specificity of the colloidal gold assay were 84.1% and 95.0%, respectively, for influenza A virus and 85.7% and 98.7% for influenza B virus. Conclusion: This colloidal gold assay may be one of the viable tools for the rapid screening for influenza viruses in an outpatient clinical practice.
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Affiliation(s)
- Wei Li
- Clinical Laboratory, Zhejiang University School of Medicine Children's Hospital, Hangzhou, China
| | - Lifang Liu
- Zhejiang University School of Medicine Children's Hospital, Hangzhou, China
| | - Luyan Chen
- Zhejiang University School of Medicine Children's Hospital, Hangzhou, China
| | - Shiqiang Shang
- Zhejiang University School of Medicine Children's Hospital, Hangzhou, China
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11
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Xiang W, Peng Z, Xu J, Shen H, Li W. Evaluation of a commercial latex agglutination test for detecting rotavirus A and human adenovirus in children's stool specimens. J Clin Lab Anal 2020; 34:e23208. [PMID: 31930752 PMCID: PMC7246382 DOI: 10.1002/jcla.23208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 01/21/2023] Open
Abstract
Objectives Rotavirus A and human adenovirus are the two most common causes of infantile diarrhea; thus, it is of great importance to find out a rapid and accurate diagnostic method. This study aimed to evaluate the diagnostic significance of latex agglutination test for detection of rotavirus A and human adenovirus. Methods A prospective study was conducted on 214 diarrhea children from September 2018 to March 2019 in our hospital. Fresh stool samples were collected for detection of rotavirus A and human adenovirus by latex agglutination test and quantitative reverse transcription polymerase chain reaction (RT‐qPCR). Then, the consistency of results detected by these two methods was analyzed. Results With performing the latex agglutination test, it was revealed that positive rates for detecting rotavirus A virus and human adenovirus were 23.83% (51/214) and 25.24% (54/214), respectively. Meanwhile, results of RT‐qPCR showed that positive rates for detecting rotavirus A virus and human adenovirus were 58 (27.10%) and 59 (27.57%), respectively. Using RT‐qPCR as the gold standard, the sensitivity and specificity of the latex agglutination test for detecting rotavirus A were 81.03% and 97.44%, and the corresponding values for detecting human adenovirus were 76.27% and 94.19%, respectively. Conclusion This latex agglutination test showed a satisfactory consistency with RT‐qPCR for detecting rotavirus A and human adenovirus. The mentioned commercial assay may be highly appropriate for rapid screening of rotavirus A and human adenovirus.
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Affiliation(s)
- Wenqing Xiang
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Zhaoyang Peng
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Jialu Xu
- Department of Neurology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Hongqiang Shen
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
| | - Wei Li
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center For Child Health, Hangzhou, China
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12
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Esposito S, Mencacci A, Cenci E, Camilloni B, Silvestri E, Principi N. Multiplex Platforms for the Identification of Respiratory Pathogens: Are They Useful in Pediatric Clinical Practice? Front Cell Infect Microbiol 2019; 9:196. [PMID: 31275863 PMCID: PMC6593267 DOI: 10.3389/fcimb.2019.00196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/21/2019] [Indexed: 01/31/2023] Open
Abstract
Respiratory tract infections (RTIs) are extremely common especially in the first year of life. Knowledge of the etiology of a RTI is essential to facilitate the appropriate management and the implementation of the most effective control measures. This perspective explains why laboratory methods that can identify pathogens in respiratory secretions have been developed over the course of many years. High-complexity multiplex panel assays that can simultaneously detect up to 20 viruses and up to four bacteria within a few hours have been marketed. However, are these platforms actually useful in pediatric clinical practice? In this manuscript, we showed that these platforms appear to be particularly important for epidemiological studies and clinical research. On the contrary, their routine use in pediatric clinical practice remains debatable. They can be used only in the hospital as they require specific equipment and laboratory technicians with considerable knowledge, training, and experience. Moreover, despite more sensitive and specific than other tests routinely used for respiratory pathogen identification, they do not offer significantly advantage for detection of the true etiology of a respiratory disease. Furthermore, knowledge of which virus is the cause of a respiratory disease is not useful from a therapeutic point of view unless influenza virus or respiratory syncytial virus are the infecting agents as effective drugs are available only for these pathogens. On the other hand, multiplex platforms can be justified in the presence of severe clinical manifestations, and in immunocompromised patients for whom specific treatment option can be available, particularly when they can be used simultaneously with platforms that allow identification of antimicrobial resistance to commonly used drugs. It is highly likely that these platforms, particularly those with high sensitivity and specificity and with low turnaround time, will become essential when new drugs effective and safe against most of the respiratory viruses will be available. Further studies on how to differentiate carriers from patients with true disease, as well as studies on the implications of coinfections and identification of antimicrobial resistance, are warranted.
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Affiliation(s)
- Susanna Esposito
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Antonella Mencacci
- Microbiology Unit, Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
| | - Elio Cenci
- Microbiology Unit, Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
| | - Barbara Camilloni
- Microbiology Unit, Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
| | - Ettore Silvestri
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
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13
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Appak Ö, Duman M, Belet N, Sayiner AA. Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients. J Med Virol 2019; 91:731-737. [PMID: 30570759 PMCID: PMC7167103 DOI: 10.1002/jmv.25379] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/16/2018] [Indexed: 12/22/2022]
Abstract
Syndromic diagnosis by multiplex nucleic acid amplification tests is the most practical approach to respiratory tract infections since the symptoms are rarely agent‐specific. The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. A total of 3162 respiratory samples collected from children between April 2011 and April 2018 tested by a multiplex real‐time PCR assay. Two different commercial assays were used during the study period, "AusDiagnostics/Respiratory Pathogens 12 (AusDiagnostics)" used between April 2011 and December 2015, which changed to "Fast Track Diagnostics/Respiratory Pathogens 21 (Fast Track Diagnostics)" after January 2016 to cover more viruses. Nucleic acid extraction was done by EZ1 Advanced XL platform (QIAGEN). Respiratory pathogens detected in 1857 of the 3162 (58.7%) samples. The most prevalent viruses during the 8‐year period were rhinovirus/enterovirus (RV/EV; 36.2%), respiratory syncytial virus (RSV; 19%), and influenza virus A/B (14.7%). Rhinovirus was the main contributor to the RV/EV group as shown by the assay used during the 2016‐2018 period. RV/EV and adenoviruses detected throughout the year. Influenza virus was most frequently detected during January to March when both RSV and metapneumovirus were also in circulation. The coinfection percentage was 10.2%. Rhinovirus was the most common virus in coinfections while RSV plus rhinovirus/enterovirus were the most frequent combination. RSV and metapneumovirus showed a similar seasonal distribution to the influenza virus, which made it necessary to use a virological diagnostic assay during the influenza season.
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Affiliation(s)
- Özgür Appak
- Department of Medical Microbiology, Division of Medical Virology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Murat Duman
- Department of Pediatrics, Division of Pediatric Emergency Care, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Nurşen Belet
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Ayça Arzu Sayiner
- Department of Medical Microbiology, Division of Medical Virology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
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The epidemiology and severity of respiratory viral infections in a tropical country: Ecuador, 2009-2016. J Infect Public Health 2018; 12:357-363. [PMID: 30573330 PMCID: PMC7102740 DOI: 10.1016/j.jiph.2018.12.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/16/2018] [Accepted: 12/06/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Respiratory viral infections (RVI) are a leading cause of mortality worldwide. We compared the epidemiology and severity of RVI in Ecuador during 2009-2016. METHODS Respiratory specimens collected within the national surveillance system were tested for influenza viruses, respiratory syncytial virus (RSV), adenovirus, parainfluenza virus, and human metapneumovirus. Overall and virus-specific positive detection rate (PDR) were calculated and compared the timing of epidemics caused by the different viruses. Logistic regression models were used to compare the age distribution and risk of death across respiratory viruses. RESULTS A total of 41,172 specimens were analyzed: influenza (PDR=14.3%) and respiratory syncytial virus (RSV) (PDR=9.5%) were the most frequently detected viruses. Influenza epidemics typically peaked in December-January and RSV epidemics in March; seasonality was less evident for the other viruses. Compared to adults, children were more frequently infected with RSV, adenovirus, parainfluenza, and influenza B, while the elderly were less frequently infected with influenza A(H1N1)p. The age-adjusted risk of death was highest for A(H1N1)p (odds ratio [OR] 1.73, 95% confidence intervals [CI] 1.38-2.17), and lowest for RSV (OR 0.75, 95%CI 0.57-0.98). CONCLUSIONS Whilst influenza and RSV were the most frequently detected pathogens, the risk of death differed by RVI, being highest for pandemic influenza and lowest for RSV.
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Yun SG, Kim MY, Choi JM, Lee CK, Lim CS, Cho Y, Suh IB. Comparison of three multiplex PCR assays for detection of respiratory viruses: Anyplex II RV16, AdvanSure RV, and Real-Q RV. J Clin Lab Anal 2017; 32. [PMID: 28397965 PMCID: PMC5836940 DOI: 10.1002/jcla.22230] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/10/2017] [Indexed: 12/25/2022] Open
Abstract
Background Due to its great sensitivity, the nucleic acid amplification test (NAAT) is widely used for detection of respiratory viruses (RV). However, few reports have described a direct comparison between multiplex RT‐PCR assays for RV. The objective of this study was to perform a direct comparison of three multiplex RT‐PCR assays for the detection of respiratory viruses. Methods A total of 201 respiratory samples (161 nasopharyngeal swab samples and 40 sputum samples) were tested with three commercial RV assays: Seegene Anyplex II RV16 (AP), LG AdvanSure RV (AD), and Biosewoom Real‐Q RV (RQ). The additional tests for the discrepant results were conducted by repeat RV assay or monoplex PCR coupled direct sequencing. Data analysis using percent agreement, kappa, and prevalence‐adjusted and bias‐adjusted kappa (PABAK) values was performed for comparisons among the three RV assays. Results Of the 201 samples, AP, AD, and RQ detected 105 (52.2%), 99 (49.3%), and 95 (47.3%) positive cases respectively. The overall agreement, kappa, and PABAK values for the three assays ranged between 97%‐98%, 0.76‐0.86, and 0.93‐0.96 respectively. The performance of the three assays was very similar, with 94%‐100% agreement for all comparisons, each virus types. The additional testing of samples showed discrepant results demonstrating that AD assay had the highest rate of concordance with original results. Conclusions We suggest that all multiplex assay would be suitable for the detection of for respiratory viruses in clinical setting.
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Affiliation(s)
- Seung Gyu Yun
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Min Young Kim
- Armed Forces Medical Research Institute, Daejeon, Korea
| | - Jong Moon Choi
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - In Bum Suh
- Department of Laboratory Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
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