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Sun B, Qiu Y, Wang L, Sun H, Wang Z, Mao L, Wu W. Viral etiology of febrile respiratory syndrome among patients in Liaoning Province, China. BMC Infect Dis 2024; 24:1060. [PMID: 39333919 PMCID: PMC11429093 DOI: 10.1186/s12879-024-09956-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Febrile respiratory syndrome (FRS) is often associated with viral infections. The aim of this study was to identify the viral pathogens responsible for FRS in Liaoning Province, China. METHODS We tested eight respiratory viruses, namely, influenza virus (IFV), rhinovirus (RV), human adenovirus (HAdV), human bocavirus (HBoV), human parainfluenza virus (HPIV), human coronavirus (HCoV), respiratory syncytial virus (RSV), and human metapneumovirus (HMPV), using reverse transcription-polymerase chain reaction (RT-PCR). Statistical analyses were performed using SPSS version 25.0, and the data were plotted using RStudio 4.2.1 software. RESULTS IFV was the most frequently identified pathogen, followed by RV, HAdV, HBoV, HPIV, HCoV, RSV, and HMPV. RSV/HBoV coinfection occurred most frequently among the mixed cases. The rate of respiratory virus detection was highest in children under one year of age and decreased significantly with age. Seasonal trends showed a peak in virus detection during the winter months. CONCLUSIONS IFV is the leading cause of FRS in Liaoning Province, China, with single-virus infections prevailing over coinfections. Observations indicate a differential virus detection rate across age groups and seasons, highlighting the need for focused preventive strategies to mitigate the transmission of respiratory viruses, particularly among susceptible populations in the colder season.
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Affiliation(s)
- Baihong Sun
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Yuzhu Qiu
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Lulu Wang
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Haibo Sun
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China
| | - Zhiqian Wang
- Research Center for Universal Health, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Lingling Mao
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang, Liaoning, China.
| | - Wei Wu
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, Liaoning, China.
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2
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Wang Y, Huang Y, Peng Y, Cao Q, Liu W, Zhou Z, Xu G, Li L, Zhou R. Development and validation of a rapid five-minute nucleic acid extraction method for respiratory viruses. Virol J 2024; 21:189. [PMID: 39155366 PMCID: PMC11331601 DOI: 10.1186/s12985-024-02381-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/02/2024] [Indexed: 08/20/2024] Open
Abstract
BACKGROUND The rapid transmission and high pathogenicity of respiratory viruses significantly impact the health of both children and adults. Extracting and detecting their nucleic acid is crucial for disease prevention and treatment strategies. However, current extraction methods are laborious and time-consuming and show significant variations in nucleic acid content and purity among different kits, affecting detection sensitivity and efficiency. Our aim is to develop a novel method that reduces extraction time, simplifies operational steps, and ensures high-quality acquisition of respiratory viral nucleic acid. METHODS We extracted respiratory syncytial virus (RSV) nucleic acid using reagents with different components and analyzed cycle threshold (Ct) values via quantitative real-time polymerase chain reaction (qRT-PCR) to optimize and validate the novel lysis and washing solution. The performance of this method was compared against magnetic bead, spin column, and precipitation methods for extracting nucleic acid from various respiratory viruses. The clinical utility of this method was confirmed by comparing it to the standard magnetic bead method for extracting clinical specimens of influenza A virus (IAV). RESULTS The solution, composed of equal parts glycerin and ethanol (50% each), offers an innovative washing approach that achieved comparable efficacy to conventional methods in a single abbreviated cycle. When combined with our A Plus lysis solution, our novel five-minute nucleic acid extraction (FME) method for respiratory viruses yielded superior RNA concentrations and purity compared to traditional methods. FME, when used with a universal automatic nucleic acid extractor, demonstrated similar efficiency as various conventional methods in analyzing diverse concentrations of respiratory viruses. In detecting respiratory specimens from 525 patients suspected of IAV infection, the FME method showed an equivalent detection rate to the standard magnetic bead method, with a total coincidence rate of 95.43% and a kappa statistic of 0.901 (P < 0.001). CONCLUSIONS The FME developed in this study enables the rapid and efficient extraction of nucleic acid from respiratory samples, laying a crucial foundation for the implementation of expedited molecular diagnosis.
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Affiliation(s)
- Yu Wang
- Guangzhou National Laboratory, Guangzhou, China
| | | | - Yuqing Peng
- Guangzhou National Laboratory, Guangzhou, China
| | - Qinglin Cao
- Guangzhou National Laboratory, Guangzhou, China
| | - Wenkuan Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Guangxin Xu
- Guangzhou National Laboratory, Guangzhou, China
| | - Lei Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science of Technology, Wuhan, China.
- GIRM Biosafety (Guangzhou) Co., Ltd, Guangzhou, China.
| | - Rong Zhou
- Guangzhou National Laboratory, Guangzhou, China.
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
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3
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Magda G. Opportunistic Infections Post-Lung Transplantation: Viral, Fungal, and Mycobacterial. Infect Dis Clin North Am 2024; 38:121-147. [PMID: 38280760 DOI: 10.1016/j.idc.2023.12.001] [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] [Indexed: 01/29/2024]
Abstract
Opportunistic infections are a leading cause of lung transplant recipient morbidity and mortality. Risk factors for infection include continuous exposure of the lung allograft to the external environment, high levels of immunosuppression, impaired mucociliary clearance and decreased cough reflex, and impact of the native lung microbiome in single lung transplant recipients. Infection risk is mitigated through careful pretransplant screening of recipients and donors, implementation of antimicrobial prophylaxis strategies, and routine surveillance posttransplant. This review describes common viral, fungal, and mycobacterial infectious after lung transplant and provides recommendations on prevention and treatment.
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Affiliation(s)
- Gabriela Magda
- Columbia University Lung Transplant Program, Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, Columbia University Vagelos College of Physicians and Surgeons, 622 West 168th Street PH-14, New York, NY 10032, USA.
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4
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Hongdan G, Yao D, Qiang C, Meng H, Xiaorong L, Zhihao X, Dongli M. A multiplex recombinase polymerase amplification assay combined with CRISPR/Cas12a for the detection of respiratory syncytial virus and respiratory adenovirus. J Int Med Res 2024; 52:3000605231223083. [PMID: 38230675 PMCID: PMC10798089 DOI: 10.1177/03000605231223083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/11/2023] [Indexed: 01/18/2024] Open
Abstract
OBJECTIVE Respiratory syncytial virus (RSV) and respiratory adenovirus (ADV) are two common pathogens that cause acute respiratory tract infections in children. We aimed to develop a rapid method for detecting both pathogens simultaneously. METHODS The recombinase polymerase isothermal amplification (RPA) method was combined with the CRISPR/Cas detection system. The assay's specificity and sensitivity were explored by designing RPA primers and CRISPR RNAs (crRNAs) through multi-sequence comparisons, optimizing the reaction conditions, and using a fluorescent reading device. The consistency of the test results of 160 clinical pharyngeal swab samples was studied using quantitative polymerase chain reaction (qPCR) results as a comparative control. RESULTS RSV and ADV could be detected at levels as low as 104 copies/mL and 103 copies/mL, respectively, within 50 minutes with no cross-reactivity with other similar pathogens. For the clinical samples, compared with the qPCR method, the sensitivities for RSV and ADV were 98.1% and 91.4%, respectively, and the detection specificities were both 100%. The Kappa values were greater than 0.95, suggesting a high degree of consistency. CONCLUSION This method for detecting RSV and ADV is rapid, sensitive, and specific. It can accurately detect mixed infections in a timely manner, making it suitable for use in areas with scarce healthcare resources.
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Affiliation(s)
- Gao Hongdan
- School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, China
- Institute of Pediatrics, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Du Yao
- School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, China
- Institute of Pediatrics, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Chai Qiang
- Shenzhen Sea Microbiology Technology Co., Ltd., Shenzhen, Guangdong, China
| | - Huang Meng
- Shenzhen Sea Microbiology Technology Co., Ltd., Shenzhen, Guangdong, China
| | - Liu Xiaorong
- Institute of Pediatrics, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Xing Zhihao
- Institute of Pediatrics, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Ma Dongli
- School of Laboratory Medicine, Bengbu Medical College, Bengbu, Anhui, China
- Institute of Pediatrics, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
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5
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Yang M, Tao C. Diagnostic efficiency of the FilmArray blood culture identification (BCID) panel: a systematic review and meta-analysis. J Med Microbiol 2023; 72. [PMID: 37712641 DOI: 10.1099/jmm.0.001608] [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] [Indexed: 09/16/2023] Open
Abstract
Introduction. The FilmArray blood culture identification panel (BCID) panel is a multiplex PCR assay with high sensitivity and specificity to identify the most common pathogens in bloodstream infections (BSIs).Hypothesis. We hypothesize that the BCID panel has good diagnostic performance for BSIs and can be popularized in clinical application.Aim: To provide summarized evidence for the diagnostic accuracy of the BCID panel for the identification of positive blood cultures.Methodology. We searched the MEDLINE, EMBASE and Cochrane databases through March 2021 and assessed the efficacy of the diagnostic test of the BCID panel. We performed a meta-analysis and calculated the summary sensitivity and specificity of the BCID panel. Systematic review protocols were registered in the International Prospective Register of Systematic Reviews (PROSPERO) (registration number CRD42021239176).Results. A total of 16 full-text articles were eligible for analysis. The overall sensitivities of the BCID panel on Gram-positive bacteria, Gram-negative bacteria and fungi were 97 % (95 % CI, 0.96-0.98), 100 % (95 % CI, 0.98-01.00) and 99 % (95 % CI, 0.87-1.00), respectively. The pooled diagnostic specificities were 99 % (95 % CI, 0.97-1.00), 100 % (95 % CI, 1.00-1.00) and 100 % (95 % CI, 1.00-1.00) for Gram-positive bacteria, Gram-negative bacteria and fungi, respectively.Conclusions. The BCID panel has high rule-in value for the early detection of BSI patients. The BCID panel can still provide valuable information for ruling out bacteremia or fungemia in populations with low pretest probability.
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Affiliation(s)
- Mei Yang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Chuanmin Tao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
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Duan Y, Jiang M, Huang Q, Jia M, Yang W, Feng L. Incidence, hospitalization, and mortality in children aged 5 years and younger with respiratory syncytial virus-related diseases: A systematic review and meta-analysis. Influenza Other Respir Viruses 2023; 17:e13145. [PMID: 37223668 PMCID: PMC10201211 DOI: 10.1111/irv.13145] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/25/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
Objectives Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infection in young children. We aimed to analyze the factors affecting the estimation of RSV-related disease burden, and to provide evidence to help establish a surveillance system. Methods We searched the English- and Chinese-language databases for articles published between January 1, 2010 and June 2, 2022. The quality of the included articles was assessed using the Agency for Healthcare Research and Quality scale. Random-effects models were used for data synthesis and subgroup analyses. This review was registered in the Prospective Register of Systematic Reviews (PROSPERO: CRD42022372972). Results We included 44 studies (149,321,171 participants), all of which were of medium or high quality. The pooled RSV-related disease incidence, hospitalization rate, in-hospital mortality, and overall mortality rates in children aged 5 years and younger were 9.0 per 100 children per year (95% confidence interval [CI]: 7.0-11.0), 1.7 per 100 children per year (95% CI: 1.3-2.1), 0.5 per 100 children per year (95% CI: 0.4-0.5), and 0.05 per 100 children per year (95% CI: 0.04-0.06), respectively. Age, economics, surveillance types, case definition, and data source were all recognized as influencing factors. Conclusions A standardized and unified RSV surveillance system is required. Case definition and surveillance types should be fully considered for surveillance of different age groups.
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Affiliation(s)
- Yuping Duan
- School of Population Medicine and Public HealthChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Mingyue Jiang
- School of Population Medicine and Public HealthChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Qiangru Huang
- School of Population Medicine and Public HealthChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Mengmeng Jia
- School of Population Medicine and Public HealthChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Weizhong Yang
- School of Population Medicine and Public HealthChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Luzhao Feng
- School of Population Medicine and Public HealthChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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Opportunistic Infections Post-Lung Transplantation: Viral, Fungal, and Mycobacterial. Clin Chest Med 2023; 44:159-177. [PMID: 36774162 DOI: 10.1016/j.ccm.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Opportunistic infections are a leading cause of lung transplant recipient morbidity and mortality. Risk factors for infection include continuous exposure of the lung allograft to the external environment, high levels of immunosuppression, impaired mucociliary clearance and decreased cough reflex, and impact of the native lung microbiome in single lung transplant recipients. Infection risk is mitigated through careful pretransplant screening of recipients and donors, implementation of antimicrobial prophylaxis strategies, and routine surveillance posttransplant. This review describes common viral, fungal, and mycobacterial infectious after lung transplant and provides recommendations on prevention and treatment.
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8
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Zhang Q, Xie Z, Xia B, Wang Y, Xu W, Zhang Y. Identification of two proposed novel human rhinovirus types: Bpat107 and Cpat58. J Med Virol 2023; 95:e28531. [PMID: 36698256 DOI: 10.1002/jmv.28531] [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: 07/22/2022] [Revised: 12/30/2022] [Accepted: 01/24/2023] [Indexed: 01/27/2023]
Abstract
Human rhinovirus (RV) is an important viral pathogen associated with severe acute respiratory tract infection. The present study retrospectively identified RV types in hospitalized patients with severe acute respiratory infection (SARI) from October 2017 to June 2019 in Henan Province, China. Real-time PCR was used to screen pharyngeal swab samples for RV. Then, the VP1 gene sequences of RV-positive samples were amplified and sequenced with nested primer PCR; subsequently, analyses of the molecular epidemiology and genetic diversity characteristics of the RV types were performed. Seventy-three out of 1015 respiratory samples were identified as RV-positive, from which 65 complete VP1 sequences were successfully sequenced. These RVs were classified into 41 different types, including 26 RV-A types, 2 RV-B types, and 13 RV-C types. The RVs showed an obvious seasonal distribution, with peaks in summer and autumn. The epidemic peak of RV-C was later than that of RV-A. In addition, two new types of species, B and C, were proposed, Bpat107 and Cpat58, respectively. Compared with other types in the same RV species, the pairwise nucleotide p-distances of the two novel RV types were 0.262~0.402 and 0.251~0.508, respectively. This study analyzed the seasonal and genetic characteristics of RV associated with SARI cases in Henan Province, China. Two novel RV types were proposed.
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Affiliation(s)
- Qiang Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhibo Xie
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Baicheng Xia
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yage Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yan Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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9
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Regassa BT, Gebrewold LA, Mekuria WT, Kassa NA. Molecular epidemiology of respiratory syncytial virus in children with acute respiratory illnesses in Africa: A systematic review and meta-analysis. J Glob Health 2023; 13:04001. [PMID: 36637855 PMCID: PMC9840062 DOI: 10.7189/jogh.13.04001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Background Globally, the respiratory syncytial virus (RSV) is the most common etiologic agent of acute respiratory illnesses in children. However, its burden has not been well addressed in developing countries. We aimed to estimate the molecular epidemiology of RSV in children less than 18 years of age with acute respiratory infections in Africa by conducting a systematic review and meta-analysis. Methods We systematically searched PubMed, Scopus, CINAHL, and Global Index Medicus databases to identify studies published from January 1, 2002, to April 27, 2022, following the PRISMA 2020 guideline. We assessed the study quality using the Joanna Brigg's Institute (JBI) critical appraisal checklists. We conducted a qualitative synthesis by describing the characteristics of included studies and performed the quantitative synthesis with random effects model using STATA-14. We checked for heterogeneity with Q statistics, quantified by I2, and determined the prediction interval. We performed subgroup analyses to explain the sources of heterogeneity and assessed publication biases by funnel plots augmented with Egger's test. Results Eighty-eight studies with 105 139 participants were included in the review. The overall pooled prevalence of RSV in children <18 years of age was 23% (95% confidence interval (CI) = 20, 25%). Considerable heterogeneity was present across the included studies. The adjusted prediction interval was found to be 19%-27%. Heterogeneities were explained by subgroups analyses. The highest prevalence of RSV was found among inpatients, 28% (95% CI = 25, 31%) compared with inpatients/outpatients and outpatients, with statistically significant differences (P < 0.01). The RSV estimate was also highest among those with acute lower respiratory tract illnesses (ALRTIs), 28% (95% CI = 25, 31%) compared with acute upper respiratory tract illnesses (AURTIs) and both acute upper/lower respiratory manifestations, with statistically different prevalence (P < 0.01). RSV infection estimates in each sub-region of Africa were statistically different (P < 0.01). There were no statistically significant differences in RSV infections by designs, specimen types, and specimen conditions, despite them contributing to heterogeneity. Conclusions We found a high prevalence of RSV in pediatric populations with acute respiratory tract illnesses in Africa, highlighting that the prevention and control of RSV infections in children deserve more attention. Registration PROSPERO CRD42022327054.
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Affiliation(s)
- Belay Tafa Regassa
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Ambo University, Ethiopia
| | - Lami Abebe Gebrewold
- Department of Public Health, College of Medicine and Health Sciences, Ambo University, Ethiopia
| | - Wagi Tosisa Mekuria
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Ambo University, Ethiopia
| | - Nega Assefa Kassa
- School of Public Health, College of Health and Medical Sciences, Haramaya University, Ethiopia
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10
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Yuan G, Wang H, Zhao Y, Mao E, Li M, Wang R, Zhou F, Jin S, Zhang Z, Xu K, Xu J, Liang S, Li X, Jiang L, Zhang L, Song J, Yang T, Guo J, Zhang H, Zhou Y, Wang S, Qiu C, Jiang N, Ai J, Wu J, Zhang W. Early identification and severity prediction of acute respiratory infection (ESAR): a study protocol for a randomized controlled trial. BMC Infect Dis 2022; 22:632. [PMID: 35858876 PMCID: PMC9296892 DOI: 10.1186/s12879-022-07552-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Background The outbreak of SARS-CoV-2 at the end of 2019 sounded the alarm for early inspection on acute respiratory infection (ARI). However, diagnosis pathway of ARI has still not reached a consensus and its impact on prognosis needs to be further explored. Methods ESAR is a multicenter, open-label, randomized controlled, non-inferiority clinical trial on evaluating the diagnosis performance and its impact on prognosis of ARI between mNGS and multiplex PCR. Enrolled patients will be divided into two groups with a ratio of 1:1. Group I will be directly tested by mNGS. Group II will firstly receive multiplex PCR, then mNGS in patients with severe infection if multiplex PCR is negative or inconsistent with clinical manifestations. All patients will be followed up every 7 days for 28 days. The primary endpoint is time to initiate targeted treatment. Secondary endpoints include incidence of significant events (oxygen inhalation, mechanical ventilation, etc.), clinical remission rate, and hospitalization length. A total of 440 participants will be enrolled in both groups. Discussion ESAR compares the efficacy of different diagnostic strategies and their impact on treatment outcomes in ARI, which is of great significance to make precise diagnosis, balance clinical resources and demands, and ultimately optimize clinical diagnosis pathways and treatment strategies. Trial registration Clinicaltrial.gov, NCT04955756, Registered on July 9th 2021.
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Affiliation(s)
- Guanmin Yuan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China
| | - Hongyu Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China
| | - Yuanhan Zhao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China
| | - Enqiang Mao
- Departments of Emergency, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Mengjiao Li
- Departments of Emergency, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ruilan Wang
- Department of Critical Care Medicine, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Fangqing Zhou
- Department of Critical Care Medicine, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Shanshan Jin
- Department of Critical Care Medicine, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ziqiang Zhang
- Department of Infectious Disease, Tongji Hospital, School of Medicine of Tongji University, Shanghai, China.,Department of Respiratory and Critical Care Medicine, Tongji Hospital, School of Medicine of Tongji University, Shanghai, China
| | - Ke Xu
- Department of Infectious Disease, Tongji Hospital, School of Medicine of Tongji University, Shanghai, China.,Department of Respiratory and Critical Care Medicine, Tongji Hospital, School of Medicine of Tongji University, Shanghai, China
| | - Jinfu Xu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shuo Liang
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiang Li
- Department of Critical Care Medicine, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Lijing Jiang
- Department of Critical Care Medicine, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Lu Zhang
- Department of Critical Care Medicine, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Jieyu Song
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China
| | - Tao Yang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China
| | - Jinxin Guo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China
| | - Haocheng Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China
| | - Yang Zhou
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China
| | - Sen Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China
| | - Chao Qiu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China
| | - Ning Jiang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China
| | - Jingwen Ai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China.
| | - Jing Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China.
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, No. 12 Middle Urumqi Road, Jing'an, Shanghai, 200040, China. .,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China. .,Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China.
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11
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Zeng H, Zhang P, Jiang X, Duan C, Yu Y, Wu Q, Yang X. Rapid RNA detection through intra-enzyme chain replacement-promoted Cas13a cascade cyclic reaction without amplification. Anal Chim Acta 2022; 1217:340009. [PMID: 35690427 DOI: 10.1016/j.aca.2022.340009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/12/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022]
Abstract
The clinical methods to detect RNA viruses and disease-related RNAs suffer from time-consuming processes, high false-positive rates, or limited sensitivity. Here, we propose a strategy for rapid RNA detection through intra-enzyme chain replacement-mediated Cas13a cascade cyclic reaction without target amplification. A hairpin RNA mediator (a cleavage substrate for target-activated Cas13a) and a guiding RNA recognized by the cleavage product through intra-enzyme chain replacement were designed and optimized. Upon the recognition and binding of the target RNA to the Cas13a/CrRNA complex, Cas13a is initially activated to cleave the mediator, and the cleavage products recognize the corresponding Cas13a/CrRNA complex by intra-enzyme chain replacement and initiate the circular cascade of Cas13a cleavage and activation. The accumulated active Cas13a cleaves fluorescent reporter probe for achieving target RNA detection. This "mix & read" RNA detection at room temperature was performed in total 30 min. Using miRNA-21 as the target, the changes in fluorescence intensity were linearly correlated to the concentrations from 10 fM to 50 pM with the detection limit of 75 aM, while no significant changes in fluorescence intensity were detected for non-targets. This method applied to the clinical sputum respiratory syncytial virus-positive samples gave results consistent with those from the clinical fluorescence immunoassay. Thus, intra-enzyme chain replacement-promoted Cas13a cascade cyclic reaction for detection of RNA viruses in the "mix & read" mode at room temperature is rapid, simple, convenient, and efficient for RNA detection and can be adapted to point-of-care testing for high throughput screening of RNA virus infections.
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Affiliation(s)
- Hongwei Zeng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Penghui Zhang
- Clinical Laboratory Center, Ministry of Education Key Laboratory of Child Development Diseases and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital, Chongqing Medical University, Chongqing, PR China
| | - Xue Jiang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Changyuan Duan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yang Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Qiaoming Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xiaolan Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
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12
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Lee H, Lee H, Hwang SH, Jeong W, Kim DE. Detection of SARS-CoV-2 RNA through tandem isothermal gene amplification without reverse transcription. Anal Chim Acta 2022; 1212:339909. [PMID: 35623783 PMCID: PMC9073641 DOI: 10.1016/j.aca.2022.339909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 11/27/2022]
Abstract
Diagnosis of SARS-CoV-2 infection through rapid, accurate, and sensitive testing is the most important and fundamental step in coping with the COVID-19 epidemic. We have developed a sensitive fluorometric assay to detect SARS-CoV-2 viral RNA without thermal cycling. This assay system, based on tandem isothermal gene amplification (TIGA), is composed of ternary rolling circle amplification (t-RCA) and subsequent strand displacement amplification (SDA) coupled with G-quadruplex-generating RCA (SDA/GQ-RCA). Without the need to convert viral RNA into cDNA, viral RNA forms a ternary complex composed of hairpin primer (HP) and dumbbell padlock DNA during the t-RCA process. t-RCA generates a long chain of single-stranded DNA (ssDNA) with tandemly repeated hairpin structures that are subjected to SDA. SDA produces multiple short ssDNAs from t-RCA products, which then serve as primers for the second RCA reaction. A long ssDNA harboring repeated copies of the G-quadruplex is produced in the second round of RCA. Emission of enhanced fluorescence by thioflavin T, which intercalates into the G-quadruplex, allows fluorometric detection of amplified viral genes. This fluorometric analysis sensitively detected SARS-CoV-2 RNA as low as 5.9 aM, with a linear range between 0.2 fM and 200 fM within 1 h. Hence, this isothermal gene amplification method without reverse transcription of viral RNA can be applied to diagnose COVID-19 with high sensitivity and accuracy as an alternative to current PCR-based diagnosis.
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13
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Luan Q, Jiang Z, Wang D, Wang S, Yin Y, Wang J. A sensitive triple nanoparticle-assisted PCR assay for detection of fowl adenovirus, infectious bursal disease virus and chicken anemia virus. J Virol Methods 2022; 303:114499. [PMID: 35217101 DOI: 10.1016/j.jviromet.2022.114499] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 10/19/2022]
Abstract
Fowl adenovirus (FAdV) infections in chickens have resulted in global economic losses in the poultry industry. Infectious bursal disease virus (IBDV) and chicken anemia virus (CAV) infections lead to immunosuppression in chickens, and concomitant co- infection with FAdV usually produces severe and lethal infections. These co-infections are common occurrences on chicken farms and affect large number of chickens. Thus, a rapid, sensitive and specific diagnostic test for these viruses becomes a prerequisite to effective control and isolation measures. We developed a triplex nanoparticle-assisted PCR (nano-PCR) assay that can simultaneously detect these 3 viruses in a single assay tube using PCR primers directed at respective specific genes of each virus. The assay was specific for FAdVs, CAV and IBDV, and it did not amplify Newcastle disease virus, infectious bronchitis virus, egg drop syndrome virus or Marek's disease virus. The minimum detection limit was 27.2 femtogram (fg) for all three viruses and was 1000-fold more sensitive than multiplex PCR using identical primers. Screening of 69 clinical samples from 40 to 50 days old chickens with obvious lesions in liver using the nano-PCR compared with a multiplex PCR yielded identical results. Of the 69 samples, 13 were detected positive including 4 for FAdV, 4 for IBDV and 6 for CAV single virus infections, respectively, as well as 5 for FAdV/CAV, 2 for FAdV/IBDV and 3 for IBDV/CAV co-infections. The triple nano-PCR assay developed in our laboratory is a sensitive, specific and simple method that can be used for detection of FAdV, CAV and IBDV as single or mixed infections.
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Affiliation(s)
- Qingdong Luan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhiyao Jiang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Dongdong Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shouchun Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yanbo Yin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Jianlin Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
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14
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Gao DQ, Hu YQ, Wang X, Zhang YZ. Hepatitis B virus in cerebrospinal fluid of a patient with purulent bacterial meningitis detected by multiplex-PCR: A case report. World J Clin Cases 2022; 10:1697-1701. [PMID: 35211611 PMCID: PMC8855277 DOI: 10.12998/wjcc.v10.i5.1697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/26/2021] [Accepted: 01/08/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Bacterial meningitis (BM) is a common central nervous system inflammatory disease. BM may cause serious complications, and early diagnosis is essential to improve the prognosis of affected patients.
CASE SUMMARY A 37-year-old man was hospitalized with purulent meningitis because of worsening headache for 12 h, accompanied by vomiting, fever, and rhinorrhea. Head computed tomography showed a lesion in the left frontal lobe. Infectious disease screening showed positivity for hepatitis B surface antigen, hepatitis B e antigen, and hepatitis B core antigen. Cerebrospinal fluid (CSF) leak was suspected based on clinical history. Streptococcus pneumoniae (S. pneumoniae) was detected in CSF by metagenomic next-generation sequencing (mNGS) technology, confirming the diagnosis of purulent BM. After treatment, multiplex PCR indicated the presence of hepatitis B virus (HBV) DNA and absence of S. pneumoniae DNA in CSF samples.
CONCLUSION We report a rare case of HBV in the CSF of a patient with purulent BM. Multiplex PCR is more sensitive than mNGS for detecting HBV DNA.
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Affiliation(s)
- Dai-Quan Gao
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Yong-Qiang Hu
- Department of Critical Care Medicine, Beijing Fengtai You'anmen Hospital, Beijing 100069, China
| | - Xin Wang
- Department of Intensive Medicine, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Yun-Zhou Zhang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
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15
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Sweet SC. Community-Acquired Respiratory Viruses Post-Lung Transplant. Semin Respir Crit Care Med 2021; 42:449-459. [PMID: 34030206 DOI: 10.1055/s-0041-1729172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Survival in lung transplant recipients (LTRs) lags behind heart, liver, and kidney transplant, in part due to the direct and indirect effects of infection. LTRs have increased susceptibility to infection due to the combination of a graft continually exposed to the outside world, multiple mechanisms for impaired mucus clearance, and immunosuppression. Community-acquired respiratory viral infections (CARVs) are common in LTRs. Picornaviruses have roughly 40% cumulative incidence followed by respiratory syncytial virus and coronaviruses. Although single-center retrospective and prospective series implicate CARV in rejection and mortality, conclusive evidence for and well-defined mechanistic links to long-term outcome are lacking. Treatment of viral infections can be challenging except for influenza. Future studies are needed to develop better treatments and clarify the links between CARV and long-term outcomes.
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Affiliation(s)
- Stuart C Sweet
- Division of Allergy and Pulmonary Medicine, Washington University in St. Louis, St. Louis, Missouri
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16
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Zhao X, Meng Y, Li D, Feng Z, Huang W, Li X, Wei H, Zeng X, Wang D. Retrospective study of clinical characteristics and viral etiologies of patients with viral pneumonia in Beijing. Pulm Circ 2021; 11:20458940211011027. [PMID: 34221349 PMCID: PMC8221751 DOI: 10.1177/20458940211011027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/30/2021] [Indexed: 12/31/2022] Open
Abstract
Aims The virus is common in patients with viral pneumonia. However, the viral etiology and clinical features of patients with viral pneumonia in China remain unclear. The main purpose of this study was to analyze the viral causes and epidemiology of patients with viral pneumonia in Beijing, which can significantly improve the pertinence and accuracy of clinical treatment of the disease. Methods Firstly, 1539 respiratory specimens of pneumonia (oropharyngeal swabs, nasopharyngeal swabs, saliva samples and bronchoalveolar lavage fluid) were collected from 19 hospitals in Beijing from September 2015 to August 2018. Then, TaqMan low-density microfluidic chip technology was used to detect viral pneumonia specimens in 1539 respiratory tract specimens of pneumonia and determine the types of viral bacteria in them. Lastly, the analysis of demographic, clinical and etiological data of patients with viral pneumonia was performed. Results The results showed that among the 1539 respiratory tract specimens with pneumonia, 760 were detected as viral pneumonia specimens, with a positive rate of 49.4%. Among which, 467 were infected with mono-viral and 293 were infected with multi-viral. Influenza A virus (Flu A), mycoplasma pneumoniae (MPn), Ebola virus (EBV) and herpes simplex virus type 1 (HSV-1) were the major viral components in the samples of these patients. Furthermore, these viral species were significantly associated with sample sources, onset season and certain clinical characteristics. Discussion Our findings may provide corresponding treatment strategies for viral pneumonia patients infected with specific viruses.
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Affiliation(s)
- Xiang Zhao
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Yao Meng
- Department of Influenza, Shaanxi Provincial Center for Disease Control and Prevention, Xian City, PR China
| | - Duo Li
- Department of Influenza, Yunnan Provincial Center for Disease Control and Prevention, Kunming City, PR China
| | - Zhaomin Feng
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Weijuan Huang
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Xiyan Li
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Hejiang Wei
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Xiaoxu Zeng
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
| | - Dayan Wang
- Department of Influenza, WHO Collaborating Centre for Reference and Research on Influenza, Chinese National Influenza Centre, National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Beijing, PR China
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17
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Shaffaf T, Ghafar-Zadeh E. COVID-19 Diagnostic Strategies. Part I: Nucleic Acid-Based Technologies. Bioengineering (Basel) 2021; 8:49. [PMID: 33920513 PMCID: PMC8072613 DOI: 10.3390/bioengineering8040049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused respiratory infection, resulting in more than two million deaths globally and hospitalizing thousands of people by March 2021. A considerable percentage of the SARS-CoV-2 positive patients are asymptomatic or pre-symptomatic carriers, facilitating the viral spread in the community by their social activities. Hence, it is critical to have access to commercialized diagnostic tests to detect the infection in the earliest stages, monitor the disease, and follow up the patients. Various technologies have been proposed to develop more promising assays and move toward the mass production of fast, reliable, cost-effective, and portable PoC diagnostic tests for COVID-19 detection. Not only COVID-19 but also many other pathogens will be able to spread and attach to human bodies in the future. These technologies enable the fast identification of high-risk individuals during future hazards to support the public in such outbreaks. This paper provides a comprehensive review of current technologies, the progress in the development of molecular diagnostic tests, and the potential strategies to facilitate innovative developments in unprecedented pandemics.
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Affiliation(s)
- Tina Shaffaf
- Biologically Inspired Sensors and Actuators Laboratory (BioSA), York University, Toronto, ON M3J1P3, Canada;
- Faculty of Science, Department of Biology, York University, Toronto, ON M3J1P3, Canada
| | - Ebrahim Ghafar-Zadeh
- Biologically Inspired Sensors and Actuators Laboratory (BioSA), York University, Toronto, ON M3J1P3, Canada;
- Faculty of Science, Department of Biology, York University, Toronto, ON M3J1P3, Canada
- Lassonde School of Engineering, Department of Electrical Engineering and Computer Science, York University, Toronto, ON M3J1P3, Canada
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18
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Hardick J, Shaw-Saliba K, McBryde B, Gaydos CA, Hsieh YH, Lovecchio F, Steele M, Talan D, Rothman RE. Identification of pathogens from the upper respiratory tract of adult emergency department patients at high risk for influenza complications in a pre-Sars-CoV-2 environment. Diagn Microbiol Infect Dis 2021; 100:115352. [PMID: 33639376 DOI: 10.1016/j.diagmicrobio.2021.115352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 11/24/2022]
Abstract
The emergence of SARS-CoV-2 and subsequent COVID-19 pandemic highlights the morbidity and potential disease severity caused by respiratory viruses. To elucidate pathogen prevalence, etiology of coinfections and URIs from symptomatic adult Emergency department patients in a pre-SARS-CoV-2 environment, we evaluated specimens from four geographically diverse Emergency departments in the United States from 2013-2014 utilizing ePlex RP RUO cartridges (Genmark Diagnostics). The overall positivity was 30.1% (241/799), with 6.6% (16/241) coinfections. Noninfluenza pathogens from most to least common were rhinovirus/enterovirus, coronavirus, human metapneumovirus and RSV, respectively. Broad differences in disease prevalence and pathogen distributions were observed across geographic regions; the site with the highest detection rate (for both mono and coinfections) demonstrated the greatest pathogen diversity. A variety of respiratory pathogens and geographic variations in disease prevalence and copathogen type were observed. Further research is required to evaluate the clinical relevance of these findings, especially considering the SARS-CoV-2 pandemic and related questions regarding SARS-CoV-2 disease severity and the presence of co-infections.
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Affiliation(s)
- Justin Hardick
- Johns Hopkins University School of Medicine, Department of Infectious Diseases, Baltimore, MD, USA.
| | - Kathryn Shaw-Saliba
- Johns Hopkins University School of Medicine, Department of Emergency Medicine, Baltimore, MD, USA
| | - Breana McBryde
- Johns Hopkins University School of Medicine, Department of Emergency Medicine, Baltimore, MD, USA
| | - Charlotte A Gaydos
- Johns Hopkins University School of Medicine, Department of Infectious Diseases, Baltimore, MD, USA; Johns Hopkins University School of Medicine, Department of Emergency Medicine, Baltimore, MD, USA
| | - Yu-Hsiang Hsieh
- Johns Hopkins University School of Medicine, Department of Emergency Medicine, Baltimore, MD, USA
| | | | | | - David Talan
- Oliver View Medical Center, Los Angeles, CA, USA
| | - Richard E Rothman
- Johns Hopkins University School of Medicine, Department of Infectious Diseases, Baltimore, MD, USA; Johns Hopkins University School of Medicine, Department of Emergency Medicine, Baltimore, MD, USA
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19
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Hanpanich O, Saito K, Shimada N, Maruyama A. One-step isothermal RNA detection with LNA-modified MNAzymes chaperoned by cationic copolymer. Biosens Bioelectron 2020; 165:112383. [PMID: 32729508 PMCID: PMC7836245 DOI: 10.1016/j.bios.2020.112383] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/13/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022]
Abstract
RNA detection permits early diagnosis of several infectious diseases and cancers, which prevent propagation of diseases and improve treatment efficacy. However, standard technique for RNA detection such as reverse transcription-quantitative polymerase chain reaction has complicated procedure and requires well-trained personnel and specialized lab equipment. These shortcomings limit the application for point-of-care analysis which is critical for rapid and effective disease management. The multicomponent nucleic acid enzymes (MNAzymes) are one of the promising biosensors for simple, isothermal and enzyme-free RNA detection. Herein, we demonstrate simple yet effective strategies that significantly enhance analytical performance of MNAzymes. The addition of the cationic copolymer and structural modification of MNAzyme significantly enhanced selectivity and activity of MNAzymes by 250 fold and 2,700 fold, respectively. The highly simplified RNA detection system achieved a detection limit of 73 fM target concentration without additional amplification. The robustness of MNAzyme in the presence of non-target RNA was also improved. Our finding opens up a route toward the development of an alternative rapid, sensitive, isothermal, and protein-free RNA diagnostic tool, which expected to be of great clinical significance.
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Affiliation(s)
- Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Ken Saito
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan.
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20
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Huang H, Chen S, Zhang X, Hong L, Zeng Y, Wu B. Detection and clinical characteristics analysis of respiratory viruses in hospitalized children with acute respiratory tract infections by a GeXP-based multiplex-PCR assay. J Clin Lab Anal 2019; 34:e23127. [PMID: 31774213 PMCID: PMC7147121 DOI: 10.1002/jcla.23127] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 12/05/2022] Open
Abstract
Background The information regarding viral epidemiology and clinical characteristics in hospitalized children with acute respiratory tract infection (ARTI) in central Fujian is limited. In this study, we aimed at analyzing the viral epidemiology and clinical characteristics of ARTI in hospitalized children admitted to The First Affiliated Hospital of Fujian Medical University. Methods Cohort of 386 hospitalized children (31 days to 15 years) diagnosed with ARTI admitted to the Department of Pediatrics from January 1, 2018, to December 31, 2018, was enrolled in this study. Nasopharyngeal swab or sputum samples on the day of hospitalization were tested for 11 viruses via a GeXP‐based multiplex‐PCR assay. The viral profiles and clinical characteristics were analyzed. Results The overall positive rate of the samples was 43.26% (167/386). Among the 167 positive samples, 134 (80.24%, 134/167) had a single virus and 33 (19.76%, 33/167) had multiple viruses. There was a significant difference in the frequency of single vs mixed infections among positive samples (80.24% vs 19.76%; χ2 = 122.168, P = .000) as well as among the total examined samples (34.72% vs 8.55%; χ2 = 77.945, P = .000). Human rhinovirus was the most prevalent virus (17.36%, 67/386), followed by influenza A (5.96%, 23/386) and human adenovirus (5.70%, 22/386). There was no significant difference in the etiological distribution of viral pathogens between males and females (χ2 = 0.480, P = .489). Viral infections were more likely to occur in the winter‐spring months than in the summer‐autumn months (52.51% vs 33.53%, χ2 = 13.830, P = .000). Conclusions The GeXP‐based multiplex PCR is an accurate and high‐throughput assay allows us to quickly detect multiple respiratory viruses simultaneously in pediatric patients. Our study provides information on the viral profiles and clinical characteristics in hospitalized children with ARTI, which would help better effective prevention strategies.
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Affiliation(s)
- Huanhuan Huang
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Suqing Chen
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiaoyan Zhang
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Linliang Hong
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yongbin Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Bin Wu
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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21
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Sitnikov IG, Fazylov VK, Silina EV. [Treatment of influenza and other acute respiratory viral infections in patients with diabetes mellitus]. TERAPEVT ARKH 2019; 91:39-47. [PMID: 32598630 DOI: 10.26442/00403660.2019.10.000333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Indexed: 11/22/2022]
Abstract
PURPOSE OF THE STUDY The study of the influenza and ARVI clinical performance, the development of patients with diabetes mellitus, evaluation of the effectiveness and safety application of antiviral therapy, carried out in the framework of routine clinical practice. MATERIALS AND METHODS 126 patients aged from 22 to 83 years (27.8% of men) with ARVI or influenza that occurred with medical care during the first 5 days of the disease (60.3% in the first 48 hours) are included. All patients suffer from diabetes, for the treatment of which oral hypoglycemic agents or insulins were constantly taken. The patients were divided into two groups: the first group received standard symptomatic treatment of ARVI; antiviral drug Kagocel. RESULTS AND CONCLUSION Diabetes and other acute respiratory viral infections. There is an increase in the incidence of bacterial complications - 2.2 times, an increase in the frequency of systemic antibiotics - 2.3 times. The purpose of the drug prescription led to a more rapid regression of all the symptoms of influenza and ARVI, but the most striking positive dynamics was observed in the symptoms of general weakness and headache. The prescription of Kagocel was accompanied by a 58% reduction in the number of bacterial complications and a 53% reduction in the use of antibiotics, which led to a reduction in the number of cases of the disease and an improvement in initial diseases, with an frequency increase in 1.8 times. The most significant effect achieved with early treatment and early initiation of antiviral therapy (in the first 48 hours of the disease).
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Affiliation(s)
| | | | - E V Silina
- Sechenov First Moscow State Medical University (Sechenov University)
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22
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Lalle E, Biava M, Nicastri E, Colavita F, Di Caro A, Vairo F, Lanini S, Castilletti C, Langer M, Zumla A, Kobinger G, Capobianchi MR, Ippolito G. Pulmonary Involvement during the Ebola Virus Disease. Viruses 2019; 11:E780. [PMID: 31450596 PMCID: PMC6784166 DOI: 10.3390/v11090780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 12/16/2022] Open
Abstract
Filoviruses have become a worldwide public health concern, especially during the 2013-2016 Western Africa Ebola virus disease (EVD) outbreak-the largest outbreak, both by number of cases and geographical extension, recorded so far in medical history. EVD is associated with pathologies in several organs, including the liver, kidney, and lung. During the 2013-2016 Western Africa outbreak, Ebola virus (EBOV) was detected in the lung of infected patients suggesting a role in lung pathogenesis. However, little is known about lung pathogenesis and the controversial issue of aerosol transmission in EVD. This review highlights the pulmonary involvement in EVD, with a special focus on the new data emerging from the 2013-2016 Ebola outbreak.
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Affiliation(s)
- Eleonora Lalle
- National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, 00149 Rome, Italy
| | - Mirella Biava
- National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, 00149 Rome, Italy
| | - Emanuele Nicastri
- National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, 00149 Rome, Italy
| | - Francesca Colavita
- National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, 00149 Rome, Italy
| | - Antonino Di Caro
- National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, 00149 Rome, Italy
- International Public Health Crisis Group, 00149 Rome, Italy
| | - Francesco Vairo
- National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, 00149 Rome, Italy
- International Public Health Crisis Group, 00149 Rome, Italy
| | - Simone Lanini
- National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, 00149 Rome, Italy
| | - Concetta Castilletti
- National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, 00149 Rome, Italy
| | - Martin Langer
- EMERGENCY Onlus NGO, Via Santa Croce 19, 20122 Milan, Italy
| | - Alimuddin Zumla
- International Public Health Crisis Group, London WC1E 6BT, UK
- Division of Infection and Immunity, National Institute for Health Research Biomedical Research Centre at University College London Hospitals NHS Foundation Trust, London WC1E 6BT, UK
| | - Gary Kobinger
- International Public Health Crisis Group, Quebec City, PQ G1V 0A6, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, PQ G1V 0A6, Canada
| | - Maria R Capobianchi
- National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, 00149 Rome, Italy
| | - Giuseppe Ippolito
- National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, 00149 Rome, Italy.
- International Public Health Crisis Group, 00149 Rome, Italy.
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Liapikou A, Cillóniz C, Torres A. Emerging strategies for the noninvasive diagnosis of nosocomial pneumonia. Expert Rev Anti Infect Ther 2019; 17:523-533. [PMID: 31237462 PMCID: PMC7103721 DOI: 10.1080/14787210.2019.1635010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Introduction: Hospital-acquired pneumonia is a common and therapeutically challenging diagnosis that can lead to severe sepsis, critical illness, and respiratory failure. In this review, we focus on efforts to enhance microbiological diagnosis of hospital-acquired pneumonia, including ventilator-associated pneumonia. Areas covered: A systematic literature review was conducted by searching Medline from inception to December 2018, including hand-searching of the reference lists for additional studies. The search strategy comprised the following common search terms: hospital pneumonia OR nosocomial pneumonia OR noninvasive OR molecular diagnostic tests (OR point-of-care systems OR VOC [i.e. volatile organic compounds]) OR rapid (or simple or quick test), including brand names for the most common commercial tests. Expert opinion: In recent years, the microbiological diagnosis of respiratory pathogens has improved significantly by the development and implementation of molecular diagnostic tests for pneumonia. Real-time polymerase chain reaction, hybridization, and mass spectrometry-based platforms dominate the scene, with microarray-based assays, multiplex polymerase chain reaction, and MALDI-TOF mass spectrometry capable of detecting the determinants of antimicrobial resistance (mainly β-lactamase genes). Introducing these assays into routine clinical practice for rapid identification of the causative microbes and their resistance patterns could transform the care of pneumonia, improving antimicrobial selection, de-escalation, and stewardship.
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Affiliation(s)
- Adamantia Liapikou
- a 6th Respiratory Department , Sotiria Chest Diseases Hospital , Athens , Greece
| | - Catia Cillóniz
- b Servei de Pneumologia , Institut Clinic del Tòrax, Hospital Clinic, Barcelona, IDIBAPS, CIBER Enfermedades Respiratorias, University of Barcelona , Barcelona , Spain
| | - Antoni Torres
- b Servei de Pneumologia , Institut Clinic del Tòrax, Hospital Clinic, Barcelona, IDIBAPS, CIBER Enfermedades Respiratorias, University of Barcelona , Barcelona , Spain
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Impact of Rapid On-demand Molecular Diagnosis of Pediatric Seasonal Influenza on Laboratory Workflow and Testing Costs: A Retrospective Study. Pediatr Infect Dis J 2019; 38:559-563. [PMID: 31117115 DOI: 10.1097/inf.0000000000002224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Seasonal influenza imposes a considerable burden worldwide. We aimed to evaluate impact of rapid pediatric seasonal influenza diagnosis on laboratory workflow and cost using a rapid antigen detection-based test combined with either a reverse transcriptase polymerase chain reaction (RT-PCR) or the Alere i Influenza A and B (Alere i) assay for confirmation of negative results as well as single Alere i testing on nasopharyngeal aspirates. A secondary objective was assessing performance of Alere i against RT-PCR. METHODS Effects of implementing the 3 diagnostic algorithms were assessed in the Emergency Department of Hospital Sant Joan de Déu (Barcelona, Spain) across the 2014-2015, 2015-2016 and 2016-2017 influenza seasons. Alere i performance against RT-PCR was determined during the 2015-2016 epidemic period. RESULTS Median time to result decreased when using Alere i as a confirmatory test of previous antigen detection and RT-PCR results or alone (9.7vs. 3.5/2.0 and 0.7 hours, P < 0.001) along with mean testing costs (&OV0556;87.3 vs. &OV0556;38.2 and &OV0556;25.0, P < 0.001). Results available before patient discharge from the emergency department increased from 42.7% for sequential testing by antigen detection and RT-PCR to 80.0% when Alere i was utilized as a stand-alone test. Alere i sensitivity and specificity values were 96.6% (95% confidence interval: 82.8%-99.4%) and 94.4% (95% confidence interval: 86.6%-97.8%), respectively. CONCLUSIONS Rapid Alere i testing facilitated efficient laboratory workflow near the patient during influenza epidemics while contributing cost savings when compared with serial testing by antigen and RT-PCR assays.
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Hindiyeh M, Mor O, Pando R, Mannasse B, Kabat A, Assraf-Zarfati H, Mendelson E, Sofer D, Mandelboim M. Comparison of the new fully automated extraction platform eMAG to the MagNA PURE 96 and the well-established easyMAG for detection of common human respiratory viruses. PLoS One 2019; 14:e0211079. [PMID: 30779757 PMCID: PMC6380621 DOI: 10.1371/journal.pone.0211079] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/07/2019] [Indexed: 11/19/2022] Open
Abstract
Respiratory viral infections constitute the majority of samples tested in the clinical virology laboratory during the winter season, and are mainly diagnosed using molecular assays, namely real-time PCR (qPCR). Therefore, a high-quality extraction process is critical for successful, reliable and sensitive qPCR results. Here we aimed to evaluate the performance of the newly launched eMAG compared to the fully automated MagNA PURE 96 (Roche, Germany) and to the semi-automated easyMAG (bioMerieux, France) extraction platforms. For this analysis, we assessed and compared the analytic and clinical performance of the three platforms, using 262 archived respiratory samples positive or negative to common viruses regularly examined in our laboratory (influenza A, B, H1N1pdm, Respiratory Syncytial Virus (RSV), human Metapneumovirus (hMPV), parainfluenza-3, adenovirus and negative samples). In addition, quantitated virus controls were used to determine the limit of detection of each extraction method. In all categories tested, eMAG results were comparable to those of the easyMAG and MagNa PURE 96, highly sensitive for all viruses and over 98% clinical specificity and sensitivity for all viruses tested. Together with its high level of automation, the bioMerieux eMAG is a high-quality extraction platform enabling effective molecular analysis and is mostly suitable for medium-sized laboratories.
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Affiliation(s)
- Musa Hindiyeh
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Rakefet Pando
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
- The Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Israel
| | - Batya Mannasse
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Areej Kabat
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Hadar Assraf-Zarfati
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Danit Sofer
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail:
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Affiliation(s)
- Marilynn Ransom Fairfax
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Clinical Microbiology Laboratories, DMC University Laboratories, 4201 St. Antoine Street, Detroit, MI 48201, USA.
| | - Martin H Bluth
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Pathology Laboratories, Michigan Surgical Hospital, 21230 Dequindre Road, Warren, MI 48091, USA
| | - Hossein Salimnia
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Clinical Microbiology Laboratories, DMC University Laboratories, 4201 St. Antoine Street, Detroit, MI 48201, USA
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Wen X, Huang Q, Tao H, Zou W, Gao M, Guo H, Yao X, Cui D, Wang X. Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study. BMC Infect Dis 2019; 19:32. [PMID: 30621623 PMCID: PMC6325799 DOI: 10.1186/s12879-018-3668-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 12/28/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Viruses are commonly found in patients with acute respiratory infections (ARIs). However, the viral etiologies and clinical characteristics of outpatients with ARIs are poorly understood in China. Here, we identified the viral etiologies in outpatients with ARIs in Huzhou, China. RESULTS Our results indicated that of 426 outpatients, 246 were positive for viruses. Of them, 221 were positive for a single virus, including influenza A, which comprised H3N2 (28.5%) and pandemic H1N1 (2009) (19.0%), enterovirus (10.4%), and influenza B (8.6%). Other single viruses were detected at less than 8.0%. Twenty-five patients were positively coinfected with two viruses. The prevalent viruses in coinfections were rhinovirus and H3N2 virus (28.0%). Viruses were major pathogens in young children (< 5 years) (75.0%). Coinfections were prevalent in older adults (11.9%) and young children (9.5%). Virus-positive outpatients presented higher temperatures and more sore throat, fatigue and shortness of breath than virus-negative outpatients. ARIs and most virus detections peaked during the winter, but enteroviruses emerged between April and September. CONCLUSION Viruses are major agents of ARIs among outpatients in Huzhou, China. There was a variation in the distribution of viruses across different age groups and seasons. These findings are beneficial for planning prevention and treatment services for outpatients with ARIs.
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Affiliation(s)
- Xiaohong Wen
- The First People's Hospital Affiliated to Huzhou University, Huzhou, 313000, China
| | - Qiuling Huang
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Hong Tao
- Department of Laboratory & Pharmacy, Suzhou Vocational Health College, Suzhou, 215009, China
| | - Weihua Zou
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Min Gao
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Huihui Guo
- The First People's Hospital Affiliated to Huzhou University, Huzhou, 313000, China
| | - Xing Yao
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Dawei Cui
- Department of Blood Transfusion, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China.
| | - Xiang Wang
- The First People's Hospital Affiliated to Huzhou University, Huzhou, 313000, China.
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Abstract
A wide variety of microorganisms are potential respiratory pathogens, and the spectrum of known pathogens for each respiratory infection syndrome has not changed markers over recent years. Detection of likely etiologic agents of respiratory infections can help direct management and can also play an important role in disease surveillance. For this purpose, we are still reliant on many traditional diagnostic tools that have been used for decades in order to determine the microbial etiology of respiratory infections. However, these tools have been increasingly supplemented by newer methods, particular molecular diagnostic techniques, which have enabled the more rapid detection of many pathogens that were previously difficult to detect. These advances have particularly lead to improvements in the ability to detect respiratory viruses and also other microorganisms that do not normally colonize the respiratory tract. Recognition of the existence of the lung microbiome has challenged the traditional views of pneumonia pathogenesis and may provide the opportunity for new diagnostic tools that are focused on more than just detection of specific known pathogens. Continued liaison between clinicians and laboratory staff is vital in order to facilitate the most cost-effective use of laboratory diagnostics.
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Rastogi M, Singh SK. Advances in Molecular Diagnostic Approaches for Biothreat Agents. DEFENSE AGAINST BIOLOGICAL ATTACKS 2019. [PMCID: PMC7123646 DOI: 10.1007/978-3-030-03071-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The advancement in Molecular techniques has been implicated in the development of sophisticated, high-end diagnostic platform and point-of-care (POC) devices for the detection of biothreat agents. Different molecular and immunological approaches such as Immunochromatographic and lateral flow assays, Enzyme-linked Immunosorbent assays (ELISA), Biosensors, Isothermal amplification assays, Nucleic acid amplification tests (NAATs), Next Generation Sequencers (NGS), Microarrays and Microfluidics have been used for a long time as detection strategies of the biothreat agents. In addition, several point of care (POC) devices have been approved by FDA and commercialized in markets. The high-end molecular platforms like NGS and Microarray are time-consuming, costly, and produce huge amount of data. Therefore, the future prospects of molecular based technique should focus on developing quick, user-friendly, cost-effective and portable devices against biological attacks and surveillance programs.
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Pedersen CJ, Rogan DT, Yang S, Quinn JV. Using a novel rapid viral test to improve triage of emergency department patients with acute respiratory illness during flu season. J Clin Virol 2018; 108:72-76. [PMID: 30261422 PMCID: PMC7106347 DOI: 10.1016/j.jcv.2018.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/01/2018] [Accepted: 09/08/2018] [Indexed: 01/13/2023]
Abstract
Seasonal viral respiratory illnesses overburden emergency department resources. Current viral testing practices are ineffective for patient management in the ED. Triage viral testing can reduce transmission risk & optimize antimicrobial therapy.
Background Acute respiratory illnesses (ARI) are mostly viral in etiology and cause significant morbidity and mortality. Point of care PCR (POC-PCR) is a promising new technology for rapid virus identification but utility in the Emergency Department (ED) is not yet defined. Objectives Primarily, to investigate the value of POC-PCR in rapidly identifying RSV and influenza in the setting of ED triage. Additionally, to assess whether rapid knowledge of accurate test results would improve patient management by preventing nosocomial transmission and optimizing the prescription of antimicrobials for ARIs. Study Design A prospective cohort study of consecutive ED patients with ARI symptoms during peak flu season was conducted. Patient nasopharyngeal swabs were collected and tested using a POC-PCR device; physicians and patients were blinded to results. Virus positive and negative groups were compared by ED patient room placement and antimicrobial therapy ordered. Specificity and sensitivity were calculated using laboratory-PCR as the gold standard. Results Of 119 participants, 52.9% were POC-PCR positive - Influenza A (42.9%), RSV (41.3%), influenza B (15.9%). Nearly 70% of virus positive patients were placed rooms shared with non-ARI patients. Antibiotics were prescribed for 27.3% of virus positive patients, and 77.8% of oseltamivir-eligible patients did not receive therapy. POC-PCR was 100% sensitive (95% CI, 80.5–100.0%) and 95.2% specific (95% CI, 76.2–99.9%). Conclusions Rapid POC-PCR for influenza and RSV in ED triage has excellent sensitivity and specificity and the potential to improve social distancing practices through better triage and increase appropriate prescription of antimicrobials.
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Affiliation(s)
- Courtney J Pedersen
- Stanford School of Medicine, Stanford University, 291 Campus Dr, Stanford, CA, 94305, USA.
| | - Daniel T Rogan
- Department of Emergency Medicine, Stanford University, Alway Building, M023, 300 Pasteur Drive - MC: 5768, Stanford, CA, 94305, USA.
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Alway Building, M023, 300 Pasteur Drive - MC: 5768, Stanford, CA, 94305, USA.
| | - James V Quinn
- Department of Emergency Medicine, Stanford University, Alway Building, M023, 300 Pasteur Drive - MC: 5768, Stanford, CA, 94305, USA.
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Walter JM, Wunderink RG. Testing for Respiratory Viruses in Adults With Severe Lower Respiratory Infection. Chest 2018; 154:1213-1222. [PMID: 29908153 PMCID: PMC6224704 DOI: 10.1016/j.chest.2018.06.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/29/2018] [Accepted: 06/04/2018] [Indexed: 12/31/2022] Open
Abstract
Viral pathogens are a common cause of severe lower respiratory tract infection in adults. Our ability to rapidly and accurately identify viral infections has dramatically improved as slow culture-based techniques have been largely replaced by multiplex high-throughput systems. Given these advances, reevaluation of the role of respiratory viral testing in adults presenting with lower respiratory tract infection is important. This article reviews the potential benefits of testing, provides an overview of the most commonly used diagnostic techniques, and considers whether current evidence supports routine testing.
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Affiliation(s)
- James M Walter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
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Meşe S, Uyanik A, Özakay A, Öztürk S, Badur S. Influenza surveillance in Western Turkey in the era of quadrivalent vaccines: A 2003-2016 retrospective analysis. Hum Vaccin Immunother 2018; 14:1899-1908. [PMID: 29543569 PMCID: PMC6149844 DOI: 10.1080/21645515.2018.1452577] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human influenza is predominantly caused by influenza A virus (IAV) - A/H1N1 and/or A/H3N2 - and influenza B virus (IBV) - B/Victoria and/or B/Yamagata, which co-circulate each season. Influenza surveillance provides important information on seasonal disease burden and circulation, and vaccine content for the following season. To study the circulating influenza subtypes/lineages in western Turkey. Community-based sentinel surveillance results during 2003-2016 (weeks 40-20 each season; but week 21, 2009 through week 20, 2010 during the pandemic) were analyzed. Nasal/nasopharyngeal swabs from patients with influenza-like illness were tested for influenza virus and characterized as A/H1N1, A/H3N2, or IBV. A subset of IBV samples was further characterized as B/Victoria or B/Yamagata. Among 14,429 specimens (9,766 collected during interpandemic influenza seasons; 4,663 during the 2009-2010 pandemic), 3,927 (27.2%) were positive. Excluding the pandemic year (2009-2010), 645 (27.4%) samples were characterized as A/H1N1 or A/H1N1/pdm09, 958 (40.7%) as A/H3N2, and 752 (31.9%) as IBV, but the dominant subtype/lineage varied widely each season. During the pandemic year (2009-2010), 98.3% of cases were A/H1N1/pdm09. IBV accounted for 0-60.2% of positive samples each season. The IBV lineages in circulation matched the vaccine IBV lineage >50% in six seasons and <50% in four seasons; with an overall mismatch of 49.7%. IBV cases tended to peak later than IAV cases within seasons. These results have important implications for vaccine composition and optimal vaccination timing. Quadrivalent vaccines containing both IBV lineages can reduce B-lineage mismatch, thus reducing the burden of IBV disease.
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Affiliation(s)
- Sevim Meşe
- National Influenza Reference Laboratory, Istanbul University, Istanbul, Turkey
| | - Aysun Uyanik
- National Influenza Reference Laboratory, Istanbul University, Istanbul, Turkey
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Respiratory Viruses and Other Relevant Viral Infections in the Lung Transplant Recipient. LUNG TRANSPLANTATION 2018. [PMCID: PMC7123387 DOI: 10.1007/978-3-319-91184-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
As advances occur in surgical technique, postoperative care, and immunosuppressive therapy, the rate of mortality in the early postoperative period following lung transplantation continues to decline. With the improvements in immediate and early posttransplant mortality, infections and their sequel as well as rejection and chronic allograft dysfunction are increasingly a major cause of posttransplant mortality. This chapter will focus on infections by respiratory viruses and other viral infections relevant to lung transplantation, including data regarding the link between viral infections and allograft dysfunction.
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Prevalence of Human Herpes Viruses in Bronchoalveolar Lavage of Critically Ill Children Undergoing Mechanical Ventilation at a Pediatric Intensive Care Unit. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2018. [DOI: 10.5812/pedinfect.12685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Hardick J, Metzgar D, Risen L, Myers C, Balansay M, Malcom T, Rothman R, Gaydos C. Initial performance evaluation of a spotted array Mobile Analysis Platform (MAP) for the detection of influenza A/B, RSV, and MERS coronavirus. Diagn Microbiol Infect Dis 2018; 91:245-247. [PMID: 29550057 PMCID: PMC6013072 DOI: 10.1016/j.diagmicrobio.2018.02.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/26/2018] [Accepted: 02/15/2018] [Indexed: 11/30/2022]
Abstract
Clinical samples were evaluated with the Mobile Analysis Platform (MAP) to determine platform performance for detecting respiratory viruses in samples previously characterized using clinical reverse transcriptase polymerase chain reaction assays. The percent agreement between MAP and clinical results was 97% for influenza A (73/75), 100% (21/21) for influenza B, 100% (6/6) for respiratory syncytial virus (RSV), and 80% (4/5) for negative specimens. The approximate limit of detection of the MAP was 30 copies/assay for RSV and 1500 copies/assay for Middle East respiratory syndrome coronavirus.
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Affiliation(s)
- Justin Hardick
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, Baltimore, MD, USA.
| | | | | | | | | | - Trent Malcom
- Johns Hopkins University Department of Emergency Medicine, Baltimore, MD, USA
| | - Richard Rothman
- Johns Hopkins University Department of Emergency Medicine, Baltimore, MD, USA
| | - Charlotte Gaydos
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, Baltimore, MD, USA
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Lavi N, Avivi I, Kra-Oz Z, Oren I, Hardak E. Community-acquired respiratory infections are common in patients with non-Hodgkin lymphoma and multiple myeloma. Support Care Cancer 2018; 26:2425-2431. [PMID: 29427192 DOI: 10.1007/s00520-018-4079-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/29/2018] [Indexed: 12/27/2022]
Abstract
PURPOSE Available data suggest that respiratory infections are associated with increased morbidity and mortality in patients hospitalized due to acute leukemia and allogeneic stem cell transplantation (allo-SCT). However, the precise incidence, risk factors, and severity of respiratory infection, mainly community-acquired, in patients with lymphoma and multiple myeloma (MM) are not fully determined. The current study aimed to investigate risk factors for respiratory infections and their clinical significance in patients with B cell non-Hodgkin lymphoma (NHL) and multiple myeloma (MM) in the first year of diagnosis. METHODS Data of consecutive patients diagnosed with NHL or MM and treated at the Rambam Hematology Inpatient and Outpatient Units between 01/2011 and 03/2012 were evaluated. Information regarding anticancer treatment, incidence and course of respiratory infections, and infection-related outcomes was analyzed. RESULTS One hundred and sixty episodes of respiratory infections were recorded in 103 (49%) of 211 (73-MM, 138-NHL) patients; 126 (79%) episodes were community-acquired, 47 (29%) of them required hospitalization. In univariate analysis, age < 60 years, MM diagnosis, and autologous SCT increased the respiratory infection risk (P = 0.058, 0.038, and 0.001, respectively). Ninety episodes (56% of all respiratory episodes) were examined for viral pathogens. Viral infections were documented in 25/90 (28%) episodes, 21 (84%) of them were community-acquired, requiring hospitalization in 5 (24%) cases. Anti-flu vaccination was performed in 119 (56%) patients. Two of the six patients diagnosed with influenza were vaccinated. CONCLUSIONS Respiratory infections, including viral ones, are common in NHL and MM. Most infections are community-acquired and have a favorable outcome. Rapid identification of viral pathogens allows avoiding antibiotic overuse in this patient population.
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Affiliation(s)
- Noa Lavi
- Department of Hematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa, Israel
| | - Irit Avivi
- Department of Hematology and Bone Marrow Transplantation, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zipora Kra-Oz
- Virology Laboratory, Rambam Health Care Campus, Haifa, Israel.,Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel
| | - Ilana Oren
- Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel.,Infectious Diseases Unit, Rambam Health Care Campus, Haifa, Israel
| | - Emilia Hardak
- Bruce Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa, Israel. .,Division of Pulmonary Medicine, Rambam Health Care Campus, 8, Ha'Aliya St., 31096, Haifa, Israel.
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Huang HS, Tsai CL, Chang J, Hsu TC, Lin S, Lee CC. Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis. Clin Microbiol Infect 2017; 24:1055-1063. [PMID: 29208560 PMCID: PMC7128951 DOI: 10.1016/j.cmi.2017.11.018] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/16/2017] [Accepted: 11/22/2017] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)-BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test (Verigene RV+) and Hologic Gen-Probe Prodesse assays-on the detection of viral respiratory infections. METHODS A comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RV+ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay. RESULTS Twenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RV+ and ProFlu+ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848-0.949), 0.949 (95% confidence interval, 0.882-0.979) and 0.954 (95% confidence interval, 0.871-0.985), respectively. The three mPCRs were comparable in terms of detection of FluA. CONCLUSIONS Point estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RV+ and ProFlu+) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments.
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Affiliation(s)
- H-S Huang
- Department of Medicine, College of Medicine, National Taiwan University Hospital, Taipei, Taiwan; Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan
| | - C-L Tsai
- Department of Medicine, College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - J Chang
- Department of Gastroenterology, Nutrition, and Hepatology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - T-C Hsu
- Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan; Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - S Lin
- Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan; Industrial Engineering and Operations Research Department at the University of California, Berkeley, California, USA
| | - C-C Lee
- Health Economics and Outcome Research Group, National Taiwan University Hospital, Taipei, Taiwan; Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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Brotons P, Henares D, Latorre I, Cepillo A, Launes C, Muñoz-Almagro C. Comparison of NxTAG Respiratory Pathogen Panel and Anyplex II RV16 Tests for Multiplex Detection of Respiratory Pathogens in Hospitalized Children. J Clin Microbiol 2016; 54:2900-2904. [PMID: 27629904 PMCID: PMC5121377 DOI: 10.1128/jcm.01243-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/22/2016] [Indexed: 12/21/2022] Open
Abstract
Multiplex molecular techniques can detect a diversity of respiratory viruses and bacteria that cause childhood acute respiratory infection rapidly and conveniently. However, currently available techniques show high variation in performance. We sought to compare the diagnostic accuracy of the novel multiplex NxTAG respiratory pathogen panel (RPP) RUO test versus a routine multiplex Anyplex II RV16 assay in respiratory specimens collected from children <18 years of age hospitalized with nonspecific symptoms of acute lower respiratory infection. Parallel testing was performed on nasopharyngeal aspirates prospectively collected at referral Children's Hospital Sant Joan de Déu (Barcelona, Spain) between June and November 2015. Agreement values between the two tests and kappa coefficients were assessed. Bidirectional sequencing was performed for the resolution of discordant results. A total of 319 samples were analyzed by both techniques. A total of 268 (84.0%) of them yielded concordant results. Positive percent agreement values ranged from 83.3 to 100%, while the negative percent agreement was more than 99% for all targets except for enterovirus/rhinovirus (EV/RV; 94.4%). Kappa coefficients ranged from 0.83 to 1.00. Discrepancy analysis confirmed 66.0% of NxTAG RPP RUO results. A total of 260 viruses were detected, with EV/RV (n = 105, 40.4%) being the most prevalent target. Viral coinfections were found in 44 (14.2%) samples. In addition, NxTAG RPP RUO detected single bacterial and mixed viral-bacterial infections in seven samples. NxTAG RPP RUO showed high positive and negative agreement with Anyplex II RV16 for main viruses that cause acute respiratory infections in children, coupled with an additional capability to detect some respiratory bacteria.
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Affiliation(s)
- Pedro Brotons
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain
- CIBERESP Epidemiologia y Salud Pública, Madrid, Spain
| | - Desiree Henares
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain
| | - Irene Latorre
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain
- Institut d'Investigació Germans Trias i Pujol, CIBERES Enfermedades Respiratorias, Badalona, Spain
| | - Antonio Cepillo
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain
| | - Cristian Launes
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain
- CIBERESP Epidemiologia y Salud Pública, Madrid, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain
- CIBERESP Epidemiologia y Salud Pública, Madrid, Spain
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Wen AM, Steinmetz NF. Design of virus-based nanomaterials for medicine, biotechnology, and energy. Chem Soc Rev 2016; 45:4074-126. [PMID: 27152673 PMCID: PMC5068136 DOI: 10.1039/c5cs00287g] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review provides an overview of recent developments in "chemical virology." Viruses, as materials, provide unique nanoscale scaffolds that have relevance in chemical biology and nanotechnology, with diverse areas of applications. Some fundamental advantages of viruses, compared to synthetically programmed materials, include the highly precise spatial arrangement of their subunits into a diverse array of shapes and sizes and many available avenues for easy and reproducible modification. Here, we will first survey the broad distribution of viruses and various methods for producing virus-based nanoparticles, as well as engineering principles used to impart new functionalities. We will then examine the broad range of applications and implications of virus-based materials, focusing on the medical, biotechnology, and energy sectors. We anticipate that this field will continue to evolve and grow, with exciting new possibilities stemming from advancements in the rational design of virus-based nanomaterials.
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Affiliation(s)
- Amy M Wen
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Nicole F Steinmetz
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA. and Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
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40
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Zhang Y, Yuan L, Zhang Y, Zhang X, Zheng M, Kyaw MH. Burden of respiratory syncytial virus infections in China: Systematic review and meta-analysis. J Glob Health 2016; 5:020417. [PMID: 26682049 PMCID: PMC4676581 DOI: 10.7189/jogh.05.020417] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is the most important cause of acute respiratory tract infection (ARTI) related morbidity and mortality worldwide. However, the disease burden due to RSV has not been systematically summarized in China. METHOD A systematic search was performed in the Chinese BioMedical Database (CBM), China National Knowledge Infrastructure (CNKI), Wanfang database and PubMed to identify available published RSV studies in China. RESULTS A total of 489 641 patients with ARTIs from 135 studies were included in the analysis. Among patients with ARTIs, RSV accounted for 18.7% (95% confidence interval CI 17.1-20.5%). The prevalence of RSV was highest in infants (26.5%, 95% CI 23.7-29.5%) and lowest in those aged ≥16 years (2.8%, 95% CI 1.3-6.1). A higher prevalence of RSV was seen in inpatients (22%, 95% CI 19.9-24.2%) than in outpatients (14%, 95% CI 9.6-19.9%). RSV type A accounted for 63.1% (95% CI 52.3-72.8%) of all RSV infections. RSV infections occurred mainly in winter and spring. The most common clinical manifestations were cough, production of sputum, wheezing and fever. CONCLUSION RSV is the leading cause of viral ARTIs in China, particularly in infants and young children. Our findings are valuable for guiding the selection of appropriate therapies for ARTIs and implementation of preventive measures against RSV infections. Our data further supports the development of a successful RSV vaccine as a high priority.
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Affiliation(s)
- Yaowen Zhang
- Infection Management and Disease Prevention Department, China-Japan Friendship Hospital, Beijing, China
| | - Lichao Yuan
- Department of Infectious Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Yongming Zhang
- Department of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiuping Zhang
- China-Japan Friendship Clinical College, Beijing University of Chinese Medicine, Beijing, China
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Millman AJ, Reed C, Kirley PD, Aragon D, Meek J, Farley MM, Ryan P, Collins J, Lynfield R, Baumbach J, Zansky S, Bennett NM, Fowler B, Thomas A, Lindegren ML, Atkinson A, Finelli L, Chaves SS. Improving Accuracy of Influenza-Associated Hospitalization Rate Estimates. Emerg Infect Dis 2016; 21:1595-601. [PMID: 26292017 PMCID: PMC4550134 DOI: 10.3201/eid2109.141665] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Adjusting for diagnostic test sensitivity enables more accurate and timely comparisons over time. Diagnostic test sensitivity affects rate estimates for laboratory-confirmed influenza–associated hospitalizations. We used data from FluSurv-NET, a national population-based surveillance system for laboratory-confirmed influenza hospitalizations, to capture diagnostic test type by patient age and influenza season. We calculated observed rates by age group and adjusted rates by test sensitivity. Test sensitivity was lowest in adults >65 years of age. For all ages, reverse transcription PCR was the most sensitive test, and use increased from <10% during 2003–2008 to ≈70% during 2009–2013. Observed hospitalization rates per 100,000 persons varied by season: 7.3–50.5 for children <18 years of age, 3.0–30.3 for adults 18–64 years, and 13.6–181.8 for adults >65 years. After 2009, hospitalization rates adjusted by test sensitivity were ≈15% higher for children <18 years, ≈20% higher for adults 18–64 years, and ≈55% for adults >65 years of age. Test sensitivity adjustments improve the accuracy of hospitalization rate estimates.
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Murdoch DR. How recent advances in molecular tests could impact the diagnosis of pneumonia. Expert Rev Mol Diagn 2016; 16:533-40. [PMID: 26891612 PMCID: PMC7103682 DOI: 10.1586/14737159.2016.1156536] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/17/2016] [Indexed: 12/21/2022]
Abstract
Molecular diagnostic tests have been the single major development in pneumonia diagnostics over recent years. Nucleic acid detection tests (NATs) have greatly improved the ability to detect respiratory viruses and bacterial pathogens that do not normally colonize the respiratory tract. In contrast, NATs do not yet have an established role for diagnosing pneumonia caused by bacteria that commonly colonize the nasopharynx due to difficulties discriminating between pathogens and coincidental carriage strains. New approaches are needed to distinguish infection from colonization, such as through use of quantitative methods and identification of discriminating cut-off levels. The recent realization that the lung microbiome exists has provided new insights into the pathogenesis of pneumonia involving the interaction between multiple microorganisms. New developments in molecular diagnostics must account for this new paradigm.
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Affiliation(s)
- David R. Murdoch
- Department of Pathology, University of Otago, Christchurch, and Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
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43
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Abstract
The increasing availability of nucleic acid amplification tests since the 1980s has revolutionised our understanding of the pathogenesis, epidemiology, clinical and laboratory aspects of known and novel viral respiratory pathogens. High-throughput, multiplex polymerase chain reaction is the most commonly used qualitative detection method, but utilisation of newer techniques such as next-generation sequencing will become more common following significant cost reductions. Rapid and readily accessible isothermal amplification platforms have also allowed molecular diagnostics to be used in a ‘point-of-care’ format. This review focuses on the current applications and limitations of molecular diagnosis for respiratory viruses.
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Liu T, Li Z, Zhang S, Song S, Julong W, Lin Y, Guo N, Xing C, Xu A, Bi Z, Wang X. Viral Etiology of acute respiratory tract infections in hospitalized children and adults in Shandong Province, China. Virol J 2015; 12:168. [PMID: 26467854 PMCID: PMC4606902 DOI: 10.1186/s12985-015-0388-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/20/2015] [Indexed: 11/17/2022] Open
Abstract
Background The dominant viral etiologies responsible for acute respiratory infections (ARIs) are poorly understood, particularly among hospitalized patients. Improved etiological insight is needed to improve clinical management and prevention of ARIs. Methods Clinical and demographic information and throat swabs were collected from 607 patients from 2011 to 2013 in Shandong Province, China. Multiplex RT-PCR (SeeplexTM RV detection, Seegene) was performed to detected 12 respiratory viral pathogens. Results A total of 607 hospitalized patients were enrolled from 2011 to 2013. Viruses were identified in 35.75 % (217/607) of cases, including 78 influenza virus A and B (IVA and IVB), 47 para-influenza viruses (PIVs), 41 respiratory syncytial virus (RSV) and 38 adenovirus (ADV). For the children under 15 year old, the common detected viruses were influenza viruses, RSV, PIVS and ADV, while the principal respiratory viruses were human coronaviruses (HCoV), PIVs, influenza viruses for the old adults. Co-infections with multiple viruses were detected in 15.67 % of patients. Children under 5 years were more likely to have one or more detectable virus associated with their ARI. The peak of ARI caused by the respiratory viruses occurred in winter. Conclusion This study demonstrated respiratory viruses were the major cause of hospitalized ARI patients in Shandong Province, influenza virus was the most common detected, RSV was the highest incidence among the young children (≤5 years). These findings also gave a better understand of virus distribution among different age and seasons, which help to consider potential therapeutic approaches and develop effective prevention strategies for respiratory virus infection.
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Affiliation(s)
- Ti Liu
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Zhong Li
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Shengyang Zhang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Shaoxia Song
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Wu Julong
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Yi Lin
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Nongjian Guo
- Jinan Central Hospital Affiliated to Shandong University, Jinan, 250014, Shandong, China.
| | - Chunyan Xing
- Jinan Central Hospital Affiliated to Shandong University, Jinan, 250014, Shandong, China.
| | - Aiqiang Xu
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Zhenqiang Bi
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Shandong University Institute for Prevention Medicine, Jinan, 250014, Shandong, China.
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Iravathy Goud K, Matam K, Madasu AML, Vempati R, Daripalli S, Pullamula M, Narreddy S, Nutankalva L. Molecular diagnosis of H1N1 virus. APOLLO MEDICINE 2015. [DOI: 10.1016/j.apme.2015.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Hardick J, Dugas A, Goheen J, Rothman R, Gaydos C. Prospective comparison of RT-PCR/ESI-MS to Prodesse ProFlu Plus and Cepheid GenXpert for the detection of Influenza A and B viruses. J Virol Methods 2015; 214:43-5. [PMID: 25681525 PMCID: PMC4560249 DOI: 10.1016/j.jviromet.2015.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 01/30/2015] [Accepted: 01/31/2015] [Indexed: 11/16/2022]
Abstract
RT-PCR/ESI-MS was compared to two gold standards, Prodesse ProFlu Plus and Cepheid ExpertFlu.
RT-PCR/ESI-MS has previously demonstrated the capability to detect and identify respiratory viral pathogens in nasopharyngeal swabs. This study expands on previous research by performing a prospective evaluation of RT-PCR/ESI-MS to detect and identify Influenza A and B viruses compared to Prodesse ProFlu Plus and combined ProFlu Plus and Cepheid Xpert Flu. ProFlu Plus was also used as a gold standard for comparison for respiratory syncytial virus detection. Using ProFlu Plus as a gold standard, RT-PCR/ESI-MS had sensitivity and specificity of 82.1% (23/28) and 100% (258/258), respectively, for Influenza A, 100% (16/16) and 99.6% (269/270), respectively for Influenza B, and 88.6% (39/44) and 99.6% (241/242) for any Influenza virus. Using matching results from ProFlu Plus and Xpert Flu as a gold standard, RT-PCR/ESI-MS had 85.2% (23/27) and 100% (259/259) sensitivity and specificity respectively for Influenza A, 100% (14/14) and 99.6% (270/272), respectively for Influenza B virus. Overall, RT-PCR/ESI-MS was not as sensitive as the combined gold standard of ProFlu Plus and Xpert Flu, although it has the capability of detecting other respiratory viruses.
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Affiliation(s)
- Justin Hardick
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, United States.
| | - Andrea Dugas
- Johns Hopkins University School of Medicine, Department of Emergency Medicine, United States
| | - Joshua Goheen
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, United States
| | - Richard Rothman
- Johns Hopkins University School of Medicine, Department of Emergency Medicine, United States
| | - Charlotte Gaydos
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, United States
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Ho A. Viral pneumonia in adults and older children in sub-Saharan Africa - epidemiology, aetiology, diagnosis and management. Pneumonia (Nathan) 2014; 5:18-29. [PMID: 31641571 PMCID: PMC5922328 DOI: 10.15172/pneu.2014.5/446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 06/27/2014] [Indexed: 01/14/2023] Open
Abstract
Community-acquired pneumonia causes substantial morbidity and mortality in sub-Saharan Africa with an estimated 131 million new cases each year. Viruses - such as influenza virus, respiratory syncytial virus and parainfluenza virus - are now recognised as important causes of respiratory disease in older children and adults in the developed world following the emergence of sensitive molecular diagnostic tests, recent severe viral epidemics, and the discovery of novel viruses. Few studies have comprehensively evaluated the viral aetiology of adult pneumonia in Africa, but it is likely to differ from Western settings due to varying seasonality and the high proportion of patients with immunosuppression and co-morbidities. Emerging data suggest a high prevalence of viral pathogens, as well as multiple viral and viral/bacterial infections in African adults with pneumonia. However, the interpretation of positive results from highly sensitive polymerase chain reaction tests can be challenging. Therapeutic and preventative options against viral respiratory infections are currently limited in the African setting. This review summarises the current state of the epidemiology, aetiology, diagnosis and management of viral pneumonia in sub-Saharan Africa.
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Affiliation(s)
- Antonia Ho
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Chichiri, Blantyre 3, Malawi
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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Zumla A, Al-Tawfiq JA, Enne VI, Kidd M, Drosten C, Breuer J, Muller MA, Hui D, Maeurer M, Bates M, Mwaba P, Al-Hakeem R, Gray G, Gautret P, Al-Rabeeah AA, Memish ZA, Gant V. Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections--needs, advances, and future prospects. THE LANCET. INFECTIOUS DISEASES 2014; 14:1123-1135. [PMID: 25189349 PMCID: PMC7106435 DOI: 10.1016/s1473-3099(14)70827-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Respiratory tract infections rank second as causes of adult and paediatric morbidity and mortality worldwide. Respiratory tract infections are caused by many different bacteria (including mycobacteria) and viruses, and rapid detection of pathogens in individual cases is crucial in achieving the best clinical management, public health surveillance, and control outcomes. Further challenges in improving management outcomes for respiratory tract infections exist: rapid identification of drug resistant pathogens; more widespread surveillance of infections, locally and internationally; and global responses to infections with pandemic potential. Developments in genome amplification have led to the discovery of several new respiratory pathogens, and sensitive PCR methods for the diagnostic work-up of these are available. Advances in technology have allowed for development of single and multiplexed PCR techniques that provide rapid detection of respiratory viruses in clinical specimens. Microarray-based multiplexing and nucleic-acid-based deep-sequencing methods allow simultaneous detection of pathogen nucleic acid and multiple antibiotic resistance, providing further hope in revolutionising rapid point of care respiratory tract infection diagnostics.
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Affiliation(s)
- Alimuddin Zumla
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK; Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia.
| | | | - Virve I Enne
- Division of Infection and Immunity, University College London, London, UK
| | - Mike Kidd
- Division of Infection and Immunity, University College London, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Judy Breuer
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Marcel A Muller
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - David Hui
- Division of Respiratory Medicine and Stanley Ho Center for emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong
| | - Markus Maeurer
- Therapeutic Immunology, Departments of Laboratory Medicine and Microbiology, Tumour and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Matthew Bates
- Division of Infection and Immunity, University College London, London, UK; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Peter Mwaba
- UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Rafaat Al-Hakeem
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Gregory Gray
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Philippe Gautret
- Assistance Publique Hôpitaux de Marseille, CHU Nord, Pôle Infectieux, Institut Hospitalo-Universitaire Méditerranée Infection & Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), Marseille, France
| | - Abdullah A Al-Rabeeah
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Ziad A Memish
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; Al-Faisal University, Riyadh, Saudi Arabia
| | - Vanya Gant
- Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
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Affiliation(s)
- Marilynn Ransom Fairfax
- Department of Pathology, Wayne State University School of Medicine, and Microbiology Division, Detroit Medical Center University Laboratories, 4201 Saint Antoine, Detroit, MI 48201, USA.
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Hardick J, Sadiq S, Perelstein E, Peterson S, Rothman R, Gaydos CA. A case-control study evaluating RT-PCR/ESI-MS technology compared to direct fluorescent antibody and xTAG RVP PCR. Diagn Microbiol Infect Dis 2014; 79:187-9. [PMID: 24657170 PMCID: PMC4557781 DOI: 10.1016/j.diagmicrobio.2014.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 02/03/2014] [Accepted: 02/11/2014] [Indexed: 11/02/2022]
Abstract
Waste nasopharyngeal swabs (N = 244) were evaluated by the reverse-transcriptase polymerase chain reaction/electrospray ionization mass spectrometry PLEX-ID Broad Respiratory Virus Surveillance Kit version 2.5 compared to direct fluorescent antibody and xTAG Respiratory Virus Panel for percent agreement, sensitivity, and specificity. Sensitivity and specificity were 91% (111/122) and 95.1% (116/122), respectively. Sensitivity by virus, except parainfluenza, was 92.9-100%, and specificity was 99-100%.
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Affiliation(s)
- Justin Hardick
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, Baltimore, MD, USA.
| | - Sufyan Sadiq
- Johns Hopkins University, Department of Emergency Medicine, Baltimore, MD, USA
| | | | - Stephen Peterson
- Johns Hopkins University, Department of Emergency Medicine, Baltimore, MD, USA
| | - Richard Rothman
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, Baltimore, MD, USA; Johns Hopkins University, Department of Emergency Medicine, Baltimore, MD, USA
| | - Charlotte A Gaydos
- Johns Hopkins University School of Medicine, Division of Infectious Diseases, Baltimore, MD, USA; Johns Hopkins University, Department of Emergency Medicine, Baltimore, MD, USA
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