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Talts T, Mosscrop LG, Williams D, Tregoning JS, Paulo W, Kohli A, Williams TC, Hoschler K, Ellis J, de Lusignan S, Zambon M. Robust and sensitive amplicon-based whole-genome sequencing assay of respiratory syncytial virus subtype A and B. Microbiol Spectr 2024; 12:e0306723. [PMID: 38411056 PMCID: PMC10986592 DOI: 10.1128/spectrum.03067-23] [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: 08/09/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
Prevention of respiratory syncytial virus (RSV) infection is now a global health priority, with a long-acting monoclonal antibody and two RSV vaccines recently licenced for clinical use. Most licenced and candidate interventions target the RSV fusion (RSV-F) protein. New interventions may be associated with the spread of mutations, reducing susceptibility to antibody neutralization in RSV-F. There is a need for ongoing longitudinal global surveillance of circulating RSV strains. To achieve this large-scale genomic surveillance, a reliable, high-throughput RSV sequencing assay is required. Here we report an improved high-throughput RSV whole-genome sequencing (WGS) assay performed directly on clinical samples without additional enrichment, using a 4-primer-pool, short-amplicon PCR-tiling approach that is suitable for short-read sequencing platforms. Using upper respiratory tract (URT) RSV-positive clinical samples obtained from a sentinel network of primary care providers and from hospital patients (29.7% and 70.2%, respectively; n = 1,037), collected over the period 2019 to 2023, this assay had a threshold of approximately 4 × 103 to 8 × 103 copies/mL (RSV-B and RSV-A sub-types, respectively) as the lowest amount of virus needed in the sample to achieve >96% of whole-genome coverage at a high-quality level. Using a Ct value of 31 as an empirical cut-off, the overall assay success rate of obtaining >90% genome coverage at a read depth minimum of 20 was 96.83% for clinical specimens successfully sequenced from a total of 1,071. The RSV WGS approach described in this study has increased sensitivity compared to previous approaches and can be applied to clinical specimens without the requirement for enrichment. The updated approach produces sequences of high quality consistently and cost-effectively, suitable for implementation to underpin national programs for the surveillance of RSV genomic variation. IMPORTANCE In this paper, we report an improved high-throughput respiratory syncytial virus (RSV) whole-genome sequencing (WGS) assay performed directly on clinical samples, using a 4-primer-pool, short-amplicon PCR-tiling approach that is suitable for short-read sequencing platforms. The RSV WGS approach described in this study has increased sensitivity compared to previous approaches and can be applied to clinical specimens without the requirement for enrichment. The updated approach produces sequences of high quality consistently and cost-effectively, suitable for implementation to underpin national and global programs for the surveillance of RSV genomic variation. The quality of sequence produced is essential for preparedness for new interventions in monitoring antigenic escape, where a single point mutation might lead to a reduction in antibody binding effectiveness and neutralizing activity, or indeed in the monitoring of retaining susceptibility to neutralization by existing and new interventions.
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Affiliation(s)
- Tiina Talts
- UK Health Security Agency, London, United Kingdom
| | | | | | | | | | | | | | | | - Joanna Ellis
- UK Health Security Agency, London, United Kingdom
| | | | - Maria Zambon
- UK Health Security Agency, London, United Kingdom
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van Roekel C, Poukka E, Turunen T, Nohynek H, Presser L, Meijer A, Heikkinen T, Kramer R, Begier E, Teirlinck AC, Knol MJ. Effectiveness of Immunization Products Against Medically Attended Respiratory Syncytial Virus Infection: Generic Protocol for a Test-Negative Case-Control Study. J Infect Dis 2024; 229:S92-S99. [PMID: 37935046 DOI: 10.1093/infdis/jiad483] [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: 07/15/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023] Open
Abstract
Monitoring the real-life effectiveness of respiratory syncytial virus (RSV) products is of major public health importance. This generic protocol for a test-negative design study aims to address currently envisioned approaches for RSV prevention (monoclonal antibodies and vaccines) to study effectiveness of these products among target groups: children, older adults, and pregnant women. The generic protocol approach was chosen to allow for flexibility in adapting the protocol to a specific setting. This protocol includes severe acute respiratory infection (SARI) and acute respiratory infection (ARI), both due to RSV, as end points. These end points can be applied to studies in hospitals, primarily targeting patients with more severe disease, but also to studies in general practitioner clinics targeting ARI.
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Affiliation(s)
- Caren van Roekel
- Centre for Infectious Disease Control, National Institute for Public Health and Environment, Bilthoven, the Netherlands
| | - Eero Poukka
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Topi Turunen
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Hanna Nohynek
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Lance Presser
- Centre for Infectious Disease Control, National Institute for Public Health and Environment, Bilthoven, the Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and Environment, Bilthoven, the Netherlands
| | - Terho Heikkinen
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | | | | | - Anne C Teirlinck
- Centre for Infectious Disease Control, National Institute for Public Health and Environment, Bilthoven, the Netherlands
| | - Mirjam J Knol
- Centre for Infectious Disease Control, National Institute for Public Health and Environment, Bilthoven, the Netherlands
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Mazur NI, Löwensteyn YN, Terstappen J, Leusen J, Schobben F, Cianci D, van de Ven PM, Nierkens S, Bont LJ. Daily intranasal palivizumab to prevent respiratory syncytial virus infection in healthy preterm infants: a phase 1/2b randomized placebo-controlled trial. EClinicalMedicine 2023; 66:102324. [PMID: 38192587 PMCID: PMC10772232 DOI: 10.1016/j.eclinm.2023.102324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 01/10/2024] Open
Abstract
Background Mucosal administration of monoclonal antibodies (mAbs) against respiratory pathogens is a promising alternative for systemic administration because lower doses are required for protection. Clinical development of mucosal mAbs is a highly active field yet clinical proof-of-concept is lacking. Methods In this investigator-initiated, double-blind, randomized placebo-controlled trial, we evaluated intranasal palivizumab for the prevention of RSV infection in preterm infants (Dutch Trial Register NTR7378 and NTR7403). We randomized infants 1:1 to receive intranasal palivizumab (1 mg/mL) or placebo once daily during the RSV season. Any RSV infection was the primary outcome and RSV hospitalization was the key secondary outcome. The primary outcome was analyzed with a mixed effect logistic regression on the modified intention-to-treat population. Findings We recruited 268 infants between Jan 14, 2019 and Jan 28, 2021, after which the trial was stopped for futility following the planned interim analysis. Adverse events were similar in both groups (22/134 (16.4%) palivizumab arm versus 26/134 (19.4%) placebo arm). There were 6 dropouts and 168 infants were excluded from the efficacy analyses due to absent RSV circulation during the SARS-CoV-2 pandemic. Any RSV infection was similar in infants in both groups (18/47 (38.3%) palivizumab arm versus 11/47 (23.4%) placebo arm; aOR 2.2, 95% CI 0.7-6.5). Interpretation Daily intranasal palivizumab did not prevent RSV infection in late preterm infants. Our findings have important implications for the clinical development of mucosal mAbs, namely the necessity of timely interim analyses and further research to understand mucosal antibody half-life. Funding Funded by the Department of Pediatrics, University Medical Centre Utrecht, the Netherlands.
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Affiliation(s)
- Natalie I. Mazur
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands
- Department of Pediatrics, St. Antonius Hospital, 3543 AZ, Utrecht, the Netherlands
| | - Yvette N. Löwensteyn
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands
| | - Jonne Terstappen
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands
| | - Jeanette Leusen
- Center for Translational Immunology, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Fred Schobben
- Department of Pharmacy, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Daniela Cianci
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands
- Julius Center for Health Sciences and Primary Care, Department of Data Science & Biostatistics, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Peter M. van de Ven
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands
- Julius Center for Health Sciences and Primary Care, Department of Data Science & Biostatistics, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Stefan Nierkens
- Center for Translational Immunology, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - Louis J. Bont
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Lundlaan 6, 3584 EA, Utrecht, the Netherlands
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Zuurbier RP, Bogaert D, de Steenhuijsen Piters WAA, Arp K, Chu MLJN, Sanders EAM, van Houten MA. Asymptomatic Viral Presence in Early Life Precedes Recurrence of Respiratory Tract Infections. Pediatr Infect Dis J 2023; 42:59-65. [PMID: 36476532 DOI: 10.1097/inf.0000000000003732] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Respiratory tract infections (RTIs) in infants are often caused by viruses. Although respiratory syncytial virus (RSV), influenza virus and human metapneumovirus (hMPV) can be considered the most pathogenic viruses in children, rhinovirus (RV) is often found in asymptomatic infants as well. Little is known about the health consequences of viral presence, especially early in life. We aimed to examine the dynamics of (a)symptomatic viral presence and relate early viral detection to susceptibility to RTIs in infants. METHODS In a prospective birth cohort of 117 infants, we tested 1304 nasopharyngeal samples obtained from 11 consecutive regular sampling moments, and during acute RTIs across the first year of life for 17 respiratory viruses by quantitative PCR. Associations between viral presence, viral (sub)type, viral load, viral co-detection and symptoms were tested by generalized estimating equation (GEE) models. RESULTS RV was the most detected virus. RV was negatively associated [GEE: adjusted odds ratio (aOR) 0.41 (95% CI 0.18-0.92)], and hMPV, RSV, parainfluenza 2 and 4 and human coronavirus HKU1 were positively associated with an acute RTI. Asymptomatic RV in early life was, however, associated with increased susceptibility to and recurrence of RTIs later in the first year of life (Kaplan-Meier survival analysis: P = 0.022). CONCLUSIONS Respiratory viruses, including the seasonal human coronaviruses, are often detected in infants, and are often asymptomatic. Early life RV presence is, though negatively associated with an acute RTI, associated with future susceptibility to and recurrence of RTIs. Further studies on potential ecologic or immunologic mechanisms are needed to understand these observations.
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Affiliation(s)
- Roy P Zuurbier
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, The Netherlands
| | - Debby Bogaert
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- Medical Research Council and University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Kayleigh Arp
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Mei Ling J N Chu
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Elisabeth A M Sanders
- From the Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marlies A van Houten
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, The Netherlands
- Department of Pediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
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5
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Wang B, Song J, Song J, Mao N, Liang J, Chen Y, Qi Y, Bai L, Xie Z, Zhang Y. An Outbreak of Severe Neonatal Pneumonia Caused by Human Respiratory Syncytial Virus BA9 in a Postpartum Care Centre in Shenyang, China. Microbiol Spectr 2022; 10:e0097422. [PMID: 35863015 PMCID: PMC9430609 DOI: 10.1128/spectrum.00974-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/18/2022] [Indexed: 11/20/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is a major pathogen of lower respiratory tract infections in children (<5 years) and older individuals, with outbreaks mainly reported among infants in hospital pediatric departments and intensive care units (ICUs). An outbreak of severe neonatal pneumonia occurred in a postpartum center in Shenyang city, China, from January to February 2021. In total, 34 respiratory samples were collected from 21 neonates and 13 nursing staff. The samples were screened for 27 pathogens using a TaqMan low-density array, and 20 samples tested positive for HRSV, including 16 neonates and 4 nursing staff samples. Among the 16 hospitalized neonates, seven were admitted to an ICU and nine to general wards. Four of the nursing staff had asymptomatic infections. To investigate the genetic characteristics of the HRSV responsible for this outbreak, the second hypervariable region (HVR2) sequences of the G gene were obtained from six neonates and two nursing staff. Phylogenetic analyses revealed that all eight sequences (SY strains) were identical, belonging to the HRSV BA9 genotype. Our findings highlight the necessity for strict hygiene and disease control measures so as to prevent cross-infection and further avoid potential outbreaks of severe infectious respiratory diseases. IMPORTANCE Human respiratory syncytial virus (HRSV) is one of the leading causes of acute lower respiratory infections (ALRI) worldwide. In this study, we first reported an outbreak of severe neonatal pneumonia caused by HRSVB BA9 at a postpartum care center in mainland China. Among 20 confirmed cases, 16 were hospitalized neonates with 7 in the ICU ward, and the other four were nursing staff with asymptomatic infections. Our findings highlighted the importance of preventing cross-infection in such postpartum centers.
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Affiliation(s)
- Bing Wang
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
- Shenyang Prefecture Center for Disease Control and Prevention, Shenyang, China
| | - Jingjing Song
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
| | - Jinhua Song
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
| | - Naiying Mao
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
| | - Jiayuan Liang
- Liaoning Provincial Center for Disease Control and Prevention, Liaoning, China
| | - Ye Chen
- Shenyang Prefecture Center for Disease Control and Prevention, Shenyang, China
| | - Ying Qi
- Shenyang Prefecture Center for Disease Control and Prevention, Shenyang, China
| | - Lina Bai
- Shenyang Prefecture Center for Disease Control and Prevention, Shenyang, China
| | - Zhibo Xie
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
| | - Yan Zhang
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO WPRO Regional Reference Measles/Rubella Laboratory, Beijing, China
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6
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Association of Nasopharyngeal and Serum Glutathione Metabolism with Bronchiolitis Severity and Asthma Risk: A Prospective Multicenter Cohort Study. Metabolites 2022; 12:metabo12080674. [PMID: 35893241 PMCID: PMC9394245 DOI: 10.3390/metabo12080674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022] Open
Abstract
Infants hospitalized for bronchiolitis are at high risk for asthma. Glutathione-related metabolites may antagonize oxidative stress, which induces airway injuries in respiratory infection and subsequent airway remodeling. However, little is known about the relationship of glutathione-related metabolites with bronchiolitis severity and the risk of asthma. In a multicenter prospective observational cohort study of infants hospitalized for bronchiolitis, we measured nasopharyngeal and serum glutathione-related metabolites by using liquid chromatography−tandem mass spectrometry. We then examined their association with bronchiolitis severity (defined by positive pressure ventilation (PPV) use). We also identified severity-related glutathione-related metabolite signatures and examined their association with asthma at age 6 years. In 1013 infants, we identified 12 nasopharyngeal and 10 serum glutathione-related metabolites. In the multivariable models, lower relative abundances of seven metabolites, e.g., substrates of glutathione, including cysteine (adjOR 0.21, 95%CI 0.06−0.76), glycine (adjOR 0.25, 95%CI 0.07−0.85), and glutamate (adjOR 0.25, 95%CI 0.07−0.88), were significantly associated with PPV use (all FDR < 0.05). These associations were consistent with serum glutathione-related metabolites. The nasopharyngeal glutathione-related metabolite signature was also associated with a significantly higher risk of asthma (adjOR 0.90, 95%CI 0.82−0.99, p = 0.04). In infants hospitalized for bronchiolitis, glutathione-related metabolites were associated with bronchiolitis severity and asthma risk.
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Li H, Ren H, Cao L, Guo J, Zhang Y, Fang Q, Xu W. Comparison of the efficacy and safety of different immunization routes induced by human respiratory syncytial virus F protein with CpG adjuvant in mice. Biochem Biophys Res Commun 2022; 618:54-60. [PMID: 35716595 DOI: 10.1016/j.bbrc.2022.06.015] [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: 05/07/2022] [Accepted: 06/06/2022] [Indexed: 11/02/2022]
Abstract
Human respiratory syncytial virus (HRSV) is a leading cause worldwide of severe respiratory illness in infants and the elderly. The ideal HRSV vaccine should induce a systemic immune response, especially mucosal immunity. In this study, mice were immunized twice with F protein combined with CpG adjuvant to compare the safety and efficacy of 4 immunization routes, including intranasal primed/intramuscular boosted immunization (CpG + F/in+im), intramuscular primed/intranasal boosted immunization (CpG + F/im+in), intramuscular primed/intramuscular boosted immunization (CpG + F/im + im) and intranasal primed/intranasal boosted immunization (CpG + F/in+in). Compared with the control group (CpG/in+im, CpG/im+in, CpG/im + im and CpG/in+in), all 4 immunization routes induced a high titer of neutralizing antibodies and a strong cellular immune response. Mice in the CpG + F/in+in group induced the highest antibody neutralization titer, and IgA antibody in bronchoalveolar lavage fluid (BALF) was the highest. The copy of HRSVs in the lung decreased by approximately 3 log10. As seen from the IgG1/IgG2a and IFN-γ/IL-4-secreting lymphocyte ratios, compared with the mice in the CpG + F/im + im group, mice in the CpG + F/in+in group induced Th1-baised humoral and cellular immune responses and significantly reduced lung pathological injury. In conclusion, among the 4 immunization routes, the safety and efficacy induced by the mice in the CpG + F/in+in group were the best. We can conclude that intranasal immunization is superior to intramuscular immunization using F protein with CpG adjuvant as vaccine candidates.
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Affiliation(s)
- Hai Li
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, China CDC), PR China
| | - Hu Ren
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, China CDC), PR China
| | - Lei Cao
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, China CDC), PR China
| | - Jinyuan Guo
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, China CDC), PR China
| | - Yan Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, China CDC), PR China
| | | | - Wenbo Xu
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, China CDC), PR China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, PR China.
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8
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Lui G, Wong CK, Chan M, Chong KC, Wong R, Chu I, Zhang M, Li T, Hui D, Lee N, Chan P. Host inflammatory response is the major marker of severe respiratory syncytial virus infection in older adults. J Infect 2021; 83:686-692. [PMID: 34614399 DOI: 10.1016/j.jinf.2021.09.024] [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: 11/23/2020] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022]
Abstract
OBJECTIVES We aim to study the viral kinetics and host inflammatory response of RSV infection in older adults, and their correlation with disease severity. METHODS We performed a prospective observational study in adults with RSV infection. We serially collected nasal-throat swabs for quantification of RSV-A and RSV-B viral load, and peripheral blood samples for measurement of cytokine/chemokine concentrations. The study endpoints were (i) requiring supplemental oxygen therapy, and (ii) non-invasive ventilation, intensive care, or died within 30 days of admission. We performed multivariable logistic regression models to identify independent variables for severe disease. RESULTS We enrolled 71 hospitalized patients and 10 outpatients treated for RSV infection (median age 75 years, 51% male, and 74% with comorbidities). Among hospitalized patients, 61% required supplemental oxygen therapy, and 18% had severe disease requiring non-invasive ventilation or intensive care, or died within 30 days. Inflammatory cytokine/chemokines IL-6, CXCL8/IL-8, CXCL9/MIG and CXCL10/IP-10 increased significantly during the acute phase of illness. IL-6 concentration was independently associated with severe disease after adjusting for confounding factors. RSV viral load was not associated with disease severity throughout the course of illness. CONCLUSION Host inflammatory response is a major marker of severe disease in older adults with RSV infection.
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Affiliation(s)
- G Lui
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region; Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region
| | - C K Wong
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region
| | - M Chan
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region; Department of Microbiology, Prince of Wales Hospital, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region
| | - K C Chong
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region; Centre for Health System and Policy Research, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region
| | - R Wong
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region
| | - I Chu
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region
| | - M Zhang
- Department of Microbiology, Prince of Wales Hospital, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region
| | - T Li
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region
| | - Dsc Hui
- Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region; Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region
| | - N Lee
- Institute for Pandemics, Dalla Lana School of Public Health, University of Toronto, Canada
| | - Pks Chan
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region; Department of Microbiology, Prince of Wales Hospital, The Chinese University of Hong Kong, China Hong Kong Special Administrative Region.
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9
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Felt SA, Sun Y, Jozwik A, Paras A, Habibi MS, Nickle D, Anderson L, Achouri E, Feemster KA, Cárdenas AM, Turi KN, Chang M, Hartert TV, Sengupta S, Chiu C, López CB. Detection of respiratory syncytial virus defective genomes in nasal secretions is associated with distinct clinical outcomes. Nat Microbiol 2021; 6:672-681. [PMID: 33795879 PMCID: PMC9098209 DOI: 10.1038/s41564-021-00882-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/23/2021] [Indexed: 02/01/2023]
Abstract
Respiratory syncytial virus (RSV) causes respiratory illness in children, immunosuppressed individuals and the elderly. However, the viral factors influencing the clinical outcome of RSV infections remain poorly defined. Defective viral genomes (DVGs) can suppress virus replication by competing for viral proteins and by stimulating antiviral immunity. We studied the association between detection of DVGs of the copy-back type and disease severity in three RSV A-confirmed cohorts. In hospitalized children, detection of DVGs in respiratory samples at or around the time of admission associated strongly with more severe disease, higher viral load and a stronger pro-inflammatory response. Interestingly, in experimentally infected adults, the presence of DVGs in respiratory secretions differentially associated with RSV disease severity depending on when DVGs were detected. Detection of DVGs early after infection associated with low viral loads and mild disease, whereas detection of DVGs late after infection, especially if DVGs were present for prolonged periods, associated with high viral loads and severe disease. Taken together, we demonstrate that the kinetics of DVG accumulation and duration could predict clinical outcome of RSV A infection in humans, and thus could be used as a prognostic tool to identify patients at risk of worse clinical disease.
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Affiliation(s)
- Sébastien A. Felt
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Present address: Department of Molecular Microbiology and Center for Women Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA.,These authors contributed equally: Sébastien A. Felt, Yan Sun
| | - Yan Sun
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Present address: Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA.,These authors contributed equally: Sébastien A. Felt, Yan Sun
| | - Agnieszka Jozwik
- Department of Infectious Disease, Imperial College London, London, UK
| | - Allan Paras
- Department of Infectious Disease, Imperial College London, London, UK
| | | | | | - Larry Anderson
- Pediatric Infectious Disease, Emory University, Atlanta, GA, USA
| | - Emna Achouri
- Department of Molecular Microbiology and Center for Women Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Kristen A. Feemster
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ana María Cárdenas
- Infectious Disease Diagnostics Laboratory, Children’s Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Present address: Becton, Dickinson and Company, Sparks, MD, USA
| | - Kedir N. Turi
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Tina V. Hartert
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shaon Sengupta
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Carolina B. López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Present address: Department of Molecular Microbiology and Center for Women Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
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10
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Redlberger-Fritz M, Kundi M, Aberle SW, Puchhammer-Stöckl E. Significant impact of nationwide SARS-CoV-2 lockdown measures on the circulation of other respiratory virus infections in Austria. J Clin Virol 2021; 137:104795. [PMID: 33761423 PMCID: PMC7962988 DOI: 10.1016/j.jcv.2021.104795] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/28/2021] [Accepted: 03/14/2021] [Indexed: 12/01/2022]
Abstract
Background Since the worldwide spread of SARS-CoV-2, different European countries reacted with temporary national lockdowns with the aim to limit the virus transmission in the population. Also Austria started a lockdown of public life in March 2020. Objectives In this study we investigated whether the circulation of different respiratory virus infections in Austria, as assessed by the established respiratory virus surveillance system, is affected by these measures as well and may reflect the success of the lockdown in limiting respiratory virus transmission. Study design Sentinel data obtained for influenza virus, respiratory syncytial virus, human metapneumovirus and rhinovirus cases were analyzed and compared between the season 2019/2020 and the five previous seasons. Results We observed a rapid and statistically significant reduction of cumulative cases for all these viruses within short time after the lockdown in March 2020, compared to previous seasons (each p < 0.001). Also, sentinel screening for SARS-CoV-2 infections was performed and a decrease of SARS-CoV-2 was seen after the lockdown. While for the seasonally occurring viruses as influenza, respiratory syncytial virus or human metapneumovirus the lockdown led to the end of the annual epidemics, a re-increase of rhinovirus infections was observed after liberalization of numerous lockdown measures. Conclusions Our data provide evidence that occurrence of different respiratory virus infections reflect not only the efficiency of lockdown measures taken against SARS-CoV-2 but it shows also the effects of lockdown releases on the transmission of respiratory viruses.
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Affiliation(s)
| | - Michael Kundi
- Department of Environmental Health, Medical University Vienna, Vienna, Austria
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11
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Wang LN, Peng XL, Xu M, Zheng YB, Jiao YY, Yu JM, Fu YH, Zheng YP, Zhu WY, Dong ZJ, He JS. Evaluation of the Safety and Immune Efficacy of Recombinant Human Respiratory Syncytial Virus Strain Long Live Attenuated Vaccine Candidates. Virol Sin 2021; 36:706-720. [PMID: 33559831 PMCID: PMC8379332 DOI: 10.1007/s12250-021-00345-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 09/18/2020] [Indexed: 11/30/2022] Open
Abstract
Human respiratory syncytial virus (RSV) infection is the leading cause of lower respiratory tract illness (LRTI), and no vaccine against LRTI has proven to be safe and effective in infants. Our study assessed attenuated recombinant RSVs as vaccine candidates to prevent RSV infection in mice. The constructed recombinant plasmids harbored (5′ to 3′) a T7 promoter, hammerhead ribozyme, RSV Long strain antigenomic cDNA with cold-passaged (cp) mutations or cp combined with temperature-sensitive attenuated mutations from the A2 strain (A2cpts) or further combined with SH gene deletion (A2cptsΔSH), HDV ribozyme (δ), and a T7 terminator. These vectors were subsequently co-transfected with four helper plasmids encoding N, P, L, and M2-1 viral proteins into BHK/T7-9 cells, and the recovered viruses were then passaged in Vero cells. The rescued recombinant RSVs (rRSVs) were named rRSV-Long/A2cp, rRSV-Long/A2cpts, and rRSV-Long/A2cptsΔSH, respectively, and stably passaged in vitro, without reversion to wild type (wt) at sites containing introduced mutations or deletion. Although rRSV-Long/A2cpts and rRSV-Long/A2cptsΔSH displayed temperature-sensitive (ts) phenotype in vitro and in vivo, all rRSVs were significantly attenuated in vivo. Furthermore, BALB/c mice immunized with rRSVs produced Th1-biased immune response, resisted wtRSV infection, and were free from enhanced respiratory disease. We showed that the combination of ΔSH with attenuation (att) mutations of cpts contributed to improving att phenotype, efficacy, and gene stability of rRSV. By successfully introducing att mutations and SH gene deletion into the RSV Long parent and producing three rRSV strains, we have laid an important foundation for the development of RSV live attenuated vaccines.
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Affiliation(s)
- Li-Nan Wang
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100044, China
| | - Xiang-Lei Peng
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100044, China
| | - Min Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100044, China
| | - Yuan-Bo Zheng
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100044, China
| | - Yue-Ying Jiao
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100044, China
| | - Jie-Mei Yu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100044, China
| | - Yuan-Hui Fu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100044, China
| | - Yan-Peng Zheng
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100044, China
| | - Wu-Yang Zhu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Zhong-Jun Dong
- School of Medicine and Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, Beijing, 100084, China
| | - Jin-Sheng He
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, 100044, China.
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12
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Haigh J, Cutino-Moguel MT, Wilks M, Welch C, Melzer M. A service evaluation of simultaneous near-patient testing for influenza, respiratory syncytial virus, Clostridium difficile and norovirus in a UK district general hospital. J Hosp Infect 2019; 103:441-446. [DOI: 10.1016/j.jhin.2019.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/29/2019] [Indexed: 10/26/2022]
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13
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de Souza RP, Ribeiro ALR, de Menezes SAF, Machado LFA. Incidence of respiratory syncytial virus infection in children with congenital heart disease undergoing immunoprophylaxis with palivizumab in Pará state, north region of Brazil. BMC Pediatr 2019; 19:299. [PMID: 31462289 PMCID: PMC6714430 DOI: 10.1186/s12887-019-1681-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 08/21/2019] [Indexed: 12/03/2022] Open
Abstract
Background Palivizumab prophylaxis for the human respiratory syncytial virus (HRSV) has been reported to reduce the risk of hospital admissions related to HRSV in children with congenital heart disease (CHD). These children are at high risk of developing severe lower respiratory tract infection (LRTI) due to HRSV infection. Our goal was to evaluate the incidence of HRSV infection in children with CHD after being submitted to immunoprophylaxis with palivizumab in Pará state, North region of Brazil. Methods A prospective and observational cohort study was performed in children ≤2 years of age with CHD who received palivizumab immunoprophylaxis between January 1 and June 31, 2016. A questionnaire about basic non-medical care measures was applied to parents/legal representatives. Data on patients’ demographic characteristics, household environment, and respiratory infections were evaluated. HRSV infection was determined by qPCR. Results There were 104 children enrolled in this investigation and the results showed a mean age of 10.6 months, an average weight of 7.3 kg and 3.5 doses of palivizumab per children during seasonality of HRSV. Respiratory infection was observed in 27.9% of cases, of which 9.6% were LRTI. No case of children who received palivizumab immunoprophylaxis and developed influenza-like symptoms tested positive for HRSV. Conclusion Although the lack of a control group doesn’t allow to affirm the effectiveness of HRSV passive immunization, the immunoprophylaxis with palivizumab appeared to be totally efficient in preventing respiratory infection by HRSV in children up to two years of age with CHD.
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Affiliation(s)
- Roseane Porfírio de Souza
- Biology of Infectious and Parasitic Agents Post-Graduate Program, Federal University of Pará, Belém, Pará, Brazil.,Gaspar Vianna Clinic Hospital Foundation, Belém, Pará, Brazil
| | - Andre Luis Ribeiro Ribeiro
- Postdoctoral fellowship, Cell Culture Laboratory, School of Dentistry, Federal University of Para - UFPA, Belém, Pará, Brazil
| | | | - Luiz Fernando Almeida Machado
- Biology of Infectious and Parasitic Agents Post-Graduate Program, Federal University of Pará, Belém, Pará, Brazil. .,Virology Laboratory, Institute of Biological Sciences, Federal University of Pará, Cidade Universitária Prof. José da Silveira Netto, Rua Augusto Correa 1, Guamá, 66.075-110, Belém, Pará, Brazil.
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14
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de Steenhuijsen Piters WAA, Jochems SP, Mitsi E, Rylance J, Pojar S, Nikolaou E, German EL, Holloway M, Carniel BF, Chu MLJN, Arp K, Sanders EAM, Ferreira DM, Bogaert D. Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine. Nat Commun 2019; 10:2981. [PMID: 31278315 PMCID: PMC6611866 DOI: 10.1038/s41467-019-10814-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 05/15/2019] [Indexed: 12/21/2022] Open
Abstract
Streptococcus pneumoniae is the main bacterial pathogen involved in pneumonia. Pneumococcal acquisition and colonization density is probably affected by viral co-infections, the local microbiome composition and mucosal immunity. Here, we report the interactions between live-attenuated influenza vaccine (LAIV), successive pneumococcal challenge, and the healthy adult nasal microbiota and mucosal immunity using an experimental human challenge model. Nasal microbiota profiles at baseline are associated with consecutive pneumococcal carriage outcome (non-carrier, low-dense and high-dense pneumococcal carriage), independent of LAIV co-administration. Corynebacterium/Dolosigranulum-dominated profiles are associated with low-density colonization. Lowest rates of natural viral co-infection at baseline and post-LAIV influenza replication are detected in the low-density carriers. Also, we detected the fewest microbiota perturbations and mucosal cytokine responses in the low-density carriers compared to non-carriers or high-density carriers. These results indicate that the complete respiratory ecosystem affects pneumococcal behaviour following challenge, with low-density carriage representing the most stable ecological state.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Medical Research Council/University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Simon P Jochems
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Elena Mitsi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Jamie Rylance
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Sherin Pojar
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Elissavet Nikolaou
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Esther L German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Mark Holloway
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Beatriz F Carniel
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Mei Ling J N Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Kayleigh Arp
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
| | - Daniela M Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands.
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands.
- Medical Research Council/University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom.
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15
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Landry ML, Foxman EF. Antiviral Response in the Nasopharynx Identifies Patients With Respiratory Virus Infection. J Infect Dis 2019; 217:897-905. [PMID: 29281100 PMCID: PMC5853594 DOI: 10.1093/infdis/jix648] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/12/2017] [Indexed: 12/19/2022] Open
Abstract
Background Despite the high burden of respiratory infection and the importance of early and accurate diagnosis, there is no simple diagnostic test to rule in viral infection as a cause of respiratory symptoms. Methods We performed RNA sequencing on human nasal epithelial cells following stimulation of the intracellular viral recognition receptor RIG-I. Next, we evaluated whether measuring identified host mRNAs and proteins from patient nasopharyngeal swabs could predict the presence of a respiratory virus in the sample. Results Our first study showed that a signature of 3 mRNAs, CXCL10, IFIT2, and OASL, predicted respiratory virus detection with an accuracy of 97% (95% confidence interval [CI], 0.9–1.0), and identified proteins correlating with virus detection. In a second study, elevated CXCL11 or CXCL10 protein levels identified samples containing respiratory viruses, including viruses not on the initial test panel. Overall area under the curve (AUC) values were: CXCL11 AUC = 0.901 (95% CI, 0.86–0.94); CXCL10 AUC = 0.85 (95% CI, 0.80–0.91). Conclusions Host antiviral mRNAs and single host proteins detectable using nasopharyngeal swabs accurately predict the presence of viral infection. This approach holds promise for developing rapid, cost-effective tests to improve management of patients with respiratory illnesses.
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Affiliation(s)
- Marie L Landry
- Department of Laboratory Medicine Yale University School of Medicine, New Haven, Connecticut.,Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Ellen F Foxman
- Department of Laboratory Medicine Yale University School of Medicine, New Haven, Connecticut
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16
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Duplex real-time RT-PCR assay for detection and subgroup-specific identification of human respiratory syncytial virus. J Virol Methods 2019; 271:113676. [PMID: 31181218 PMCID: PMC7172218 DOI: 10.1016/j.jviromet.2019.113676] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/26/2023]
Abstract
Human respiratory syncytial virus (HRSV) is a leading cause of acute respiratory illness in young children worldwide. Reliable detection and identification of HRSV subgroup A and B infections are essential for accurate disease burden estimates in anticipation of licensure of novel HRSV vaccines and immunotherapies. To ensure continued reliability, molecular assays must remain current with evolving virus strains. We have developed a HRSV subgroup-specific real-time RT-PCR (rRT-PCR) assay for detection and subgroup identification using primers and subgroup-specific probes targeting a conserved region of the nucleoprotein gene combined in a single duplex reaction using all genome sequence data currently available in GenBank. The assay was validated for analytical sensitivity, specificity, reproducibility, and clinical performance with a geographically diverse collection of viral isolates and respiratory specimens in direct comparison with an established pan-HRSV rRT-PCR reference test. The assay was sensitive, reproducibly detecting as few as 5-10 copies/reaction of target RNA. The assay was specific, showing no amplification with a panel of 16 other common respiratory pathogens or predicted by in silico primer/probe analysis. The duplex rRT-PCR assay based on the most current available genome sequence data permits rapid, sensitive and specific detection and subgroup identification of HRSV.
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17
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Liu GS, Niu PH, Zhao SC, Lu RJ, Tan WJ. Detection of six common human paramyxoviruses in patients with acute febrile respiratory symptoms using a novel multiplex real-time RT-PCR assay. J Med Virol 2018; 91:564-569. [PMID: 30358912 PMCID: PMC7167037 DOI: 10.1002/jmv.25350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/18/2018] [Indexed: 11/16/2022]
Abstract
Human metapneumovirus (hMPV), respiratory syncytial virus type A (RSV‐A), RSV‐B, and human parainfluenza viruses 1, 2, and 3 (HPIV‐1, HPIV‐2, and HPIV‐3) are common respiratory paramyxoviruses. Here, we developed a two‐tube triplex one‐step real‐time reverse‐transcription polymerase chain reaction (real‐time RT‐PCR) and evaluated its performance using clinical samples. The data showed that this novel assay was 100% consistent with the monoplex real‐time RT‐PCR assay (in‐house), which was superior to the commercial routine multiplex‐ligation‐NAT‐based assay. Meanwhile, the clinical nasopharyngeal swabs of 471 patients with the acute febrile respiratory syndrome (AFRS) were analyzed using the established method. The results showed that 52 (11.7%) cases were positive for paramyxovirus. Among them, HPIVs and RSV‐A had the highest detection rate. The age and seasonal distribution of human paramyxovirus infection were analyzed. In conclusion, we developed a novel multiplex real‐time RT‐PCR assay for the rapid detection of six common human paramyxoviruses, which were dominant in patients with AFRS in Qinghai. We developed a novel multiplex real‐time RT‐PCR assay for the rapid detection of six common human paramyxoviruses for patients with AFRS in Qinghai. This method provides a new approach with a higher quality of performance (accuracy, speed, and higher sensitivity) for the detection of common respiratory paramyxoviruses in clinical specimens. The method is more specimen‐ and time‐ saving and more cost‐effective, without compromising quality, compared with monoplex real time RT PCR and commercial routine multiplex ligation‐NAT‐based RF 22.
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Affiliation(s)
- Gao-Shan Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Key Laboratory of Medical Virology, Biotech Center for Viral Disease Emergency, Beijing, China
| | - Pei-Hua Niu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Key Laboratory of Medical Virology, Biotech Center for Viral Disease Emergency, Beijing, China
| | - Sheng-Cang Zhao
- Center for Disease Control and Prevention of Qinghai Province, Department of Virus Detection, Xining, China
| | - Rou-Jian Lu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Key Laboratory of Medical Virology, Biotech Center for Viral Disease Emergency, Beijing, China
| | - Wen-Jie Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Key Laboratory of Medical Virology, Biotech Center for Viral Disease Emergency, Beijing, China
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18
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Goggin RK, Bennett CA, Bassiouni A, Bialasiewicz S, Vreugde S, Wormald PJ, Psaltis AJ. Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites. Front Cell Infect Microbiol 2018; 8:334. [PMID: 30283747 PMCID: PMC6156342 DOI: 10.3389/fcimb.2018.00334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022] Open
Abstract
Background: With the emergence of the microbiome as an important factor in health and disease in the respiratory tract standardised, validated techniques are required for its accurate characterisation. No standardised technique has been reported specifically for viral sampling in the sinonasal passages. Aim: To optimise viral sampling techniques from the sinonasal cavity. Methods: Sterile cytology brushes were used under endoscopic guidance to sample the sinonasal mucosa at time of endoscopic sinus surgery at both the middle and inferior meatuses (MM and IM). DNA and RNA were extracted from the samples and underwent PCR or RT-PCR testing, respectively, for a panel of 15 common upper respiratory tract viruses. Results: Twenty-four adult patients were recruited for this study. 18/24 (75%) patients were positive for virus in at least one site, while 8/24 (33%) were positive for virus at both sites. The mean number of viruses identified at the two sites were similar (0.875 ± 0.899 at the MM vs. 0.750 ± 1.032 at the IM). 6/24 (25%) of patients showed no virus at either site, while 3/24 (12.5%) demonstrated the same viral species at both sites. Conclusion: Although the number of viruses present at different sites with the nasal cavity are similar, discord exists in the viral species between sites. It is therefore recommended that both sites are sampled in the clinical and research setting better to characterise the viral species within the nasal cavity.
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Affiliation(s)
- Rachel K Goggin
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Catherine A Bennett
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Ahmed Bassiouni
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Seweryn Bialasiewicz
- Queensland Paediatric Infectious Diseases Laboratory, Children's Health Queensland, Brisbane, QLD, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Sarah Vreugde
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Peter-John Wormald
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Alkis J Psaltis
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
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19
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Zhao L, Wang J, Li GX, Qiu FZ, Chen C, Zhao MC, Wang L, Duan SX, Feng ZS, Ma XJ. A highly sensitive 1-tube nested real-time RT-PCR assay using LNA-modified primers for detection of respiratory syncytial virus. Diagn Microbiol Infect Dis 2018; 93:101-106. [PMID: 30266400 PMCID: PMC7126397 DOI: 10.1016/j.diagmicrobio.2018.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/23/2018] [Accepted: 09/03/2018] [Indexed: 12/31/2022]
Abstract
Respiratory syncytial virus (RSV) causes serious respiratory tract infection worldwide. The relatively low RSV load makes it difficult to detect in frail, elderly, and severely immune-compromised patients. In the present study, we developed a locked nucleic acid–-based 1-tube nested real-time RT-PCR (OTNRT-PCR) assay with the advantages of extremely high sensitivity, facile operability, and less likelihood of cross-contamination. The sensitivity, specificity, and clinical performance of the OTNRT-PCR assay were compared in parallel with a conventional TaqMan probe-based real-time PCR (qRT-PCR) assay and a traditional 2-step nested RT-PCR assay. The limit of detection of the OTNRT-PCR assay was 1.02 × 10−1 TCID50/mL, equivalent to the traditional 2-step nested RT-PCR assay and 25-fold lower than the qRT-PCR assay. Of 616 nasopharyngeal aspirates tested, 143 RSV-negative samples by qRT-PCR were confirmed as positive by sequencing the OTNRT-PCR products. We therefore conclude that OTNRT-PCR is more sensitive than qRT-PCR for detection of RSV in clinical samples.
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Affiliation(s)
- Li Zhao
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China; Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Ji Wang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Gui-Xia Li
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Fang-Zhou Qiu
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China; Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Chen Chen
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Meng-Chuan Zhao
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Le Wang
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Su-Xia Duan
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Zhi-Shan Feng
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Xue-Jun Ma
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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20
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Comparison of the Xpert Flu/RSV XC and Xpress Flu/RSV Assays. J Clin Microbiol 2018; 56:JCM.00278-18. [PMID: 29769281 DOI: 10.1128/jcm.00278-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/15/2018] [Indexed: 11/20/2022] Open
Abstract
Molecular diagnostics for influenza and respiratory syncytial virus (RSV) have become commonplace, and various tests and systems have been cleared by the FDA for use in the United States. We performed a retrospective study to compare the Cepheid Xpress Flu/RSV assay with the Xpert Flu/RSV XC assay, using laboratory-developed tests (LDTs) as the reference method. The Xpress assay was 100% accurate compared to LDTs, whereas the Xpert Flu/RSV XC assay was 96.0% accurate. The Xpress test was determined to be faster and more sensitive than the XC assay.
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21
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Meidani M, Mirmohammad Sadeghi SA. Respiratory Viruses in Febrile Neutropenic Patients with Respiratory Symptoms. Adv Biomed Res 2018; 7:5. [PMID: 29456976 PMCID: PMC5812103 DOI: 10.4103/abr.abr_433_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Respiratory infections are a frequent cause of fever in neutropenic patients, whereas respiratory viral infections are not frequently considered as a diagnosis, which causes high morbidity and mortality in these patients. Materials and Methods: This prospective study was performed on 36 patients with neutropenia who admitted to hospital were eligible for inclusion with fever (single temperature of >38.3°C or a sustained temperature of >38°C for more than 1 h), upper and lower respiratory symptoms. Sampling was performed from the throat of the patient by the sterile swab. All materials were analyzed by quantitative real-time multiplex polymerase chain reaction covering the following viruses; influenza, parainfluenza virus (PIV), rhinovirus (RV), human metapneumovirus, and respiratory syncytial virus (RSV). Results: RV was the most frequently detected virus and then RSV was the most. PIV was not present in any of the tested samples. Furthermore, no substantial differences in the distribution of specific viral species were observed based on age, sex, neutropenia duration, hematological disorder, and respiratory tract symptoms and signs (P > 0.05). Conclusion: Our prospective study supports the hypothesis that respiratory viruses play an important role in the development of neutropenic fever, and thus has the potential to individualize infection treatment and to reduce the extensive use of antibiotics in immunocompromised patients with neutropenia.
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Affiliation(s)
- Mohsen Meidani
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.,Infectious Diseases and Tropical Medicine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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22
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Construction and Characterization of a Recombinant Human Respiratory Syncytial Virus Encoding Enhanced Green Fluorescence Protein for Antiviral Drug Screening Assay. BIOMED RESEARCH INTERNATIONAL 2018; 2018:8431243. [PMID: 29568767 PMCID: PMC5820570 DOI: 10.1155/2018/8431243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/25/2017] [Accepted: 12/04/2017] [Indexed: 11/17/2022]
Abstract
Human respiratory syncytial virus (RSV) is the single most important cause of lower respiratory tract disease in infants and young children and a major viral agent responsible for respiratory tract disease in immunosuppressed individuals and the elderly, but no vaccines and antiviral drugs are available. Herein the recombinant RSV (rRSV) encoding enhanced green fluorescence protein (EGFP, rRSV-EGFP) was constructed and the potential for screening anti-RSV drugs was investigated. The recombinant plasmid of pBRATm-rRSV-EGFP, containing T7 transcription cassette composed of T7 promoter, RSV antigenomic cDNA with EGFP gene, HDV ribozyme (δ), and T7 terminator in the order of 5' to 3', was constructed and cotransfected into BHK/T7-9 cells together with helper plasmids encoding N, P, L, and M2-1 gene, respectively. The rescued rRSV-EGFP was confirmed by increasing expression of EGFP over blind passages and by RT-PCR. rRSV-EGFP was comparable to the other two recombinant RSVs encoding red fluorescent protein (RFP, rRSV-RFP) or luciferase (Luc, rRSV-Luc) in the growth kinetic, and there was a difference in sensitivity between them for screening anti-RSV agents based on infection of HEp-2 cells. The EGFP-encoding rRSV has been constructed and rescued successfully and has the potential for high-throughput anti-RSV drug screening in vitro.
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23
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A Built-In CpG Adjuvant in RSV F Protein DNA Vaccine Drives a Th1 Polarized and Enhanced Protective Immune Response. Viruses 2018; 10:v10010038. [PMID: 29342954 PMCID: PMC5795451 DOI: 10.3390/v10010038] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/08/2018] [Accepted: 01/09/2018] [Indexed: 01/03/2023] Open
Abstract
Human respiratory syncytial virus (RSV) is the most significant cause of acute lower respiratory infection in children. However, there is no licensed vaccine available. Here, we investigated the effect of five or 20 copies of C-Class of CpG ODN (CpG-C) motif incorporated into a plasmid DNA vaccine encoding RSV fusion (F) glycoprotein on the vaccine-induced immune response. The addition of CpG-C motif enhanced serum binding and virus-neutralizing antibody responses in BALB/c mice immunized with the DNA vaccines. Moreover, mice vaccinated with CpG-modified vaccines, especially with the higher 20 copies, resulted in an enhanced shift toward a Th1-biased antibody and T-cell response, a decrease in pulmonary pathology and virus replication, and a decrease in weight loss after RSV challenge. This study suggests that CpG-C motif, cloned into the backbone of DNA vaccine encoding RSV F glycoprotein, functions as a built-in adjuvant capable of improving the efficacy of DNA vaccine against RSV infection.
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24
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Song J, Wang H, Shi J, Cui A, Huang Y, Sun L, Xiang X, Ma C, Yu P, Yang Z, Li Q, Ng TI, Zhang Y, Zhang R, Xu W. Emergence of BA9 genotype of human respiratory syncytial virus subgroup B in China from 2006 to 2014. Sci Rep 2017; 7:16765. [PMID: 29196726 PMCID: PMC5711796 DOI: 10.1038/s41598-017-17055-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/21/2017] [Indexed: 01/10/2023] Open
Abstract
A study was conducted to investigate the circulation of HRSV subgroup B (HRSVB) in China in recent years. HRSVB sequences from 365 samples collected in 1991, 2004 and 2008-2014 in China, together with 332 Chinese HRSVB sequences obtained from GenBank were analyzed to determine the geographic and yearly distribution of HRSVB. Phylogenetic analysis revealed these HRSVB sequences clustered into 4 genotypes with different frequencies: BA (83%), CB1 (11%), SAB (3.0%) and GB3 (0.7%). Between 2005 and 2013, there was a co-circulation of BA and non-BA genotypes in China. Genotypes BA9 and BA10 were two of the main BA genotypes detected in this study. Genotype BA9 was first detected in China in 2006 and became the predominant HRSVB genotype circulating in China from 2008 to 2014. Three different lineages were detected for both genotypes BA9 and BA10. Time to the most recent common ancestor for genotypes BA9 and BA10 was estimated for years 1997 and 1996, respectively. Results of this study not only contribute to the understanding of the circulation pattern, but also the phylogenetic pattern and evolution of HRSVB in China from 1991 to 2014.
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Affiliation(s)
- Jinhua Song
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Huiling Wang
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Jing Shi
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China.,Lu Juan Community Health Center of Daxing region, Beijing, People's Republic of China
| | - Aili Cui
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yanzhi Huang
- Jilin Children's Medical Center, Children's Hospital of Changchun, Changchun, People's Republic of China
| | - Liwei Sun
- Jilin Children's Medical Center, Children's Hospital of Changchun, Changchun, People's Republic of China
| | - Xingyu Xiang
- Hunan Provincial Centers for Disease Control and Prevention, Changsha, People's Republic of China
| | - Chaofeng Ma
- Xian Center for Disease Control and Prevention, Xian, People's Republic of China
| | - Pengbo Yu
- Shaanxi Provincial Centers for Disease Control and Prevention, Xian, People's Republic of China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Qi Li
- Hebei Provincial Centers for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | | | - Yan Zhang
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China.
| | - Rongbo Zhang
- Medical College, Anhui University of Science & Technology, Huainan, People's Republic of China.
| | - Wenbo Xu
- WHO WPRO Regional Reference Measles/Rubella Laboratory and Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, People's Republic of China. .,Medical College, Anhui University of Science & Technology, Huainan, People's Republic of China.
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25
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Abstract
Nucleic acid based diagnostic techniques are routinely used for the detection of infectious agents. Most of these assays rely on nucleic acid extraction platforms for the extraction and purification of nucleic acids and a separate real-time PCR platform for quantitative nucleic acid amplification tests (NATs). Several microfluidic lab on chip (LOC) technologies have been developed, where mechanical and chemical methods are used for the extraction and purification of nucleic acids. Microfluidic technologies have also been effectively utilized for chip based real-time PCR assays. However, there are few examples of microfluidic systems which have successfully integrated these two key processes. In this study, we have implemented an electro-actuation based LOC micro-device that leverages multi-frequency actuation of samples and reagents droplets for chip based nucleic acid extraction and real-time, reverse transcription (RT) PCR (qRT-PCR) amplification from clinical samples. Our prototype micro-device combines chemical lysis with electric field assisted isolation of nucleic acid in a four channel parallel processing scheme. Furthermore, a four channel parallel qRT-PCR amplification and detection assay is integrated to deliver the sample-to-detection NAT chip. The NAT chip combines dielectrophoresis and electrostatic/electrowetting actuation methods with resistive micro-heaters and temperature sensors to perform chip based integrated NATs. The two chip modules have been validated using different panels of clinical samples and their performance compared with standard platforms. This study has established that our integrated NAT chip system has a sensitivity and specificity comparable to that of the standard platforms while providing up to 10 fold reduction in sample/reagent volumes.
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26
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Gibson J, Schechter-Perkins EM, Mitchell P, Mace S, Tian Y, Williams K, Luo R, Yen-Lieberman B. Multi-center evaluation of the cobas ® Liat ® Influenza A/B & RSV assay for rapid point of care diagnosis. J Clin Virol 2017; 95:5-9. [PMID: 28818691 DOI: 10.1016/j.jcv.2017.08.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 08/04/2017] [Accepted: 08/06/2017] [Indexed: 11/26/2022]
Abstract
Point of Care Testing (POCT) provides the capability for rapid laboratory test results in patient care environments where a traditional clinical laboratory is not available. POCTs have shorter turn-around times (TATs), they may be performed by non-laboratory personnel, and the need for transport time is eliminated. The Food and Drug Administration (FDA) recently granted Clinical Laboratory Improvements Amendment (CLIA) waiver status to the cobas® Influenza A/B & RSV assay, a rapid, accurate point-of-care test for Influenza and respiratory syncytial virus (RSV) performed on the Liat® System. The performance characteristics of this test were determined though a multi-site study consisting of different point of care testing environments. Prospectively collected Nasopharyngeal (NP) swabs from 1361 patients seen at 8 primary care clinics and 4 emergency departments (EDs) and 295 retrospectively identified specimens were tested for Influenza A/B and RSV on the cobas® Liat® platform. Performance characteristics were determined through comparison to ProFlu+, a laboratory-based PCR test for Influenza A/B and RSV (reference test). Discordant specimens were adjudicated following bi-directional sequencing. The cobas® Influenza A/B and RSV assay showed sensitivities of 99.6%, 99.3%, and 96.8% for Influenza A, Influenza B, and RSV, respectively as determined from percent positive agreement (PPA) following comparison to the reference test. Sequencing confirmed cobas® Influenza A/B and RSV results in 49.2% of reference test discordant specimens, while crossing threshold data suggest increased sensitivity compared to the reference test. The cobas® Influenza A/B and RSV assay was found to be a rapid, sensitive POCT for the detection of these viruses, and provides laboratory-quality PCR-based diagnostic results in point of care settings.
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Affiliation(s)
- Jane Gibson
- Department of Clinical Sciences, University of Central Florida College of Medicine, United States.
| | - Elissa M Schechter-Perkins
- Department of Emergency Medicine, Boston Medical Center, Boston University School of Medicine, United States
| | - Patricia Mitchell
- Department of Emergency Medicine, Boston Medical Center, Boston University School of Medicine, United States
| | - Sharon Mace
- Cleveland Clinic, Emergency Department & Department of Laboratory Medicine, United States
| | - Yu Tian
- Roche Molecular Systems, United States
| | | | | | - Belinda Yen-Lieberman
- Cleveland Clinic, Emergency Department & Department of Laboratory Medicine, United States
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27
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Emergence of ON1 genotype of human respiratory syncytial virus subgroup A in China between 2011 and 2015. Sci Rep 2017; 7:5501. [PMID: 28710393 PMCID: PMC5511225 DOI: 10.1038/s41598-017-04824-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 05/22/2017] [Indexed: 11/23/2022] Open
Abstract
A molecular epidemiological study of human respiratory syncytial virus (HRSV) was conducted to examine the distribution of its subgroups and genotypes, as well as to identify its transmission pattern in China. A total of 705 samples collected from 9 provinces in China between January 2008 and February 2015 were identified as HRSV-positive and were subsequently sequenced. Of these, 336 samples were HRSV subgroup A (HRSVA), 368 samples were HRSV subgroup B (HRSVB), and 1 sample contained both HRSVA and HRSVB. These 705 HRSV sequences, together with 766 HRSV sequences downloaded from GenBank, were analyzed to understand the recent circulation patterns of HRSV in China. HRSVB predominated in the 2008/2009 and 2009/2010 seasons, whereas HRSVA predominated in the 2010/2011 and 2011/2012 seasons; HRSVA and HRSVB co-circulated during 2012/2013 and 2014/2015. Phylogenetic analysis showed most of the HRSVA sequences clustered into 2 genotypes, namely, NA1 and ON1. The ON1 genotype was first detected in China in 2011, and it quickly replaced the NA1 genotype to become the most prevalent HRSVA genotype circulating in China between 2013 and 2015. Continuous epidemiological surveillance and molecular characterization of HRSV should be conducted to monitor the evolution of HRSV in China.
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28
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A single intranasal administration of virus-like particle vaccine induces an efficient protection for mice against human respiratory syncytial virus. Antiviral Res 2017; 144:57-69. [PMID: 28529001 DOI: 10.1016/j.antiviral.2017.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 05/08/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022]
Abstract
Human respiratory syncytial virus (RSV) is an important pediatric pathogen causing acute viral respiratory disease in infants and young children. However, no licensed vaccines are currently available. Virus-like particles (VLPs) may bring new hope to producing RSV VLP vaccine with high immunogenicity and safety. Here, we constructed the recombinants of matrix protein (M) and fusion glycoprotein (F) of RSV, respectively into a replication-deficient first-generation adenoviral vector (FGAd), which were used to co-infect Vero cells to assemble RSV VLPs successfully. The resulting VLPs showed similar immunoreactivity and function to RSV virion in vitro. Moreover, Th1 polarized response, and effective mucosal virus-neutralizing antibody and CD8+ T-cell responses were induced by a single intranasal (i.n.) administration of RSV VLPs rather than intramuscular (i.m.) inoculation, although the comparable RSV F-specific serum IgG and long-lasting RSV-specific neutralizing antibody were detected in the mice immunized by both routes. Upon RSV challenge, VLP-immunized mice showed increased viral clearance but decreased signs of enhanced lung pathology and fewer eosinophils compared to mice immunized with formalin-inactivated RSV (FI-RSV). In addition, a single i.n. RSV VLP vaccine has the capability to induce RSV-specific long-lasting neutralizing antibody responses observable up to 15 months. Our results demonstrate that the long-term and memory immune responses in mice against RSV were induced by a single i.n. administration of RSV VLP vaccine, suggesting a successful approach of RSV VLPs as an effective and safe mucosal vaccine against RSV infection, and an applicable and qualified platform of FGAd-infected Vero cells for VLP production.
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29
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Essaidi-Laziosi M, Lyon M, Mamin A, Fernandes Rocha M, Kaiser L, Tapparel C. A new real-time RT-qPCR assay for the detection, subtyping and quantification of human respiratory syncytial viruses positive- and negative-sense RNAs. J Virol Methods 2016; 235:9-14. [PMID: 27180039 DOI: 10.1016/j.jviromet.2016.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 11/17/2022]
Abstract
Human respiratory syncytial virus (RSV) is a major health problem and the main cause of hospitalization due to bronchiolitis. RSV is divided into two antigenic subgroups, RSV-A and -B that co-circulate worldwide. Rapid and sensitive detection is desirable for proper patient handling while assessment of viral load may help to evaluate disease severity and progression. Finally RSV subtyping is needed to determine the prevalence and pathogenicity of each RSV subgroup, as well as their sensitivity to treatment. In this study, we took into account the most recent circulating RSV variants and designed two quantitative TaqMan one-step RT-PCR assays to detect and quantify both RSV subgroups separately. Standard dilutions of transcripts of positive and negative polarities were included in the assay validation to assess potential differences in sensitivity on negative-sense genomes and positive-sense RNAs. In addition, RSV detection in respiratory specimens of different types and sampled in different populations was compared to commercially available RSV diagnostic tools. Altogether, the RSV-A and -B assays revealed sensitive and quantitative over a wide range of viral loads, with a slight improved sensitivity of the RSV-B assay on positive sense transcripts, and allowed accurate RSV subtyping. We thus provide a useful tool for both RSV diagnostics and research.
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Affiliation(s)
- Manel Essaidi-Laziosi
- Faculty of Medicine of Geneva, Department of Microbiology and Molecular medicine, 1 rue Michel Servet, 1211 Geneva 4, Switzerland; Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
| | - Matthieu Lyon
- Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
| | - Aline Mamin
- Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
| | - Mélanie Fernandes Rocha
- Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
| | - Laurent Kaiser
- Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
| | - Caroline Tapparel
- Faculty of Medicine of Geneva, Department of Microbiology and Molecular medicine, 1 rue Michel Servet, 1211 Geneva 4, Switzerland; Geneva University Hospitals, Infectious Diseases Divisions, Rue Gabrielle-Perret-Gentil 4, 1211 Geneva 4, Switzerland.
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30
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Esposito S, Scarselli E, Lelii M, Scala A, Vitelli A, Capone S, Fornili M, Biganzoli E, Orenti A, Nicosia A, Cortese R, Principi N. Antibody response to respiratory syncytial virus infection in children <18 months old. Hum Vaccin Immunother 2016; 12:1700-6. [PMID: 26901128 DOI: 10.1080/21645515.2016.1145847] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The development of a safe and effective respiratory syncytial virus (RSV) vaccine might be facilitated by knowledge of the natural immune response to this virus. The aims of this study were to evaluate the neutralizing antibody response of a cohort of healthy children <18 months old to RSV infection. During the RSV season, 89 healthy children <18 months old were enrolled and followed up weekly for 12 weeks. At each visit, a nasopharyngeal swab was obtained for RSV detection by real-time polymerase chain reaction (PCR). During the study period, 2 blood samples were drawn and they were used to determine RSV geometric mean neutralizing antibody titres (GMT) against RSV. A total of 35 (39.3%) children had RSV detected during the study period. Among RSV-positive patients, children ≥7 months showed a significantly higher increase in antibody response (p<0.001). A significantly higher number of patients with a ≥4 -fold increase in GMT were ≥7 months old (p = 0.02) and presented lower respiratory tract infections (LRTIs) during the study period (p = 0.01). Viral shedding was longer among children aged ≥7 months (p = 0.06), those with viral load ≥10(6) copies/mL (p = 0.03), and those with LRTIs during the study period (p = 0.03), but it was not associated with the immune response (p = 0.41). In conclusion, natural RSV infection seems to evoke a low immune response in younger children. To be effective in this infant population, which is at highest risk of developing severe LRTIs, vaccines must be able to induce in the first months of life a stronger immune response than that produced by the natural infection.
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Affiliation(s)
- Susanna Esposito
- a Paediatric Highly Intensive Care Unit , Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milan , Italy
| | - Elisa Scarselli
- b ReiThera Srl (formerly Okairos) , Viale Città d'Europa 679, Rome , Italy
| | - Mara Lelii
- a Paediatric Highly Intensive Care Unit , Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milan , Italy
| | - Alessia Scala
- a Paediatric Highly Intensive Care Unit , Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milan , Italy
| | - Alessandra Vitelli
- b ReiThera Srl (formerly Okairos) , Viale Città d'Europa 679, Rome , Italy
| | - Stefania Capone
- b ReiThera Srl (formerly Okairos) , Viale Città d'Europa 679, Rome , Italy
| | - Marco Fornili
- c Unit of Medical Statistics, Biometry and Bioinformatics "G.A. Maccacaro"; Università degli Studi di Milano, Fondazione IRCCS Istituto Nazionale Tumori , Milan , Italy
| | - Elia Biganzoli
- c Unit of Medical Statistics, Biometry and Bioinformatics "G.A. Maccacaro"; Università degli Studi di Milano, Fondazione IRCCS Istituto Nazionale Tumori , Milan , Italy
| | - Annalisa Orenti
- c Unit of Medical Statistics, Biometry and Bioinformatics "G.A. Maccacaro"; Università degli Studi di Milano, Fondazione IRCCS Istituto Nazionale Tumori , Milan , Italy
| | - Alfredo Nicosia
- b ReiThera Srl (formerly Okairos) , Viale Città d'Europa 679, Rome , Italy
| | | | - Nicola Principi
- a Paediatric Highly Intensive Care Unit , Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milan , Italy
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31
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Baronti C, Piorkowski G, Leparc-Goffart I, de Lamballerie X, Dubot-Pérès A. Rapid next-generation sequencing of dengue, EV-A71 and RSV-A viruses. J Virol Methods 2015; 226:7-14. [PMID: 26376168 DOI: 10.1016/j.jviromet.2015.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 09/08/2015] [Accepted: 09/10/2015] [Indexed: 11/16/2022]
Abstract
Accurate characterisation of viral strains constitutes a crucial objective for the management of modern virus collections. Next-generation sequencing (NGS) provides technical solution for fast and cost-effective full genome sequencing. Here, we report protocols for rapid full-genome characterisation of RNA viruses of medical importance: dengue virus, enterovirus A71 and respiratory syncytial virus A, based on a specific amplification step followed by NGS-sequencing. A subset of full-length genome sequences representing the genetic diversity of each virus type was selected in GenBank and used to design primer sets allowing the amplification of the complete genome in 3-8 overlapping PCR fragments. The technique was used for characterising 53 strains (33 DENV, 8 EV-A71, 12 RSV-A) from various genotypes and origins. In a single assay, and in just 4 days, it provided for all strains an excellent genomic coverage (∼ 99% including complete ORF for all strains) and accurate sequences with high number of reads per position (250-3500 on average). The elaboration of specific PCR-based full-genome sequencing protocols for diverse virus groups is likely to revolutionise the characterisation of viral isolates in modern collection, but also to contribute in the next future to the study of RNA viruses directly from biological samples.
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Affiliation(s)
- Cécile Baronti
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13005 Marseille, France; IHU Méditerranée Infection, APHM Public Hospitals of Marseille, 13005 Marseille, France.
| | - Géraldine Piorkowski
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13005 Marseille, France; IHU Méditerranée Infection, APHM Public Hospitals of Marseille, 13005 Marseille, France
| | - Isabelle Leparc-Goffart
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13005 Marseille, France; French National Reference Centre for Arboviruses, IRBA, 13013 Marseille, France
| | - Xavier de Lamballerie
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13005 Marseille, France; IHU Méditerranée Infection, APHM Public Hospitals of Marseille, 13005 Marseille, France
| | - Audrey Dubot-Pérès
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13005 Marseille, France; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, PDR Vientiane, Lao Democratic People's Republic; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Churchill Hospital, Oxford OX3 7LJ, UK
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32
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Cebey-López M, Herberg J, Pardo-Seco J, Gómez-Carballa A, Martinón-Torres N, Salas A, Martinón-Sánchez JM, Gormley S, Sumner E, Fink C, Martinón-Torres F. Viral Co-Infections in Pediatric Patients Hospitalized with Lower Tract Acute Respiratory Infections. PLoS One 2015; 10:e0136526. [PMID: 26332375 PMCID: PMC4558027 DOI: 10.1371/journal.pone.0136526] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/04/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Molecular techniques can often reveal a broader range of pathogens in respiratory infections. We aim to investigate the prevalence and age pattern of viral co-infection in children hospitalized with lower tract acute respiratory infection (LT-ARI), using molecular techniques. METHODS A nested polymerase chain reaction approach was used to detect Influenza (A, B), metapneumovirus, respiratory syncytial virus (RSV), parainfluenza (1-4), rhinovirus, adenovirus (A-F), bocavirus and coronaviruses (NL63, 229E, OC43) in respiratory samples of children with acute respiratory infection prospectively admitted to any of the GENDRES network hospitals between 2011-2013. The results were corroborated in an independent cohort collected in the UK. RESULTS A total of 204 and 97 nasopharyngeal samples were collected in the GENDRES and UK cohorts, respectively. In both cohorts, RSV was the most frequent pathogen (52.9% and 36.1% of the cohorts, respectively). Co-infection with multiple viruses was found in 92 samples (45.1%) and 29 samples (29.9%), respectively; this was most frequent in the 12-24 months age group. The most frequently observed co-infection patterns were RSV-Rhinovirus (23 patients, 11.3%, GENDRES cohort) and RSV-bocavirus / bocavirus-influenza (5 patients, 5.2%, UK cohort). CONCLUSION The presence of more than one virus in pediatric patients admitted to hospital with LT-ARI is very frequent and seems to peak at 12-24 months of age. The clinical significance of these findings is unclear but should warrant further analysis.
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Affiliation(s)
- Miriam Cebey-López
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Jethro Herberg
- Section of Paediatrics, Division of Infectious Disease, Imperial College of London, South Kensington Campus, London, United Kingdom
| | - Jacobo Pardo-Seco
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Alberto Gómez-Carballa
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Nazareth Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - José María Martinón-Sánchez
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Stuart Gormley
- Section of Paediatrics, Division of Infectious Disease, Imperial College of London, South Kensington Campus, London, United Kingdom
| | - Edward Sumner
- Micropathology Ltd., University of Warwick Science Park, Coventry, United Kingdom
| | - Colin Fink
- Micropathology Ltd., University of Warwick Science Park, Coventry, United Kingdom
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Translational Pediatrics and Infectious Diseases Section, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
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Gouriet F, Levy PY, Casalta JP, Zandotti C, Collart F, Lepidi H, Cautela J, Bonnet JL, Thuny F, Habib G, Raoult D. Etiology of Pericarditis in a Prospective Cohort of 1162 Cases. Am J Med 2015; 128:784.e1-8. [PMID: 25770033 DOI: 10.1016/j.amjmed.2015.01.040] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/26/2015] [Accepted: 01/26/2015] [Indexed: 01/09/2023]
Abstract
BACKGROUND Pericarditis is a common disorder that is present in various pathologies and may be the first manifestation of an underlying systemic disease. The aims of this study were to describe the different causes of infectious and noninfectious pericarditis and compare them with those in the literature. METHODS Between May 2007 and September 2012, we prospectively evaluated a strategy using a systematic prescription of tests for the different etiological causes of pericarditis in patients with acute pericarditis who were hospitalized in the Cardiology and Cardiac Surgery Department or admitted to the Emergency Department (University Hospital of Marseille). A total of 1162 patients with suspected pericarditis were included. A standardized diagnosis procedure was performed for 800 patients, and 362 had pericardiocentesis. RESULTS Acute pericarditis was diagnosed in 933 patients. No diagnosis was established in 516 patients (55%), 197 patients suffered from postinjury syndromes, and 156 had previously known diseases that were associated with pericarditis. Our survey allowed us to relate the probable cause of pericarditis in 64 cases. An infectious etiological diagnosis was established in 53 cases. In our study, postinjury syndrome was the leading cause of pericarditis, a new diagnosis was made in 6.7% of cases, and 16% of the diagnoses were linked to a secondary, underlying disease. CONCLUSION Using this strategy, we were able to reduce the number of idiopathic cases. In many cases, the etiologies were still identified. Long-term follow-up in the management of idiopathic pericarditis should remain of great interest for the future diagnosis of other disorders that remain hidden.
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Affiliation(s)
- Frédérique Gouriet
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - Pierre-Yves Levy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - Jean-Paul Casalta
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - Christine Zandotti
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - Frédéric Collart
- Département de Chirurgie Cardiaque, Hôpital de La Timone, AP-HM, Aix-Marseille University, Marseille, France
| | - Hubert Lepidi
- Département d'anathomopathologie, Hôpital de La Timone, AP-HM, Aix-Marseille University, Marseille, France
| | - Jennifer Cautela
- Département de Cardiologie, Hôpital Nord, AP-HM, Aix-Marseille University, Marseille, France
| | - Jean Louis Bonnet
- Département de Cardiologie, Hôpital de La Timone, AP-HM, Aix-Marseille Université, Marseille, France
| | - Franck Thuny
- Département de Cardiologie, Hôpital Nord, AP-HM, Aix-Marseille University, Marseille, France
| | - Gilbert Habib
- Département de Cardiologie, Hôpital de La Timone, AP-HM, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Aix-Marseille Université, Marseille, France.
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Benkouiten S, Charrel R, Belhouchat K, Drali T, Nougairede A, Salez N, Memish ZA, Al Masri M, Fournier PE, Raoult D, Brouqui P, Parola P, Gautret P. Respiratory viruses and bacteria among pilgrims during the 2013 Hajj. Emerg Infect Dis 2015; 20:1821-7. [PMID: 25341199 PMCID: PMC4214309 DOI: 10.3201/eid2011.140600] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The most common pathogens detected were coronaviruses, rhinoviruses, influenza viruses, and Streptococcus pneumoniae. Pilgrims returning from the Hajj might contribute to international spreading of respiratory pathogens. Nasal and throat swab specimens were obtained from 129 pilgrims in 2013 before they departed from France and before they left Saudi Arabia, and tested by PCR for respiratory viruses and bacteria. Overall, 21.5% and 38.8% of pre-Hajj and post-Hajj specimens, respectively, were positive for ≥1 virus (p = 0.003). One third (29.8%) of the participants acquired ≥1 virus, particularly rhinovirus (14.0%), coronavirus E229 (12.4%), and influenza A(H3N2) virus (6.2%) while in Saudi Arabia. None of the participants were positive for the Middle East respiratory syndrome coronavirus. In addition, 50.0% and 62.0% of pre-Hajj and post-Hajj specimens, respectively, were positive for Streptococcus pneumoniae (p = 0.053). One third (36.3%) of the participants had acquired S. pneumoniae during their stay. Our results confirm high acquisition rates of rhinovirus and S. pneumoniae in pilgrims and highlight the acquisition of coronavirus E229.
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Thiberville SD, Gaudart J, Raoult D, Charrel RN. Influenza-attributable deaths in south-eastern France (1999 to 2010): mortality predictions were undependable. BMC Public Health 2015; 15:539. [PMID: 26049715 PMCID: PMC4458058 DOI: 10.1186/s12889-015-1887-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/29/2015] [Indexed: 11/13/2022] Open
Abstract
Background Following the 2009 influenza pandemic, several studies showed that the mortality pattern associated with the A(H1N1)2009 virus primarily affected children and young adults. In this study, we aimed to estimate the influenza-attributable deaths during the periods from 1999 to 2010, in the Provence-Alpes-Côte-d’Azur (PACA) region of south-eastern France in order to corroborate the hypothesis that (i) influenza-attributable deaths caused by A(H1N1)2009 strain were much lower than initially expected. Methods In order to compare our results with published data, we used the same statistical model of an Austrian team, using a Poisson model adjusted on co-circulating respiratory syncytial virus to explain the weekly mortality. Results We assessed that 5.7 % of the respiratory deaths were attributable to influenza virus during the 2009–2010 pandemic season. This mortality was lower than that observed during the ten preceding epidemic periods (13.8 % on average). Age group- based analysis revealed that during the pandemic period, the groups under 65 had a systematically higher excess of respiratory mortality while the age group over 65 had a much lower mortality than during the seasonal epidemic seasons. Similarly, among the less specific outcome (non violent and cardiovascular mortality) the age groups over 45 had higher excess of mortality during the seasonal epidemics than during the pandemic period. Conclusions Since most of the influenza mortality is commonly observed in the elderly group (>65 year-old), the moderate elderly mortality during the 2009 pandemic period has impacted the total mortality, and has resulted in a reduced total mortality despite an increased mortality in the young age group. Despite using identical parameters and the same approach as in a previously published study using an Austrian population sample, we observed a lower excess respiratory mortality in the south-eastern France than in Vienna. Thus, the pandemic virus caused less death than the epidemic viruses that circulated during the preceding years. In contrast with catastrophic predictions made in the early phase of the pandemic, human lives were saved during the circulation period of A(H1N1)2009 virus, resulting in a lower overall mortality.
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Affiliation(s)
- Simon-Djamel Thiberville
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13385, Marseille, France. .,IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France.
| | - Jean Gaudart
- Aix-Marseille Univ, UMR912, SESSTIM (AMU, IRD, INSERM), Marseille, France.
| | - Didier Raoult
- IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France.
| | - Remi N Charrel
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", 13385, Marseille, France. .,IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France.
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36
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Esposito S, Piralla A, Zampiero A, Bianchini S, Di Pietro G, Scala A, Pinzani R, Fossali E, Baldanti F, Principi N. Characteristics and Their Clinical Relevance of Respiratory Syncytial Virus Types and Genotypes Circulating in Northern Italy in Five Consecutive Winter Seasons. PLoS One 2015; 10:e0129369. [PMID: 26047100 PMCID: PMC4457818 DOI: 10.1371/journal.pone.0129369] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/07/2015] [Indexed: 12/30/2022] Open
Abstract
In order to investigate the genetic diversity and patterns of the co-circulating genotypes of respiratory syncytial virus (RSV) and their possible relationships with the severity of RSV infection, we studied all of the RSV-positive nasopharyngeal samples collected from children during five consecutive winters (2009–2010, 2010–2011, 2011–2012, 2012–2013 and 2013–2014). The RSVs were detected using the respiratory virus panel fast assay and single-tube RT-PCR, their nucleotides were sequenced, and they were tested for positive selection. Of the 165 positive samples, 131 (79.4%) carried RSV-A and 34 (20.6%) RSV-B; both groups co-circulated in all of the study periods, with RSV-A predominating in all the seasons except for winter 2010–2011, which had a predominance of RSV-B. Phylogenetic analysis of the RSV-A sequences identified genotypes NA1 and ON1, the second replacing the first during the last two years of the study period. The RSV-B belonged to genotypes BA9 and BA10. BA9 was detected in all the years of the study whereas BA only desultorily. Comparison of the subjects infected by RSV-A and RSV-B types did not reveal any significant differences, but the children infected by genotype A/NA1 more frequently had lower respiratory tract infections (p<0.0001) and required hospitalisation (p = 0.007) more often than those infected by genotype A/ON1. These findings show that RSV has complex patterns of circulation characterised by the periodical replacement of the predominant genotypes, and indicate that the circulation and pathogenic role of the different RSV strains should be investigated as each may have a different impact on the host. A knowledge of the correlations between types, genotypes and disease severity may also be important in order to be able to include the more virulent strains in future vaccines.
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Affiliation(s)
- Susanna Esposito
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- * E-mail:
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alberto Zampiero
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sonia Bianchini
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giada Di Pietro
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessia Scala
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Raffaella Pinzani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Emilio Fossali
- Emergency Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Section of Microbiology, Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Nicola Principi
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
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Borremans B, Vossen R, Becker-Ziaja B, Gryseels S, Hughes N, Van Gestel M, Van Houtte N, Günther S, Leirs H. Shedding dynamics of Morogoro virus, an African arenavirus closely related to Lassa virus, in its natural reservoir host Mastomys natalensis. Sci Rep 2015; 5:10445. [PMID: 26022445 PMCID: PMC4448520 DOI: 10.1038/srep10445] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/10/2015] [Indexed: 12/15/2022] Open
Abstract
Arenaviruses can cause mild to severe hemorrhagic fevers. Humans mainly get infected through contact with infected rodents or their excretions, yet little is known about transmission dynamics within rodent populations. Morogoro virus (MORV) is an Old World arenavirus closely related to Lassa virus with which it shares the same host species Mastomys natalensis. We injected MORV in its host, and sampled blood and excretions at frequent intervals. Infection in adults was acute; viral RNA disappeared from blood after 18 days post infection (dpi) and from excretions after 39 dpi. Antibodies were present from 7 dpi and never disappeared. Neonatally infected animals acquired a chronic infection with RNA and antibodies in blood for at least 3 months. The quantified excretion and antibody patterns can be used to inform mathematical transmission models, and are essential for understanding and controlling transmission in the natural rodent host populations.
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Affiliation(s)
- Benny Borremans
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Raphaël Vossen
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | | | - Sophie Gryseels
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Nelika Hughes
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Mats Van Gestel
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | | | - Stephan Günther
- Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
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Performance Characteristics of Xpert Flu/RSV XC Assay. J Clin Microbiol 2015; 53:2720-1. [PMID: 26019209 DOI: 10.1128/jcm.00972-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/19/2015] [Indexed: 11/20/2022] Open
Abstract
The Xpert Flu/RSV XC assay was compared to laboratory-developed tests (LDTs) (n = 207) and the Xpert Flu assay (n = 147) using archived nasopharyngeal swabs. The percentages of positive agreements with LDTs were 97.8% for influenza A, 97.2% for influenza B, and 89.3% for RSV. The sensitivity of influenza detection was improved with the Xpert Flu/RSV XC assay compared to the Xpert Flu assay.
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Lee N, Chan MCW, Lui GCY, Li R, Wong RYK, Yung IMH, Cheung CSK, Chan ECY, Hui DSC, Chan PKS. High Viral Load and Respiratory Failure in Adults Hospitalized for Respiratory Syncytial Virus Infections. J Infect Dis 2015; 212:1237-40. [PMID: 25904604 PMCID: PMC7539363 DOI: 10.1093/infdis/jiv248] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/16/2015] [Indexed: 12/11/2022] Open
Abstract
A prospective study among adults hospitalized for polymerase chain reaction-confirmed respiratory syncytial virus infections (n = 123) showed frequent occurrence of lower respiratory-tract complications causing respiratory insufficiency (52.8%), requirement for assisted ventilation (16.3%), and intensive care unit admission/death (12.2%). High viral RNA concentration was detected at time of hospitalization, including in patients who presented later than 2 days of illness (day 1-2, 7.29 ± 1.47; day 3-4, 7.28 ± 1.41; day 5-8, 6.66 ± 1.87 log10 copies/mL). RNA concentration was independently associated with risk of complications and respiratory insufficiency (adjusted odds ratio 1.40 per log10 copies/mL increase, 95% confidence interval, 1.03-1.90; P = .034). Our data indicate the need and provide a basis for clinical research on antiviral therapy in this population.
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Affiliation(s)
- Nelson Lee
- Department of Medicine and Therapeutics Stanley Ho Centre for Emerging Infectious Diseases
| | - Martin C W Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR PRC
| | | | - Ran Li
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Beijing Institute of Respiratory Medicine, Capital Medical University, China
| | | | | | | | - Eugenia C Y Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR PRC
| | - David S C Hui
- Department of Medicine and Therapeutics Stanley Ho Centre for Emerging Infectious Diseases
| | - Paul K S Chan
- Stanley Ho Centre for Emerging Infectious Diseases Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR PRC
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Acute otorrhea in children with tympanostomy tubes: prevalence of bacteria and viruses in the post-pneumococcal conjugate vaccine era. Pediatr Infect Dis J 2015; 34:355-60. [PMID: 25764097 DOI: 10.1097/inf.0000000000000595] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Acute tympanostomy-tube otorrhea is a common sequela in children with tympanostomy tubes. Acute tympanostomy-tube otorrhea is generally a symptom of an acute middle ear infection, whereby middle ear fluid drains through the tube. The widespread use of pneumococcal conjugate vaccination (PCV) has changed the bacterial prevalence in the upper respiratory tract of children, but its impact on bacterial and viral pathogens causing acute tympanostomy-tube otorrhea is yet unknown. METHODS This study was performed in the post-PCV7 era parallel to a randomized clinical trial of the clinical and cost-effectiveness of ototopical and systemic antibiotics and initial observation in 230 children aged 1 to 10 years with untreated, uncomplicated acute tympanostomy-tube otorrhea. Otorrhea and nasopharyngeal samples were collected at baseline (before treatment) and at 2 weeks (after treatment). Conventional bacterial culture was performed followed by antimicrobial-resistance assessment. Viruses were identified by polymerase chain reaction. RESULTS At baseline, Haemophilus influenzae (41%), Staphylococcus aureus (40%) and Pseudomonas aeruginosa (18%) were the most prevalent bacteria in otorrhea, followed by Streptococcus pneumoniae (7%) and Moraxella catarrhalis (4%). Most pneumococci were non-PCV7 serotypes. Viruses were detected in 45 otorrhea samples at baseline (21%). Most infections were polymicrobial and overall antimicrobial resistance was low. CONCLUSIONS H. influenzae, S. aureus and P. aeruginosa are the most common microorganisms in children with untreated uncomplicated acute tympanostomy-tube otorrhea. Prevalence of S. pneumoniae has decreased since the introduction of PCV and most pneumococci are nonvaccine serotypes.
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Salez N, Nougairede A, Ninove L, Zandotti C, de Lamballerie X, Charrel RN. Prospective and retrospective evaluation of the Cepheid Xpert® Flu/RSV XC assay for rapid detection of influenza A, influenza B, and respiratory syncytial virus. Diagn Microbiol Infect Dis 2015; 81:256-8. [PMID: 25662018 PMCID: PMC7172894 DOI: 10.1016/j.diagmicrobio.2015.01.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/15/2015] [Accepted: 01/18/2015] [Indexed: 12/02/2022]
Abstract
A total of 281 clinical specimens (nasal swabs and nasopharyngeal aspirates) were tested with the Xpert® Flu/RSV XC. The results were compared to those obtained with the real-time retro transcriptase-polymerase chain reaction assays routinely used in our laboratory. The Xpert® Flu/RSV XC showed sensitivity/specificity of 97.8%/100% and 97.9%/100% for flu and respiratory syncytial virus, respectively. Real-time RT-PCR is gold standard for diagnosis of influenza and RSV in human samples. Xpert® Flu/RSV XC assay sensitivity >97.75% and 100% specificity for both viruses. Similar performances using nasal swabs or and nasopharyngeal aspirate specimens. Turnaround time is 63 min, minimal training, suitable for point-of-care settings. No need for confirmation of the results.
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Affiliation(s)
- Nicolas Salez
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France.
| | - Antoine Nougairede
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
| | - Laetitia Ninove
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
| | - Christine Zandotti
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
| | - Xavier de Lamballerie
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
| | - Remi N Charrel
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 "Emergence des Pathologies Virales", & IHU Méditerranée Infection, APHM Public Hospitals of Marseille 13385, Marseille, France
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Clinical performance evaluation of the Sofia RSV FIA rapid antigen test for diagnosis of respiratory syncytial virus infection. J Clin Microbiol 2014; 53:684-6. [PMID: 25428155 DOI: 10.1128/jcm.03324-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A recently introduced Sofia respiratory syncytial virus (RSV) fluorescent immunoassay (FIA) was evaluated against the BinaxNOW RSV card and the SD Bioline RSV test using 348 respiratory samples. The Sofia, BinaxNOW, and SD Bioline kits showed sensitivities of 66%, 65%, and 64%, respectively, for detecting RSV-A, and 71%, 63%, and 65% for detecting RSV-B, respectively.
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Comparison of the IMDx influenza A virus, influenza B virus, and respiratory syncytial virus A/B assay on the m2000 platform with real-time reverse transcriptase PCR assays. J Clin Microbiol 2014; 52:4441-2. [PMID: 25275003 DOI: 10.1128/jcm.02565-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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44
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Evaluation of the Alere I influenza A&B nucleic acid amplification test by use of respiratory specimens collected in viral transport medium. J Clin Microbiol 2014; 52:3992-5. [PMID: 25210070 DOI: 10.1128/jcm.01639-14] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Alere i Influenza A&B assay is a newly developed rapid molecular assay which has the potential to generate results within 15 min from sample collection. In this study, we evaluated the Alere i Influenza A&B assay by using salvaged frozen respiratory specimens that were collected in viral transport medium from children ages 10 months to 19 years. Alere i Influenza A&B assay test results were compared with viral culture and ProFlu(+) real-time reverse transcription-PCR (RT-PCR) assay results. We found that the overall sensitivity and specificity of the Alere i Influenza A&B assay were 93.3% and 94.5% for the detection of influenza A virus and 100% and 100% for the detection of influenza B virus, respectively, compared to viral culture. In comparison to ProFlu(+) real-time RT-PCR, overall sensitivity and specificity of the Alere i Influenza A&B assay for the detection of influenza A virus were 88.8% and 98.3% and 100% and 100% for detecting influenza B virus. Overall, the Alere i Influenza A&B assay performed well compared to either virus cell culture or RT-PCR.
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Bell JJ, Anderson EJ, Greene WH, Romero JR, Merchant M, Selvarangan R. Multicenter clinical performance evaluation of BD Veritor™ system for rapid detection of respiratory syncytial virus. J Clin Virol 2014; 61:113-7. [PMID: 25034375 DOI: 10.1016/j.jcv.2014.05.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/26/2014] [Accepted: 05/30/2014] [Indexed: 11/28/2022]
Abstract
BACKGROUND BD Veritor™ System for Rapid Detection of Respiratory Syncytial Virus (RSV) is a new-generation lateral flow immunochromatographic assay for objective detection of RSV in respiratory specimens from children. OBJECTIVE To evaluate the performance of BD Veritor™ System for Rapid Detection of RSV in respiratory specimens collected from pediatric patients. STUDY DESIGN A prospective, multicenter clinical trial was undertaken at five study sites representing geographically diverse regions of the U.S. to assess the performance of the BD Veritor™ System for Rapid Detection of RSV in comparison to R-mix shell vial culture and ProFlu+ reverse transcription-PCR assay (Gen-Probe/Prodesse). RESULTS 440 nasopharyngeal washes/aspirates (NPW/A) and 706 nasopharyngeal swab (NPS) specimens from U.S. subjects<20 years of age were collected and tested using the BD Veritor™ System and compared with shell vial culture and real-time RT-PCR results. Analysis of the data indicates the overall sensitivity and specificity for BD Veritor™ System for all sample types combined was 90% and 97.0% versus shell vial culture and 75.5% and 98.7% versus RT-PCR respectively. CONCLUSION Overall, the BD Veritor™ System for the Rapid Detection of RSV performed well when compared to both viral cell culture and RT-PCR in children.
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Affiliation(s)
- J Jeremiah Bell
- Children's Mercy Hospitals and Clinics, Kansas City, MO 64108, United States; University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, United States
| | - Evan J Anderson
- Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Wallace H Greene
- Penn State University College of Medicine, Hershey, PA, United States; Penn State Hershey Medical Center, Hershey, PA, United States
| | - José R Romero
- University of Arkansas for Medical Sciences, Little Rock, AR, United States; Arkansas Children's Hospital, Little Rock, AR, United States
| | - Moheet Merchant
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Rangaraj Selvarangan
- Children's Mercy Hospitals and Clinics, Kansas City, MO 64108, United States; University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, United States.
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Multicenter clinical evaluation of the novel Alere™ i Influenza A&B isothermal nucleic acid amplification test. J Clin Virol 2014; 61:81-6. [PMID: 24973813 DOI: 10.1016/j.jcv.2014.06.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/29/2014] [Accepted: 06/01/2014] [Indexed: 01/14/2023]
Abstract
BACKGROUND Rapid detection of influenza infection is important for patient management and timely anti-viral therapy. Rapid antigen detection tests for influenza have inferior sensitivity when compared to nucleic acid-based amplification tests. An isothermal nucleic acid amplification test that offers the potential for rapid molecular testing at the clinical point-of-care with simple equipment can improve influenza detection rates. OBJECTIVES To evaluate the performance of Alere™ i Influenza A&B isothermal nucleic acid amplification test to detect influenza A and B in comparison to viral cell culture as reference method. STUDY DESIGN A prospective, multicenter, clinical study to evaluate the clinical performance of the Alere™ i Influenza A&B assay in a point-of-care setting using prospectively enrolled specimens from both children and adults was conducted in seven sites. RESULTS In comparison with viral cell culture, the overall sensitivity and specificity of the Alere™ i Influenza A&B assay was 97.8% and 85.6% for the detection of influenza A, and 91.8% and 96.3% for the detection of influenza B, respectively. Following resolution of discrepant results by real-time RT-PCR the sensitivity and specificity of the Alere™ i Influenza A&B assay improved to 99.3% and 98.1% for influenza A, and 97.6% and 100% for influenza B, respectively. CONCLUSIONS The Alere™ i Influenza A&B isothermal nucleic acid amplification test is an ideal point-of-care test for influenza detection in children and adults due to its high sensitivity and specificity and ability to generate results within 15 min from specimen receipt.
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Comparison of Simplexa Flu A/B & RSV PCR with cytospin-immunofluorescence and laboratory-developed TaqMan PCR in predominantly adult hospitalized patients. J Clin Microbiol 2014; 52:3057-9. [PMID: 24850350 DOI: 10.1128/jcm.00738-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To compare Simplexa Flu A/B & RSV PCR with cytospin-immunofluorescence and laboratory-developed TaqMan PCR methods, 445 nasopharyngeal samples were tested. Of these, 199 were positive (46 for respiratory syncytial virus [RSV], 120 for influenza A, and 33 for influenza B) and 246 were negative. The direct fluorescent-antibody assay (DFA) detected 132 (66.3%) positive samples, Simplexa direct detected 162 (81.4%), Simplexa using extracts detected 177 (88.9%), and lab-developed TaqMan PCR reference methods detected 199 (100%). The specificities were 99.6%, 100%, 100%, and 100%, respectively. The two Simplexa methods were more sensitive than the DFA (P = 0.0001) but less sensitive than the TaqMan reverse transcriptase PCR (P = 0.0001).
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Delangue J, Roca Sanchez Y, Piorkowski G, Bessaud M, Baronti C, Thirion-Perrier L, Mafayle RL, Ardaya CA, Aguilera GA, Guzman JR, Riera JL, de Lamballerie X. Viral aetiology influenza like illnesses in Santa Cruz, Bolivia (2010-2012). Virol J 2014; 11:35. [PMID: 24564892 PMCID: PMC4015617 DOI: 10.1186/1743-422x-11-35] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/10/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Acute respiratory infections represent a serious public health issue worldwide but virological aetiologies of Influenza Like Illnesses (ILIs) remain largely unknown in developing countries. This study represents the first attempt to characterise viral aetiologies of ILIs in Bolivia. METHODS It was performed in Santa Cruz city from January 2010 to September 2012, based on 564 naso-pharyngeal swabs collected in a National Reference Laboratory and real-time PCR techniques, viral cultures and phylogenetic analyses. RESULTS 50.2% of samples were positive for at least one virus with influenza viruses (Flu A: ~15%; Flu B: ~9%), rhinoviruses (~8%), coronaviruses (~5%) and hRSV (~4%) being the most frequently identified. The pattern of viral infections varied according to age groups. The elucidation rate was the highest (>60%) amongst patients under 10 yo and the lowest (<40%) amongst patients ≥60 yo. Nearly 3% of samples showed dual viral infections. Epidemiological peaks were associated with a predominant virus but generally included 30-50% of infections by different viruses. Unexpectedly, the frequency of influenza in the 0-4 yo population was very low and a complete hRSV eclipse occurred in 2011. Genetic analyses indicated that distinct evolutionary lineages of Flu A(H1N1)pdm2009, Flu A/H3N2 and Flu B have co-circulated in Bolivia in the study period, originating from Central and North America, Europe, Asia and Australia. CONCLUSION Our results emphasise the requirement for a reinforced epidemiological and genetic follow-up of influenza and other ILIs in Bolivia to further inform the preparation of vaccines used in the region, guide vaccination campaigns and improve the medical management of patients.
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Affiliation(s)
- Julie Delangue
- IRD French Institute of Research for Development, EHESP French School of Public Health, UMR_D 190 "Emergence des Pathologies Virales", Aix Marseille Univ, 13005 Marseille, France.
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Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control. BMC Infect Dis 2014; 14:15. [PMID: 24405747 PMCID: PMC3897990 DOI: 10.1186/1471-2334-14-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 12/20/2013] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Carefully conducted, community-based, longitudinal studies are required to gain further understanding of the nature and timing of respiratory viruses causing infections in the population. However, such studies pose unique challenges for field specimen collection, including as we have observed the appearance of mould in some nasal swab specimens. We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. METHODS Anterior nasal swab samples were collected from infants participating in an ongoing community-based, longitudinal, dynamic birth cohort study. The samples were first collected from each infant shortly after birth and weekly thereafter. They were then mailed to the laboratory where they were catalogued, stored at -80°C and later screened by PCR for 17 respiratory viruses. The quality of specimen collection was assessed by screening for human deoxyribonucleic acid (DNA) using endogenous retrovirus 3 (ERV3). The impact of ERV3 load upon respiratory virus detection and the impact of visible mould observed in a subset of swabs reaching the laboratory upon both ERV3 loads and respiratory virus detection was determined. RESULTS In total, 4933 nasal swabs were received in the laboratory. ERV3 load in nasal swabs was associated with respiratory virus detection. Reduced respiratory virus detection (odds ratio 0.35; 95% confidence interval 0.27-0.44) was observed in samples where the ERV3 could not be identified. Mould was associated with increased time of samples reaching the laboratory and reduced ERV3 loads and respiratory virus detection. CONCLUSION Suboptimal sample collection and high levels of visible mould can impact negatively upon sample quality. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies.
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Recent advances in diagnosis, prevention, and treatment of human respiratory syncytial virus. Adv Virol 2013; 2013:595768. [PMID: 24382964 PMCID: PMC3872095 DOI: 10.1155/2013/595768] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/30/2013] [Indexed: 12/25/2022] Open
Abstract
Human respiratory syncytial virus (RSV) is a common cause of respiratory infection in infants and the elderly, leading to significant morbidity and mortality. The interdisciplinary fields, especially biotechnology and nanotechnology, have facilitated the development of modern detection systems for RSV. Many anti-RSV compounds like fusion inhibitors and RNAi molecules have been successful in laboratory and clinical trials. But, currently, there are no effective drugs for RSV infection even after decades of research. Effective diagnosis can result in effective treatment, but the progress in both of these facets must be concurrent. The development in prevention and treatment measures for RSV is at appreciable pace, but the implementation into clinical practice still seems a challenge. This review attempts to present the promising diverse research approaches and advancements in the area of diagnosis, prevention, and treatment that contribute to RSV management.
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