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Mengual-Chuliá B, Tamayo-Trujillo R, Mira-Iglesias A, Cano L, García-Esteban S, Ferrús ML, Puig-Barberà J, Díez-Domingo J, López-Labrador FX. Enterovirus D68 disease burden and epidemiology in hospital-admitted influenza-like illness, Valencia region of Spain, 2014-2020 influenza seasons. J Med Virol 2024; 96:e29810. [PMID: 39049549 DOI: 10.1002/jmv.29810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/15/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
Enterovirus D68 (EV-D68) is an emerging agent for which data on the susceptible adult population is scarce. We performed a 6-year analysis of respiratory samples from influenza-like illness (ILI) admitted during 2014-2020 in 4-10 hospitals in the Valencia Region, Spain. EV-D68 was identified in 68 (3.1%) among 2210 Enterovirus (EV)/Rhinovirus (HRV) positive samples. Phylogeny of 59 VP1 sequences showed isolates from 2014 clustering in B2 (6/12), B1 (5/12), and A2/D1 (1/12) subclades; those from 2015 (n = 1) and 2016 (n = 1) in B3 and A2/D1, respectively; and isolates from 2018 in A2/D3 (42/45), and B3 (3/45). B1 and B2 viruses were mainly detected in children (80% and 67%, respectively); B3 were equally distributed between children and adults; whereas A2/D1 and A2/D3 were observed only in adults. B3 viruses showed up to 16 amino acid changes at predicted antigenic sites. In conclusion, two EV-D68 epidemics linked to ILI hospitalized cases occurred in the Valencia Region in 2014 and 2018, with three fatal outcomes and one ICU admission. A2/D3 strains from 2018 were associated with severe respiratory infection in adults. Because of the significant impact of non-polio enteroviruses in ILI and the potential neurotropism, year-round surveillance in respiratory samples should be pursued.
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Affiliation(s)
- Beatriz Mengual-Chuliá
- Virology Laboratory, Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Tamayo-Trujillo
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | - Ainara Mira-Iglesias
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Vaccine Research Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Laura Cano
- Virology Laboratory, Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Sandra García-Esteban
- Virology Laboratory, Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Maria Loreto Ferrús
- Virology Laboratory, Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Joan Puig-Barberà
- Vaccine Research Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - Javier Díez-Domingo
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Vaccine Research Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
| | - F Xavier López-Labrador
- Virology Laboratory, Genomics and Health Area, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO-Public Health), Valencia, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Department of Microbiology & Ecology, Medical School, University of Valencia, Valencia, Spain
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2
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Ju DU, Park D, Kim IH, Kim S, Yoo HM. Development of Human Rhinovirus RNA Reference Material Using Digital PCR. Genes (Basel) 2023; 14:2210. [PMID: 38137032 PMCID: PMC10742479 DOI: 10.3390/genes14122210] [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: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.
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Affiliation(s)
- Dong U Ju
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Dongju Park
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Il-Hwan Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Seil Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
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3
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Pichler I, Schmutz S, Ziltener G, Zaheri M, Kufner V, Trkola A, Huber M. Rapid and sensitive single-sample viral metagenomics using Nanopore Flongle sequencing. J Virol Methods 2023; 320:114784. [PMID: 37516367 DOI: 10.1016/j.jviromet.2023.114784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/11/2023] [Accepted: 07/25/2023] [Indexed: 07/31/2023]
Abstract
The ability of viral metagenomic Next-Generation Sequencing (mNGS) to unbiasedly detect nucleic acids in a clinical sample is a powerful tool for advanced diagnosis of viral infections. When clinical symptoms do not provide a clear differential diagnosis, extensive laboratory testing with virus-specific PCR and serology can be replaced by a single viral mNGS analysis. However, widespread diagnostic use of viral mNGS is thus far limited by long sample-to-result times, as most protocols rely on Illumina sequencing, which provides high and accurate sequencing output but is time-consuming and expensive. Here, we describe the development of an mNGS protocol based on the more cost-effective Nanopore Flongle sequencing with decreased turnaround time and lower, yet sufficient sequencing output to provide sensitive virus detection. Sample preparation (6 h) and sequencing (2 h) times are substantially reduced compared to Illumina mNGS and allow detection of DNA/RNA viruses at low input (up to 33-38 cycle threshold of specific qPCR). Although Flongles yield lower sequencing output, direct comparison with Illumina mNGS on diverse clinical samples showed similar results. Collectively, the novel Nanopore mNGS approach is specifically tailored for use in clinical diagnostics and provides a rapid and cost-effective mNGS strategy for individual testing of severe cases.
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Affiliation(s)
- Ian Pichler
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Gabriela Ziltener
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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4
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Alsayed AR, Abed A, Abu-Samak M, Alshammari F, Alshammari B. Etiologies of Acute Bronchiolitis in Children at Risk for Asthma, with Emphasis on the Human Rhinovirus Genotyping Protocol. J Clin Med 2023; 12:3909. [PMID: 37373604 DOI: 10.3390/jcm12123909] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/22/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
This research aims to determine acute bronchiolitis' causative virus(es) and establish a viable protocol to classify the Human Rhinovirus (HRV) species. During 2021-2022, we included children 1-24 months of age with acute bronchiolitis at risk for asthma. The nasopharyngeal samples were taken and subjected to a quantitative polymerase chain reaction (qPCR) in a viral panel. For HRV-positive samples, a high-throughput assay was applied, directing the VP4/VP2 and VP3/VP1 regions to confirm species. BLAST searching, phylogenetic analysis, and sequence divergence took place to identify the degree to which these regions were appropriate for identifying and differentiating HRV. HRV ranked second, following RSV, as the etiology of acute bronchiolitis in children. The conclusion of the investigation of all available data in this study distributed sequences into 7 HRV-A, 1 HRV-B, and 7 HRV-C types based on the VP4/VP2 and VP3/VP1 sequences. The nucleotide divergence between the clinical samples and the corresponding reference strains was lower in the VP4/VP2 region than in the VP3/VP1 region. The results demonstrated the potential utility of the VP4/VP2 region and the VP3/VP1 region for differentiating HRV genotypes. Confirmatory outcomes were yielded, indicating how nested and semi-nested PCR can establish practical ways to facilitate HRV sequencing and genotyping.
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Affiliation(s)
- Ahmad R Alsayed
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Mahmoud Abu-Samak
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan
| | - Farhan Alshammari
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 2440, Saudi Arabia
| | - Bushra Alshammari
- Department of Medical Surgical Nursing, College of Nursing, University of Hail, Hail 2440, Saudi Arabia
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5
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Fu L, Zhang XY, Jin WP, Wang C, Qian SS, Wang MJ, Wang WH, Meng SL, Guo J, Wang ZJ, Chen XQ, Shen S. Identification of a Conserved, Linear Epitope on VP3 of Enterovirus A Species Recognized by a Broad-Spectrum Monoclonal Antibody. Viruses 2023; 15:v15041028. [PMID: 37113008 PMCID: PMC10145497 DOI: 10.3390/v15041028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Outbreaks of hand, foot and mouth disease (HFMD) have occurred frequently in the Asian-Pacific region over the last two decades, caused mainly by the serotypes in Enterovirus A species. High-quality monoclonal antibodies (mAbs) are needed to improve the accuracy and efficiency of the diagnosis of enteroviruses associated HFMD. In this study, a mAb 1A11 was generated using full particles of CV-A5 as an immunogen. In indirect immunofluorescence and Western blotting assays, 1A11 bound to the viral proteins of CV-A2, CV-A4, CV-A5, CV-A6, CV-A10, CV-A16, and EV-A71 of the Enterovirus A and targeted VP3. It has no cross-reactivity to strains of Enterovirus B and C. By mapping with over-lapped and truncated peptides, a minimal and linear epitope 23PILPGF28 was identified, located at the N-terminus of the VP3. A BLAST sequence search of the epitope in the NCBI genus Enterovirus (taxid: 12059) protein database indicates that the epitope sequence is highly conserved among the Enterovirus A species, but not among the other enterovirus species, first reported by us. By mutagenesis analysis, critical residues for 1A11 binding were identified for most serotypes of Enterovirus A. It may be useful for the development of a cost-effective and pan-Enterovirus A antigen detection for surveillance, early diagnosis and differentiation of infections caused by the Enterovirus A species.
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Affiliation(s)
- Lie Fu
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Xiao-Yu Zhang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Wei-Ping Jin
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Chen Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Sha-Sha Qian
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Meng-Jun Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Wen-Hui Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Sheng-Li Meng
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Jing Guo
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Ze-Jun Wang
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Xiao-Qi Chen
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
| | - Shuo Shen
- Wuhan Institute of Biological Products Co., Ltd., Wuhan 430207, China
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Zanella MC, Vu DL, Hosszu-Fellous K, Neofytos D, Van Delden C, Turin L, Poncet A, Simonetta F, Masouridi-Levrat S, Chalandon Y, Cordey S, Kaiser L. Longitudinal Detection of Twenty DNA and RNA Viruses in Allogeneic Hematopoietic Stem Cell Transplant Recipients Plasma. Viruses 2023; 15:v15040928. [PMID: 37112908 PMCID: PMC10142697 DOI: 10.3390/v15040928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Metagenomics revealed novel and routinely overlooked viruses, representing sources of unrecognized infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aim to describe DNA and RNA virus prevalence and kinetics in allo-HSCT recipients' plasma for one year post HSCT. We included 109 adult patients with first allo-HSCT from 1 March 2017 to 31 January 2019 in this observational cohort study. Seventeen DNA and three RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays using plasma samples collected at 0, 1, 3, 6, and 12 months post HSCT. TTV infected 97% of patients, followed by HPgV-1 (prevalence: 26-36%). TTV (median 3.29 × 105 copies/mL) and HPgV-1 (median 1.18 × 106 copies/mL) viral loads peaked at month 3. At least one Polyomaviridae virus (BKPyV, JCPyV, MCPyV, HPyV6/7) was detected in >10% of patients. HPyV6 and HPyV7 prevalence reached 27% and 12% at month 3; CMV prevalence reached 27%. HSV, VZV, EBV, HHV-7, HAdV and B19V prevalence remained <5%. HPyV9, TSPyV, HBoV, EV and HPg-V2 were never detected. At month 3, 72% of patients had co-infections. TTV and HPgV-1 infections were highly prevalent. BKPyV, MCPyV and HPyV6/7 were frequently detected relative to classical culprits. Further investigation is needed into associations between these viral infections and immune reconstitution or clinical outcomes.
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Affiliation(s)
- Marie-Céline Zanella
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Diem-Lan Vu
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Krisztina Hosszu-Fellous
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
| | - Dionysios Neofytos
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Chistian Van Delden
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Lara Turin
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Antoine Poncet
- Center for Clinical Research, Department of Health and Community Medicine, University of Geneva, 1206 Geneva, Switzerland
- Division of Clinical Epidemiology, Department of Health and Community Medicine, University Hospital of Geneva, 1211 Geneva, Switzerland
| | - Federico Simonetta
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Stavroula Masouridi-Levrat
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Yves Chalandon
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
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7
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Filipe IC, Tee HK, Prados J, Piuz I, Constant S, Huang S, Tapparel C. Comparison of tissue tropism and host response to enteric and respiratory enteroviruses. PLoS Pathog 2022; 18:e1010632. [PMID: 35789345 PMCID: PMC9286751 DOI: 10.1371/journal.ppat.1010632] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 07/15/2022] [Accepted: 06/01/2022] [Indexed: 11/21/2022] Open
Abstract
Enteroviruses (EVs) are among the most prevalent viruses worldwide. They are characterized by a high genetic and phenotypic diversity, being able to cause a plethora of symptoms. EV-D68, a respiratory EV, and EV-D94, an enteric EV, represent an interesting paradigm of EV tropism heterogeneity. They belong to the same species, but display distinct phenotypic characteristics and in vivo tropism. Here, we used these two viruses as well as relevant 3D respiratory, intestinal and neural tissue culture models, to highlight key distinctive features of enteric and respiratory EVs. We emphasize the critical role of temperature in restricting EV-D68 tissue tropism. Using transcriptomic analysis, we underscore fundamental differences between intestinal and respiratory tissues, both in the steady-state and in response to infection. Intestinal tissues present higher cell proliferation rate and are more immunotolerant than respiratory tissues. Importantly, we highlight the different strategies applied by EV-D94 and EV-D68 towards the host antiviral response of intestinal and respiratory tissues. EV-D68 strongly activates antiviral pathways while EV-D94, on the contrary, barely induces any host defense mechanisms. In summary, our study provides an insightful characterization of the differential pathogenesis of EV-D68 and EV-D94 and the interplay with their main target tissues. Enteroviruses (EVs) are important human pathogens, associated with more than 20 clinical presentations. They replicate predominantly in the intestinal and/or respiratory mucosae. The respiratory EV-D68 can be considered an emerging virus because it caused an unprecedent outbreak in 2014, and contemporary isolates display increased virulence and novel neurotropic potential. The genetically related enteric EV-D94 is less common and its pathogenesis remains poorly defined, however, its infection has also been associated with neurological symptoms such as acute flaccid paralysis. To decipher the pathogenic mechanisms of these two viruses, we investigated their tropism and innate immunity induction in relevant human respiratory, intestinal and neural tissue culture models. Our results highlight the critical role of temperature in restricting EV-D68 tropism. Furthermore, using transcriptomic analysis, we identified key differences between respiratory and intestinal tissues, with the latter exhibiting higher cell proliferation and being more immunotolerant. More importantly, we could demonstrate the different strategies applied by EV-D94 and EV-D68 towards the host antiviral response, with EV-D68 strongly activating antiviral pathways and EV-D94, in contrast, inducing few host antiviral transcripts. This work identifies key differences in the pathogenesis of these representative respiratory and enteric EVs, which may contribute to the development of targeted antiviral therapies.
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Affiliation(s)
- Ines Cordeiro Filipe
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Han Kang Tee
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Julien Prados
- Bioinformatics Support Platform, University of Geneva, Geneva, Switzerland
| | - Isabelle Piuz
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | | | - Song Huang
- Epithelix SAS Geneva, Geneva, Switzerland
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
- * E-mail:
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8
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Mwita Morobe J, Kamau E, Murunga N, Gatua W, Luka MM, Lewa C, Cheruiyot R, Mutunga M, Odundo C, James Nokes D, Agoti CN. Trends and Intensity of Rhinovirus Invasions in Kilifi, Coastal Kenya, Over a 12-Year Period, 2007-2018. Open Forum Infect Dis 2021; 8:ofab571. [PMID: 34988244 PMCID: PMC8694214 DOI: 10.1093/ofid/ofab571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/11/2021] [Indexed: 12/05/2022] Open
Abstract
Background Rhinoviruses (RVs) are ubiquitous pathogens and the principal etiological agents of common cold. Despite the high frequency of RV infections, data describing their long-term epidemiological patterns in a defined population remain limited. Methods Here, we analyzed 1070 VP4/VP2 genomic region sequences sampled at Kilifi County Hospital on the Kenya coast. The samples were collected between 2007 and 2018 from hospitalized pediatric patients (<60 months of age) with acute respiratory illness. Results Of 7231 children enrolled, RV was detected in 1497 (20.7%) and VP4/VP2 sequences were recovered from 1070 samples (71.5%). A total of 144 different RV types were identified (67 Rhinovirus A, 18 Rhinovirus B, and 59 Rhinovirus C) and at any month, several types co-circulated with alternating predominance. Within types, multiple genetically divergent variants were observed. Ongoing RV infections through time appeared to be a combination of (1) persistent types (observed up to 7 consecutive months), (2) reintroduced genetically distinct variants, and (3) new invasions (average of 8 new types annually). Conclusions Sustained RV presence in the Kilifi community is mainly due to frequent invasion by new types and variants rather than continuous transmission of locally established types/variants.
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Affiliation(s)
- John Mwita Morobe
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nickson Murunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Winfred Gatua
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Martha M Luka
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Clement Lewa
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Robinson Cheruiyot
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Martin Mutunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Calleb Odundo
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
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Abstract
Enterovirus D68 (EV-D68) causes a range of clinical manifestations, including asthma-like illness, severe respiratory disease, and acute flaccid myelitis. EV-D68 has caused worldwide outbreaks since 2014 and is now recognized as a reemerging infection in many countries. EV-D68-specific PCR assays are widely used for the diagnosis of EV-D68 infection; however, assay sensitivity is a concern because of genetic changes in recently circulated EV-D68. To address this, we summarized EV-D68 sequences from previously reported world outbreaks from 2014 through 2020 on GenBank, and found several mutations at the primer and probe binding sites of the existing EV-D68-specific PCR assays. Subsequently, we designed two novel assays corresponding to the recently reported EV-D68 sequences: an EV-D68-specific real-time and seminested PCR. In an analysis of 22 EV-D68 confirmed cases during a recent EV-D68 outbreak in Japan, the new real-time PCR had higher sensitivity than the existing assay (100% versus 45%, P < 0.01) and a lower median CT value (27.8 versus 32.8, P = 0.005). Sensitivity was higher for the new nonnested PCR (91%) than for the existing seminested PCR assay (50%, P < 0.01). The specificity of the new real-time PCR was 100% using samples from non-EV-D68-infected cases (n = 135). In conclusion, our novel assays had higher sensitivity than the existing assay and might lead to more accurate diagnosis of recently circulating EV-D68. To prepare for future EV-D68 outbreaks, EV-D68-specific assays must be continuously monitored and updated.
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Menu E, Driouich JS, Luciani L, Morand A, Ranque S, L’Ollivier C. Detection of Pneumocystis jirovecii in Hospitalized Children Less Than 3 Years of Age. J Fungi (Basel) 2021; 7:jof7070546. [PMID: 34356925 PMCID: PMC8306698 DOI: 10.3390/jof7070546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Abstract
Few data are available in the literature regarding Pneumocystis jirovecii infection in children under 3 years old. This retrospective cohort study aimed to describe medically relevant information among them. All children under 3 years old treated in the same medical units from April 2014 to August 2020 and in whom a P. jirovecii evaluation was undertaken were enrolled in the study. A positive case was defined as a child presenting at least one positive PCR for P. jirovecii in a respiratory sample. Medically relevant information such as demographical characteristics, clinical presentation, microbiological co-infections, and treatments were collected. The objectives were to describe the characteristics of these children with P. jirovecii colonization/infection to determine the key underlying diseases and risk factors, and to identify viral respiratory pathogens associated. The PCR was positive for P. jirovecii in 32 children. Cardiopulmonary pathologies (21.9%) were the most common underlying disease in them, followed by severe combined immunodeficiency (SCID) (18.8%), hyaline membrane disease (15.6%), asthma (9.4%) and acute leukaemia (6.3%). All SCID children were diagnosed with pneumocystis pneumonia. Co-infection with Pj/Rhinovirus (34.4%) was not significant. Overall mortality was 18.8%. Paediatric pneumocystis is not restricted to patients with HIV or SCID and should be considered in pneumonia in children under 3 years old.
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Affiliation(s)
- Estelle Menu
- Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France; (J.-S.D.); (S.R.); (C.L.)
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, 13385 Marseille, France
- Correspondence:
| | - Jean-Sélim Driouich
- Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France; (J.-S.D.); (S.R.); (C.L.)
- Unité des Virus Emergents (UVE), Aix Marseille Université, IRD 190, INSERM 1207, IHU-Méditerranée Infection, 13385 Marseille, France;
| | - Léa Luciani
- Unité des Virus Emergents (UVE), Aix Marseille Université, IRD 190, INSERM 1207, IHU-Méditerranée Infection, 13385 Marseille, France;
| | - Aurélie Morand
- Institut de Recherche pour le Développement IRD, Aix-Marseille Université, Assistance Publique-Hôpitaux de Marseille, AP-HM, MEPHI: Microbes, Evolution, Phylogénie et Infection, IHU-Méditerranée-Infection, 13385 Marseille, France;
| | - Stéphane Ranque
- Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France; (J.-S.D.); (S.R.); (C.L.)
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, 13385 Marseille, France
| | - Coralie L’Ollivier
- Laboratoire de Parasitologie-Mycologie, IHU Méditerranée Infection, 13385 Marseille, France; (J.-S.D.); (S.R.); (C.L.)
- Institut de Recherche pour le Développement, Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille, Service de Santé des Armées, VITROME: Vecteurs-Infections Tropicales et Méditerranéennes, 13385 Marseille, France
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11
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Steiner F, Schmutz S, Gosert R, Huder JB, Redli PM, Capaul R, Hirsch HH, Böni J, Zbinden A. Usefulness of the GenMark ePlex RPP assay for the detection of respiratory viruses compared to the FTD21 multiplex RT-PCR. Diagn Microbiol Infect Dis 2021; 101:115424. [PMID: 34111651 DOI: 10.1016/j.diagmicrobio.2021.115424] [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: 02/09/2021] [Revised: 04/26/2021] [Accepted: 05/01/2021] [Indexed: 11/26/2022]
Abstract
Cartridge-based multiplex panels covering numerous pathogens offer an advantage of minimal hands-on-time and short time to result to commercial RT-PCR assays. In this study, we evaluated the performance of the ePlex respiratory pathogen panel (RPP) compared to the Fast Track Diagnostics Respiratory pathogens 21 multiplex RT-PCR assay (FTD21) using 400 clinical respiratory samples. Discrepant results were further analysed by a reference nucleic acid amplification testing (NAT) and a composite reference approach was used for final interpretation. Discordant results were observed in 56 targets corresponding to 54 samples. Sensitivities and specificities were 85.5% and 99.9% for the ePlex RPP and 95.8% and 99.7% for the FTD21 system, respectively. Altogether, the ePlex RPP is a valuable tool for the rapid detection of a number of different respiratory viruses with the exception of the coronavirus family (low sensitivity ranging from 50-80%) and samples with a low pathogen load (Ct values >33).
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Affiliation(s)
- Fiona Steiner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Rainer Gosert
- Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland; Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Jon B Huder
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Patrick M Redli
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Riccarda Capaul
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hans H Hirsch
- Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland; Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Andrea Zbinden
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
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Brahim Belhaouari D, Wurtz N, Grimaldier C, Lacoste A, Pires de Souza GA, Penant G, Hannat S, Baudoin JP, La Scola B. Microscopic Observation of SARS-Like Particles in RT-qPCR SARS-CoV-2 Positive Sewage Samples. Pathogens 2021; 10:516. [PMID: 33923138 PMCID: PMC8146039 DOI: 10.3390/pathogens10050516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022] Open
Abstract
The ongoing outbreak of novel coronavirus pneumonia (COVID-19) caused by SARS-CoV-2 infection has spread rapidly worldwide. The major transmission routes of SARS-CoV-2 are recognised as inhalation of aerosol/droplets and person-to-person contact. However, some studies have demonstrated that live SARS-CoV-2 can be isolated from the faeces and urine of infected patients, which can then enter the wastewater system. The currently available evidence indicates that the viral RNA present in wastewater may become a potential source of epidemiological data. However, to investigate whether wastewater may present a risk to humans such as sewage workers, we investigated whether intact particles of SARS-CoV-2 were observable and whether it was possible to isolate the virus in wastewater. Using a correlative strategy of light microscopy and electron microscopy (CLEM), we demonstrated the presence of intact and degraded SARS-like particles in RT-qPCR SARS-CoV-2-positive sewage sample collected in the city of Marseille. However, the viral infectivity assessment of SARS-CoV-2 in the wastewater was inconclusive, due to the presence of other viruses known to be highly resistant in the environment such as enteroviruses, rhinoviruses, and adenoviruses. Although the survival and the infectious risk of SARS-CoV-2 in wastewater cannot be excluded from our study, additional work may be required to investigate the stability, viability, fate, and decay mechanisms of SARS-CoV-2 thoroughly in wastewater.
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Affiliation(s)
- Djamal Brahim Belhaouari
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Clio Grimaldier
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
| | - Alexandre Lacoste
- Bataillon des Marins Pompiers de Marseille, 13003 Marseille, France;
| | - Gabriel Augusto Pires de Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Gwilherm Penant
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
| | - Sihem Hannat
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Jean-Pierre Baudoin
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
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Detection of Parechovirus A1 with Monoclonal Antibody against Capsid Protein VP0. Microorganisms 2020; 8:microorganisms8111794. [PMID: 33207765 PMCID: PMC7696872 DOI: 10.3390/microorganisms8111794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/11/2020] [Accepted: 11/15/2020] [Indexed: 01/11/2023] Open
Abstract
Parechovirus A (PeV-A; human parechovirus) causes mild infections and severe diseases such as neonatal sepsis, encephalitis, and cardiomyopathy in young children. Among the 19 types of PeV-A, PeV-A1 is the most common type of infection. We have previously established an immunofluorescence assay for detecting multiple PeV-A types with a polyclonal antibody against the conserved epitope of VP0. Although the polyclonal antibody is useful for PeV-A diagnosis, it could not distinguish the PeV-A genotypes. Thus, the development of a specific monoclonal antibody for identifying the common infection of PeV-A1 would be beneficial in clinical diagnosis practice. In this study, the recombinant full-length PeV-A1 VP0 protein was used in mouse immunization; a total 10 hybridomas were established. After evaluation by immunoblotting and fluorescence assays, six hybridoma clones with monoclonal antibody (mAb) production were confirmed. These mAbs, which specifically recognize viral protein PeV-A1 VP0 without cross-reactivity to PeV-A3, will prove useful in research and PeV-A1 diagnosis.
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Enteroviruses from Humans and Great Apes in the Republic of Congo: Recombination within Enterovirus C Serotypes. Microorganisms 2020; 8:microorganisms8111779. [PMID: 33202777 PMCID: PMC7709013 DOI: 10.3390/microorganisms8111779] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/07/2020] [Accepted: 11/11/2020] [Indexed: 11/28/2022] Open
Abstract
Enteroviruses (EVs) are viruses of the family Picornaviridae that cause mild to severe infections in humans and in several animal species, including non-human primates (NHPs). We conducted a survey and characterization of enteroviruses circulating between humans and great apes in the Congo. Fecal samples (N = 24) of gorillas and chimpanzees living close to or distant from humans in three Congolese parks were collected, as well as from healthy humans (N = 38) living around and within these parks. Enteroviruses were detected in 29.4% of gorilla and 13.15% of human feces, including wild and human-habituated gorillas, local humans and eco-guards. Two identical strains were isolated from two humans coming from two remote regions. Their genomes were similar and all genes showed their close similarity to coxsackieviruses, except for the 3C, 3D and 5′-UTR regions, where they were most similar to poliovirus 1 and 2, suggesting recombination. Recombination events were found between these strains, poliovirus 1 and 2 and EV-C99. It is possible that the same EV-C species circulated in both humans and apes in different regions in the Congo, which must be confirmed in other investigations. In addition, other studies are needed to further investigate the circulation and genetic diversity of enteroviruses in the great ape population, to draw a definitive conclusion on the different species and types of enteroviruses circulating in the Republic of Congo.
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15
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Scagnolari C, Bitossi C, Frasca F, Viscido A, Brazzini G, Trancassini M, Pietropaolo V, Midulla F, Cimino G, Palange P, Pierangeli A, Antonelli G. Differential toll like receptor expression in cystic fibrosis patients' airways during rhinovirus infection. J Infect 2020; 81:726-735. [PMID: 32712204 DOI: 10.1016/j.jinf.2020.07.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/27/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVES Since an inappropriate and sustained activation of TLRs may contribute to a chronic inflammatory response resulting in detrimental effects in cystic fibrosis (CF) patients, we sought to examine whether HRV infection might alter the respiratory expression of TLRs according to the microbiological status of CF patients. METHODS Respiratory samples were collected from the respiratory tract of CF patients (n = 294) over a period of 12 months. In addition to the usual microbiological investigation, HRV-RNA detection and typing were performed by RT-PCR and sequencing. HRV viral load and TLRs levels were measured by RT-Real Time PCR. RESULTS HRV-RNA was detected in 80 out of 515 respiratory samples (15.5%) with a similar rate in all age groups (0-10 years, 11-24 years, ≥ 25 years). Patients infected with different HRV A, B and C species exhibited higher levels of TLR2, TLR4 and TLR8 as compared to HRV negative patients. Moreover, the expression level of TLR2, TLR4 and TLR8 correlated with high level of HRV viral load. HRV positive patients co-colonized by Staphylococcus aureus or Pseudomonas aeruginosa showed also enhanced amounts of TLR2 and TLR2/4-mRNAs expression respectively. In the case of presence of both bacteria, TLR2, TLR4, TLR8 and TLR9 levels are elevated in positive HRV patients. CONCLUSIONS TLRs, especially TLR2 and TLR4, increased in HRV positive CF individuals and varies according to the presence of S. aureus, P. aeruginosa and both bacteria.
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Affiliation(s)
- Carolina Scagnolari
- Virology Laboratory, Department of Molecular Medicine, Affiliated to Pasteur Institute Italy, Cenci Bolognetti Foundation, Sapienza University, Viale di Porta Tiburtina, 28, 00185 Rome, Italy.
| | - Camilla Bitossi
- Virology Laboratory, Department of Molecular Medicine, Affiliated to Pasteur Institute Italy, Cenci Bolognetti Foundation, Sapienza University, Viale di Porta Tiburtina, 28, 00185 Rome, Italy
| | - Federica Frasca
- Virology Laboratory, Department of Molecular Medicine, Affiliated to Pasteur Institute Italy, Cenci Bolognetti Foundation, Sapienza University, Viale di Porta Tiburtina, 28, 00185 Rome, Italy
| | - Agnese Viscido
- Virology Laboratory, Department of Molecular Medicine, Affiliated to Pasteur Institute Italy, Cenci Bolognetti Foundation, Sapienza University, Viale di Porta Tiburtina, 28, 00185 Rome, Italy
| | - Gabriele Brazzini
- Virology Laboratory, Department of Molecular Medicine, Affiliated to Pasteur Institute Italy, Cenci Bolognetti Foundation, Sapienza University, Viale di Porta Tiburtina, 28, 00185 Rome, Italy
| | - Maria Trancassini
- Department of Public Health and Infectious Diseases, Sapienza University, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, Sapienza University, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Fabio Midulla
- Department of Pediatrics, Policlinico Umberto I University Hospital, Sapienza University, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Giuseppe Cimino
- Lazio Reference Center for Cystic Fibrosis, Policlinico Umberto I University Hospital, Sapienza University, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Paolo Palange
- Department of Public Health and Infectious Diseases, Sapienza University, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Alessandra Pierangeli
- Virology Laboratory, Department of Molecular Medicine, Affiliated to Pasteur Institute Italy, Cenci Bolognetti Foundation, Sapienza University, Viale di Porta Tiburtina, 28, 00185 Rome, Italy
| | - Guido Antonelli
- Virology Laboratory, Department of Molecular Medicine, Affiliated to Pasteur Institute Italy, Cenci Bolognetti Foundation, Sapienza University, Viale di Porta Tiburtina, 28, 00185 Rome, Italy
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16
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Pradier A, Masouridi-Levrat S, Bosshard C, Dantin C, Vu DL, Zanella MC, Boely E, Tapparel C, Kaiser L, Chalandon Y, Simonetta F, Roosnek E. Torque Teno Virus as a Potential Biomarker for Complications and Survival After Allogeneic Hematopoietic Stem Cell Transplantation. Front Immunol 2020; 11:998. [PMID: 32536920 PMCID: PMC7267041 DOI: 10.3389/fimmu.2020.00998] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/27/2020] [Indexed: 12/20/2022] Open
Abstract
Impaired immune reconstitution after allogeneic hematopoietic stem cell transplantation (HSCT) contributes to increased risk of cancer relapse and infection resulting in significant morbidity and mortality. Unfortunately, effective strategies to functionally assess the quality of immune reconstitution are still missing. Quantification of in vivo replication of the ubiquitous, non-pathogenic virus Torque Teno Virus (TTV) has been reported in small series as a test to functionally evaluate the quality of post-transplant immune reconstitution. In the present study, we analyzed by quantitative PCR TTV titers in plasma samples from a large cohort of 168 allogeneic HSCT recipients. Our analysis confirms that TTV titers peaked at 100 days post-transplant, followed by progressive normalization thereafter. Negative correlation of TTV titers with T cell absolute numbers during the first year post-transplant points to the restoration of an active anti-TTV immunity. Univariable and multivariable linear regression analysis demonstrated that donor CMV positive serostatus, donor type and immune suppression resulting from GVHD treatment affected the restoration of anti-TTV immunity. Importantly, higher TTV titers at 100 days after transplantation were associated with worse overall survival and higher risk of acute GVHD and infections. Our results provide new insights into the factors affecting the dynamics of TTV replication and indicate that TTV is a potentially useful biomarker to assess immune reconstitution and to predict complications and outcomes of allogeneic HSCT.
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Affiliation(s)
- Amandine Pradier
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Stavroula Masouridi-Levrat
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Carine Bosshard
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Carole Dantin
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Diem-Lan Vu
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Marie-Céline Zanella
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Elsa Boely
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Caroline Tapparel
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Yves Chalandon
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Federico Simonetta
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland.,Translational Research Center for Oncohematology, Department of Internal Medicine Specialties, University of Geneva, Geneva, Switzerland
| | - Eddy Roosnek
- Division of Hematology, Department of Oncology, Faculty of Medicine, Geneva University Hospitals, Geneva, Switzerland
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Point-of-care multiplexed diagnosis of meningitis using the FilmArray® ME panel technology. Eur J Clin Microbiol Infect Dis 2020; 39:1573-1580. [DOI: 10.1007/s10096-020-03859-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/03/2020] [Indexed: 12/30/2022]
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18
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Nakauchi M, Takayama I, Takahashi H, Semba S, Saito S, Kubo H, Kaida A, Oba K, Nagata S, Odagiri T, Kageyama T. Development of real-time fluorescent reverse transcription loop-mediated isothermal amplification assays for rhinovirus detection. J Med Virol 2019; 91:1232-1238. [PMID: 30735248 PMCID: PMC7166982 DOI: 10.1002/jmv.25427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 02/04/2023]
Abstract
Human rhinoviruses (RVs) belong to the genus Enterovirus of the family Picornaviridae, and are classified into RV-A, -B, and -C species. Two assays were developed to detect RVs by a real-time fluorescent reverse transcription loop-mediated isothermal amplification method: one was designed based on the 5'-untranslated regions (UTRs) of RV-A and -B, and the other was designed based on the 5'-UTR of RV-C. The competence of both assays for the diagnosis of RV infection was tested using isolated viruses and compared with real-time reverse transcription polymerase chain reaction assays on clinical specimens. Neither assay demonstrated cross-reactivity with other tested enteroviruses, and they detected 19 out of 21 tested RV-As and seven out of eight tested RV-Cs. The specificity of the assays was 100% for the detection of RVs and their sensitivity for RV-A and RV-C was 86.3% and 77.3%, respectively, on clinical specimens by the combined use of both assays. Considering that both developed assays were highly specific and detected the majority of recently circulating RVs, they are helpful for the diagnosis of RV infection. Consequently, the results generated by these assays will enhance the surveillance of respiratory illness and the study of the roles of RVs associated with clinical features and disease severity.
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Affiliation(s)
- Mina Nakauchi
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Ikuyo Takayama
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Hitoshi Takahashi
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Shohei Semba
- Eiken Chemical Co, Ltd, Taito, Taito-ku, Tokyo, Japan
| | - Shinji Saito
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Hideyuki Kubo
- Division of Microbiology, Osaka Institute of Public Health, Tojo-cho, Tennoji-ku, Osaka, Japan
| | - Atsushi Kaida
- Division of Microbiology, Osaka Institute of Public Health, Tojo-cho, Tennoji-ku, Osaka, Japan
| | - Kunihiro Oba
- Department of Pediatrics, Showa General Hospital, Hanakoganei, Kodaira-shi, Tokyo, Japan
| | - Shiho Nagata
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Takato Odagiri
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
| | - Tsutomu Kageyama
- Influenza Virus Research Center, National Institute of Infectious Diseases, Gakuen, Musashimuyayama-shi, Tokyo, Japan
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19
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Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clin Microbiol Rev 2018; 32:32/1/e00042-18. [PMID: 30541871 DOI: 10.1128/cmr.00042-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.
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20
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Azuma J, Yamamoto T, Sakurai M, Amou R, Yamada C, Hashimoto K, Kajita S, Yamamoto K, Kijima E, Mizoguchi Y, Nakata K, Shimotsuji T, Ozono K. Urinary β2-microglobulin as an early marker of infantile enterovirus and human parechovirus infections. Medicine (Baltimore) 2018; 97:e12930. [PMID: 30412100 PMCID: PMC6221734 DOI: 10.1097/md.0000000000012930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Enterovirus and human parechovirus (HPeV) are RNA viruses belonging to the family Picornaviridae that frequently infect infants. These infections show a wide variety of clinical manifestations, from mild to severe. However, there are no known early clinical markers for diagnosis and prediction of disease severity. The aim of this study was to examine the clinical utility of urinary beta 2-microglobulin (β2MG) for the early detection and prognosis of infantile enterovirus and HPeV infections.This retrospective study included 108 full-term infants younger than 60 days of age, including 15 with enterovirus or HPeV-3 (enterovirus/HPeV-3), 22 with respiratory syncytial virus (RSV), and 24 with bacterial infections. Laboratory data and clinical characteristics were compared among these 3 groups. Of the 15 patients with enterovirus/HPeV-3, 6 were treated with intravenous immunoglobulin (IVIG subgroup) because of severe clinical conditions.Urinary β2MG to creatinine ratio (β2MG/Cr) was significantly higher in the enterovirus/HPeV-3 group compared to bacterial and RSV infection groups (both P < .001). In the enterovirus/HPeV-3 group, mean peak urinary β2MG/Cr was observed on day 1 or 2. Urinary β2MG/Cr values were significantly higher in the IVIG subgroup than the non-IVIG subgroup (P < .001).Increased urinary β2MG/Cr in early-stage infection may be a useful clinical marker for the detection and prediction of infantile enterovirus and HPeV infection severity.
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Affiliation(s)
- Junji Azuma
- Department of Pediatrics, Minoh City Hospital
| | | | | | - Ryuko Amou
- Department of Pediatrics, Minoh City Hospital
| | | | | | | | | | - Eri Kijima
- Department of Pediatrics, Minoh City Hospital
| | | | - Keiko Nakata
- Department of Infectious Diseases, Osaka Institute of Public Health, Osaka, Japan
| | | | - Keiichi Ozono
- Department of Pediatrics, Osaka University Graduate School of Medicine
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21
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Royston L, Essaidi-Laziosi M, Pérez-Rodríguez FJ, Piuz I, Geiser J, Krause KH, Huang S, Constant S, Kaiser L, Garcin D, Tapparel C. Viral chimeras decrypt the role of enterovirus capsid proteins in viral tropism, acid sensitivity and optimal growth temperature. PLoS Pathog 2018; 14:e1006962. [PMID: 29630666 PMCID: PMC5908207 DOI: 10.1371/journal.ppat.1006962] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 04/19/2018] [Accepted: 03/08/2018] [Indexed: 11/19/2022] Open
Abstract
Despite their genetic similarities, enteric and respiratory enteroviruses (EVs) have highly heterogeneous biophysical properties and cause a vast diversity of human pathologies. In vitro differences include acid sensitivity, optimal growth temperature and tissue tropism, which reflect a preferential in vivo replication in the respiratory or gastrointestinal tract and are thus key determinants of EV virulence. To investigate the underlying cause of these differences, we generated chimeras at the capsid-level between EV-D68 (a respiratory EV) and EV-D94 (an enteric EV). Although some chimeras were nonfunctional, EV-D94 with both the capsid and 2A protease or the capsid only of EV-D68 were both viable. Using this latter construct, we performed several functional assays, which indicated that capsid proteins determine acid sensitivity and tropism in cell lines and in respiratory, intestinal and neural tissues. Additionally, capsid genes were shown to also participate in determining the optimal growth temperature, since EV-D94 temperature adaptation relied on single mutations in VP1, while constructs with EV-D68 capsid could not adapt to higher temperatures. Finally, we demonstrate that EV-D68 maintains residual binding-capacity after acid-treatment despite a loss of infectivity. In contrast, non-structural rather than capsid proteins modulate the innate immune response in tissues. These unique biophysical insights expose another layer in the phenotypic diversity of one of world's most prevalent pathogens and could aid target selection for vaccine or antiviral development.
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Affiliation(s)
- Léna Royston
- University of Geneva Faculty of Medicine, Department of Microbiology and Molecular Medicine, 1 Rue Michel-Servet, Geneva, Switzerland
| | - Manel Essaidi-Laziosi
- University of Geneva Faculty of Medicine, Department of Microbiology and Molecular Medicine, 1 Rue Michel-Servet, Geneva, Switzerland
| | - Francisco J. Pérez-Rodríguez
- University of Geneva Faculty of Medicine, Department of Microbiology and Molecular Medicine, 1 Rue Michel-Servet, Geneva, Switzerland
| | - Isabelle Piuz
- University of Geneva Faculty of Medicine, Department of Microbiology and Molecular Medicine, 1 Rue Michel-Servet, Geneva, Switzerland
| | - Johan Geiser
- University of Geneva Faculty of Medicine, Department of Microbiology and Molecular Medicine, 1 Rue Michel-Servet, Geneva, Switzerland
| | - Karl-Heinz Krause
- University of Geneva Faculty of Medicine, Department of Pathology and Immunology, 1 Rue Michel-Servet, Geneva, Switzerland
| | - Song Huang
- Epithelix Sàrl, 18 Chemin des Aulx, Geneva, Switzerland
| | | | - Laurent Kaiser
- Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 4 Rue Gabrielle Perret-Gentil, Geneva 14, Switzerland
| | - Dominique Garcin
- University of Geneva Faculty of Medicine, Department of Microbiology and Molecular Medicine, 1 Rue Michel-Servet, Geneva, Switzerland
| | - Caroline Tapparel
- University of Geneva Faculty of Medicine, Department of Microbiology and Molecular Medicine, 1 Rue Michel-Servet, Geneva, Switzerland
- * E-mail:
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22
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Deschildre A, Pichavant M, Engelmann I, Langlois C, Drumez E, Pouessel G, Boileau S, Romero-Cubero D, Decleyre-Badiu I, Dewilde A, Hober D, Néve V, Thumerelle C, Lejeune S, Mordacq C, Gosset P. Virus-triggered exacerbation in allergic asthmatic children: neutrophilic airway inflammation and alteration of virus sensors characterize a subgroup of patients. Respir Res 2017; 18:191. [PMID: 29137638 PMCID: PMC5686805 DOI: 10.1186/s12931-017-0672-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/01/2017] [Indexed: 12/11/2022] Open
Abstract
Background Viruses are important triggers of asthma exacerbations. They are also detected outside of exacerbation. Alteration of anti-viral response in asthmatic patients has been shown although the mechanisms responsible for this defect remain unclear. The objective of this study was to compare in virus-infected and not-infected allergic asthmatic children, aged 6 to 16 years, admitted to hospital for a severe exacerbation, the innate immune response and especially the expression of pattern recognition receptor (PRR) and their function. Methods Virus identification was performed both during the exacerbation and at steady state (eight weeks later). Data assessed at both periods included clinical features, anti-viral response and inflammation (in sputum and plasma), and PRR expression/function in blood mononuclear cells. Results Viruses were identified in 46 out of 72 children (median age 8.9 years) during exacerbation, and among them, in 17 at steady state. IFN-β, IFN-γ and IL-29 levels in sputum and plasma were similar between infected and not infected patients at both times, as well as the expression of TLR3, RIG-I and MDA5 in blood monocytes and dendritic cells. Airway inflammation in infected patients was characterized by significantly higher IL-5 concentration and eosinophil count. Compared to patients only infected at exacerbation, the re-infected children significantly exhibited lower levels of IFN-γ in plasma and sputum at exacerbation associated with modifications in PRR expression and function in blood mononuclear cells. These re-infected patients also presented an airway neutrophilic inflammation at steady state. Conclusion Our results reports in asthmatic children that impaired anti-viral response during virus-induced exacerbation is more pronounced in a subgroup of patients prone to re-infection by virus. This subgroup is characterized by altered PRR function and a different pattern of airway inflammation. Trial registration This multicenter prospective study was approved by the regional investigational review board (ref: 08/07). Electronic supplementary material The online version of this article (10.1186/s12931-017-0672-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antoine Deschildre
- University Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France. .,CNRS, UMR 8204, F-59000, Lille, France. .,Inserm, U1019, F-59000, Lille, France. .,CHU Lille, F-59000, Lille, France. .,Institut Pasteur de Lille, F-59000, Lille, France. .,CHU Lille, Unité de Pneumologie et Allergologie Pédiatrique, Hopital Jeanne de Flandre, F-59000, Lille, France. .,INSERM U1019-CNRS UMR8204, CIIL, "Lung infection and innate immunity" research group, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, F-59019, Lille cedex, France.
| | - Muriel Pichavant
- University Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France.,CNRS, UMR 8204, F-59000, Lille, France.,Inserm, U1019, F-59000, Lille, France.,CHU Lille, F-59000, Lille, France.,Institut Pasteur de Lille, F-59000, Lille, France
| | - Ilka Engelmann
- CHU Lille, Service de Virologie, F-59000, Lille, France.,University Lille, EA 3610 - Pathogenèse virale du diabète de type 1, F-59000, Lille, France
| | - Carole Langlois
- CHU Lille, Departement de Biostatistiques, F-59000, Lille, France
| | - Elodie Drumez
- CHU Lille, Departement de Biostatistiques, F-59000, Lille, France.,University Lille, EA 2694 - Santé publique: épidémiologie et qualité des soins, Département de Biostatistique, F-59000, Lille, France
| | - Guillaume Pouessel
- CH Roubaix, Service de Pédiatrie, Hôpital Victor Provo, F-59100, Roubaix, France
| | - Sophie Boileau
- CHU Lille, Unité de Pneumologie et Allergologie Pédiatrique, Hopital Jeanne de Flandre, F-59000, Lille, France
| | - David Romero-Cubero
- CHU Lille, Unité de Pneumologie et Allergologie Pédiatrique, Hopital Jeanne de Flandre, F-59000, Lille, France
| | - Irina Decleyre-Badiu
- CHU Lille, Unité de Pneumologie et Allergologie Pédiatrique, Hopital Jeanne de Flandre, F-59000, Lille, France
| | - Anny Dewilde
- CHU Lille, Service de Virologie, F-59000, Lille, France.,University Lille, EA 3610 - Pathogenèse virale du diabète de type 1, F-59000, Lille, France
| | - Didier Hober
- CHU Lille, Service de Virologie, F-59000, Lille, France.,University Lille, EA 3610 - Pathogenèse virale du diabète de type 1, F-59000, Lille, France
| | - Véronique Néve
- University Lille, EA 2694 - Santé publique: épidémiologie et qualité des soins, Département de Biostatistique, F-59000, Lille, France.,CHU Lille, Service d'Exploration Fonctionnelle Respiratoire, F-5900, Lille, France
| | - Caroline Thumerelle
- University Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France.,CNRS, UMR 8204, F-59000, Lille, France.,Inserm, U1019, F-59000, Lille, France.,CHU Lille, F-59000, Lille, France.,Institut Pasteur de Lille, F-59000, Lille, France.,CHU Lille, Unité de Pneumologie et Allergologie Pédiatrique, Hopital Jeanne de Flandre, F-59000, Lille, France
| | - Stéphanie Lejeune
- University Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France.,CNRS, UMR 8204, F-59000, Lille, France.,Inserm, U1019, F-59000, Lille, France.,CHU Lille, F-59000, Lille, France.,Institut Pasteur de Lille, F-59000, Lille, France.,CHU Lille, Unité de Pneumologie et Allergologie Pédiatrique, Hopital Jeanne de Flandre, F-59000, Lille, France
| | - Clémence Mordacq
- University Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France.,CNRS, UMR 8204, F-59000, Lille, France.,Inserm, U1019, F-59000, Lille, France.,CHU Lille, F-59000, Lille, France.,Institut Pasteur de Lille, F-59000, Lille, France.,CHU Lille, Unité de Pneumologie et Allergologie Pédiatrique, Hopital Jeanne de Flandre, F-59000, Lille, France
| | - Philippe Gosset
- University Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France. .,CNRS, UMR 8204, F-59000, Lille, France. .,Inserm, U1019, F-59000, Lille, France. .,CHU Lille, F-59000, Lille, France. .,Institut Pasteur de Lille, F-59000, Lille, France. .,INSERM U1019-CNRS UMR8204, CIIL, "Lung infection and innate immunity" research group, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, F-59019, Lille cedex, France.
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23
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Cordey S, Vu DL, Zanella MC, Turin L, Mamin A, Kaiser L. Novel and classical human astroviruses in stool and cerebrospinal fluid: comprehensive screening in a tertiary care hospital, Switzerland. Emerg Microbes Infect 2017; 6:e84. [PMID: 28928418 PMCID: PMC5625321 DOI: 10.1038/emi.2017.71] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/03/2017] [Accepted: 07/18/2017] [Indexed: 01/26/2023]
Abstract
Classical human astroviruses (HAstV) are the third most common cause of non-bacterial acute gastroenteritis. Due to the lack of routine molecular assays, novel HAstV are underdiagnosed and the magnitude of their contribution to clinical disease remains unknown. To better understand their prevalence and the susceptible patient profile, we conducted a comprehensive screening of novel and classical HAstV in stool and cerebrospinal fluid (CSF) samples collected for clinical care in a tertiary care hospital using a specially designed rRT-PCR panel for the detection of novel (MLB1-3 and VA1-4) and classical HAstV. Of the 654 stool samples, 20 were positive for HAstV, and the novel (n=10; 3 MLB1, 4 MLB2; 3 VA2) and classical (n=10) serotypes were equally prevalent. None of the 105 CSF samples were positive. Investigating the patient profile, we found a higher prevalence (P=0.0002) of both novel and classical HAstV in pediatric stool samples (3.4% and 3%, respectively) compared with adult stool samples (0.5% and 0.7%, respectively). Furthermore, all novel and classical HAstV-positive pediatric subjects were ≤four years old, demonstrating similar susceptible populations. Forty-five percent of positive patients were immunocompromised (novel: 40%, classical: 50%). A comparison of novel and classical HAstV-positive cases showed a lower viral load for novel HAstV (P=0.0007) with significantly more upper respiratory symptoms (70% of subjects; P=0.02); this observation may suggest a unique pathogenic pathway. This study confirms the clinical and epidemiological relevance of novel HAstV and identifies a target population in which routine screening may yield clinically valuable information.
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Affiliation(s)
- Samuel Cordey
- Laboratory of Virology, Infectious Diseases Service, University Hospitals of Geneva, 1211 Geneva, Switzerland
- University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Diem-Lan Vu
- Laboratory of Virology, Infectious Diseases Service, University Hospitals of Geneva, 1211 Geneva, Switzerland
- University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Marie-Celine Zanella
- Laboratory of Virology, Infectious Diseases Service, University Hospitals of Geneva, 1211 Geneva, Switzerland
- University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Lara Turin
- Laboratory of Virology, Infectious Diseases Service, University Hospitals of Geneva, 1211 Geneva, Switzerland
- University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Aline Mamin
- Laboratory of Virology, Infectious Diseases Service, University Hospitals of Geneva, 1211 Geneva, Switzerland
- University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, Infectious Diseases Service, University Hospitals of Geneva, 1211 Geneva, Switzerland
- University of Geneva Medical School, 1211 Geneva, Switzerland
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24
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Lewandowska DW, Zagordi O, Geissberger FD, Kufner V, Schmutz S, Böni J, Metzner KJ, Trkola A, Huber M. Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples. MICROBIOME 2017; 5:94. [PMID: 28789678 PMCID: PMC5549297 DOI: 10.1186/s40168-017-0317-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/25/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sequence-specific PCR is the most common approach for virus identification in diagnostic laboratories. However, as specific PCR only detects pre-defined targets, novel virus strains or viruses not included in routine test panels will be missed. Recently, advances in high-throughput sequencing allow for virus-sequence-independent identification of entire virus populations in clinical samples, yet standardized protocols are needed to allow broad application in clinical diagnostics. Here, we describe a comprehensive sample preparation protocol for high-throughput metagenomic virus sequencing using random amplification of total nucleic acids from clinical samples. RESULTS In order to optimize metagenomic sequencing for application in virus diagnostics, we tested different enrichment and amplification procedures on plasma samples spiked with RNA and DNA viruses. A protocol including filtration, nuclease digestion, and random amplification of RNA and DNA in separate reactions provided the best results, allowing reliable recovery of viral genomes and a good correlation of the relative number of sequencing reads with the virus input. We further validated our method by sequencing a multiplexed viral pathogen reagent containing a range of human viruses from different virus families. Our method proved successful in detecting the majority of the included viruses with high read numbers and compared well to other protocols in the field validated against the same reference reagent. Our sequencing protocol does work not only with plasma but also with other clinical samples such as urine and throat swabs. CONCLUSIONS The workflow for virus metagenomic sequencing that we established proved successful in detecting a variety of viruses in different clinical samples. Our protocol supplements existing virus-specific detection strategies providing opportunities to identify atypical and novel viruses commonly not accounted for in routine diagnostic panels.
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Affiliation(s)
- Dagmara W Lewandowska
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Osvaldo Zagordi
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | | | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Karin J Metzner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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25
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Shinomoto M, Kawasaki T, Sugahara T, Nakata K, Kotani T, Yoshitake H, Yuasa K, Saeki M, Fujiwara Y. First report of human parechovirus type 3 infection in a pregnant woman. Int J Infect Dis 2017; 59:22-24. [PMID: 28347852 DOI: 10.1016/j.ijid.2017.03.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/15/2022] Open
Abstract
Human parechovirus type 3 (HPeV3) can cause serious conditions in neonates, such as sepsis and encephalitis, but data for adults are lacking. The case of a pregnant woman with HPeV3 infection is reported herein. A 28-year-old woman at 36 weeks of pregnancy was admitted because of myalgia and muscle weakness. Her grip strength was 6.0kg for her right hand and 2.5kg for her left hand. The patient's symptoms, probably due to fasciitis and not myositis, improved gradually with conservative treatment, however labor pains with genital bleeding developed unexpectedly 3 days after admission. An obstetric consultation was obtained and a cesarean section was performed, with no complications. A real-time PCR assay for the detection of viral genomic ribonucleic acid against HPeV showed positive results for pharyngeal swabs, feces, and blood, and negative results for the placenta, umbilical cord, umbilical cord blood, amniotic fluid, and breast milk. The HPeV3 was genotyped by sequencing of the VP1 region. The woman made a full recovery and was discharged with her infant in a stable condition.
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Affiliation(s)
- Makiko Shinomoto
- Department of Neurology, Matsushita Memorial Hospital, Osaka, Japan.
| | - Tatsuya Kawasaki
- Department of General Internal Medicine, Matsushita Memorial Hospital, Osaka, Japan
| | - Takuya Sugahara
- Department of Obstetrics and Gynecology, Matsushita Memorial Hospital, Osaka, Japan
| | - Keiko Nakata
- Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Tomoya Kotani
- Department of General Internal Medicine, Matsushita Memorial Hospital, Osaka, Japan
| | - Hidetaka Yoshitake
- Department of General Internal Medicine, Matsushita Memorial Hospital, Osaka, Japan
| | - Kento Yuasa
- Department of General Internal Medicine, Matsushita Memorial Hospital, Osaka, Japan
| | - Masashi Saeki
- Department of Neurology, Matsushita Memorial Hospital, Osaka, Japan
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26
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Cordey S, Schibler M, L'Huillier AG, Wagner N, Gonçalves AR, Ambrosioni J, Asner S, Turin L, Posfay-Barbe KM, Kaiser L. Comparative analysis of viral shedding in pediatric and adult subjects with central nervous system-associated enterovirus infections from 2013 to 2015 in Switzerland. J Clin Virol 2017; 89:22-29. [PMID: 28214758 DOI: 10.1016/j.jcv.2017.01.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/25/2017] [Accepted: 01/28/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND Several enterovirus (EV) genotypes can result in aseptic meningitis, but their routes of access to the central nervous system remain to be elucidated and may differ between the pediatric and adult populations. OBJECTIVE To assess the pattern of viral shedding in pediatric and adult subjects with acute EV meningitis and to generate EV surveillance data for Switzerland. STUDY DESIGN All pediatric and adult subjects admitted to the University Hospitals of Geneva with a diagnosis of EV meningitis between 2013 and 2015 were enrolled. A quantitative EV real-time reverse transcriptase (rRT)-PCR was performed on the cerebrospinal fluid (CSF), blood, stool, urine and respiratory specimens to assess viral shedding and provide a comparative analysis of pediatric and adult populations. EV genotyping was systematically performed. RESULTS EV positivity rates differed significantly between pediatric and adult subjects; 62.5% of pediatric cases (no adult case) were EV-positive in stool and blood for subjects for whom these samples were all collected. Similarly, the EV viral load in blood was significantly higher in pediatric subjects. Blood C-reactive protein levels were lower and the number of leucocytes/mm3 in the CSF were higher in non-viremic than in viremic pediatric subjects, respectively. A greater diversity of EV genotypes was observed in pediatric cases, with a predominance of echovirus 30 in children ≥3 years old and adults. CONCLUSION In contrast to adults, EV-disseminated infections are predominant in pediatric subjects and show different patterns of EV viral shedding. This observation may be useful for clinicians and contribute to modify current practices of patient care.
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Affiliation(s)
- S Cordey
- Laboratory of Virology, Infectious Diseases Service, University Hospitals of Geneva, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland; University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland.
| | - M Schibler
- Laboratory of Virology, Infectious Diseases Service, University Hospitals of Geneva, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland; University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland
| | - A G L'Huillier
- University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland; Pediatric Infectious Diseases Unit, Division of General Pediatrics, Department of Pediatrics, University Hospitals of Geneva, 6 Rue Willy-Donzé, 1211 Geneva 14, Switzerland
| | - N Wagner
- University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland; Pediatric Infectious Diseases Unit, Division of General Pediatrics, Department of Pediatrics, University Hospitals of Geneva, 6 Rue Willy-Donzé, 1211 Geneva 14, Switzerland
| | - A R Gonçalves
- Laboratory of Virology, Infectious Diseases Service, University Hospitals of Geneva, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland; University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland
| | - J Ambrosioni
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, 149 Carrer del Rosselló, 08036 Barcelona, Spain
| | - S Asner
- Pediatric Infectious Diseases and Vaccinology Unit, Department of Pediatrics, University Hospital Center, 46 Rue du Bugnon, 1011 Lausanne, Switzerland; Service of Infectious Diseases, Department of Internal Medicine, University Hospital Center, 46 Rue du Bugnon, 1011 Lausanne, Switzerland
| | - L Turin
- Laboratory of Virology, Infectious Diseases Service, University Hospitals of Geneva, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland; University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland
| | - K M Posfay-Barbe
- University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland; Pediatric Infectious Diseases Unit, Division of General Pediatrics, Department of Pediatrics, University Hospitals of Geneva, 6 Rue Willy-Donzé, 1211 Geneva 14, Switzerland
| | - L Kaiser
- Laboratory of Virology, Infectious Diseases Service, University Hospitals of Geneva, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland; University of Geneva Medical School, 1 Rue Michel-Servet, 1211 Geneva 4, Switzerland
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Rhinovirus Infections and Associated Respiratory Morbidity in Infants: A Prospective Cohort Study. Pediatr Infect Dis J 2016; 35:1069-74. [PMID: 27254029 DOI: 10.1097/inf.0000000000001240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Risk factors promoting rhinovirus (RV) infections are inadequately described in healthy populations, especially infants. OBJECTIVES To determine the frequency of symptomatic and asymptomatic RV infections and identify possible risk factors from host and environment among otherwise healthy infants. METHODS In a prospective birth cohort, respiratory health was assessed in 41 term-born infants by weekly telephonic interviews during the first year of life, and weekly nasal swabs were collected to determine RV prevalence. In a multilevel logistic regression model, associations between prevalence and respiratory symptoms during RV infections and host/environmental factors were determined. RESULTS Twenty-seven percent of nasal swabs in 41 infants tested positive for RVs. Risk factors for RV prevalence were autumn months [odds ratio (OR) = 1.71, P = 0.01, 95% confidence interval (CI): 1.13-2.61], outdoor temperatures between 5 and 10°C (OR = 2.33, P = 0.001, 95% CI: 1.41-3.86), older siblings (OR = 2.60, P = 0.001, 95% CI: 1.50-4.51) and childcare attendance (OR = 1.53, P = 0.07, 95% CI: 0.96-2.44). Fifty-one percent of RV-positive samples were asymptomatic. Respiratory symptoms during RV infections were less likely during the first 3 months of life (OR = 0.34, P = 0.003, 95% CI: 0.17-0.69) and in infants with atopic mothers (OR = 0.44, P = 0.008, 95% CI: 0.24-0.80). Increased tidal volume (OR = 1.67, P = 0.03, 95% CI: 1.04-2.68) and outdoor temperatures between 2 and 5°C (OR = 2.79, P = 0.02, 95% CI: 1.17-6.61) were associated with more symptoms. CONCLUSIONS RVs are highly prevalent during the first year of life, and most infections are asymptomatic. Frequency of RV infections is associated with environmental factors, while respiratory symptoms during RV infections are linked to host determinants like infant age, maternal atopy or premorbid lung function.
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L'Huillier AG, Kaiser L, Petty TJ, Kilowoko M, Kyungu E, Hongoa P, Vieille G, Turin L, Genton B, D'Acremont V, Tapparel C. Molecular Epidemiology of Human Rhinoviruses and Enteroviruses Highlights Their Diversity in Sub-Saharan Africa. Viruses 2015; 7:6412-23. [PMID: 26670243 PMCID: PMC4690871 DOI: 10.3390/v7122948] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/16/2015] [Accepted: 11/19/2015] [Indexed: 11/16/2022] Open
Abstract
Human rhinoviruses (HRVs) and enteroviruses (HEVs) belong to the Enterovirus genus and are the most frequent cause of infection worldwide, but data on their molecular epidemiology in Africa are scarce. To understand HRV and HEV molecular epidemiology in this setting, we enrolled febrile pediatric patients participating in a large prospective cohort assessing the causes of fever in Tanzanian children. Naso/oropharyngeal swabs were systematically collected and tested by real-time RT-PCR for HRV and HEV. Viruses from positive samples were sequenced and phylogenetic analyses were then applied to highlight the HRV and HEV types as well as recombinant or divergent strains. Thirty-eight percent (378/1005) of the enrolled children harboured an HRV or HEV infection. Although some types were predominant, many distinct types were co-circulating, including a vaccinal poliovirus, HEV-A71 and HEV-D68. Three HRV-A recombinants were identified: HRV-A36/HRV-A67, HRV-A12/HRV-A67 and HRV-A96/HRV-A61. Four divergent HRV strains were also identified: one HRV-B strain and three HRV-C strains. This is the first prospective study focused on HRV and HEV molecular epidemiology in sub-Saharan Africa. This systematic and thorough large screening with careful clinical data management confirms the wide genomic diversity of these viruses, brings new insights about their evolution and provides data about associated symptoms.
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Affiliation(s)
- Arnaud G L'Huillier
- Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Laurent Kaiser
- Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Tom J Petty
- Swiss Institute of Bioinformatics, Centre Medical Universitraire, 1 rue Michel-Servet, 1211 Geneva 4, Switzerland.
| | - Mary Kilowoko
- Amana Regional Referral Hospital, PO box 25411, Dar es Salaam TZ-02, United Republic of Tanzania.
| | - Esther Kyungu
- St-Francis Hospital, PO box 73, Ifakara TZ-16, United Republic of Tanzania.
| | - Philipina Hongoa
- St-Francis Hospital, PO box 73, Ifakara TZ-16, United Republic of Tanzania.
| | - Gaël Vieille
- Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Lara Turin
- Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Blaise Genton
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland.
- Centre Hospitalier Universitaire Vaudois, 21 rue du Bugnon, Lausanne 1011, Switzerland.
| | - Valérie D'Acremont
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland.
- Centre Hospitalier Universitaire Vaudois, 21 rue du Bugnon, Lausanne 1011, Switzerland.
| | - Caroline Tapparel
- Geneva University Hospitals and Medical School, 4 rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
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Eccles R, Winther B, Johnston SL, Robinson P, Trampisch M, Koelsch S. Efficacy and safety of iota-carrageenan nasal spray versus placebo in early treatment of the common cold in adults: the ICICC trial. Respir Res 2015; 16:121. [PMID: 26438038 PMCID: PMC4595062 DOI: 10.1186/s12931-015-0281-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/18/2015] [Indexed: 12/03/2022] Open
Abstract
Abstract Iota-carrageenan (I-C) is active against respiratory viruses in vitro and was effective as nasal spray in three previous clinical trials. The current trial served to further investigate I-C in patients with early common cold symptoms. Methods This randomized, placebo-controlled, double-blind phase IV trial was conducted in 200 adult patients with self-diagnosed colds of <48 h’ duration that were confirmed by baseline cold symptom scores. Patients were to self-administer 0.12 % I-C or placebo spray (NaCl 0.5 %) four times daily for four to ten days and record symptom information for ten days. Common respiratory viruses were quantified by RT-PCR during pretreatment and on Day 3 or 4. The primary endpoint was the mean total symptom score (TSS) of eight cold symptoms on Days 2–4 (TSS2–4). Results Patients in both treatment groups had similar baseline TSSs (mean TSS: 6.75 for I-C and 6.79 for placebo). Viruses were detected in baseline samples from 53 of 98 I-C patients (54.1 %) and 54 of 97 placebo patients (55.7 %). Mean ± SE for TSS2–4 was 5.78 ± 0.25 for I-C patients and 6.39 ± 0.25 for placebo (p = 0.0895). Exploratory analyses after unblinding (TSS2–4 excluding a patient with aberrantly high symptom scores [TSS2–4, ex 1pt]; mean of TSS over Days 1–4 [TSS1–4]; change in TSS1–4 relative to baseline [TSS1–4, rel]) demonstrated treatment differences in favor of I-C (p = 0.0364, p = 0.0495 and p = 0.0421, respectively). For patients with quantifiable rhinovirus/enterovirus at baseline, there was a trend towards greater reduction of virus load at Day 3 or 4 (p = 0.0958; I-C: 90.2 % reduction in viral load; placebo: 72.0 %). Treatments were well tolerated with no differences in adverse event rates. Conclusions The primary endpoint did not demonstrate a statistically significant difference between I-C and placebo but showed a trend towards I-C benefit. Exploratory analyses indicated significant reduction of cold symptoms in the I-C group relative to placebo during the first four days when symptoms were most severe, and also substantiated I-C’s activity against rhinovirus/enterovirus. Trial registration NCT01944631 (clinicaltrials.gov)
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Affiliation(s)
- R Eccles
- Common Cold Centre, Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - B Winther
- Respiratory Disease Study Center, University of Virginia, Charlottesville, VA, USA
| | - S L Johnston
- Airway Disease Infection Section & MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, National Heart and Lung Institute, Imperial College, London, UK
| | - P Robinson
- Boehringer Ingelheim Pharmaceuticals Inc., Therapeutic Area Virology, Ridgefield, CT, USA
| | - M Trampisch
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biometrics & Data Management, Ingelheim/Rhein, 55216, Germany
| | - S Koelsch
- Boehringer Ingelheim Pharma GmbH & Co. KG, CHC Development, Medicine & Regulatory Affairs, Ingelheim/Rhein, 55216, Germany.
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Aubry F, Nougairède A, de Fabritus L, Piorkowski G, Gould EA, de Lamballerie X. "ISA-Lation" of Single-Stranded Positive-Sense RNA Viruses from Non-Infectious Clinical/Animal Samples. PLoS One 2015; 10:e0138703. [PMID: 26407018 PMCID: PMC4583506 DOI: 10.1371/journal.pone.0138703] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/02/2015] [Indexed: 01/25/2023] Open
Abstract
Isolation of viral pathogens from clinical and/or animal samples has traditionally relied on either cell cultures or laboratory animal model systems. However, virus viability is notoriously susceptible to adverse conditions that may include inappropriate procedures for sample collection, storage temperature, support media and transportation. Using our recently described ISA method, we have developed a novel procedure to isolate infectious single-stranded positive-sense RNA viruses from clinical or animal samples. This approach, that we have now called "ISA-lation", exploits the capacity of viral cDNA subgenomic fragments to re-assemble and produce infectious viral RNA in susceptible cells. Here, it was successfully used to rescue enterovirus, Chikungunya and Tick-borne encephalitis viruses from a variety of inactivated animal and human samples. ISA-lation represents an effective option to rescue infectious virus from clinical and/or animal samples that may have deteriorated during the collection and storage period, but also potentially overcomes logistic and administrative difficulties generated when complying with current health and safety and biosecurity guidelines associated with shipment of infectious viral material.
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Affiliation(s)
- Fabien Aubry
- 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
- * E-mail:
| | - Antoine Nougairède
- 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
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Lauriane de Fabritus
- 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
| | - 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", 13385, Marseille, France
| | - Ernest A. Gould
- 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
| | - 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", 13385, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
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Abstract
Human rhinoviruses (HRV) cause respiratory infections and are associated with asthma development. We assessed HRV prevalence, types and association with respiratory symptoms in the first year of life in 20 unselected infants. HRV was detected in 32% of 825 weekly nasal swabs. Seventy-four different types of all three species were identified. HRV presence and related respiratory symptoms are highly heterogeneous.
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Lewandowska DW, Zagordi O, Zbinden A, Schuurmans MM, Schreiber P, Geissberger FD, Huder JB, Böni J, Benden C, Mueller NJ, Trkola A, Huber M. Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains. Diagn Microbiol Infect Dis 2015; 83:133-8. [PMID: 26231254 PMCID: PMC7172999 DOI: 10.1016/j.diagmicrobio.2015.06.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 06/01/2015] [Accepted: 06/25/2015] [Indexed: 02/09/2023]
Abstract
Multiplex PCR assays for respiratory viruses are widely used in routine diagnostics, as they are highly sensitive, rapid, and cost effective. However, depending on the assay system, cross-reactivity between viruses that share a high sequence homology as well as detection of rare virus isolates with sequence variations can be problematic. Virus sequence-independent metagenomic high-throughput sequencing allows for accurate detection of all virus species in a given sample, as we demonstrate here for human Enterovirus and Rhinovirus in a lung transplant patient. While early in infection a commercial PCR assay recorded Rhinovirus, high-throughput sequencing correctly identified human Enterovirus C104 as the source of infection, highlighting the potential of the technology and the benefit of applying open assay formats in complex diagnostic situations. Commercial test produced ambivalent results regarding Enterovirus/Rhinovirus infection. To resolve etiology of infection, we performed unbiased metagenomic sequencing. We detected HEV-C104 and other coinfecting viruses. We identified sequence variations in HEV-C104 responsible for low sensitivity. Metagenomics can complement specific routine diagnostics in complex cases.
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Affiliation(s)
- Dagmara W Lewandowska
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Osvaldo Zagordi
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Andrea Zbinden
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Macé M Schuurmans
- Division of Pulmonary Medicine, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Peter Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland
| | | | - Jon B Huder
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Christian Benden
- Division of Pulmonary Medicine, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Nicolas J Mueller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland.
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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Detection of enterovirus D68 in Canadian laboratories. J Clin Microbiol 2015; 53:1748-51. [PMID: 25740765 DOI: 10.1128/jcm.03686-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
The recent emergence of a severe respiratory disease caused by enterovirus D68 prompted investigation into whether Canadian hospital and provincial laboratories can detect this virus using commercial and laboratory-developed assays. This study demonstrated analytical sensitivity differences between commercial and laboratory-developed assays for the detection of enterovirus D68.
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Morikawa S, Hiroi S, Kase T. Detection of respiratory viruses in gargle specimens of healthy children. J Clin Virol 2015; 64:59-63. [PMID: 25728080 PMCID: PMC7106489 DOI: 10.1016/j.jcv.2015.01.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/26/2014] [Accepted: 01/10/2015] [Indexed: 11/28/2022]
Abstract
Gargle samples were collected from children and tested respiratory viruses. In 45(45/200; 22.5%) episodes, some respiratory viruses detected without symptoms. Under asymptomatic conditions, detected viruses were mainly RVs and EV/RV untyped. PIVs, RSV and hCoV OC43 were detected only when clinical symptom was seen. Asymptomatic infections may play an important role in the viral circulation.
Background Respiratory tract viral infection is one of the most common and important diseases in children. Polymerase chain reaction (PCR) tests are often used to detect viruses in samples, it is difficult to interpret the clinical significance of PCR positivity, which may reflect a past, imminent or active asymptomatic infection due to their high sensitivity. Although single respiratory viruses have been detected in samples from children with symptoms, other respiratory viruses can also be detected simultaneously. However, the clinical importance of these findings for the symptoms is not known. Objectives To investigate the prevalence of respiratory viruses among children without any symptoms such as acute respiratory illness and/or fever. Study design From week twenty-five 2013 to week twenty-six 2014, gargle samples were collected from children once a week and these samples were subjected to real-time PCR to detect respiratory viruses. On each sampling day, we asked the parents about their children’s health condition. Results Among the 286 samples collected, 200 were from asymptomatic children. In the asymptomatic condition, human parechovirus, adenovirus, enterovirus, rhinovirus, coronavirus 229E and HKU1 were observed in 45 episodes. In samples from symptomatic children, parainfluenza viruses, respiratory syncytial virus and coronavirus OC43 were detected in addition to those mentioned above. Conclusions Various viruses of different species were detected in the specimens from the children regardless of their health status. It might be speculated that host factors such as the function of the immune system influence the clinical outcome of the infection. However, this needs to be studied further.
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Affiliation(s)
- Saeko Morikawa
- Division of Virology, Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan.
| | - Satoshi Hiroi
- Division of Virology, Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan.
| | - Tetsuo Kase
- Division of Virology, Department of Infectious Diseases, Osaka Prefectural Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka 537-0025, Japan.
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Selvaggi C, Pierangeli A, Fabiani M, Spano L, Nicolai A, Papoff P, Moretti C, Midulla F, Antonelli G, Scagnolari C. Interferon lambda 1-3 expression in infants hospitalized for RSV or HRV associated bronchiolitis. J Infect 2014; 68:467-77. [PMID: 24389019 PMCID: PMC7172705 DOI: 10.1016/j.jinf.2013.12.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 12/19/2013] [Accepted: 12/24/2013] [Indexed: 12/30/2022]
Abstract
OBJECTIVES The airway expression of type III interferons (IFNs) was evaluated in infants hospitalized for respiratory syncytial virus (RSV) or rhinovirus (HRV) bronchiolitis. As an additional objective we sought to determine whether a different expression of IFN lambda 1-3 was associated with different harboring viruses, the clinical course of bronchiolitis or with the levels of well established IFN stimulated genes (ISGs), such as mixovirus resistance A (MxA) and ISG56. METHODS The analysis was undertaken in 118 infants with RSV or HRV bronchiolitis. Nasopharyngeal washes were collected for virological studies and molecular analysis of type III IFN responses. RESULTS RSV elicited higher levels of IFN lambda subtypes when compared with HRV. A similar expression of type III IFN was found in RSVA or RSVB infected infants and in those infected with HRVA or HRVC viruses. Results also indicate that IFN lambda 1 and IFN lambda 2-3 levels were correlated with each other and with MxA and ISG56-mRNAs. In addition, a positive correlation exists between the IFN lambda1 levels and the clinical score index during RSV infection. In particular, higher IFN lambda 1 levels are associated to an increase of respiratory rate. CONCLUSIONS These findings show that differences in the IFN lambda 1-3 levels in infants with RSV or HRV infections are present and that the expression of IFN lambda 1 correlates with the severity of RSV bronchiolitis.
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Affiliation(s)
- Carla Selvaggi
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Alessandra Pierangeli
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Marco Fabiani
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Lucia Spano
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Ambra Nicolai
- Department of Pediatrics PICU, Sapienza University of Rome, Rome, Italy
| | - Paola Papoff
- Department of Pediatrics PICU, Sapienza University of Rome, Rome, Italy
| | - Corrado Moretti
- Department of Pediatrics PICU, Sapienza University of Rome, Rome, Italy
| | - Fabio Midulla
- Department of Pediatrics PICU, Sapienza University of Rome, Rome, Italy
| | - Guido Antonelli
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Carolina Scagnolari
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy.
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Improved molecular typing assay for rhinovirus species A, B, and C. J Clin Microbiol 2014; 52:2461-71. [PMID: 24789198 DOI: 10.1128/jcm.00075-14] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Human rhinoviruses (RVs), comprising three species (A, B, and C) of the genus Enterovirus, are responsible for the majority of upper respiratory tract infections and are associated with severe lower respiratory tract illnesses such as pneumonia and asthma exacerbations. High genetic diversity and continuous identification of new types necessitate regular updating of the diagnostic assays for the accurate and comprehensive detection of circulating RVs. Methods for molecular typing based on phylogenetic comparisons of a variable fragment in the 5' untranslated region were improved to increase assay sensitivity and to eliminate nonspecific amplification of human sequences, which are observed occasionally in clinical samples. A modified set of primers based on new sequence information and improved buffers and enzymes for seminested PCR assays provided higher specificity and sensitivity for virus detection. In addition, new diagnostic primers were designed for unequivocal species and type assignments for RV-C isolates, based on phylogenetic analysis of partial VP4/VP2 coding sequences. The improved assay was evaluated by typing RVs in >3,800 clinical samples. RVs were successfully detected and typed in 99% of the samples that were RV positive in multiplex diagnostic assays.
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Ambrosioni J, Bridevaux PO, Wagner G, Mamin A, Kaiser L. Epidemiology of viral respiratory infections in a tertiary care centre in the era of molecular diagnosis, Geneva, Switzerland, 2011-2012. Clin Microbiol Infect 2014; 20:O578-84. [PMID: 24382326 PMCID: PMC7128668 DOI: 10.1111/1469-0691.12525] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/11/2013] [Accepted: 12/22/2013] [Indexed: 11/27/2022]
Abstract
Few studies have examined the epidemiology of respiratory viral infections in large tertiary centres over more than one season in the era of molecular diagnosis. Respiratory clinical specimens received between 1 January 2011 and 31 December 2012 were analysed. Respiratory virus testing was performed using a large panel of real‐time PCR or RT‐PCR. Results were analysed according to sample type (upper versus lower respiratory tract) and age group. In all, 2996 (2469 (82.4%) upper; 527 (17.6%) lower) specimens were analysed. Overall positivity rate was 47.4% and 23.7% for upper and lower respiratory samples, respectively. The highest positivity rate was observed in patients under 18 years old (p <0.001); picornaviruses were the most frequent viruses detected over the year. Influenza virus, respiratory syncytial virus, human metapneumovirus and coronaviruses showed a seasonal peak during the winter season, while picornaviruses and adenoviruses were less frequently detected in these periods. Multiple viral infections were identified in 12% of positive cases and were significantly more frequent in children (p <0.001). In conclusion, we observed significant differences in viral infection rates and virus types among age groups, clinical sample types and seasons. Follow‐up of viral detection over several seasons allows a better understanding of respiratory viral epidemiology.
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Affiliation(s)
- J Ambrosioni
- Laboratory of Virology, Division of Laboratory Medicine, University of Geneva Hospitals, Geneva, Switzerland; Division of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland
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Kaida A, Kubo H, Takakura KI, Sekiguchi JI, Yamamoto SP, Kohdera U, Togawa M, Amo K, Shiomi M, Ohyama M, Goto K, Hase A, Kageyama T, Iritani N. Associations between Co-Detected Respiratory Viruses in Children with Acute Respiratory Infections. Jpn J Infect Dis 2014; 67:469-75. [DOI: 10.7883/yoken.67.469] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Tapparel C, Sobo K, Constant S, Huang S, Van Belle S, Kaiser L. Growth and characterization of different human rhinovirus C types in three-dimensional human airway epithelia reconstituted in vitro. Virology 2013; 446:1-8. [DOI: 10.1016/j.virol.2013.06.031] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/10/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
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Simultaneous detection and differentiation of human rhino- and enteroviruses in clinical specimens by real-time PCR with locked nucleic Acid probes. J Clin Microbiol 2013; 51:3960-7. [PMID: 24048533 DOI: 10.1128/jcm.01646-13] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Human rhinoviruses (HRVs) and human enteroviruses (HEVs) are significant respiratory pathogens. While HRV infections are restricted to the respiratory tract, HEV infections may spread to secondary target organs. The method of choice for sensitive specific detection of these viruses is reverse transcription (RT)-PCR with primers targeting the conserved 5' noncoding region of the viral RNA. On the other hand, sequence similarities between HRVs and HEVs complicate their differential detection. In this study, we describe the use of locked nucleic acid (LNA) analogues in short double-dye probes which contained only two selectively HRV- or HEV-specific bases. The double-stranded DNA dye BOXTO (4-[6-(benzoxazole-2-yl-(3-methyl-)-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene)]-1-methyl-quinolinium chloride) was used with the LNA probes in a tricolor real-time PCR assay to allow specific detection of HRVs (probes labeled with 6-carboxyfluorescein [FAM] [green]) and HEVs (Cy5 [red]) with additional melting curve analysis (BOXTO [yellow]). The functionality of the probes was validated in PCR and RT-PCR assays using plasmids containing viral cDNA, quantified viral RNA transcripts, cultivated rhino- and enterovirus prototypes, and clinical specimens. Of 100 HRV and 63 HEV prototypes, the probes correctly identified all HEVs except one that produced only a BOXTO signal. Among 118 clinical specimens with sequencing results, concordant results were obtained for 116 specimens. Two specimens were reactive with both probes, but sequencing yielded only a single virus. Real-time PCR with LNA probes allowed sensitive group-specific identification of HRVs and HEVs and would enable relative copy number determination. The assay is suitable for rapid and accurate differential detection of HRVs and HEVs in a diagnostic laboratory setting.
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Kieninger E, Singer F, Tapparel C, Alves MP, Latzin P, Tan HL, Bossley C, Casaulta C, Bush A, Davies JC, Kaiser L, Regamey N. High rhinovirus burden in lower airways of children with cystic fibrosis. Chest 2013. [PMID: 23188200 DOI: 10.1378/chest.12-0954] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Rhinovirus (RV)-induced pulmonary exacerbations are common in cystic fibrosis (CF) and have been associated with impaired virus clearance by the CF airway epithelium in vitro. Here, we assess in vivo the association of RV prevalence and load with antiviral defense mechanisms, airway inflammation, and lung function parameters in children with CF compared with a control group and children with other chronic respiratory diseases. METHODS RV presence and load were measured by real-time reverse transcription-polymerase chain reaction in BAL samples and were related to antiviral and inflammatory mediators measured in BAL and to clinical parameters. RESULTS BAL samples were obtained from children with CF (n = 195), non-CF bronchiectasis (n = 40), or asthma (n = 29) and from a control group (n = 35) at a median (interquartile range [IQR]) age of 8.2 (4.0-11.7) years. RV was detected in 73 samples (24.4%). RV prevalence was similar among groups. RV load (median [IQR] x 10(3) copies/mL) was higher in children with CF (143.0 [13.1-1530.0]), especially during pulmonary exacerbations, compared with children with asthma (3.0 [1.3-25.8], P = .006) and the control group (0.5 [0.3-0.5], P < .001), but similar to patients with non-CF bronchiectasis (122.1 [2.7-4423.5], P = not significant). In children with CF, RV load was negatively associated with interferon (IFN)- b and IFN- l , IL-1ra levels, and FEV 1 , and positively with levels of the cytokines CXCL8 and CXCL10. CONCLUSIONS RV load in CF BAL is high, especially during exacerbated lung disease. Impaired production of antiviral mediators may lead to the high RV burden in the lower airways of children with CF. Whether high RV load is a cause or a consequence of inflammation needs further investigation in longitudinal studies.
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Affiliation(s)
- Elisabeth Kieninger
- Division of Pediatric Respiratory Medicine, Department of Pediatrics, University Hospital, Bern, Switzerland; Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Florian Singer
- Division of Pediatric Respiratory Medicine, Department of Pediatrics, University Hospital, Bern, Switzerland
| | - Caroline Tapparel
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University of Geneva Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marco P Alves
- Division of Pediatric Respiratory Medicine, Department of Pediatrics, University Hospital, Bern, Switzerland; Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Division of Pediatric Respiratory Medicine, Department of Pediatrics, University Hospital, Bern, Switzerland; Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Hui-Leng Tan
- Department of Pediatric Respiratory Medicine, Royal Brompton Hospital, London, England
| | - Cara Bossley
- Department of Pediatric Respiratory Medicine, Royal Brompton Hospital, London, England
| | - Carmen Casaulta
- Division of Pediatric Respiratory Medicine, Department of Pediatrics, University Hospital, Bern, Switzerland
| | - Andrew Bush
- Department of Pediatric Respiratory Medicine, Royal Brompton Hospital, London, England
| | - Jane C Davies
- Department of Pediatric Respiratory Medicine, Royal Brompton Hospital, London, England
| | - Laurent Kaiser
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University of Geneva Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Nicolas Regamey
- Division of Pediatric Respiratory Medicine, Department of Pediatrics, University Hospital, Bern, Switzerland; Department of Clinical Research, University of Bern, Bern, Switzerland.
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Renois F, Lévêque N, Deliège PG, Fichel C, Bouin A, Abely M, N'Guyen Y, Andréoletti L. Enteroviruses as major cause of microbiologically unexplained acute respiratory tract infections in hospitalized pediatric patients. J Infect 2013; 66:494-502. [PMID: 23542784 PMCID: PMC7172623 DOI: 10.1016/j.jinf.2013.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 02/20/2013] [Accepted: 03/12/2013] [Indexed: 12/26/2022]
Abstract
OBJECTIVE To assess the etiological role and the clinical characteristics of HRV and HEV infections in pediatric patients hospitalized for acute respiratory tract infections (ARTIs). METHODS RT-qPCR assays and molecular sequencing methods were used to identify HRV and HEV strains in nasopharyngeal aspirates of 309 hospitalized pediatric patients with microbiologically unexplained ARTIs and in 210 hospitalized pediatric patients without respiratory symptoms from September 2009 to June 2010 in France. RESULTS Among the 309 ARTI cases, 15 HEV and 172 HRV strains were identified whereas only 1 HEV and 37 HRV strains were observed in control patients (187 vs. 38: P < 10(-3)). HRV strains were identified in 150 of the 164 lower ARTIs whereas HEV strains were identified in only 14 of these cases. Among bronchiolitis and asthma exacerbation cases (n = 133), HEV infected cases were older (Median age (months) 36 vs. 11, P = 0.003) and were more frequently associated with a respiratory distress (P = 0.01) and a need for oxygen supply at the time of admission (P = 0.01) than cases infected by HRV strains. CONCLUSION HRV and HEV strains were identified as potential etiological causes of 60.5% of microbiologically unexplained ARTIs diagnosed in hospitalized pediatric cases. A higher clinical severity was observed in HEV infected bronchiolitis or asthma exacerbation cases in comparison to HRV infected cases.
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Affiliation(s)
- Fanny Renois
- Clinical and Molecular Virology Unit, EA4684-CardioVir Medicine Faculty, University Hospital Centre, Reims, France
| | - Nicolas Lévêque
- Clinical and Molecular Virology Unit, EA4684-CardioVir Medicine Faculty, University Hospital Centre, Reims, France
| | - Pierre-Guillaume Deliège
- Clinical and Molecular Virology Unit, EA4684-CardioVir Medicine Faculty, University Hospital Centre, Reims, France
| | - Caroline Fichel
- Clinical and Molecular Virology Unit, EA4684-CardioVir Medicine Faculty, University Hospital Centre, Reims, France
| | - Alexis Bouin
- Clinical and Molecular Virology Unit, EA4684-CardioVir Medicine Faculty, University Hospital Centre, Reims, France
| | - Michel Abely
- Pediatric Unit A, American Memorial Hospital, University Hospital Centre, Reims, France
| | - Yohan N'Guyen
- Clinical and Molecular Virology Unit, EA4684-CardioVir Medicine Faculty, University Hospital Centre, Reims, France
| | - Laurent Andréoletti
- Clinical and Molecular Virology Unit, EA4684-CardioVir Medicine Faculty, University Hospital Centre, Reims, France
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Sansone M, Andersson M, Brittain-Long R, Andersson LM, Olofsson S, Westin J, Lindh M. Rhinovirus infections in western Sweden: a four-year molecular epidemiology study comparing local and globally appearing types. Eur J Clin Microbiol Infect Dis 2013; 32:947-54. [PMID: 23435753 PMCID: PMC7087832 DOI: 10.1007/s10096-013-1832-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/24/2013] [Indexed: 11/07/2022]
Abstract
Human rhinovirus (HRV) is a highly prevalent pathogen and a major cause of acute respiratory tract infection (ARTI). HRV express less seasonality than other viral ARTIs, which typically appear as seasonal epidemics lasting for 1–2 months. The aim of this study was to investigate the seasonal patterns of HRV types over four consecutive years in one geographic region. HRV identified in respiratory samples from 114 patients over a four-year period were analysed by VP4/VP2 sequencing. HRV-A was found in 64, HRV-B in 11 and HRV-C in 37 cases. Overall, 33 different HRV-A types, nine B types and 21 C types were found. As many as 21 of the HRV types appeared during several seasons, with a maximum time-span of four years. Some types appeared during successive seasons and, in some cases, phylogenetic analysis indicated extended periods of circulation locally. Most of the strains were closely related to HRV identified in other parts of the world during the same time period. HRV strains that circulate locally represent many types and seem to reflect that HRV infections are highly globalised. The existence of simultaneous or successive epidemics with different HRV types in combination with the ability of each type to remain in the local population over extended periods of time may contribute to explaining the high rate of HRV infections.
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Affiliation(s)
- M Sansone
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10B, 413 36 Gothenburg, Sweden
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44
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Enterovirus 68 in pediatric patients hospitalized for acute airway diseases. J Clin Microbiol 2012; 51:640-3. [PMID: 23224095 DOI: 10.1128/jcm.02640-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterovirus 68 was detected in 10 respiratory specimens from pediatric patients hospitalized for acute wheezing or bronchitis during 2009 in the northeast of France. Viral loads ranged from 2 × 10(5) to 7.2 × 10(7) copies/ml. Alignment of 5' nontranslated regions and phylogenetic analysis of partial VP1 gene sequences show that these viruses clustered and belonged to clade C.
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45
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Point: is the era of viral culture over in the clinical microbiology laboratory? J Clin Microbiol 2012; 51:2-4. [PMID: 23052302 DOI: 10.1128/jcm.02593-12] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Conventional tube culture systems have long been the mainstay in clinical virology for the growth and identification of viruses from clinical specimens. Innovations such as centrifugation-enhanced shell vial and multiwell plate cultures and the use of genetically engineered and mixed cell lines, coupled with faster detection of viral replication, have allowed for reasonable turnaround times for even some of the most slowly growing clinically important human viruses. However, molecular methods, in particular, the PCR, have usurped the role of viral culture in many laboratories, limiting the use of this traditional method of virus detection or replacing it altogether. Advances and improvements in molecular technology over time have also resulted in newer generations of more rapid and accurate molecular assays for the detection, quantification, and genetic characterization of viruses. For this point-counterpoint, we have asked two individuals, Richard L. Hodinka of the Children's Hospital of Philadelphia, a clinical virologist whose laboratory has completely eliminated viral culture in favor of molecular methods, and Laurent Kaiser, head of the Virology Laboratory at the University of Geneva Hospital, who continues to be a strong advocate of viral culture, to discuss the relevance of viral culture in the molecular age.
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Family outbreak of an infection with a recombinant Coxsackie A virus in eastern Switzerland. Infection 2012; 41:231-5. [PMID: 23055150 DOI: 10.1007/s15010-012-0340-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 09/12/2012] [Indexed: 10/27/2022]
Abstract
PURPOSE We report on an unusual familial outbreak of a coxsackie virus infection in Switzerland in which five family members were affected. Most of the patients presented with signs of meningitis, and four were hospitalized. METHODS In three individuals, the virus was detected in the cerebrospinal fluid, pharynx, and stool, respectively. The genome was sequenced in specimens of two patients. RESULTS The nucleotide sequences of both virus strains were identical. Blast search revealed that the first half of the sequence was 88 % homologous to Enterovirus 75 (EV-75), 87 % with Echovirus 11 (E-11), and 84 % homologous to Coxsackie virus A9 (CV-A9). The second half of the sequence was 77 % homologous to EV-75, 75 % to E-11, and 91 % to CV-A9. CONCLUSION We propose that the isolated virus strain is a recombinant strain with a 5' untranslated region and with the start of the VP4 sequence originating from E-11/EV-75 and the rest of the genome originating from CV-A9. Interestingly, this novel virus strain showed an exceptional virulence and rapid spread. Two weeks after the initial outbreak in this family, a similar outbreak was observed in a second geographic area roughly 100 km distant to the primary identification site, and another 2 months later this virus strain was found to circulate in the western part of Switzerland some 250 km distant to the primary locus. These findings suggest that genetic recombination has resulted in a novel enterovirus with features of high virulence, contagiosity, and spreading.
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47
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Cordey S, Petty TJ, Schibler M, Martinez Y, Gerlach D, van Belle S, Turin L, Zdobnov E, Kaiser L, Tapparel C. Identification of site-specific adaptations conferring increased neural cell tropism during human enterovirus 71 infection. PLoS Pathog 2012; 8:e1002826. [PMID: 22910880 PMCID: PMC3406088 DOI: 10.1371/journal.ppat.1002826] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 06/16/2012] [Indexed: 01/04/2023] Open
Abstract
Enterovirus 71 (EV71) is one of the most virulent enteroviruses, but the specific molecular features that enhance its ability to disseminate in humans remain unknown. We analyzed the genomic features of EV71 in an immunocompromised host with disseminated disease according to the different sites of infection. Comparison of five full-length genomes sequenced directly from respiratory, gastrointestinal, nervous system, and blood specimens revealed three nucleotide changes that occurred within a five-day period: a non-conservative amino acid change in VP1 located within the BC loop (L97R), a region considered as an immunogenic site and possibly important in poliovirus host adaptation; a conservative amino acid substitution in protein 2B (A38V); and a silent mutation in protein 3D (L175). Infectious clones were constructed using both BrCr (lineage A) and the clinical strain (lineage C) backgrounds containing either one or both non-synonymous mutations. In vitro cell tropism and competition assays revealed that the VP1₉₇ Leu to Arg substitution within the BC loop conferred a replicative advantage in SH-SY5Y cells of neuroblastoma origin. Interestingly, this mutation was frequently associated in vitro with a second non-conservative mutation (E167G or E167A) in the VP1 EF loop in neuroblastoma cells. Comparative models of these EV71 VP1 variants were built to determine how the substitutions might affect VP1 structure and/or interactions with host cells and suggest that, while no significant structural changes were observed, the substitutions may alter interactions with host cell receptors. Taken together, our results show that the VP1 BC loop region of EV71 plays a critical role in cell tropism independent of EV71 lineage and, thus, may have contributed to dissemination and neurotropism in the immunocompromised patient.
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Affiliation(s)
- Samuel Cordey
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva, Geneva, Switzerland.
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Puig-Barberà J, Díez-Domingo J, Arnedo-Pena A, Ruiz-García M, Pérez-Vilar S, Micó-Esparza JL, Belenguer-Varea A, Carratalá-Munuera C, Gil-Guillén V, Schwarz-Chavarri H. Effectiveness of the 2010-2011 seasonal influenza vaccine in preventing confirmed influenza hospitalizations in adults: a case-case comparison, case-control study. Vaccine 2012; 30:5714-20. [PMID: 22819720 PMCID: PMC7115682 DOI: 10.1016/j.vaccine.2012.07.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 07/01/2012] [Accepted: 07/06/2012] [Indexed: 12/03/2022]
Abstract
Introduction We estimated influenza vaccine effectiveness (IVE) to prevent laboratory-confirmed influenza-related hospitalizations in patients 18 years old or older during the 2010–2011 influenza season. Methods We conducted a prospective case-control study in five hospitals, in Valencia, Spain. Study subjects were consecutive emergency hospitalizations for predefined conditions associated with an influenza-like illness episode <8 days before admission. Patients were considered immunized if vaccinated ≥14 days before influenza-like illness onset. Cases were those with a real time reverse transcriptase polymerase chain reaction (RT-PCR) positive for influenza and controls were RT-PCR positive for other respiratory viruses. Adjusted IVE was estimated as 100 × (1 − adjusted odds ratio). To account for indication bias we computed adjusted IVE for respiratory syncytial virus related hospitalizations. Results Of 826 eligible hospitalized patients, 102 (12%) were influenza positive and considered cases, and 116 (14%) were positive for other respiratory viruses and considered controls. Adjusted IVE was 54% (95% confidence interval, 11–76%). By subgroup, adjusted IVE was 53% (4–77%) for those with high-risk conditions, 59% (16–79%) for those ≥60 years of age, and, 54% (4–79%) for those ≥60 years of age with high-risk conditions. No influenza vaccine effect was observed against respiratory syncytial virus related hospitalization. Conclusion Influenza vaccination was associated with a significant reduction on the risk of confirmed influenza hospitalization, irrespective of age and high-risk conditions.
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Affiliation(s)
- J Puig-Barberà
- Centro Superior de Investigación en Salud Pública CSISP, Valencia, Spain. puig
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Critical analysis of rhinovirus RNA load quantification by real-time reverse transcription-PCR. J Clin Microbiol 2012; 50:2868-72. [PMID: 22718934 DOI: 10.1128/jcm.06752-11] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhinoviruses are the most frequent cause of human respiratory infections, and quantitative rhinovirus diagnostic tools are needed for clinical investigations. Although results obtained by real-time reverse-transcription PCR (RT-PCR) assays are frequently converted to viral RNA loads, this presents several limitations regarding accurate virus RNA quantification, particularly given the need to reliably quantify all known rhinovirus genotypes with a single assay. Using an internal extraction control and serial dilutions of an in vitro-transcribed rhinovirus RNA reference standard, we validated a quantitative one-step real-time PCR assay. We then used chimeric rhinovirus genomes with 5'-untranslated regions (5'UTRs) originating from the three rhinovirus species and from one enterovirus to estimate the impact of the 5'UTR diversity. Respiratory specimens from infected patients were then also analyzed. The assay quantification ability ranged from 4.10 to 9.10 log RNA copies/ml, with an estimated error margin of ±10%. This variation was mainly linked to target variability and interassay variability. Taken together, our results indicate that our assay can reliably estimate rhinovirus RNA load, provided that the appropriate error margin is used. In contrast, due to the lack of a universal rhinovirus RNA standard and the variability related to sample collection procedures, accurate absolute rhinovirus RNA quantification in respiratory specimens is currently hardly feasible.
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50
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Lau SKP, Yip CCY, Lung DC, Lee P, Que TL, Lau YL, Chan KH, Woo PCY, Yuen KY. Detection of human rhinovirus C in fecal samples of children with gastroenteritis. J Clin Virol 2012; 53:290-6. [PMID: 22317907 PMCID: PMC7108355 DOI: 10.1016/j.jcv.2012.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/04/2012] [Accepted: 01/09/2012] [Indexed: 12/31/2022]
Abstract
Background Despite recent discovery of the novel human rhinovirus species, HRV-C, little is known about the association of HRV-C in diseases other than respiratory tract infections. Objectives To investigate the presence of HRV-C in fecal samples of children with gastroenteritis. Study design 734 fecal samples from hospitalized children with gastroenteritis were subject to picornavirus detection by RT-PCR of the conserved 5′-NCR. Positive samples were subject to VP4 and 3Dpol gene analysis for species determination. The clinical and molecular epidemiology of HRV-C and other picornaviruses was analyzed. Results Picornaviruses were detected in 113 (15.4%) of 734 fecal samples from children with gastroenteritis by RT-PCR of 5′-NCR, with 58 containing potential HRVs and 55 containing other enteroviruses. PCR of the VP4 and 3Dpol regions was positive in 21 and 19 samples respectively (both regions positive in 8 samples). Sequencing analysis showed the presence of HRV-C in four samples, and diverse picornaviruses including HRV-A (n = 2), HEV-A (n = 2), HEV-B (n = 2), HEV-C (n = 21) and HPeV (n = 2) in other samples, with co-detection of HRV-C and HPeV in one sample. Of the four children with HRV-C detected in fecal samples, three presented with diarrhea in the absence of respiratory symptoms, while one also had acute bronchiolitis. The four HRV-C strains from fecal samples belonged to the existing clade of diverse HRV-C genotypes, indistinguishable from previous respiratory strains. Conclusions HRV-C can be detected in fecal samples of children with gastroenteritis, in the absence of respiratory symptoms. This study also represented the first to detect HPeV in our population.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.
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