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Berginc N, Sočan M, Prosenc Trilar K, Petrovec M. Seasonality and Genotype Diversity of Human Rhinoviruses during an Eight-Year Period in Slovenia. Microorganisms 2024; 12:341. [PMID: 38399745 PMCID: PMC10893136 DOI: 10.3390/microorganisms12020341] [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: 12/21/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Due to the high socioeconomic burden of rhinoviruses, the development of prevention and treatment strategies is of high importance. Understanding the epidemiological and clinical features of rhinoviruses is essential in order to address these issues. Our study aimed to define the seasonality and molecular epidemiology of rhinoviruses in Slovenia. Over a period of eight years, a total of 20,425 patients from sentinel primary healthcare settings and sentinel hospitals were examined for a panel of respiratory viruses in the national programme for the surveillance of influenza-like illnesses and acute respiratory infections. The patients were from all age groups and had respiratory infections of various severity. Infection with a rhinovirus was confirmed using an RT-rPCR in 1834 patients, and 1480 rhinoviruses were genotyped. The molecular analysis was linked to demographical and meteorological data. We confirmed the year-round circulation of rhinoviruses with clear seasonal cycles, resulting in two seasonal waves with peaks in spring and autumn. High levels of genotype variability and co-circulation were confirmed between and within seasons and were analysed in terms of patient age, the patient source reflecting disease severity, and meteorological factors. Our study provides missing scientific information on the genotype diversity of rhinoviruses in Slovenia. As most previous investigations focused on exclusive segments of the population, such as children or hospitalised patients, and for shorter study periods, our study, with its design, size and length, contributes complementary aspects and new evidence-based knowledge to the regional and global understanding of rhinovirus seasonality and molecular epidemiology.
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Affiliation(s)
- Nataša Berginc
- Department of Public Health Microbiology, National Laboratory of Health, Environment and Food, 1000 Ljubljana, Slovenia;
| | - Maja Sočan
- Centre for Infectious Diseases, National Institute of Public Health, 1000 Ljubljana, Slovenia
| | - Katarina Prosenc Trilar
- Department of Public Health Microbiology, National Laboratory of Health, Environment and Food, 1000 Ljubljana, Slovenia;
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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Castañeda-Ribeyro A, Martins-Luna J, Verne E, Aguila-Luis MA, Silva-Caso W, Ugarte C, Carrillo-Ng H, Cornejo-Tapia A, Tarazona-Castro Y, del Valle-Mendoza J. High prevalence and clinical characteristics of respiratory infection by human rhinovirus in children from Lima-Peru during years 2009–2010. PLoS One 2022; 17:e0271044. [PMID: 35839227 PMCID: PMC9286243 DOI: 10.1371/journal.pone.0271044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 06/22/2022] [Indexed: 11/18/2022] Open
Abstract
Introduction
Human rhinovirus is a major cause of acute respiratory infections (ARIs) worldwide. Epidemiological data on human rhinovirus (RV) in Peru is still scarce, as well as its role in respiratory infections in children. Therefore, the aim of this study was to describe the prevalence of rhinovirus and to identify the circulating species in nasopharyngeal swabs from children with acute respiratory infections.
Materials and methods
We analyzed nasopharyngeal swab samples that were collected from children younger than 17 years old, who had a clinical diagnosis of ARI from the “Hospital Nacional Cayetano Heredia” between May 2009 and December 2010. The original study recruited 767 inpatients with ARI, 559 samples of which were included and analyzed in the current study. Detection of rhinovirus and determination of rhinovirus species were characterized by PCR.
Results
Rhinovirus was detected in 42.22% samples (236/559), RV-A was detected in 10.17% (24/236) of the cases, RV-B in 16.53% (39/236), and RV-C in 73.31% (173/236). The age group with the highest number of cases was the 0–5 months group with 45.97%, followed by the 1–5 years group with 25.22%. Most of the positive RV cases, i.e., 86.44% (204/236), were hospitalized. The most common signs and symptoms found in patients who tested positive for RV were cough (72.88%), fever (68.64%), rhinorrhea (68.22%), and respiratory distress (61.44%). Infection with RV-A was associated with wheezing (p = 0.02). Furthermore, RV-C was related to cough (p = 0.01), wheezing (p = 0.002), and conjunctival injection (p = 0.03). A peak in RV-C cases was found in March (32 cases in 2010); June (18 cases in 2009 and 12 cases in 2010), which corresponds to the fall season in Peru; and also November (17 cases in 2009 and 4 cases in 2010), which corresponds to spring. RV-A and RV-B cases were constant throughout the year.
Conclusion
In conclusion, we found a high prevalence of rhinovirus C infection among pediatric patients with acute respiratory infections in Lima, Peru. This viral infection was more common in children between 0 to 5 months old, and was associated with cough, wheezing, and conjunctival injection. Epidemiological surveillance of this virus should be strengthened/encouraged in Peru to determine its real impact on respiratory infections.
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Affiliation(s)
- Ariana Castañeda-Ribeyro
- School of Medicine, Research Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Johanna Martins-Luna
- School of Medicine, Research Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
- Laboratory of Molecular Biology, Instituto de Investigación Nutricional, Lima, Peru
| | - Eduardo Verne
- School of Medicine Alberto Hurtado, Universidad Peruana Cayetano Heredia, Lima, Peru
- Pediatrics Service, Hospital Nacional Cayetano Heredia, Lima, Peru
| | - Miguel Angel Aguila-Luis
- School of Medicine, Research Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
- Laboratory of Molecular Biology, Instituto de Investigación Nutricional, Lima, Peru
| | - Wilmer Silva-Caso
- School of Medicine, Research Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
- Laboratory of Molecular Biology, Instituto de Investigación Nutricional, Lima, Peru
| | - Claudia Ugarte
- School of Medicine Alberto Hurtado, Universidad Peruana Cayetano Heredia, Lima, Peru
- Pediatrics Service, Hospital Nacional Cayetano Heredia, Lima, Peru
| | - Hugo Carrillo-Ng
- School of Medicine, Research Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
- Laboratory of Molecular Biology, Instituto de Investigación Nutricional, Lima, Peru
| | - Angela Cornejo-Tapia
- School of Medicine, Research Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Yordi Tarazona-Castro
- School of Medicine, Research Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
- Laboratory of Molecular Biology, Instituto de Investigación Nutricional, Lima, Peru
| | - Juana del Valle-Mendoza
- School of Medicine, Research Center of the Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
- Laboratory of Molecular Biology, Instituto de Investigación Nutricional, Lima, Peru
- * E-mail:
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Galindo-Fraga A, Guerra de Blas PDC, Ortega-Villa AM, Mateja A, Ruiz Quiñones JA, Cervantes PR, Barrientos FL, Ortiz-Hernández AA, Llamosas-Gallardo B, Ramírez-Venegas A, Vázquez RV, Chepitel DN, Moreno-Espinosa S, Powers JH, Lourdes Guerrero M, Ruiz-Palacios GM, Beigel J. DIFFERENT CLINICAL PRESENTATIONS OF HUMAN RHINOVIRUS (HRV) SPECIES INFECTION IN CHILDREN AND ADULTS IN MEXICO. Open Forum Infect Dis 2022; 9:ofac303. [PMID: 35891697 PMCID: PMC9308452 DOI: 10.1093/ofid/ofac303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/15/2022] [Indexed: 11/26/2022] Open
Abstract
Background Human rhinoviruses (HRVs) are a common cause of influenza-like illness, with the ability to infect the upper and lower respiratory tracts. In this study we aim to describe the clinical and molecular features of HRV infection in Mexican children and adults. Methods We performed a hospital-based, 4-year multicenter prospective observational cohort study of patients with influenza-like illness. Participants who tested positive for HRV were included. We described demographic, clinical, and laboratory characteristics and the association between HRV types, illness severity, and clinical outcomes. Results Of the 5662 subjects recruited, 1473 (26%) had HRV; of those, 988 (67.1%) were adults (≥18 years) and 485 (32.9%) were children. One hundred sixty-seven (11.33%) samples were sequenced; 101 (60.5%) were rhinovirus species A (HRV-A), 22 (13.2%) were rhinovirus species B (HRV-B), and 44 (26.3%) were rhinovirus species C (HRV-C). Among children and adults, 30.5% and 23.5%, respectively, were hospitalized (non–intensive care unit [ICU]). The odds of HRV-C are higher than HRV-A for participants in the ICU (compared to outpatient) and when platelets, lymphocytes, white blood cells, and lactate dehydrogenase are increased. The odds of HRV-C are higher than HRV-A and HRV-B with shortness of breath. The odds of HRV-A are higher than HRV-B, and the odds of HRV-B are higher than HRV-C, when mild symptoms like muscle ache and headache occur. Conclusions Rhinoviruses are a common cause of influenza-like illness. It is necessary to improve the surveillance, testing, and species identification for these viruses to understand different clinical presentations and risk factors associated with worse outcomes. Clinical Trials Registration. NCT01418287.
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Affiliation(s)
- Arturo Galindo-Fraga
- Departamento de Epidemiología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán , Mexico City , Mexico
| | | | - Ana M Ortega-Villa
- National Institute of Allergy and Infectious Diseases , Bethesda, MD , USA
| | - Allyson Mateja
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research , Frederick, Maryland , United States of America
| | - Jesus Arturo Ruiz Quiñones
- Departamento de Epidemiología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán , Mexico City , Mexico
| | - Pilar Ramos Cervantes
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán , Mexico City , Mexico
| | - Fernando Ledesma Barrientos
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán , Mexico City , Mexico
| | - Ana A Ortiz-Hernández
- División de Desarrollo y Enlace Interinstitucional, Instituto Nacional de Pediatría Mexico City , Mexico
| | - Beatriz Llamosas-Gallardo
- División de Desarrollo y Enlace Interinstitucional, Instituto Nacional de Pediatría Mexico City , Mexico
| | - Alejandra Ramírez-Venegas
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas” , Mexico City , Mexico
| | - Rafael Valdéz Vázquez
- Departamento de Infectología, Hospital General “Dr. Manuel Gea González” , Mexico City , Mexico
| | - Daniel Noyola Chepitel
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luís Potosí , San Luis Potosí , Mexico
| | - Sarbelio Moreno-Espinosa
- Departamento de Infectología, Hospital Infantil de México Federico Gómez, Instituto Nacional de Salud , Mexico City , Mexico
| | - John H Powers
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Frederick , Maryland , United States of America
| | - M Lourdes Guerrero
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán , Mexico City , Mexico
| | - Guillermo M Ruiz-Palacios
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán , Mexico City , Mexico
| | - John Beigel
- National Institute of Allergy and Infectious Diseases , Bethesda, MD , USA
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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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A Multicenter Study of Viral Aetiology of Community-Acquired Pneumonia in Hospitalized Children in Chinese Mainland. Virol Sin 2021; 36:1543-1553. [PMID: 34523109 PMCID: PMC8440149 DOI: 10.1007/s12250-021-00437-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/18/2021] [Indexed: 12/25/2022] Open
Abstract
Community-acquired pneumonia (CAP) is one of the leading causes of morbidity and mortality in children worldwide. In this study, we aimed to describe the aetiology of viral infection of pediatric CAP in Chinese mainland. During November 2014 to June 2016, the prospective study was conducted in 13 hospitals. The hospitalized children under 18 years old who met the criteria for CAP were enrolled. The throat swabs or nasopharyngeal aspirates (NPAs) were collected which were then screened 18 respiratory viruses using multiplex PCR assay. Viral pathogens were present in 56.6% (1539/2721) of the enrolled cases, with the detection rate of single virus in 39.8% of the cases and multiple viruses in 16.8% of the cases. The most frequently detected virus was respiratory syncytial virus (RSV) (15.2%, 414/2721). The highest detection rate of virus was in < 6-month-age group (70.7%, 292/413). RSV, human metapneumovirus (HMPV), human parainfluenza viruses (HPIVs) and influenza B virus (Flu B) showed the similar prevalence patterns both in north and south China, but HPIVs, Flu A, human bocavirus (HBoV), human adenovirus (HAdV) and human coronaviruses (HCoVs) showed the distinct circulating patterns in north and south China. Human enterovirus/human rhinovirus (HEV/HRV) (27.6%, 27/98), HBoV (18.4%, 18/98), RSV (16.3%, 16/98) and HMPV (14.3%, 14/98) were the most commonly detected viruses in severe pneumonia cases with single virus infection. In conclusion, viral pathogens are frequently detected in pediatric CAP cases and may therefore play a vital role in the aetiology of CAP. RSV was the most important virus in hospitalized children with CAP in Chinese mainland.
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Seyfoori A, Shokrollahi Barough M, Mokarram P, Ahmadi M, Mehrbod P, Sheidary A, Madrakian T, Kiumarsi M, Walsh T, McAlinden KD, Ghosh CC, Sharma P, Zeki AA, Ghavami S, Akbari M. Emerging Advances of Nanotechnology in Drug and Vaccine Delivery against Viral Associated Respiratory Infectious Diseases (VARID). Int J Mol Sci 2021; 22:6937. [PMID: 34203268 PMCID: PMC8269337 DOI: 10.3390/ijms22136937] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/19/2021] [Accepted: 06/19/2021] [Indexed: 12/12/2022] Open
Abstract
Viral-associated respiratory infectious diseases are one of the most prominent subsets of respiratory failures, known as viral respiratory infections (VRI). VRIs are proceeded by an infection caused by viruses infecting the respiratory system. For the past 100 years, viral associated respiratory epidemics have been the most common cause of infectious disease worldwide. Due to several drawbacks of the current anti-viral treatments, such as drug resistance generation and non-targeting of viral proteins, the development of novel nanotherapeutic or nano-vaccine strategies can be considered essential. Due to their specific physical and biological properties, nanoparticles hold promising opportunities for both anti-viral treatments and vaccines against viral infections. Besides the specific physiological properties of the respiratory system, there is a significant demand for utilizing nano-designs in the production of vaccines or antiviral agents for airway-localized administration. SARS-CoV-2, as an immediate example of respiratory viruses, is an enveloped, positive-sense, single-stranded RNA virus belonging to the coronaviridae family. COVID-19 can lead to acute respiratory distress syndrome, similarly to other members of the coronaviridae. Hence, reviewing the current and past emerging nanotechnology-based medications on similar respiratory viral diseases can identify pathways towards generating novel SARS-CoV-2 nanotherapeutics and/or nano-vaccines.
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Affiliation(s)
- Amir Seyfoori
- Laboratory for Innovations in Micro Engineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada; (A.S.); (T.W.)
- Biomaterials and Tissue Engineering Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran 1517964311, Iran
| | - Mahdieh Shokrollahi Barough
- Department of Immunology, Iran University of Medical Sciences, Tehran 1449614535, Iran;
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran 1517964311, Iran
| | - Pooneh Mokarram
- Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran;
- Autophagy Research Center, Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran
| | - Mazaher Ahmadi
- Department of Analytical Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan 6517838695, Iran; (M.A.); (T.M.)
| | - Parvaneh Mehrbod
- Influenza and Respiratory Viruses Department, Pasteur Institute of IRAN, Tehran 1316943551, Iran;
| | - Alireza Sheidary
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 14155-6451, Iran;
| | - Tayyebeh Madrakian
- Department of Analytical Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan 6517838695, Iran; (M.A.); (T.M.)
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 14155-6451, Iran;
| | - Mohammad Kiumarsi
- Department of Human Anatomy and Cell Science, Rady College of Medicine, Max Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
| | - Tavia Walsh
- Laboratory for Innovations in Micro Engineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada; (A.S.); (T.W.)
| | - Kielan D. McAlinden
- Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
| | - Chandra C. Ghosh
- Roger Williams Medical Center, Immuno-Oncology Institute (Ix2), Providence, RI 02908, USA;
| | - Pawan Sharma
- Center for Translational Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Jane & Leonard Korman Respiratory Institute, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Amir A. Zeki
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, U.C. Davis Lung Center, Davis School of Medicine, University of California, Davis, CA 95817, USA;
- Veterans Affairs Medical Center, Mather, CA 95817, USA
| | - Saeid Ghavami
- Autophagy Research Center, Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran
- Department of Human Anatomy and Cell Science, Rady College of Medicine, Max Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
- Biology of Breathing Theme, Children Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Research Institute of Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Mohsen Akbari
- Laboratory for Innovations in Micro Engineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada; (A.S.); (T.W.)
- Biotechnology Center, Silesian University of Technology, Akademicka 2A, 44-100 Gliwice, Poland
- Center for Advanced Materials and Related Technologies, University of Victoria, Victoria, BC V8P 5C2, Canada
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7
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Sánchez-González L, Quandelacy TM, Johansson M, Torres-Velásquez B, Lorenzi O, Tavarez M, Torres S, Alvarado LI, Paz-Bailey G. Viral etiology and seasonal trends of pediatric acute febrile illness in southern Puerto Rico; a seven-year review. PLoS One 2021; 16:e0247481. [PMID: 33606839 PMCID: PMC7895389 DOI: 10.1371/journal.pone.0247481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 02/08/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Acute febrile illness (AFI) is an important cause for seeking health care among children. Knowledge of the most common etiologic agents of AFI and its seasonality is limited in most tropical regions. METHODOLOGY/PRINCIPAL FINDINGS To describe the viral etiology of AFI in pediatric patients (≤18 years) recruited through a sentinel enhanced dengue surveillance system (SEDSS) in Southern Puerto Rico, we analyzed data for patients enrolled from 2012 to May 2018. To identify seasonal patterns, we applied time-series analyses to monthly arboviral and respiratory infection case data. We calculated coherence and phase differences for paired time-series to quantify the association between each time series. A viral pathogen was found in 47% of the 14,738 patients. Influenza A virus was the most common pathogen detected (26%). The incidence of Zika and dengue virus etiologies increased with age. Arboviral infections peaked between June and September throughout the times-series. Respiratory infections have seasonal peaks occurring in the fall and winter months of each year, though patterns vary by individual respiratory pathogen. CONCLUSIONS/SIGNIFICANCE Distinct seasonal patterns and differences in relative frequency by age groups seen in this study can guide clinical and laboratory assessment in pediatric patients with AFI in Puerto Rico.
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Affiliation(s)
| | - Talia M. Quandelacy
- Dengue Branch, Centers for Disease Control and Prevention, CDC, San Juan, Puerto Rico
| | - Michael Johansson
- Dengue Branch, Centers for Disease Control and Prevention, CDC, San Juan, Puerto Rico
| | | | - Olga Lorenzi
- Dengue Branch, Centers for Disease Control and Prevention, CDC, San Juan, Puerto Rico
| | - Mariana Tavarez
- Saint Luke’s Episcopal Hospital Consortium, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Sanet Torres
- Saint Luke’s Episcopal Hospital Consortium, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Luisa I. Alvarado
- Saint Luke’s Episcopal Hospital Consortium, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Gabriela Paz-Bailey
- Dengue Branch, Centers for Disease Control and Prevention, CDC, San Juan, Puerto Rico
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8
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Biggs HM, Nix WA, Zhang J, Rogers S, Clara W, Jara JH, Gonzalez R, Luciani K, Brizuela YS, Estripeaut D, Castillo JM, De Leon T, Corro M, Vergara O, Rauda R, Chong EG, Watson JT, Azziz-Baumgartner E, Gerber SI, Tong S, Dawood FS. Enterovirus D68 infection among hospitalized children with severe acute respiratory illness in El Salvador and Panama, 2012-2013. Influenza Other Respir Viruses 2020; 15:181-187. [PMID: 33280235 PMCID: PMC7902261 DOI: 10.1111/irv.12815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022] Open
Abstract
We assessed EV‐D68 epidemiology and phylogenetics among children aged ≤9 years hospitalized with severe acute respiratory illnesses at five sites in Panama and El Salvador during 2012‐2013. Respiratory specimens positive for enterovirus or rhinovirus were tested by real‐time RT‐PCR for EV‐D68, and partial VP1 gene sequences were determined. Of 715 enrolled children, 17 from sites in both countries were EV‐D68‐positive and commonly had a history of asthma or wheezing. Phylogenetically, 15 of 16 sequences fell into Clade B1, and one into Clade A2. The Central American EV‐D68s were closely related genetically to contemporaneous strains from North America, South America, and the Caribbean.
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Affiliation(s)
- Holly M Biggs
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - W Allan Nix
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jing Zhang
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shannon Rogers
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Wilfrido Clara
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jorge H Jara
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Rosalba Gonzalez
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Kathia Luciani
- Hospital De Especialidades Pediátricas Omar Torrijos, Panama City, Panama
| | | | | | | | - Tirza De Leon
- Hospital Materno Infantil José Domingo De Obaldía, David, Panama
| | - Mary Corro
- Hospital De Especialidades Pediátricas Omar Torrijos, Panama City, Panama
| | | | - Rafael Rauda
- Hospital San Juan De Dios, Santa Ana, El Salvador
| | - Evens G Chong
- Hospital Materno Infantil José Domingo De Obaldía, David, Panama
| | - John T Watson
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Eduardo Azziz-Baumgartner
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Susan I Gerber
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suxiang Tong
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Fatimah S Dawood
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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9
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Grunberg M, Sno R, Adhin MR. Epidemiology of respiratory viruses in patients with severe acute respiratory infections and influenza-like illness in Suriname. Influenza Other Respir Viruses 2020; 15:72-80. [PMID: 32881286 PMCID: PMC7767960 DOI: 10.1111/irv.12791] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/12/2020] [Indexed: 12/13/2022] Open
Abstract
Background Influenza has been well studied in developed countries with temperate climates, in contrast to low‐ and middle‐income (LMIC) countries, thus hampering the effort to attain representative global data. Furthermore, data on non‐influenza respiratory infections are also limited. Insight in viral respiratory infections in Suriname, a tropical LMIC in South America, would contribute to improved local preventive measures and a better global understanding of respiratory viruses. Methods From May 2016 through April 2018, all patients (n = 1096) enrolled in the national severe acute respiratory infection and influenza‐like illness surveillance were screened for the presence of 10 respiratory viruses with singleplex RT‐PCR. Results The overall viral‐positive detection rate was 45.3%, specified as RSV (19.4%), influenza (15.5%), hMPV (4.9%), AdV (4.6%), and parainfluenza (3.8%). Co‐infections were detected in 6.2% of the positive cases. Lower overall positivity was observed in the SARI vs ILI surveillance and influenza prevalence was higher in outpatients (45.0% vs 6.7%), while RSV exhibited the reverse (4.8% vs 23.8%). Respiratory infections in general were more common in children than in adults (54.4% vs 29.5%), although children were significantly less affected by influenza (11.5% vs 22.7%). None of the respiratory viruses displayed a clear seasonal pattern, and viral interference was observed between RSV and influenza. Conclusions The comprehensive information presented for Suriname, including first data on non‐influenza respiratory viruses, displayed distinct differences between the viruses, in seasonality, within age groups and between SARI/ILI, accentuating the need, especially for tropical LMIC countries to continue ongoing surveillance and accumulate local data.
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Affiliation(s)
- Meritha Grunberg
- Prof. Dr. Paul C. Flu" Institute for Biomedical Sciences, Paramaribo, Suriname
| | - Rachel Sno
- Prof. Dr. Paul C. Flu" Institute for Biomedical Sciences, Paramaribo, Suriname
| | - Malti R Adhin
- Prof. Dr. Paul C. Flu" Institute for Biomedical Sciences, Paramaribo, Suriname.,Department of Biochemistry, Faculty of Medical Sciences, Anton de Kom Universiteit van Suriname, Paramaribo, Suriname
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10
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Viral Etiology of Acute Respiratory Infections in Pediatric Patients in Lebanon. Mediterr J Hematol Infect Dis 2019; 11:e2019059. [PMID: 31700584 PMCID: PMC6827722 DOI: 10.4084/mjhid.2019.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/25/2019] [Indexed: 11/08/2022] Open
Abstract
Background Acute respiratory infections (ARI) are the leading cause of death worldwide, especially among children. The majority of these infections in children are of viral etiology. In this study, we evaluated the incidence of viral ARI among children in Lebanon. Patients and Methods Children presenting with symptoms of ARI were prospectively recruited between September 2009 to February 2012. Nasopharyngeal aspirates were obtained from patients and screened for 11 respiratory viruses using a multiplex Luminex-based PCR assay. Results Two hundred twenty-one patients were recruited with a median age of 1 year (IQR: 0 - 5). Out of 221 patients, 116 (52.5%) were positive for at least one virus, the majority (103/116; 88.8%) of which were in children under 6-year of age. Overall, 188 viruses were detected. Rhinovirus (RhV) was the most common virus detected in 81 (69.8%) patients followed by coxsackie virus and echovirus (CVEV) which were detected as one target in the panel in 45 (38.8%), and parainfluenza viruses (PIV types: 1, 2, 3, 4) in 24 (20.7%) patients. Coinfection with more than one virus was detected in 49 (42.9%) patients. RhV and CVEV were the most common viruses associated with co-infections and higher risk of rhinorrhea. Conclusions Viral pathogens account for at least half of the ARIs in Lebanon, with a high frequency of co-infections being detected.
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11
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Molecular Subtyping of Human Rhinovirus in Children from Three Sub-Saharan African Countries. J Clin Microbiol 2019; 57:JCM.00723-19. [PMID: 31270180 PMCID: PMC6711929 DOI: 10.1128/jcm.00723-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/24/2019] [Indexed: 11/20/2022] Open
Abstract
The pathogenesis of human rhinovirus (HRV) during severe respiratory disease remains undefined; thus, we aimed to explore the relationship between the HRV molecular subtyping results obtained during severe and asymptomatic childhood infections. Nasopharyngeal/oropharyngeal swabs from children (1 to 59 months of age) hospitalized with pneumonia and from age-frequency-matched controls were collected between August 2011 and August 2013. The pathogenesis of human rhinovirus (HRV) during severe respiratory disease remains undefined; thus, we aimed to explore the relationship between the HRV molecular subtyping results obtained during severe and asymptomatic childhood infections. Nasopharyngeal/oropharyngeal swabs from children (1 to 59 months of age) hospitalized with pneumonia and from age-frequency-matched controls were collected between August 2011 and August 2013. Swabs were tested for respiratory pathogens, including HRV, using quantitative real-time PCR assays. HRV-positive samples were sequenced for phylogenetic analysis by targeting the 5′ noncoding region (5′NCR). Our data showed that there were no differences in the prevalence of HRV detection among cases and controls (21% versus 20%, P = 0.693); however, among children 13 to 59 months old, HRV detection was more often case associated (21% versus 16%; P = 0.009), with the results mainly driven by HRV-C (12% versus 7%; P = 0.001). Overall, there were no differences in the results of molecular subtyping of the HRV species prevalence among cases (for HRV-A, 48%; for HRV-B, 7%; for HRV-C, 45%) and controls (for HRV-A, 45%; for HRV-B, 10%; for HRV-C, 45% [P = 0.496]). Those with pneumonia and HRV-C were older (12.1 versus 9.4 months, P = 0.033) and more likely to present with wheeze (35% versus 25%, P = 0.031) than those with HRV-A cases. Thus, the rate of HRV detection was high, with similar degrees of genetic diversity among cases and controls, confounding the interpretation of the presence of HRV in nasopharyngeal samples for attribution of a causal role in the pathogenesis of severe pneumonia in infants. However, among children 13 to 59 months of age, HRV detection, in particular, HRV-C detection, was associated with case status, especially among children with wheezing disease.
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12
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Morobe JM, Nyiro JU, Brand S, Kamau E, Gicheru E, Eyase F, Otieno GP, Munywoki PK, Agoti CN, Nokes DJ. Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance. Wellcome Open Res 2019; 3:128. [PMID: 30483602 PMCID: PMC6234744 DOI: 10.12688/wellcomeopenres.14836.2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Human rhinovirus (HRV) is the predominant cause of upper respiratory tract infections, resulting in a significant public health burden. The virus circulates as many different types (168), each generating strong homologous, but weak heterotypic, immunity. The influence of these features on transmission patterns of HRV in the community is understudied. Methods: Nasopharyngeal swabs were collected from patients with symptoms of acute respiratory infection (ARI) at nine out-patient facilities across a Health and Demographic Surveillance System between December 2015 and November 2016. HRV was diagnosed by real-time RT-PCR, and the VP4/VP2 genomic region of the positive samples sequenced. Phylogenetic analysis was used to determine the HRV types. Classification models and G-test statistic were used to investigate HRV type spatial distribution. Demographic characteristics and clinical features of ARI were also compared. Results: Of 5,744 NPS samples collected, HRV was detected in 1057 (18.4%), of which 817 (77.3%) were successfully sequenced. HRV species A, B and C were identified in 360 (44.1%), 67 (8.2%) and 390 (47.7%) samples, respectively. In total, 87 types were determined: 39, 10 and 38 occurred within species A, B and C, respectively. HRV types presented heterogeneous temporal patterns of persistence. Spatially, identical types occurred over a wide distance at similar times, but there was statistically significant evidence for clustering of types between health facilities in close proximity or linked by major road networks. Conclusion: This study records a high prevalence of HRV in out-patient presentations exhibiting high type diversity. Patterns of occurrence suggest frequent and independent community invasion of different types. Temporal differences of persistence between types may reflect variation in type-specific population immunity. Spatial patterns suggest either rapid spread or multiple invasions of the same type, but evidence of similar types amongst close health facilities, or along road systems, indicate type partitioning structured by local spread.
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Affiliation(s)
- John Mwita Morobe
- Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, +254, Kenya.,Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Joyce U Nyiro
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Samuel Brand
- Zeeman Institute of Systems Biology and Infectious Disease Research (SBIDER), University of Warwick, Coventry, UK.,School of Life Sciences, University of Warwick, Coventry, UK
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Elijah Gicheru
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Fredrick Eyase
- Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, +254, Kenya
| | - Grieven P Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Patrick K Munywoki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya.,Public Health, Pwani University, Kilifi, +254, Kenya
| | - C N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya.,Public Health, Pwani University, Kilifi, +254, Kenya
| | - D J Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya.,Zeeman Institute of Systems Biology and Infectious Disease Research (SBIDER), University of Warwick, Coventry, UK.,School of Life Sciences, University of Warwick, Coventry, UK.,Public Health, Pwani University, Kilifi, +254, Kenya
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13
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Ortiz‐Hernández AA, Nishimura KK, Noyola DE, Moreno‐Espinosa S, Gamiño A, Galindo‐Fraga A, Valdéz Vázquez R, Magaña Aquino M, Ramirez‐Venegas A, Valdés Salgado R, Andrade‐Platas D, Estevez‐Jimenéz J, Ruiz‐Palacios GM, Guerrero ML, Beigel J, Smolskis MC, Hunsberger S, Freimanis‐Hence L, Llamosas‐Gallardo B. "Differential risk of hospitalization among single virus infections causing influenza-like illnesses". Influenza Other Respir Viruses 2019; 13:36-43. [PMID: 30137695 PMCID: PMC6304313 DOI: 10.1111/irv.12606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/24/2018] [Accepted: 08/16/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Acute respiratory infections are a major cause of morbidity in children and are often caused by viruses. However, the relative severity of illness associated with different viruses is unclear. The objective of this study was to evaluate the risk of hospitalization from different viruses in children presenting with an influenza-like illness (ILI). METHODS Data from children 5 years old or younger participating in an ILI natural history study from April 2010 to March 2014 was analyzed. The adjusted odds ratio for hospitalization was estimated in children with infections caused by respiratory syncytial virus (RSV), metapneumovirus, bocavirus, parainfluenza viruses, rhinovirus/enterovirus, coronavirus, adenovirus, and influenza. RESULTS A total of 1486 children (408 outpatients and 1078 inpatients) were included in this analysis. At least one virus was detected in 1227 (82.6%) patients. The most frequent viruses detected as single pathogens were RSV (n = 286), rhinovirus/enterovirus (n = 251), parainfluenza viruses (n = 104), and influenza A or B (n = 99). After controlling for potential confounders (age, sex, recruitment site, days from symptom onset to enrollment, and underlying illnesses), children with RSV and metapneumovirus infections showed a greater likelihood of hospitalization than those infected by parainfluenza viruses (OR 2.7 and 1.9, respectively), rhinovirus/enterovirus (OR 3.1 and 2.1, respectively), coronaviruses (OR 4.9 and 3.4, respectively), adenovirus (OR 4.6 and 3.2, respectively), and influenza (OR 6.3 and 4.4, respectively). CONCLUSIONS Children presenting with ILI caused by RSV and metapneumovirus were at greatest risk for hospitalization, while children with rhinovirus/enterovirus, parainfluenza, coronavirus, adenovirus, and influenza were at lower risk of hospitalization.
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Affiliation(s)
| | - Katherine K. Nishimura
- National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMaryland
| | | | | | - Ana Gamiño
- Hospital Infantil de México Dr. Federico GómezCiudad de MéxicoMéxico
| | - Arturo Galindo‐Fraga
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiranCiudad de MéxicoMéxico
| | | | | | | | | | | | | | | | - Maria Lourdes Guerrero
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador ZubiranCiudad de MéxicoMéxico
| | - John Beigel
- Frederick National Laboratory for Cancer ResearchLeidos Biomedical Research, Inc.FrederickMaryland
| | - Mary C. Smolskis
- National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMaryland
| | - Sally Hunsberger
- National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMaryland
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14
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Morobe JM, Nyiro JU, Brand S, Kamau E, Gicheru E, Eyase F, Otieno GP, Munywoki PK, Agoti C, Nokes D. Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance. Wellcome Open Res 2018; 3:128. [DOI: 10.12688/wellcomeopenres.14836.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2018] [Indexed: 01/02/2023] Open
Abstract
Background: Human rhinovirus (HRV) is the predominant cause of upper respiratory tract infections, resulting in a significant public health burden. The virus circulates as many different types (~160), each generating strong homologous, but weak heterotypic, immunity. The influence of these features on transmission patterns of HRV in the community is understudied. Methods: Nasopharyngeal swabs were collected from patients with symptoms of acute respiratory infection (ARI) at nine out-patient facilities across a Health and Demographic Surveillance System between December 2015 and November 2016. HRV was diagnosed by real-time RT-PCR, and the VP4/VP2 genomic region of the positive samples sequenced. Phylogenetic analysis was used to determine the HRV types. Classification models and G-test statistic were used to investigate HRV type spatial distribution. Demographic characteristics and clinical features of ARI were also compared. Results: Of 5,744 NPS samples collected, HRV was detected in 1057 (18.4%), of which 817 (77.3%) were successfully sequenced. HRV species A, B and C were identified in 360 (44.1%), 67 (8.2%) and 390 (47.7%) samples, respectively. In total, 87 types were determined: 39, 10 and 38 occurred within species A, B and C, respectively. HRV types presented heterogeneous temporal patterns of persistence. Spatially, identical types occurred over a wide distance at similar times, but there was statistically significant evidence for clustering of types between health facilities in close proximity or linked by major road networks. Conclusion: This study records a high prevalence of HRV in out-patient presentations exhibiting high type diversity. Patterns of occurrence suggest frequent and independent community invasion of different types. Temporal differences of persistence between types may reflect variation in type-specific population immunity. Spatial patterns suggest either rapid spread or multiple invasions of the same type, but evidence of similar types amongst close health facilities, or along road systems, indicate type partitioning structured by local spread.
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15
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Review on Clinical and Molecular Epidemiology of Human Rhinovirus-Associated Lower Respiratory Tract Infections in African and Southeast Asian Children. Pediatr Infect Dis J 2018; 37:e185-e194. [PMID: 29893746 DOI: 10.1097/inf.0000000000001897] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The detection of human rhinoviruses (HRV) is highly prevalent in children with pneumonia, bronchiolitis, acute asthma and croup; however, there is also evidence that HRV is common in asymptomatic individuals. The majority of studies on the role of different HRV serotypes during acute respiratory tract infections episodes have limited sample size to fully characterize the epidemiology of HRV infection, including those from low-middle income countries, where the burden of childhood respiratory disease is greatest. METHODS We systematically reviewed HRV clinical and molecular epidemiology in low- and middle-income countries in Africa and Southeast Asia before November 2015. RESULTS We identified 31 studies, which included data from 13 African and 6 Southeast Asian countries, emphasizing the gaps in knowledge surrounding HRV infections. HRV was one of the most prevalent respiratory viruses detected during childhood respiratory disease (13%-59%); however, many studies could not determine the attributable role of HRV in the pathogenesis of acute respiratory infections due to high prevalence of detection among asymptomatic individuals (6%-50%). A meta-analysis showed no significant difference in the prevalence of HRV identification between children of different age groups; or between children with severe disease compared with asymptomatic children. CONCLUSIONS These data highlight the need for large-scale surveillance projects to determine the attributable etiologic role of HRV in respiratory disease.
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16
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Chen X, Guo J, Li J, Li Q, Ai J, Sun S, Xie Z. Serotypes of human enteroviruses causing pediatric viral encephalitis and meningitis in Hebei province, China, from 2013 to 2015. Pediatr Investig 2018; 2:98-104. [PMID: 32851241 PMCID: PMC7331305 DOI: 10.1002/ped4.12037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
IMPORTANCE Viral encephalitis and meningitis are severe infectious diseases responsible for substantial morbidity and mortality in children. Enteroviruses are typically the most common causative agents of viral encephalitis and meningitis. OBJECTIVE This study aimed to investigate the etiology of viral encephalitis and meningitis among children in Hebei province, China. METHODS Cerebrospinal fluid samples from children with viral encephalitis (n=309) and meningitis (n=133) were collected between Nov 2013 and Dec 2015 and viral pathogens were identified by real-time and multiplex PCR. Amplification and sequencing of partial VP1 genes was used to type enteroviruses. RESULTS The causative pathogen was successfully detected in 176 (57%) patients with viral encephalitis and 82 (61.7%) patients with viral meningitis. The most common causative agents of both viral encephalitis and meningitis were enteroviruses (55.7% and 64.6% of cases, respectively). The most common enterovirus serotypes identified were echovirus 18, echovirus 6 and echovirus 30. Echovirus 18 accounted for 74.4% of all typed enteroviruses and caused a viral encephalitis and meningitis outbreak in Hebei province in 2015. By contrast, the major enterovirus serotypes circulating in 2014 were echovirus 6 and echovirus 30. INTERPRETATION Enteroviruses were the main causative agents of viral encephalitis and meningitis in children in Hebei province from Nov 2013 to Dec 2015. Echovirus 18 became the leading cause of viral encephalitis and meningitis for the first time in Hebei province in 2015.
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Affiliation(s)
- Xiangpeng Chen
- Key Laboratory of Major Diseases in ChildrenMinistry of EducationBeijing Key Laboratory of Pediatric Respiratory Infection DiseasesVirology LaboratoryBeijing Pediatric Research InstituteBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Jiayun Guo
- Key Laboratory of Major Diseases in ChildrenMinistry of EducationBeijing Key Laboratory of Pediatric Respiratory Infection DiseasesVirology LaboratoryBeijing Pediatric Research InstituteBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Jingjie Li
- Department of NeurologyChildren's Hospital of Hebei ProvinceShijiazhuangChina
| | - Qiuping Li
- Key Laboratory of Major Diseases in ChildrenMinistry of EducationBeijing Key Laboratory of Pediatric Respiratory Infection DiseasesVirology LaboratoryBeijing Pediatric Research InstituteBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Junhong Ai
- Key Laboratory of Major Diseases in ChildrenMinistry of EducationBeijing Key Laboratory of Pediatric Respiratory Infection DiseasesVirology LaboratoryBeijing Pediatric Research InstituteBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Suzhen Sun
- Department of NeurologyChildren's Hospital of Hebei ProvinceShijiazhuangChina
| | - Zhengde Xie
- Key Laboratory of Major Diseases in ChildrenMinistry of EducationBeijing Key Laboratory of Pediatric Respiratory Infection DiseasesVirology LaboratoryBeijing Pediatric Research InstituteBeijing Children's HospitalCapital Medical UniversityNational Center for Children's HealthBeijingChina
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17
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Swamy MA, Malhotra B, Janardhan Reddy PV, Tiwari J. Profile of Respiratory Pathogens Causing Acute Respiratory Infections in Hospitalised Children at Rajasthan a 4 Year’s Study. Indian J Med Microbiol 2018; 36:163-171. [DOI: 10.4103/ijmm.ijmm_18_84] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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18
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Reis J, Shaman J. Simulation of four respiratory viruses and inference of epidemiological parameters. Infect Dis Model 2018; 3:23-34. [PMID: 30839912 PMCID: PMC6326234 DOI: 10.1016/j.idm.2018.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 02/20/2018] [Accepted: 03/18/2018] [Indexed: 12/02/2022] Open
Abstract
While influenza has been simulated extensively to better understand its behavior and predict future outbreaks, most other respiratory viruses have seldom been simulated. In this study, we provide an overview of four common respiratory viral infections: respiratory syncytial virus (RSV), respiratory adenovirus, rhinovirus and parainfluenza, present specimen data collected 2004–2014, and simulate outbreaks in 19 overlapping regions in the United States. Pairing a compartmental model and data assimilation methods, we infer key epidemiological parameters governing transmission: the basic reproductive number R0 and length of infection D. RSV had been previously simulated, and our mean estimate of D and R0 of 5.2 days and 2.8, respectively, are within published clinical and modeling estimates. Among the four virus groupings, mean estimates of R0 range from 2.3 to 3.0, with a lower and upper quartile range of 2.0–2.8 and 2.6–3.2, respectively. As rapid PCR testing becomes more common, estimates of the observed virulence and duration of infection for these viruses could inform decision making by clinicians and officials for managing patient treatment and response.
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Affiliation(s)
- Julia Reis
- Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
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19
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Zheng X, Song Z, Li Y, Zhang J, Wang XL. Possible interference between seasonal epidemics of influenza and other respiratory viruses in Hong Kong, 2014-2017. BMC Infect Dis 2017; 17:772. [PMID: 29246199 PMCID: PMC5732536 DOI: 10.1186/s12879-017-2888-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 12/06/2017] [Indexed: 12/03/2022] Open
Abstract
Background Unlike influenza viruses, little is known about the prevalence and seasonality of other respiratory viruses because laboratory surveillance for non-influenza respiratory viruses is not well developed or supported in China and other resource-limited countries. We studied the interference between seasonal epidemics of influenza viruses and five other common viruses that cause respiratory illnesses in Hong Kong from 2014 to 2017. Methods The weekly laboratory-confirmed positive rates of each virus were analyzed from 2014 to 2017 in Hong Kong to describe the epidemiological trends and interference between influenza viruses, respiratory syncytial virus (RSV), parainfluenza virus (PIV), adenovirus, enterovirus and rhinovirus. A sinusoidal model was established to estimate the peak timing of each virus by phase angle parameters. Results Seasonal features of the influenza viruses, PIV, enterovirus and adenovirus were obvious, whereas annual peaks of RSV and rhinovirus were not observed. The incidence of the influenza viruses usually peaked in February and July, and the summer peaks in July were generally caused by the H3 subtype of influenza A alone. When influenza viruses were active, other viruses tended to have a low level of activity. The peaks of the influenza viruses were not synchronized. An epidemic of rhinovirus tended to shift the subsequent epidemics of the other viruses. Conclusion The evidence from recent surveillance data in Hong Kong suggests that viral interference during the epidemics of influenza viruses and other common respiratory viruses might affect the timing and duration of subsequent epidemics of a certain or several viruses.
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Affiliation(s)
- Xueying Zheng
- Department of Biostatistics and Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China.,Collaborative Innovation Center of Social Risks Governance in Health, Fudan University, Shanghai, China
| | - Zhengyu Song
- Department of Biostatistics and Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Yapeng Li
- Department of Biostatistics and Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Juanjuan Zhang
- Department of Biostatistics and Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Xi-Ling Wang
- Department of Biostatistics and Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China. .,Collaborative Innovation Center of Social Risks Governance in Health, Fudan University, Shanghai, China. .,Shanghai Key Laboratory of Meteorology and Health, Shanghai, China.
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20
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Taylor S, Lopez P, Weckx L, Borja-Tabora C, Ulloa-Gutierrez R, Lazcano-Ponce E, Kerdpanich A, Angel Rodriguez Weber M, Mascareñas de Los Santos A, Tinoco JC, Safadi MAP, Lim FS, Hernandez-de Mezerville M, Faingezicht I, Cruz-Valdez A, Feng Y, Li P, Durviaux S, Haars G, Roy-Ghanta S, Vaughn DW, Nolan T. Respiratory viruses and influenza-like illness: Epidemiology and outcomes in children aged 6 months to 10 years in a multi-country population sample. J Infect 2016; 74:29-41. [PMID: 27667752 PMCID: PMC7112512 DOI: 10.1016/j.jinf.2016.09.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 06/01/2016] [Accepted: 09/16/2016] [Indexed: 11/26/2022]
Abstract
BACKGROUND Better population data on respiratory viruses in children in tropical and southern hemisphere countries is needed. METHODS The epidemiology of respiratory viruses among healthy children (6 months to <10 years) with influenza-like illness (ILI) was determined in a population sample derived from an influenza vaccine trial (NCT01051661) in 17 centers in eight countries (Australia, South East Asia and Latin America). Active surveillance for ILI was conducted for approximately 1 year (between February 2010 and August 2011), with PCR analysis of nasal and throat swabs. RESULTS 6266 children were included, of whom 2421 experienced 3717 ILI episodes. Rhinovirus/enterovirus had the highest prevalence (41.5%), followed by influenza (15.8%), adenovirus (9.8%), parainfluenza and respiratory syncytial virus (RSV) (both 9.7%), coronavirus (5.6%), human metapneumovirus (5.5%) and human bocavirus (HBov) (2.0%). Corresponding incidence per 100 person-years was 29.78, 11.34, 7.03, 6.96, 6.94, 4.00, 3.98 and 1.41. Except for influenza, respiratory virus prevalence declined with age. The incidence of medically-attended ILI associated with viral infection ranged from 1.03 (HBov) to 23.69 (rhinovirus/enterovirus). The percentage of children missing school or daycare ranged from 21.4% (HBov) to 52.1% (influenza). CONCLUSIONS Active surveillance of healthy children provided evidence of respiratory illness burden associated with several viruses, with a substantial burden in older children.
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Affiliation(s)
| | - Pio Lopez
- Centro de Estudios en Infectologia Pediatrica, Cali, Colombia
| | - Lily Weckx
- Pediatric Infectious Diseases, Department of Pediatrics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Charissa Borja-Tabora
- Research Institute for Tropical Medicine, Department of Health, Alabang, Muntinlupa City, Philippines
| | | | | | - Angkool Kerdpanich
- Infectious Diseases Unit, Department of Pediatrics, Phramongkutklao Hospital, Thailand
| | | | | | | | - Marco Aurelio P Safadi
- Faculdade de Ciências Médicas da Santa Casa de São Paulo and Associação Fundo de Incentivo à Pesquisa, Department of Pediatrics, São Paulo, Brazil
| | - Fong Seng Lim
- National Healthcare Group Polyclinics, National University of Singapore, Singapore
| | | | - Idis Faingezicht
- Instituto Costarricense de Investigaciones Clínicas, San José, Costa Rica
| | | | | | - Ping Li
- GSK Vaccines, King of Prussia, PA, USA
| | | | | | | | | | - Terry Nolan
- Murdoch Children's Research Institute and Melbourne School of Population and Global Health, University of Melbourne, Carlton, Victoria, Australia
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Zhou Y, Fernandez S, Yoon IK, Simasathien S, Watanaveeradej V, Yang Y, Marte-Salcedo OA, Shuck-Lee DJ, Thomas SJ, Hang J, Jarman RG. Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens and Identification of Human Enteroviruses at a Thailand Hospital. Am J Trop Med Hyg 2016; 95:663-669. [PMID: 27352877 PMCID: PMC5014275 DOI: 10.4269/ajtmh.16-0062] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/12/2016] [Indexed: 12/11/2022] Open
Abstract
Numerous pathogens cause respiratory infections with similar symptoms. Routine diagnostics detect only a limited number of pathogens, leaving a gap in respiratory illness etiology surveillance. This study evaluated next-generation sequencing for unbiased pathogen identification. Respiratory samples collected in Thailand, Philippines, Bhutan, and Nepal, that were negative by several molecular and immunofluorescence assays, underwent viral cultivation. Samples which demonstrated cytopathic effect in culture (N = 121) were extracted and tested by Luminex xTAG respiratory viral panel (RVP) assay and deep sequencing by Roche 454 FLX Titanium system. Using RVP assay, 52 (43%) samples were positive for enterovirus or rhinovirus and another three were positive for respiratory syncytial virus B, parainfluenza 4, and adenovirus. Deep sequencing confirmed the Luminex assay results and identified additional viral pathogens. Human enteroviruses, including Enterovirus A type 71 and 12 types of Enterovirus B (EV-B) were identified from a hospital in Bangkok. Phylogenetic and recombination analysis showed high correlation of VP1 gene-based phylogeny with genome-wide phylogeny and the frequent genetic exchange among EV-B viruses. The high number and diversity of enteroviruses in the hospital in Bangkok suggests prevalent existence. The metagenomic approach used in our study enabled comprehensive diagnoses of respiratory viruses.
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Affiliation(s)
- Yanfei Zhou
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Stefan Fernandez
- Department of Virology, U.S. Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - In-Kyu Yoon
- International Vaccine Institute, Seoul, Republic of Korea.,Department of Virology, U.S. Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | | | - Yu Yang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Omely A Marte-Salcedo
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Deidra J Shuck-Lee
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Stephen J Thomas
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jun Hang
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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Fall A, Dia N, Kébé O, Sarr FD, Kiori DE, Cissé EHAK, Sy S, Goudiaby D, Richard V, Diop OM, Niang MN. Enteroviruses and Rhinoviruses: Molecular Epidemiology of the Most Influenza-Like Illness Associated Viruses in Senegal. Am J Trop Med Hyg 2016; 95:339-47. [PMID: 27246444 DOI: 10.4269/ajtmh.15-0799] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 04/04/2016] [Indexed: 12/31/2022] Open
Abstract
Different viruses have been identified as etiologic agents of respiratory tract infections, including severe cases. Among these, human rhinoviruses (HRVs) and human enteroviruses (HEVs) are recognized as leading causes. The present study describes the molecular epidemiology of HRVs and HEVs in Senegal over a 3-year surveillance period. From January 2012 to December 2014, nasopharyngeal and oropharyngeal swabs specimen were collected from patients with influenza-like illness (ILI). A real-time reverse transcription polymerase chain reaction was performed for HRV and HEV detection using the RV16 kit. Two regions were targeted for the molecular characterization of RVs: 5' untranslated region (5'UTR) and viral protein 4/viral protein 2 (VP4/VP2) transition region. For enteroviruses (EVs) phylogeny, VP1 gene was targeted. A total of 4,194 samples were collected. Children up to 5 years accounted for 52.9%. Among them, 1,415 (33.7%) were positive for HRV, 857 (20.4%) for HEV, and 437 cases of dual infections HRV/HEV. HRVs and HEVs were identified significantly in children aged 5 years or less. Only cough and vomiting signs were observed with significant association with viral infection. Both viruses co-circulated all year long with a marked increase of activity during rainy and cold period. All HRV types circulate in Senegal. HRV-A and C groups were the most common. HEV serotyping identified coxsackie B viruses (CBV) only. VP1 region revealed different CBV (CBV1, CBV2, CBV3, CBV4, and CBV5), echoviruses, coxsackieviruses A4-like strains and a poliovirus 2. The results suggest strong year-round respiratory picornavirus activity in children up to 5 years of age. Molecular studies identified a wide variety of RVs along with diverse EVs in samples from patients with ILI.
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Affiliation(s)
- Amary Fall
- Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal
| | - Ndongo Dia
- Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal
| | - Ousmane Kébé
- Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal
| | - Fatoumata Diene Sarr
- Unité d'Epidémiologie des Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Sénégal
| | - Davy E Kiori
- Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal
| | | | - Sara Sy
- Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal
| | - Deborah Goudiaby
- Unité de Virologie Médicale, Institut Pasteur de Dakar, Dakar, Sénégal
| | - Vincent Richard
- Unité d'Epidémiologie des Maladies Infectieuses, Institut Pasteur de Dakar, Dakar, Sénégal
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Royston L, Tapparel C. Rhinoviruses and Respiratory Enteroviruses: Not as Simple as ABC. Viruses 2016; 8:E16. [PMID: 26761027 PMCID: PMC4728576 DOI: 10.3390/v8010016] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/09/2015] [Accepted: 12/28/2015] [Indexed: 12/21/2022] Open
Abstract
Rhinoviruses (RVs) and respiratory enteroviruses (EVs) are leading causes of upper respiratory tract infections and among the most frequent infectious agents in humans worldwide. Both are classified in the Enterovirus genus within the Picornaviridae family and they have been assigned to seven distinct species, RV-A, B, C and EV-A, B, C, D. As viral infections of public health significance, they represent an important financial burden on health systems worldwide. However, the lack of efficient antiviral treatment or vaccines against these highly prevalent pathogens prevents an effective management of RV-related diseases. Current advances in molecular diagnostic techniques have revealed the presence of RV in the lower respiratory tract and its role in lower airway diseases is increasingly reported. In addition to an established etiological role in the common cold, these viruses demonstrate an unexpected capacity to spread to other body sites under certain conditions. Some of these viruses have received particular attention recently, such as EV-D68 that caused a large outbreak of respiratory illness in 2014, respiratory EVs from species C, or viruses within the newly-discovered RV-C species. This review provides an update of the latest findings on clinical and fundamental aspects of RV and respiratory EV, including a summary of basic knowledge of their biology.
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Affiliation(s)
- Léna Royston
- University of Geneva Faculty of Medicine, 1 Rue Michel-Servet, 1205 Geneva, Switzerland.
- Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Caroline Tapparel
- University of Geneva Faculty of Medicine, 1 Rue Michel-Servet, 1205 Geneva, Switzerland.
- Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland.
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Molecular Evolution and Intraclade Recombination of Enterovirus D68 during the 2014 Outbreak in the United States. J Virol 2015; 90:1997-2007. [PMID: 26656685 DOI: 10.1128/jvi.02418-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED In August 2014, an outbreak of enterovirus D68 (EV-D68) occurred in North America, causing severe respiratory disease in children. Due to a lack of complete genome sequence data, there is only a limited understanding of the molecular evolution and epidemiology of EV-D68 during this outbreak, and it is uncertain whether the differing clinical manifestations of EV-D68 infection are associated with specific viral lineages. We developed a high-throughput complete genome sequencing pipeline for EV-D68 that produced a total of 59 complete genomes from respiratory samples with a 95% success rate, including 57 genomes from Kansas City, MO, collected during the 2014 outbreak. With these data in hand, we performed phylogenetic analyses of complete genome and VP1 capsid protein sequences. Notably, we observed considerable genetic diversity among EV-D68 isolates in Kansas City, manifest as phylogenetically distinct lineages, indicative of multiple introductions of this virus into the city. In addition, we identified an intersubclade recombination event within EV-D68, the first recombinant in this virus reported to date. Finally, we found no significant association between EV-D68 genetic variation, either lineages or individual mutations, and a variety of demographic and clinical variables, suggesting that host factors likely play a major role in determining disease severity. Overall, our study revealed the complex pattern of viral evolution within a single geographic locality during a single outbreak, which has implications for the design of effective intervention and prevention strategies. IMPORTANCE Until recently, EV-D68 was considered to be an uncommon human pathogen, associated with mild respiratory illness. However, in 2014 EV-D68 was responsible for more than 1,000 disease cases in North America, including severe respiratory illness in children and acute flaccid myelitis, raising concerns about its potential impact on public health. Despite the emergence of EV-D68, a lack of full-length genome sequences means that little is known about the molecular evolution of this virus within a single geographic locality during a single outbreak. Here, we doubled the number of publicly available complete genome sequences of EV-D68 by performing high-throughput next-generation sequencing, characterized the evolutionary history of this outbreak in detail, identified a recombination event, and investigated whether there was any correlation between the demographic and clinical characteristics of the patients and the viral variant that infected them. Overall, these results will help inform the design of intervention strategies for EV-D68.
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Lin CH, Wang YB, Chen SH, Hsiung CA, Lin CY. Precise genotyping and recombination detection of Enterovirus. BMC Genomics 2015; 16 Suppl 12:S8. [PMID: 26678286 PMCID: PMC4682392 DOI: 10.1186/1471-2164-16-s12-s8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception, http://symbiont.iis.sinica.edu.tw/evidence), for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution.
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Torres JP, Farfan MJ, Izquierdo G, Piemonte P, Henriquez J, O'Ryan ML. Enterovirus D68 infection, Chile, Spring 2014. Emerg Infect Dis 2015; 21:728-9. [PMID: 25811806 PMCID: PMC4378481 DOI: 10.3201/eid2104.141766] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Enterovirus D68 detected in children with severe acute respiratory illness in Brazil. Emerg Microbes Infect 2015; 4:e66. [PMID: 26576342 PMCID: PMC4631932 DOI: 10.1038/emi.2015.66] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/31/2015] [Accepted: 08/31/2015] [Indexed: 11/16/2022]
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Poelman R, Schuffenecker I, Van Leer-Buter C, Josset L, Niesters HGM, Lina B. European surveillance for enterovirus D68 during the emerging North-American outbreak in 2014. J Clin Virol 2015; 71:1-9. [PMID: 26364237 DOI: 10.1016/j.jcv.2015.07.296] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 07/13/2015] [Accepted: 07/16/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND In August and September 2014, unexpected clusters of enterovirus-D68 (EV-D68) infections associated with severe respiratory disease emerged from North-America. In September, the European Centre for Disease Prevention and Control (ECDC) asked European countries to strengthen respiratory sample screening for enterovirus detection and typing in cases with severe respiratory presentations. OBJECTIVES To provide a detailed picture of EV-D68 epidemiology in Europe by conducting a retrospective and prospective laboratory analysis of clinical specimens. STUDY DESIGN An initiative supported by the European Society for Clinical Virology (ESCV) and ECDC was launched to screen for EV-D68 in respiratory specimens between July 1st and December 1st 2014 in Europe and to sequence the VP1 region of detected viruses for phylogenetic analytic purposes. RESULTS Forty-two institutes, representing 51 laboratories from 17 European countries, analyzed 17,248 specimens yielding 389 EV-D68 positive samples (2.26%) in 14 countries. The proportion of positive samples ranged between 0 and 25% per country. These infections resulted primarily in mild respiratory disease, mainly detected in young children presenting with wheezing and in immuno-compromised adults. The viruses detected in Europe are genetically very similar to those of the North-American epidemic and the majority (83%) could be assigned to clade B. Except for 3 acute flaccid paralysis (AFP) cases, one death and limited ICU admissions, no severe cases were reported. CONCLUSIONS The European study showed that EV-D68 circulated in Europe during summer and fall of 2014 with a moderate disease burden and different pathogenic profile compared to the North-American epidemic.
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Affiliation(s)
- Randy Poelman
- The University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Division of Clinical Virology, Groningen, The Netherlands.
| | - Isabelle Schuffenecker
- National Enterovirus Reference Centre, Laboratoire de Virologie, Centre de Biologie Est des Hospices Civils de Lyon, Bron, France
| | - Coretta Van Leer-Buter
- The University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Division of Clinical Virology, Groningen, The Netherlands
| | - Laurence Josset
- National Enterovirus Reference Centre, Laboratoire de Virologie, Centre de Biologie Est des Hospices Civils de Lyon, Bron, France; Virpath Lab, EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon1, Université de Lyon, Lyon, France
| | - Hubert G M Niesters
- The University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Division of Clinical Virology, Groningen, The Netherlands
| | - Bruno Lina
- National Enterovirus Reference Centre, Laboratoire de Virologie, Centre de Biologie Est des Hospices Civils de Lyon, Bron, France; Virpath Lab, EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon1, Université de Lyon, Lyon, France
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BUBBA L, PELLEGRINELLI L, PARIANI E, PRIMACHE V, AMENDOLA A, BINDA S. A novel multiplex one-step real-time RT-PCR assay for the simultaneous identification of enterovirus and parechovirus in clinical fecal samples. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2015; 56:E57-60. [PMID: 26789989 PMCID: PMC4718355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/26/2015] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Enterovirus (EV) and parechovirus (PeV) can either infect humans asymptomatically or can cause gastroenteritis, respiratory symptoms and, sometimes, severe disease. As the number of newly identified EV and PeV genotypes keeps increasing, diagnostic methods need to be updated. To this end, we described a novel multiplex one-step real-time RT-PCR to detect EV and human PeV (HPeV) simultaneously in fecal samples collected from children with rotavirus group A (RV-A)-related gastroenteritis. METHODS The specificity and sensitivity of the EV/HPeV realtime RT-PCR were evaluated with two 2011 Quality Control for Molecular Diagnostics (QCMD) panels for EV and HPeV detection. RNA was extracted from 111 RV-A-positive fecal samples collected from children up to 5 years of age who had been hospitalized for gastroenteritis from September 2010 to August 2011. RESULTS The EV/HPeV real-time RT-PCR showed a 100% sensitivity and specificity for EV and 91% and 91.7% for HPeV, respectively. Of the 111 RV-A-positive stool specimens, 28 (25.2%) were EV-positive and 7 (6.3%) were HPeV-positive. No clinical differences between children with single or double infections were observed. DISCUSSION In our study, the frequency of EV and HPeV infections was surprisingly high, thus underlining the importance of including EV and HPeV detection in diagnostic panels. The multiplex real-time RT-PCR presented in this paper can therefore be a useful method in a diagnostic setting.
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Affiliation(s)
- L. BUBBA
- Correspondence: Laura Bubba, Department of Biomedical Sciences for Health, University of Milan, via C. Pascal 36, 20133 Milan, Italy - Tel. +39 02 50315132 - Fax +39 02 50315120 - E-mail:
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del Valle Mendoza J, Cornejo-Tapia A, Weilg P, Verne E, Nazario-Fuertes R, Ugarte C, del Valle LJ, Pumarola T. Incidence of respiratory viruses in Peruvian children with acute respiratory infections. J Med Virol 2015; 87:917-24. [PMID: 25784285 PMCID: PMC7167149 DOI: 10.1002/jmv.24159] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2015] [Indexed: 11/08/2022]
Abstract
Acute respiratory infections are responsible for high morbi-mortality in Peruvian children. However, the etiological agents are poorly identified. This study, conducted during the pandemic outbreak of H1N1 influenza in 2009, aims to determine the main etiological agents responsible for acute respiratory infections in children from Lima, Peru. Nasopharyngeal swabs collected from 717 children with acute respiratory infections between January 2009 and December 2010 were analyzed by multiplex RT-PCR for 13 respiratory viruses: influenza A, B, and C virus; parainfluenza virus (PIV) 1, 2, 3, and 4; and human respiratory syncytial virus (RSV) A and B, among others. Samples were also tested with direct fluorescent-antibodies (DFA) for six respiratory viruses. RT-PCR and DFA detected respiratory viruses in 240 (33.5%) and 85 (11.9%) cases, respectively. The most common etiological agents were RSV-A (15.3%), followed by influenza A (4.6%), PIV-1 (3.6%), and PIV-2 (1.8%). The viruses identified by DFA corresponded to RSV (5.9%) and influenza A (1.8%). Therefore, respiratory syncytial viruses (RSV) were found to be the most common etiology of acute respiratory infections. The authors suggest that active surveillance be conducted to identify the causative agents and improve clinical management, especially in the context of possible circulation of pandemic viruses.
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Affiliation(s)
- Juana del Valle Mendoza
- School of Medicine, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas-UPC, Lima, Perú; Nutrition Research Institute, Lima, Perú
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Aponte FE, Taboada B, Espinoza MA, Arias-Ortiz MA, Monge-Martínez J, Rodríguez-Vázquez R, Díaz-Hernández F, Zárate-Vidal F, Wong-Chew RM, Firo-Reyes V, del Río-Almendárez CN, Gaitán-Meza J, Villaseñor-Sierra A, Martínez-Aguilar G, García-Borjas M, Noyola DE, Pérez-Gónzalez LF, López S, Santos-Preciado JI, Arias CF. Rhinovirus is an important pathogen in upper and lower respiratory tract infections in Mexican children. Virol J 2015; 12:31. [PMID: 25889995 PMCID: PMC4349319 DOI: 10.1186/s12985-015-0262-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/10/2015] [Indexed: 11/17/2022] Open
Abstract
Background Most of the studies characterizing the incidence of rhinovirus (RV) have been carried out in hospitalized children and in developed countries. In those studies, RV-C has been associated with more severe respiratory tract infections than RV species A and B. In this study we determined the frequency and diversity of RV strains associated with upper and lower respiratory tract infections (URTI, LRTI) in Mexico, and describe the clinical characteristics of the illness associated with different RV species. Methods A prospective surveillance of 526 and 250 children with URTI and LRTI was carried out. Respiratory samples were analyzed by RT-PCR for viruses. The 5′ untranslated region of the RV genome was amplified and sequenced. Results In the case of URTI, 17.5% were positive for RV, while this virus was found in 24.8% of LRTI. The RV species was determined in 73 children with URTI: 61.6% were RV-A, 37% RV-C and, 1.4% RV-B; and in 43 children with LRTI: 51.2% were RV-A, 41.8% RV-C, and 7% RV-B. No significant differences in clinical characteristics were found in patients with RV-A or RV-C infections. A high genetic diversity of RV strains was found in both URTI and LRTI. Conclusions Both RV-A and RV-C species were frequently found in hospitalized as well as in outpatient children. This study underlines the high prevalence and genetic diversity of RV strains in Mexico and the potential severity of disease associated with RV-A and RV-C infections.
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Affiliation(s)
- Fernando E Aponte
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av.Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico.
| | - Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av.Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico.
| | - Marco A Espinoza
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av.Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico.
| | | | | | | | | | | | - Rosa María Wong-Chew
- Facultad de Medicina, Universidad Nacional Autónoma de México, México, D F, Mexico.
| | | | | | - Jesús Gaitán-Meza
- Nuevo Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico.
| | | | | | | | - Daniel E Noyola
- Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico.
| | | | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av.Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico.
| | | | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av.Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico.
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Epidemiologic, clinical, and virologic characteristics of human rhinovirus infection among otherwise healthy children and adults: rhinovirus among adults and children. J Clin Virol 2015; 64:74-82. [PMID: 25728083 PMCID: PMC4347877 DOI: 10.1016/j.jcv.2015.01.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/06/2015] [Accepted: 01/10/2015] [Indexed: 11/23/2022]
Abstract
BACKGROUND human rhinovirus (HRV) is a major cause of influenza-like illness (ILI) in adults and children. Differences in disease severity by HRV species have been described among hospitalized patients with underlying illness. Less is known about the clinical and virologic characteristics of HRV infection among otherwise healthy populations, particularly adults. OBJECTIVES to characterize molecular epidemiology of HRV and association between HRV species and clinical presentation and viral shedding. STUDY DESIGN observational, prospective, facility-based study of ILI was conducted from February 2010 to April 2012. Collection of nasopharyngeal specimens, patient symptoms, and clinical information occurred on days 0, 3, 7, and 28. Patients recorded symptom severity daily for the first 7 days of illness in a symptom diary. HRV was identified by RT-PCR and genotyped for species determination. Cases who were co-infected with other viral respiratory pathogens were excluded from the analysis. We evaluated the associations between HRV species, clinical severity, and patterns of viral shedding. RESULTS eighty-four HRV cases were identified and their isolates genotyped. Of these, 62 (74%) were >18 years. Fifty-four were HRV-A, 11HRV-B, and 19HRV-C. HRV-C infection was more common among children than adults (59% vs. 10%, P<0.001). Among adults, HRV-A was associated with higher severity of upper respiratory symptoms compared to HRV-B (P=0.02), but no such association was found in children. In addition, adults shed HRV-A significantly longer than HRV-C (P trend=0.01). CONCLUSIONS among otherwise healthy adults with HRV infection, we observed species-specific differences in respiratory symptom severity and duration of viral shedding.
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Marcone DN, Culasso A, Carballal G, Campos R, Echavarría M. Genetic diversity and clinical impact of human rhinoviruses in hospitalized and outpatient children with acute respiratory infection, Argentina. J Clin Virol 2014; 61:558-64. [PMID: 25453332 PMCID: PMC7185656 DOI: 10.1016/j.jcv.2014.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/09/2014] [Accepted: 10/12/2014] [Indexed: 01/01/2023]
Abstract
Human rhinoviruses (HRV) were detected in 40% of children with ARI without comorbidities. HRV were identified as a risk factor associated with hospitalization (OR: 2.47). All HRV species co-circulated, being HRV-A and C the most frequently detected. Demographic and clinical outcome were similar for HRV-A and C infections. A high turnover rate of HRV genotypes was observed.
Background Human rhinoviruses (HRV) are recognized as a cause of upper and lower acute respiratory infections (ARI). The circulating species and their clinical impact were not described in Argentina. Objectives To describe the molecular epidemiology of HRV in children and to determine the association of HRV species with outcome and severity. Study design: Hospitalized and outpatients children <6 years old with ARI without comorbidities (n = 620) were enrolled (2008–2010). Demographic, clinical data and outcome were analyzed. HRV were identified by RT-PCR. Phylogenetic analysis and demographic reconstruction for HRV were performed in selected samples. Results HRV were detected in 252/620 (40.6%) of children; 8.5% in viral coinfection. Bronchiolitis (55%) and pneumonia (13%) were the most frequent clinical diagnosis. Of 202 inpatients with HRV: 72% required oxygen supplementation, 11% intensive care unit and 3% mechanical ventilation. HRV were identified as a risk factor for hospitalization (OR: 2.47). All three HRV species were detected being HRV-A (55%) and HRV-C (43%) the most frequent; HRV-B was infrequent (2%). Of 44 sequenced HRV, 30 genotypes were detected. Seven of them were the most prevalent and circulated during limited periods of time. The demographic reconstruction revealed a constant population size and a high turnover rate of genotypes. Demographic and clinical outcome were similar for HRV-A and HRV-C infections. Conclusion This study highlights the clinical impact of HRV in children without comorbidities as a cause of lower ARI and hospitalization. The high frequency of HRV infections may be associated with the simultaneous circulation of genotypes and their high turnover rate.
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Affiliation(s)
- Débora Natalia Marcone
- Virology Unit and Clinical Virology Laboratory, Hospital Universitario CEMIC, Av. Galván 4102, Buenos Aires, Argentina.
| | - Andrés Culasso
- Department of Virology, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, Buenos Aires, Argentina
| | - Guadalupe Carballal
- Virology Unit and Clinical Virology Laboratory, Hospital Universitario CEMIC, Av. Galván 4102, Buenos Aires, Argentina
| | - Rodolfo Campos
- Department of Virology, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 954, Buenos Aires, Argentina
| | - Marcela Echavarría
- Virology Unit and Clinical Virology Laboratory, Hospital Universitario CEMIC, Av. Galván 4102, Buenos Aires, Argentina
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Linder JE, Plachco TE, Libster R, Miller EK. Sequencing human rhinoviruses: direct sequencing versus plasmid cloning. J Virol Methods 2014; 211:64-9. [PMID: 25286177 DOI: 10.1016/j.jviromet.2014.09.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 09/17/2014] [Accepted: 09/24/2014] [Indexed: 01/08/2023]
Abstract
Human rhinoviruses (RV) are associated with the majority of viral respiratory illnesses in infants, children and adults. Over the last several years, researchers have begun to sequence the many different species and strains of RV in order to determine if certain species were associated with increased disease severity. There are a variety of techniques employed to prepare samples for sequencing. One method utilizes plasmid-cloning, which is expensive and takes several hours to complete. Recently, some investigators have instead used direct sequencing to sequence RV strains, allowing for omission of the time- and labor-intensive cloning step. This study formally compares and contrasts the sequencing results obtained from plasmid-cloning and direct Sanger sequencing of a 500 base pair PCR product covering the VP4/VP2 region of RV. A slightly longer sequence (by 65 base pairs on average) was obtained when specimens were plasmid-cloned, and the sequences were 86% similar. After trimming the extra base pairs from the cloned sequences, the sequences were 99.7% identical. Overall success of directly sequencing samples was similar to that of cloning, 5% on average failed for each technique. Therefore, in many instances, directly sequencing samples may be considered in lieu of the more expensive and time-consuming plasmid-cloning technique.
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Affiliation(s)
- Jodell E Linder
- Department of Pediatrics, Vanderbilt University School of Medicine, Medical Center North, Nashville, TN 37232, United States.
| | - Tatyana E Plachco
- Hospital de Pediatria SAMIC Prof. Dr. Juan P Garrahan, Buenos Aires, Argentina; Hospital Materno Infantil Ramon Sarda, Buenos Aires, Argentina.
| | | | - E Kathryn Miller
- Department of Pediatrics, Vanderbilt University School of Medicine, Medical Center North, Nashville, TN 37232, United States.
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Huaman JL, Carrion G, Ampuero JS, Gomez J, Ocaña V, Paz I, Gomez E, Chavez E, Sarmiento F, Pozo E, Laguna-Torres VA, Halsey ES. Non-rhinovirus enteroviruses associated with respiratory infections in Peru (2005-2010). Virol J 2014; 11:169. [PMID: 25244984 PMCID: PMC4192742 DOI: 10.1186/1743-422x-11-169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 09/15/2014] [Indexed: 11/10/2022] Open
Abstract
Background Enteroviruses (EVs) are a common cause of respiratory tract infections and are classified into seven species (EVA-D and rhinoviruses [RHVs] A-C) with more than 200 different serotypes. Little is known about the role of non-RHV EVs in respiratory infections in South America. The aim of this study was to describe the epidemiology of non-RHV EVs detected in patients with influenza-like illness enrolled in a passive surveillance network in Peru. Methods Throat swabs and epidemiological data were collected from participants after obtaining verbal consent. Viral isolation was performed in cell culture and identified by immunofluorescence assay. Serotype identification of EV isolates was performed using commercial monoclonal antibodies. Identification of non-serotypeable isolations was carried out by reverse transcriptase-PCR, followed by sequencing. Results Between 2005 and 2010, 24,239 samples were analyzed, and 9,973 (41.1%) possessed at least one respiratory virus. EVs were found in 175 samples (0.7%). Our results revealed a clear predominance of EVB species, 90.9% (159/175). No EVDs were isolated. The mean and median ages of EV-positive subjects were 9.1 and 4.0 years, respectively, much younger than the population sampled, 17.6 and 12.0 years. Sixteen serotypes were identified, four EVA, 11 EVB, and one EVC species. The most common serotypes were coxsackievirus B1, coxsackievirus B2, coxsackievirus B5, and coxsackievirus B3. Conclusion This study provides data about the serotypes of EVs circulating in Peru and sets the need for further studies.
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