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Boukli N, Flamand C, Chea KL, Heng L, Keo S, Sour K, In S, Chhim P, Chhor B, Kruy L, Feenstra JDM, Gandhi M, Okafor O, Ulekleiv C, Auerswald H, Horm VS, Karlsson EA. One assay to test them all: Multiplex assays for expansion of respiratory virus surveillance. Front Med (Lausanne) 2023; 10:1161268. [PMID: 37168265 PMCID: PMC10165998 DOI: 10.3389/fmed.2023.1161268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Molecular multiplex assays (MPAs) for simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza and respiratory syncytial virus (RSV) in a single RT-PCR reaction reduce time and increase efficiency to identify multiple pathogens with overlapping clinical presentation but different treatments or public health implications. Clinical performance of XpertXpress® SARS-CoV-2/Flu/RSV (Cepheid, GX), TaqPath™ COVID-19, FluA/B, RSV Combo kit (Thermo Fisher Scientific, TP), and PowerChek™ SARS-CoV-2/Influenza A&B/RSV Multiplex RT-PCR kit II (KogeneBiotech, PC) was compared to individual Standards of Care (SoC). Thirteen isolates of SARS-CoV-2, human seasonal influenza, and avian influenza served to assess limit of detection (LoD). Then, positive and negative residual nasopharyngeal specimens, collected under public health surveillance and pandemic response served for evaluation. Subsequently, comparison of effectiveness was assessed. The three MPAs confidently detect all lineages of SARS-CoV-2 and influenza viruses. MPA-LoDs vary from 1 to 2 Log10 differences from SoC depending on assay and strain. Clinical evaluation resulted in overall agreement between 97 and 100%, demonstrating a high accuracy to detect all targets. Existing differences in costs, testing burden and implementation constraints influence the choice in primary or community settings. TP, PC and GX, reliably detect SARS-CoV-2, influenza and RSV simultaneously, with reduced time-to-results and simplified workflows. MPAs have the potential to enhance diagnostics, surveillance system, and epidemic response to drive policy on prevention and control of viral respiratory infections.
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Affiliation(s)
- Narjis Boukli
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Claude Flamand
- Epidemiology and Public Health Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, CNRS, Paris, France
| | - Kim Lay Chea
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Leangyi Heng
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Seangmai Keo
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Kimhoung Sour
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sophea In
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Panha Chhim
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Bunthea Chhor
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Lomor Kruy
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | | | - Manoj Gandhi
- Thermo Fisher Scientific, South San Francisco CA, United States
| | - Obiageli Okafor
- Thermo Fisher Scientific, South San Francisco CA, United States
| | | | - Heidi Auerswald
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Viseth Srey Horm
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Erik A. Karlsson
- Virology Unit, National Influenza Center, WHO H5 Regional Reference Laboratory, World Health Organization COVID-19 Global Referral Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
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von Mollendorf C, Berger D, Gwee A, Duke T, Graham SM, Russell FM, Mulholland EK. Aetiology of childhood pneumonia in low- and middle-income countries in the era of vaccination: a systematic review. J Glob Health 2022; 12:10009. [PMID: 35866332 PMCID: PMC9305023 DOI: 10.7189/jogh.12.10009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background This systematic review aimed to describe common aetiologies of severe and non-severe community acquired pneumonia among children aged 1 month to 9 years in low- and middle-income countries. Methods We searched the MEDLINE, EMBASE, and PubMed online databases for studies published from January 2010 to August 30, 2020. We included studies on acute community-acquired pneumonia or acute lower respiratory tract infection with ≥1 year of continuous data collection; clear consistent case definition for pneumonia; >1 specimen type (except empyema studies where only pleural fluid was required); testing for >1 pathogen including both viruses and bacteria. Two researchers reviewed the studies independently. Results were presented as a narrative summary. Quality of evidence was assessed with the Quality Assessment Tool for Quantitative Studies. The study was registered on PROSPERO [CRD42020206830]. Results We screened 5184 records; 1305 duplicates were removed. The remaining 3879 titles and abstracts were screened. Of these, 557 articles were identified for full-text review, and 55 met the inclusion criteria - 10 case-control studies, three post-mortem studies, 11 surveillance studies, eight cohort studies, five cross-sectional studies, 12 studies with another design and six studies that included patients with pleural effusions or empyema. Studies which described disease by severity showed higher bacterial detection (Streptococcus pneumoniae, Staphylococcus aureus) in severe vs non-severe cases. The most common virus causing severe disease was respiratory syncytial virus (RSV). Pathogens varied by age, with RSV and adenovirus more common in younger children. Influenza and atypical bacteria were more common in children 5-14 years than younger children. Malnourished and HIV-infected children had higher rates of pneumonia due to bacteria or tuberculosis. Conclusions Several viral and bacterial pathogens were identified as important targets for prevention and treatment. Bacterial pathogens remain an important cause of moderate to severe disease, particularly in children with comorbidities despite widespread PCV and Hib vaccination.
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Affiliation(s)
- Claire von Mollendorf
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Daria Berger
- Royal Children's Hospital, Parkville, Victoria, Australia
| | - Amanda Gwee
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Royal Children's Hospital, Parkville, Victoria, Australia
| | - Trevor Duke
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Royal Children's Hospital, Parkville, Victoria, Australia
| | - Stephen M Graham
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Royal Children's Hospital, Parkville, Victoria, Australia
| | - Fiona M Russell
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - E Kim Mulholland
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
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Hwang JK, Na JY, Kim J, Oh JW, Kim YJ, Choi YJ. Age-Specific Characteristics of Adult and Pediatric Respiratory Viral Infections: A Retrospective Single-Center Study. J Clin Med 2022; 11:jcm11113197. [PMID: 35683584 PMCID: PMC9181129 DOI: 10.3390/jcm11113197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 11/16/2022] Open
Abstract
This study aimed to identify age-specific characteristics of respiratory viral infections. Hospitalized patients with confirmed viral respiratory infections were included in the sample. The patients were divided into the pediatric group (<19 years old) and the adult group (≥19 years old). The groups were then subdivided based on age: 0−6, 7−12, 13−18, 19−49, 50−64, and ≥65 years old. These groups were compared to evaluate the differences in the pattern of respiratory viral infections. Among a total of 4058 pediatric patients (mean age 3.0 ± 2.9 years, n = 1793 females), 2829 (48.9%) had mono-infections, while 1229 (51.1%) had co-infections. Co-infections were the most common in the 0−6-year-old group (31.6%). Among 1550 adult patients (mean age 70.2 ± 15.3 years, n = 710 females), 1307 (85.6%) had mono-infections and 243 (14.4%) had co-infections. Co-infections were most common in the ≥65-year-old group (16.8%). Viral infection and co-infection rates decreased with age in pediatric patients but increased with increasing age in adults. In pediatric patients, the rates of viral infections and co-infections were high; the rate of co-infections was higher in younger patients. In adult patients, the rates of viral infections and co-infections were lower than those in pediatric patients; the rate of co-infections was higher in older patients.
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Affiliation(s)
- Jae Kyoon Hwang
- Department of Pediatrics, Hanyang University Guri Hospital, Guri 11923, Korea; (J.K.H.); (J.-W.O.)
| | - Jae Yoon Na
- Department of Pediatrics, Hanyang University Seoul Hospital, Seoul 04763, Korea; (J.Y.N.); (J.K.); (Y.J.K.)
| | - Jihye Kim
- Department of Pediatrics, Hanyang University Seoul Hospital, Seoul 04763, Korea; (J.Y.N.); (J.K.); (Y.J.K.)
| | - Jae-Won Oh
- Department of Pediatrics, Hanyang University Guri Hospital, Guri 11923, Korea; (J.K.H.); (J.-W.O.)
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Yong Joo Kim
- Department of Pediatrics, Hanyang University Seoul Hospital, Seoul 04763, Korea; (J.Y.N.); (J.K.); (Y.J.K.)
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Young-Jin Choi
- Department of Pediatrics, Hanyang University Guri Hospital, Guri 11923, Korea; (J.K.H.); (J.-W.O.)
- Correspondence:
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Choi YJ, Lee KS, Lee YS, Kim KR, Oh JW. Analysis of the Association Among Air Pollutants, Allergenic Pollen, and Respiratory Virus Infection of Children in Guri, Korea During Recent 5 Years. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2022; 14:289-299. [PMID: 35557494 PMCID: PMC9110915 DOI: 10.4168/aair.2022.14.3.289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 03/05/2022] [Accepted: 03/14/2022] [Indexed: 12/31/2022]
Abstract
PURPOSE Concerns about the spread of infectious diseases have increased due to the coronavirus disease pandemic. Knowing the factors that exacerbate or increase the contagiousness of a virus could be a key to pandemic prevention. Therefore, we investigated whether the pandemic potential of infectious diseases correlates with the concentration of atmospheric substances. We also investigated whether environmental deterioration causes an increase in viral infections. METHODS Pediatric patients (0-18 years old; n = 6,223) were recruited from those hospitalized for aggravated respiratory symptoms at Hanyang University Guri Hospital between January 1, 2015 and December 31, 2019. The number of viral infections was defined as the total number of virus-infected patients hospitalized for respiratory symptoms. We analyzed the association between the number of viral infections/week and the average concentrations of atmospheric substances including particulate matter (PM)10, PM2.5, O₃, NO₂, CO, SO₂, and allergenic pollen) for that week. The cross-correlation coefficient between the weekly measures of pollens and viral infections was checked to determine which time point had the most influence. The association of atmospheric substances in that time, with the number of viral infections/week was investigated using multiple linear regression analysis to identify factors with the greatest influence. RESULTS In spring the tree pollen average concentration one week earlier (t-1) had the greatest correlation with the average virus infection of a given week (t) (ρXY (h) =0.5210). The number of viral infections showed a statistically significant correlation with especially tree pollen concentration of 1 week prior (adj R²=0.2280). O₃ concentration was correlated to the number of viral infections within that week (adj R²=0.2552) in spring, and weed pollen and CO concentration correlated (adj R²=0.1327) in autumn. CONCLUSIONS Seasonal co-exposure to air pollutants and allergenic pollens may enhance respiratory viral infection susceptibility in children. Therefore, reducing the concentrations of air pollutants and pollens may help prevent future epidemics.
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Affiliation(s)
- Young-Jin Choi
- Department of Pediatrics, Hanyang University Guri Hospital, Guri, Korea
| | - Kyung Suk Lee
- Department of Pediatrics, Hanyang University Guri Hospital, Guri, Korea
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul, Korea
| | - Young-Seop Lee
- Department of Statistics, College of Science, Dongguk University, Seoul, Korea
| | - Kyu Rang Kim
- Impact-based Forecast Research Team, High Impact Weather Research Department, National Institute of Meteorological Sciences, Gangneung, Korea
| | - Jae-Won Oh
- Department of Pediatrics, Hanyang University Guri Hospital, Guri, Korea
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul, Korea.
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Kamata K, Thein KN, Di Ja L, Win NC, Win SMK, Suzuki Y, Ito A, Osada H, Chon I, Phyu WW, Aizawa Y, Ikuse T, Ota T, Kyaw Y, Tin HH, Shobugawa Y, Watanabe H, Saito R, Saitoh A. Clinical manifestations and outcome of viral acute lower respiratory infection in hospitalised children in Myanmar. BMC Infect Dis 2022; 22:350. [PMID: 35395744 PMCID: PMC8992414 DOI: 10.1186/s12879-022-07342-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/25/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Acute lower respiratory infection (ALRI) remains the leading cause of death in children worldwide, and viruses have been the major cause of ALRI. In Myanmar, ALRI is associated with high morbidity and mortality in children, and detailed information on ALRI is currently lacking. METHODS This prospective study investigated the viral aetiologies, clinical manifestations, and outcomes of ALRI in hospitalised children aged 1 month to 12 years at the Yankin Children Hospital, Yangon, Myanmar from May 2017 to April 2019. The sample size was set to 300 patients for each year. Two nasopharyngeal swabs were obtained for the patients with suspected viral ALRI; one for rapid tests for influenza and respiratory syncytial virus (RSV), and the other for real-time PCR for the 16 ALRI-causing viruses. Pneumococcal colonization rates were also investigated using real-time PCR. Clinical information was extracted from the medical records, and enrolled patients were categorised by age and severity for comparison. RESULTS Among the 5463 patients admitted with a diagnosis of ALRI, 570 (10.4%) were enrolled in this study. The median age of the patients was 8 months (interquartile range, 4-15 months). The most common symptoms were cough (93%) and difficulty in breathing (73%), while the most common signs of ALRI were tachypnoea (78%) and chest indrawing (67%). A total of 16 viruses were detected in 502 of 570 patients' samples (88%), with RSV B (36%) and rhinovirus (28%) being the most commonly detected. Multiple viruses were detected in 221 of 570 samples (37%) collected from 570 patients. Severe ALRI was diagnosed in 107 of 570 patients (19%), and RSV B and human rhinovirus were commonly detected. The mortality rate was 5%; influenza virus A (29%) and RSV B (21%) were commonly detected, and stunting and lack of immunization were frequently observed in such cases. Additionally, 45% (259/570) of the patients had pneumococcal colonization. CONCLUSIONS Viral ALRI in hospitalised children with a median of 8 months has significant morbidity and mortality rates in Myanmar. RSV and rhinovirus were the most commonly detected from nasopharyngeal swabs, while influenza virus and RSV were the most frequently associated with fatal cases.
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Grants
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
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Affiliation(s)
- Kazuhiro Kamata
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | | | - Lasham Di Ja
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
| | - Nay Chi Win
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
| | - Su Mon Kyaw Win
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
| | - Yuko Suzuki
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Ai Ito
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Hidekazu Osada
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
- Division of International Health, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Irina Chon
- Division of International Health, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Wint Wint Phyu
- Division of International Health, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Yuta Aizawa
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Tatsuki Ikuse
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Tomomi Ota
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
| | - Yadanar Kyaw
- Respiratory Medicine Department, Thingangyun Sanpya General Hospital, Yangon, Myanmar
| | - Htay Htay Tin
- Department of Medical Services, National Health Laboratory, Ministry of Health and Sports, Yangon, Myanmar
| | - Yugo Shobugawa
- Division of International Health, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Hisami Watanabe
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
| | - Reiko Saito
- Division of International Health, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Akihiko Saitoh
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan.
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Johnson EK, Sylte D, Chaves SS, Li Y, Mahe C, Nair H, Paget J, van Pomeren T, Shi T, Viboud C, James SL. Hospital utilization rates for influenza and RSV: a novel approach and critical assessment. Popul Health Metr 2021; 19:31. [PMID: 34126993 PMCID: PMC8204427 DOI: 10.1186/s12963-021-00252-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/31/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Influenza and respiratory syncytial virus (RSV) contribute significantly to the burden of acute lower respiratory infection (ALRI) inpatient care, but heterogeneous coding practices and availability of inpatient data make it difficult to estimate global hospital utilization for either disease based on coded diagnoses alone. METHODS This study estimates rates of influenza and RSV hospitalization by calculating the proportion of ALRI due to influenza and RSV and applying this proportion to inpatient admissions with ALRI coded as primary diagnosis. Proportions of ALRI attributed to influenza and RSV were extracted from a meta-analysis of 360 total sources describing inpatient hospital admissions which were input to a Bayesian mixed effects model over age with random effects over location. Results of this model were applied to inpatient admission datasets for 44 countries to produce rates of hospital utilization for influenza and RSV respectively, and rates were compared to raw coded admissions for each disease. RESULTS For most age groups, these methods estimated a higher national admission rate than the rate of directly coded influenza or RSV admissions in the same inpatient sources. In many inpatient sources, International Classification of Disease (ICD) coding detail was insufficient to estimate RSV burden directly. The influenza inpatient burden estimates in older adults appear to be substantially underestimated using this method on primary diagnoses alone. Application of the mixed effects model reduced heterogeneity between countries in influenza and RSV which was biased by coding practices and between-country variation. CONCLUSIONS This new method presents the opportunity of estimating hospital utilization rates for influenza and RSV using a wide range of clinical databases. Estimates generally seem promising for influenza and RSV associated hospitalization, but influenza estimates from primary diagnosis seem highly underestimated among older adults. Considerable heterogeneity remains between countries in ALRI coding (i.e., primary vs non-primary cause), and in the age profile of proportion positive for influenza and RSV across studies. While this analysis is interesting because of its wide data utilization and applicability in locations without laboratory-confirmed admission data, understanding the sources of variability and data quality will be essential in future applications of these methods.
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Affiliation(s)
- Emily K Johnson
- Institute of Health Metrics and Evaluation, University of Washington, Seattle, USA.
| | - Dillon Sylte
- Institute of Health Metrics and Evaluation, University of Washington, Seattle, USA
| | - Sandra S Chaves
- Foundation for Influenza Epidemiology, Fondation de France, Paris, France
- Vaccine Epidemiology and Modeling Department, Sanofi Pasteur, Lyon, France
| | - You Li
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Cedric Mahe
- Foundation for Influenza Epidemiology, Fondation de France, Paris, France
- Vaccine Epidemiology and Modeling Department, Sanofi Pasteur, Lyon, France
| | - Harish Nair
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - John Paget
- Netherlands Institute for Health Services Research (Nivel), Utrecht, Netherlands
| | - Tayma van Pomeren
- Netherlands Institute for Health Services Research (Nivel), Utrecht, Netherlands
| | - Ting Shi
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, USA
| | - Spencer L James
- Institute of Health Metrics and Evaluation, University of Washington, Seattle, USA
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Ríos Quituizaca P, Calderón L, Piedra S, Guerrero J, Narváez A. [Proposal for territorial analysis to face the SARS-CoV-2 pandemic based on the Profile of pneumonia and Influenza in Ecuador 2016-2018]. Aten Primaria 2021; 53:102021. [PMID: 33887602 PMCID: PMC7901493 DOI: 10.1016/j.aprim.2021.102021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/28/2020] [Accepted: 01/07/2021] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE The present study seeks to analyse sociodemographic determinants related to severe acute respiratory infections (SARI) and calculate the priorization index in the cantons of Ecuador to identify areas probably most vulnerable to COVID-19 transmission. DESIGN This descriptive ecological observational study. SETTING 224 cantons (geographical area) of Ecuador with secondary data sources of hospital information. PARTICIPANTS The unit of measurement was 224 cantons of Ecuador, in which analysed morbidity and lethality rates for SARI using hospital release data (2016-2018). MAIN MEASUREMENTS Eight sociodemographic indicators were structuralized, and correlation tests applied for a multiple regression model. The priorization index was created with criteria of efficiency, efficacy, effect size (IRR) and equity. Using the sum of the index for each indicator, the priorization score was calculated and localized in a territorial map. RESULTS Morbidity associated factors where: school attendance years, urbanization and population density; for mortality resulted: school attendance and ethnics (indigenous) IRR: 1.09 (IC95%:1.06-1.15) and IRR: 1.024 (IC95%:102-1.03) respectively. With lethality where related cantons, with population older than 60 years, IRR: 1.049 (IC95%: 1.03-1.07); 87 cantons had high priority mostly localized in the mountain region and the Morona Santiago Province. CONCLUSIONS Morbidity and mortality of SARI in Ecuador are associated to social and demographic factors. Priorization exercises considering these factors permit the identification of vulnerable territories facing respiratory disease propagation. The social determinants characteristic for each territory should be added to known individual factors to analyse the risk and vulnerability for COVID in the population.
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Affiliation(s)
- Paulina Ríos Quituizaca
- Universidad Central del Ecuador, Facultad de Ciencias Médicas, Quito, Ecuador; Universidad de Sao Paulo, Facultad de Medicina de Ribeirao Preto, Sao Paulo, Brasil.
| | - Lilian Calderón
- Universidad de Sao Paulo, Facultad de Medicina de Ribeirao Preto, Sao Paulo, Brasil
| | - Santiago Piedra
- Hospital de Especialidades Carlos Andrade Marín. Quito, Ecuador
| | - Jhon Guerrero
- Universidad Central del Ecuador, Facultad de Ciencias Médicas, Quito, Ecuador
| | - Alberto Narváez
- Universidad Central del Ecuador, Facultad de Ciencias Médicas, Quito, Ecuador
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Loevinsohn G, Hardick J, Sinywimaanzi P, Fenstermacher KZJ, Shaw-Saliba K, Monze M, Gaydos CA, Rothman RE, Pekosz A, Thuma PE, Sutcliffe CG. Respiratory pathogen diversity and co-infections in rural Zambia. Int J Infect Dis 2020; 102:291-298. [PMID: 33127501 PMCID: PMC7817328 DOI: 10.1016/j.ijid.2020.10.054] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 11/26/2022] Open
Abstract
Objectives: The role of respiratory co-infections in modulating disease severity remains understudied in southern Africa, particularly in rural areas. This study was performed to characterize the spectrum of respiratory pathogens in rural southern Zambia and the prognostic impact of co-infections. Methods: Respiratory specimens collected from inpatient and outpatient participants in a viral surveillance program in 2018–2019 were tested for selected viruses and a typical bacteria using the Xpert Xpress Flu/RSV assay and FilmArray Respiratory Panel EZ. Participants were followed for 3–5 weeks to assess their clinical course. Multivariable regression was used to examine the role of co-infections in influencing disease severity. Results: A respiratory pathogen was detected in 63.2% of samples from 671 participants who presented with influenza-like illness. Common pathogens identified included influenza virus (18.2% of samples), respiratory syncytial virus (RSV) (11.8%), rhinovirus (26.4%), and coronavirus (6.0%). Overall, 6.4% of participants were co-infected with multiple respiratory pathogens. Compared to mono-infections, co-infections were found not to be associated with severe clinical illness either overall (relative risk (RR) 0.72, 95% confidence interval (CI) 0.39–1.32) or specifically with influenza virus (RR 0.80, 95% CI 0.14–4.46) or RSV infections (RR 0.44, 95% CI 0.17–1.11). Conclusions: Respiratory infections in rural southern Zambia were associated with a wide range of viruses. Respiratory co-infections in this population were not associated with clinical severity.
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Affiliation(s)
- Gideon Loevinsohn
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA; Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Justin Hardick
- Division of Infectious Diseases, Department of Medicine Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Kathryn Shaw-Saliba
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mwaka Monze
- Virology Laboratory, University Teaching Hospital, Lusaka, Zambia
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard E Rothman
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Philip E Thuma
- Macha Research Trust, Macha, Zambia; Virology Laboratory, University Teaching Hospital, Lusaka, Zambia
| | - Catherine G Sutcliffe
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA.
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9
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Rafeek RAM, Divarathna MVM, Noordeen F. A review on disease burden and epidemiology of childhood parainfluenza virus infections in Asian countries. Rev Med Virol 2020; 31:e2164. [PMID: 32996257 DOI: 10.1002/rmv.2164] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022]
Abstract
Human parainfluenza viruses (HPIVs) are an important cause of acute respiratory tract infections (ARTIs) in children less than 5 years, second only to human respiratory syncytial viruses (HRSVs). Generally, patients infected with HPIVs are treated in outpatient clinics, yet also contribute to ARTI-associated hospitalization in children. Although HPIV infections are well studied in developed countries, these infections remain under-investigated and not considered in the routine laboratory diagnosis of childhood ARTI in many developing countries in Asia. We performed an extensive literature search on the prevalence, epidemiology, and burden of HPIV infections in children less than 5 years in Asia using PubMed and PubMed Central search engines. Based on the literature, the prevalence of HPIV infection in Asia ranges from 1% to 66%. According to many studies, HPIV-3 is the major virus circulating among children; however, several studies failed to detect HPIV-4 due to unavailability of diagnostic tools. In Asian countries, HPIV contributes a substantial disease burden in children. The data in this review should assist researchers and public health authorities to plan preventive measures, including accelerating research on vaccines and antiviral drugs.
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Affiliation(s)
- Rukshan A M Rafeek
- Faculty of Medicine, Department of Microbiology, University of Peradeniya, Peradeniya, Sri Lanka
| | - Maduja V M Divarathna
- Faculty of Medicine, Department of Microbiology, University of Peradeniya, Peradeniya, Sri Lanka
| | - Faseeha Noordeen
- Faculty of Medicine, Department of Microbiology, University of Peradeniya, Peradeniya, Sri Lanka
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10
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Viral Etiology of Acute Lower Respiratory Tract Infections in Hospitalized Children in Nagasaki, a Regional City of Japan in 2013-2015. Pediatr Infect Dis J 2020; 39:687-693. [PMID: 32221164 DOI: 10.1097/inf.0000000000002668] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND Acute lower respiratory tract infections (ALRIs) are the most common disease for hospitalized children in Japan. The aim of this study was to identify viruses in children hospitalized for ALRIs and to demonstrate epidemiologic and clinical characteristics in Japan. METHODS During a 2-year period from February 2013 to January 2015, we collected nasopharyngeal swab specimens from almost all hospitalized children with ALRIs in Nagasaki, a regional city of Japan, and its environs. Viruses were detected by multiplex polymerase chain reaction from these samples. RESULTS We detected one or more viruses from 259 (69%) of 374 patients, 227 of whom were infected with a single virus, 30 with 2, and 2 with 3 viruses. Detected viruses in this study were rhinovirus (46.4%), respiratory syncytial virus (29.7%), human metapneumovirus (6.8%), parainfluenza virus (5.5%), enterovirus D68 (3.4%), influenza virus (2.7%), adenovirus (2.4%), bocavirus (2.0%) and Coxsackie virus (1.0%). We detected a seasonal shift in respiratory syncytial virus outbreaks from the 2013-2014 to the 2014-2015 seasons. There was no significant difference in clinical course and severity among those viruses. Patients with a history of asthma or underlying diseases were older and more frequently required oxygen therapy than previously healthy patients. CONCLUSIONS Viral etiology in hospitalized children with ALRIs in Nagasaki, Japan, was similar to that in many other countries. Enterovirus D68, which was recently recognized as a causative agent of severe ALRIs, was also identified in this study area. Severity of ALRIs may depend on underlying disease rather than type of etiologic virus.
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11
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Wen S, Lv F, Chen X, Zhu L, Li H, Lin L, Zhang H. Application of a nucleic acid-based multiplex kit to identify viral and atypical bacterial aetiology of lower respiratory tract infection in hospitalized children. J Med Microbiol 2019; 68:1211-1218. [PMID: 31225788 DOI: 10.1099/jmm.0.001006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Shunhang Wen
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Fangfang Lv
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Xiaofang Chen
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Lili Zhu
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Haiyan Li
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Li Lin
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
| | - Hailin Zhang
- Department of Children's Respiration Disease, Second Affiliated Hospital & Yuying Children's Hospital, Wenzhou Medical University, Wenzhou 325000, Zhejiang, PR China
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12
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Li YT, Liang Y, Ling YS, Duan MQ, Pan L, Chen ZG. The spectrum of viral pathogens in children with severe acute lower respiratory tract infection: A 3-year prospective study in the pediatric intensive care unit. J Med Virol 2019; 91:1633-1642. [PMID: 31081548 PMCID: PMC7167151 DOI: 10.1002/jmv.25502] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/17/2019] [Accepted: 05/08/2019] [Indexed: 12/17/2022]
Abstract
Background No comprehensive analysis is available on the viral etiology and clinical characterization among children with severe acute lower respiratory tract infection (SALRTI) in Southern China. Methods Cohort of 659 hospitalized children (2 months to 14 years) with SALRTI admitted to the Pediatric Intensive Care Unit (PICU) in the Guangzhou from May 2015 to April 2018 was enrolled in this study. Nasopharyngeal aspirate specimens or induced sputum were tested for eight categories respiratory viral targets. The viral distribution and its clinical characters were statistically analyzed. Results Viral pathogen was detected in 326 (49.5%) of children with SALRTI and there were 36 (5.5%) viral coinfections. Overall, the groups of viruses identified were, in descending order of prevalence: Influenza virus (IFV) (n = 94, 14.3%), respiratory syncytial virus (RSV) (n = 75, 11.4%), human rhinovirus (HRV) (n = 56, 8.5%), adenovirus (ADV) (n = 55, 8.3%), parainfluenza (PIV) (n = 47, 7.1%), human coronavirus (HCoV) (n = 15, 2.3%), human metapneumovirus (HMPV) (n = 14, 2.1%) and human bocavirus (HBoV) (n = 11, 1.7%). The positive rate in younger children (< 5 years) was significantly higher than the positive rate detected in elder children (> 5 years) (52.5% vs 35.1%, P = 0.001). There were clear seasonal peaks for IFV, RSV, HRV, ADV, PIV, and HMPV. And the individuals with different viral infection varied significantly in terms of clinical profiles. Conclusions Viral infections are present in a consistent proportion of patients admitted to the PICU. IFV, RSV, HRV, and ADV accounted for more than two‐thirds of all viral SALRTI. Our findings could help the prediction, prevention and potential therapeutic approaches of SALRTI in children. Viral infections are present in a consistent proportion of patients admitted to the Pediatric Intensive Care Unit. Influenza virus, respiratory syncytial virus, human rhinovirus and adenovirus accounted for more than two‐thirds of all viral SALRTI.
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Affiliation(s)
- Ya-Ting Li
- Department of Pediatric Intensive Care Unit, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Ying Liang
- Department of Pediatric Intensive Care Unit, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Ye-Sheng Ling
- Department of Pediatric Intensive Care Unit, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Meng-Qi Duan
- Department of Pediatric Intensive Care Unit, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Li Pan
- Department of Pediatric Intensive Care Unit, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Zhuang-Gui Chen
- Department of Pediatric Intensive Care Unit, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
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13
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Walker GJ, Stelzer-Braid S, Shorter C, Honeywill C, Wynn M, Willenborg C, Barnes P, Kang J, Pierse N, Crane J, Howden-Chapman P, Rawlinson WD. Viruses associated with acute respiratory infection in a community-based cohort of healthy New Zealand children. J Med Virol 2019; 94:454-460. [PMID: 31017663 PMCID: PMC7228279 DOI: 10.1002/jmv.25493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/16/2022]
Abstract
Acute respiratory infections (ARIs) are a major cause of morbidity among children. Respiratory viruses are commonly detected in both symptomatic and asymptomatic periods. The rates of infection and community epidemiology of respiratory viruses in healthy children needs further definition to assist interpretation of molecular diagnostic assays in this population. Children otherwise healthy aged 1 to 8 years were prospectively enrolled in the study during two consecutive winters, when ARIs peak in New Zealand. Parents completed a daily symptom diary for 8 weeks, during which time they collected a nasal swab from the child for each clinical ARI episode. A further nasal swab was collected by research staff during a clinic visit at the conclusion of the study. All samples were tested for 15 respiratory viruses commonly causing ARI using molecular multiplex polymerase chain reaction assays. There were 575 ARIs identified from 301 children completing the study, at a rate of 1.04 per child‐month. Swabs collected during an ARI were positive for a respiratory virus in 76.8% (307 of 400), compared with 37.3% (79 of 212) of swabs collected during asymptomatic periods. The most common viruses detected were human rhinovirus, coronavirus, parainfluenza viruses, influenzavirus, respiratory syncytial virus, and human metapneumovirus. All of these were significantly more likely to be detected during ARIs than asymptomatic periods. Parent‐administered surveillance is a useful mechanism for understanding infectious disease in healthy children in the community. Interpretation of molecular diagnostic assays for viruses must be informed by understanding of local rates of asymptomatic infection by such viruses. During winter, children experienced acute respiratory infections at a rate of 1.04/month. A virus was detected in 76.8% of acute respiratory infections. Specific viruses are more likely to be associated with respiratory symptoms.
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Affiliation(s)
- Gregory J Walker
- Virology Research Laboratory, Prince of Wales Hospital, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Prince of Wales Hospital, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Caroline Shorter
- Department of Medicine, University of Otago, Wellington, New Zealand
| | - Claire Honeywill
- Department of Medicine, University of Otago, Wellington, New Zealand
| | - Matthew Wynn
- Virology Research Laboratory, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Christiana Willenborg
- Virology Research Laboratory, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Phillipa Barnes
- Department of Medicine, University of Otago, Wellington, New Zealand
| | - Janice Kang
- Department of Medicine, University of Otago, Wellington, New Zealand
| | - Nevil Pierse
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Julian Crane
- Department of Medicine, University of Otago, Wellington, New Zealand
| | | | - William D Rawlinson
- Virology Research Laboratory, Prince of Wales Hospital, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.,Serology and Virology Division, South Eastern Area Laboratory Services Microbiology, Prince of Wales Hospital, Sydney, Australia.,School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
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14
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Rudge JW, Inthalaphone N, Pavlicek R, Paboriboune P, Flaissier B, Monidarin C, Steenkeste N, Davong V, Vongsouvath M, Bonath KA, Messaoudi M, Saadatian-Elahi M, Newton P, Endtz H, Dance D, Paranhos Baccala G, Sanchez Picot V. "Epidemiology and aetiology of influenza-like illness among households in metropolitan Vientiane, Lao PDR": A prospective, community-based cohort study. PLoS One 2019; 14:e0214207. [PMID: 30951544 PMCID: PMC6450629 DOI: 10.1371/journal.pone.0214207] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 03/08/2019] [Indexed: 11/18/2022] Open
Abstract
Respiratory diseases are a major contributor to morbidity and mortality in many tropical countries, including Lao PDR. However, little has been published regarding viral or bacterial pathogens that can contribute to influenza-like illness (ILI) in a community setting. We report on the results of a community-based surveillance that prospectively monitored the incidence of ILI and its causative pathogens in Vientiane capital in Lao PDR. A cohort of 995 households, including 4885 study participants, were followed-up between May 2015 and May 2016. Nasopharyngeal swabs, throat swabs, and sputum specimens were collected from ILI cases identified through active case-finding. Real-Time PCR was used to test nasopharyngeal swabs for 21 respiratory pathogens, while throat and sputum samples were subjected to bacterial culture. Generalized linear mixed models were used to assess potential risk factors for associations with ILI. In total, 548 episodes of ILI were reported among 476 (9.7%) of the study participants and 330 (33.2%) of the study households. The adjusted estimated incidence of ILI within the study area was 10.7 (95%CI: 9.4-11.9) episodes per 100 person-years. ILI was significantly associated with age group (p<0.001), sex (p<0.001), and number of bedrooms (p = 0.04) in multivariate analysis. In 548 nasopharyngeal swabs, the most commonly detected potential pathogens were Streptococcus pneumoniae (17.0%), Staphylococcus aureus (11.3%), influenza A (11.1%; mostly subtype H3N2), rhinovirus (7.5%), and influenza B (8.0%). Streptococci were isolated from 42 (8.6%) of 536 throat swabs, most (27) of which were Lancefield Group G. Co-infections were observed in 132 (24.1%) of the 548 ILI episodes. Our study generated valuable data on respiratory disease burden and patterns of etiologies associated with community-acquired acute respiratory illness Laos. Establishment of a surveillance strategy in Laos to monitor trends in the epidemiology and burden of acute respiratory infections is required to minimize their impact on human health.
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Affiliation(s)
- James W. Rudge
- Communicable Diseases Policy Research Group, Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, United Kingdom; Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Nui Inthalaphone
- Center of Infectiology Christophe Mérieux of Laos, Vientiane, Laos
| | | | | | | | | | | | - Viengmon Davong
- Mahidol Oxford Tropical Medicine Research Unit, Vientiane, Laos
| | | | - K. A. Bonath
- University of Health Sciences, Phnom Penh, Cambodia
| | | | | | - Paul Newton
- Mahidol Oxford Tropical Medicine Research Unit, Vientiane, Laos
| | | | - David Dance
- Mahidol Oxford Tropical Medicine Research Unit, Vientiane, Laos
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15
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Obodai E, Odoom JK, Adiku T, Goka B, Wolff T, Biere B, Schweiger B, Reiche J. The significance of human respiratory syncytial virus (HRSV) in children from Ghana with acute lower respiratory tract infection: A molecular epidemiological analysis, 2006 and 2013-2014. PLoS One 2018; 13:e0203788. [PMID: 30199549 PMCID: PMC6130863 DOI: 10.1371/journal.pone.0203788] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/27/2018] [Indexed: 12/01/2022] Open
Abstract
Background Acute lower respiratory tract infection (ALRI) is a leading cause of childhood morbidity and mortality in developing countries. Globally, human respiratory syncytial virus (HRSV) is the most common pathogen of ALRI in infants and children. However, age-stratified HRSV disease burden data are largely absent from Africa, which is a key gap in informing an evidence-based recommendation for the introduction of an HRSV vaccine by the WHO. Methods This study investigated the presence of HRSV in respiratory specimens from 552 children <5 years old with ALRI from Accra, Ghana in 2006 and 2013–2014 by real-time PCR. Of HRSV-positive samples the second hypervariable region of the viral G protein gene was sequenced and analyzed for phylogeny, characteristic amino acid substitutions, and potential glycosylation patterns. Further, HRSV infections have been characterized by age, symptoms and timely occurrence. Results HRSV was observed in 23% (127/552) of the children with ALRI, with the highest incidence in infants younger than one year (33%, 97/295, p = 0.013). Within the observed seasonal circulation time of HRSV from June (mid-wet season) to December (beginning of the dry season) the incidence of ALRI due to HRSV was as high as 46% (125/273). HRSV disease was significantly associated with (broncho-) pneumonia, bronchiolitis, LRTI, and difficulty in breathing. Phylogenetic characterization of HRSV strains from Ghana identified the circulation of the currently worldwide prevailing genotypes ON1 and BA9, and shows evidence of an independent molecular evolution of ON1 and BA9 strains in Ghana resulting in potentially new subgenotypes within ON1 and BA9, provisionally named ON1.5, ON1.6, and BA9-IV. Conclusion This study addresses important knowledge gaps in the forefront of introducing the HRSV vaccine by providing information on the molecular evolution and incidence of HRSV in Accra (Ghana, Africa).
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Affiliation(s)
- Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
- * E-mail: (EO); (JR)
| | - John Kofi Odoom
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Theophilus Adiku
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Volta Region, Ghana
| | - Bamenla Goka
- Department of Child Health, School of Medicine and Dentistry, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Thorsten Wolff
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Barbara Biere
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Brunhilde Schweiger
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Janine Reiche
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
- * E-mail: (EO); (JR)
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16
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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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17
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Li X, Li J, Meng L, Zhu W, Liu X, Yang M, Yu D, Niu L, Shen X. Viral etiologies and epidemiology of patients with acute respiratory infections based on sentinel hospitals in Gansu Province, Northwest China, 2011-2015. J Med Virol 2018; 90:828-835. [PMID: 29388679 PMCID: PMC7166685 DOI: 10.1002/jmv.25040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/17/2018] [Indexed: 01/01/2023]
Abstract
Understanding etiological role and epidemiological profile is needed to improve clinical management and prevention of acute respiratory infections (ARIs). A 5-year prospective study about active surveillance for outpatients and inpatients with ARIs was conducted in Gansu province, China, from January 2011 to November 2015. Respiratory specimens were collected from patients and tested for eight respiratory viruses using polymerase chain reaction (PCR) or reverse transcription polymerase chain reaction (RT-PCR). In this study, 2768 eligible patients with median age of 43 years were enrolled including pneumonia (1368, 49.2%), bronchitis (435, 15.7%), upper respiratory tract infection or URTI (250, 9.0%), and unclassified ARI (715, 25.8%). Overall, 29.2% (808/2768) were positive for any one of eight viruses, of whom 130 cases were identified with two or more viruses. Human rhinovirus (HRV) showed the highest detection rate (8.6%), followed by influenza virus (Flu, 7.3%), respiratory syncytial virus (RSV, 6.1%), human coronavirus (hCoV, 4.3%), human parainfluenza (PIV, 4.0%), adenovirus (ADV, 2.1%), human metapneumovirus (hMPV, 1.6%), and human bocavirus (hBoV, 0.7%). Compared with URTI, RSV was more likely identified in pneumonia (χ2 = 12.720, P < 0.001) and hCoV was more commonly associated with bronchitis than pneumonia (χ2 = 15.019, P < 0.001). In patients aged less than 5 years, RSV showed the highest detection rate and hCoV was the most frequent virus detected in adults and elderly. The clear epidemical seasons were observed in HRV, Flu, and hCoV infections. These findings could serve as a reference for local health authorities in drawing up further plans to prevent and control ARIs associated with viral etiologies.
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Affiliation(s)
- Xuechao Li
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Juansheng Li
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Lei Meng
- Centers' for Disease Control and Prevention, Gansu Province, P.R. China
| | - Wanqi Zhu
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Xinfeng Liu
- Centers' for Disease Control and Prevention, Gansu Province, P.R. China
| | - Mei Yang
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Deshan Yu
- Centers' for Disease Control and Prevention, Gansu Province, P.R. China
| | - Lixia Niu
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Xiping Shen
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
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18
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Yan Y, Huang L, Wang M, Wang Y, Ji W, Zhu C, Chen Z. Clinical and epidemiological profiles including meteorological factors of low respiratory tract infection due to human rhinovirus in hospitalized children. Ital J Pediatr 2017; 43:23. [PMID: 28270165 PMCID: PMC5341482 DOI: 10.1186/s13052-017-0346-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/28/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Lower respiratory tract infection (LRTI) is a major cause of morbidity and mortality in children. Human rhinovirus (HRV) is confirmed to be associated with pediatric lower respiratory tract infection. Seasonal and meteorological factors may play a key role in the epidemiology of HRV. The purposes of this study were to investigate the frequency, seasonal distribution, and clinical characteristics of hospitalized children with LRTI caused by HRVs. In addition, associations between incidence of HRVs and meteorological factors in a subtropical region of China were discussed. METHODS Hospitalized children <14 years old admitted to the Respiratory Department of the Children's Hospital, which is affiliated to Soochow University, between January 1, 2013 and December 31, 2015, were enrolled in this study. Multi-pathogens were detected in nasopharyngeal aspirate samples. Meanwhile, meteorological factors were recorded. RESULTS The average incidence of HRVs infection was 11.4% (707/6194) and 240 cases of which were co-infection cases with other pathogens. Children with co-infection presented more frequent fever and tachypnea compared to children infected with HRVs only (both P < 0.05). Among 707 HRV positive children, the mean age was 23.2 months (range 1 to 140 months). Among all respiratory infections, the highest incidence of HRVs cases occurred in children age 13-36 months old (15.1%, 203/1341). Of all 228 HRV cases in 2014, 85 cases (37.3%) were HRV-C positive. HRVs and HRV-C infection occurred throughout the year during the study period, although a higher incidence was observed in summer and autumn seasons. HRVs or HRV-C incidence in hospitalized children with LRTI was associated with the monthly mean temperature (both P < 0.05). CONCLUSION HRV was one of the most common viral pathogen detected in hospitalized children with LRTI at the Children's Hospital of Suzhou, China, and had its own seasonal distribution including HRV-C, which was partly caused by temperature.
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Affiliation(s)
- Yongdong Yan
- Department of Respiratory Disease, Children's Hospital of Soochow University, NO.303, Jingde Road, Suzhou, Jiangsu Province, 215003, People's Republic of China
| | - Li Huang
- Department of Respiratory Disease, Children's Hospital of Soochow University, NO.303, Jingde Road, Suzhou, Jiangsu Province, 215003, People's Republic of China
| | - Meijuan Wang
- Department of Respiratory Disease, Children's Hospital of Soochow University, NO.303, Jingde Road, Suzhou, Jiangsu Province, 215003, People's Republic of China
| | - Yuqing Wang
- Department of Respiratory Disease, Children's Hospital of Soochow University, NO.303, Jingde Road, Suzhou, Jiangsu Province, 215003, People's Republic of China
| | - Wei Ji
- Department of Respiratory Disease, Children's Hospital of Soochow University, NO.303, Jingde Road, Suzhou, Jiangsu Province, 215003, People's Republic of China
| | - Canhong Zhu
- Department of Respiratory Disease, Children's Hospital of Soochow University, NO.303, Jingde Road, Suzhou, Jiangsu Province, 215003, People's Republic of China.
| | - Zhengrong Chen
- Department of Respiratory Disease, Children's Hospital of Soochow University, NO.303, Jingde Road, Suzhou, Jiangsu Province, 215003, People's Republic of China.
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Abstract
Human rhinovirus (HRV) and coronavirus (HCoV) infections are associated with both upper respiratory tract illness (“the common cold”) and lower respiratory tract illness (pneumonia). New species of HRVs and HCoVs have been diagnosed in the past decade. More sensitive diagnostic tests such as reverse transcription-polymerase chain reaction have expanded our understanding of the role these viruses play in both immunocompetent and immunosuppressed hosts. Recent identification of severe acute respiratory syndrome and Middle East respiratory syndrome viruses causing serious respiratory illnesses has led to renewed efforts for vaccine development. The role these viruses play in patients with chronic lung disease such as asthma makes the search for antiviral agents of increased importance.
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Affiliation(s)
- Stephen B Greenberg
- Department of Medicine, Ben Taub Hospital, Baylor College of Medicine, Houston, Texas
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20
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Lefebvre A, Manoha C, Bour JB, Abbas R, Fournel I, Tiv M, Pothier P, Astruc K, Aho-Glélé LS. Human metapneumovirus in patients hospitalized with acute respiratory infections: A meta-analysis. J Clin Virol 2016; 81:68-77. [PMID: 27337518 PMCID: PMC7106388 DOI: 10.1016/j.jcv.2016.05.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/26/2016] [Accepted: 05/30/2016] [Indexed: 12/31/2022]
Abstract
This meta-analysis aimed to estimate the prevalence of human metapneumovirus (hMPV) infections in patients hospitalized for acute respiratory infection (ARI) and to study factors associated with this prevalence. Medline and ScienceDirect databases were searched for prospective observational studies that screened hospitalized patients with ARI for hMPV by RT-PCR, with data available at December 27, 2014. The risk of bias was assessed regarding participation rate, definition of ARI, description of diagnostic technique, method of inclusion identical for all subjects, standardized and identical sampling method for all subjects, analysis performed according to the relevant subgroups, and presentation of data sources. Random-effect meta-analysis with arcsine transformation and meta-regressions was used. In the 75 articles included, the prevalence of hMPV among hospitalized ARI was 6.24% (95% CI 5.25-7.30). An effect of the duration of the inclusion period was observed (p=0.0114), with a higher prevalence of hMPV in studies conducted during periods of 7-11 months (10.56%, 95% CI 5.97-16.27) or complete years (7.55%, 95% CI 5.90-9.38) than in periods of 6 months or less (5.36%, 95% CI 4.29-6.54). A significant increase in the incidence with increasing distance from the equator was observed (p=0.0384). hMPV should be taken into account as a possible etiology in hospitalized ARI.
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Affiliation(s)
- Annick Lefebvre
- Epidemiology and infection control unit, Dijon University Hospital, France.
| | | | | | - Rachid Abbas
- Epidemiology and infection control unit, Dijon University Hospital, France
| | - Isabelle Fournel
- Epidemiology and infection control unit, Dijon University Hospital, France
| | - Michel Tiv
- Epidemiology and infection control unit, Dijon University Hospital, France
| | | | - Karine Astruc
- Epidemiology and infection control unit, Dijon University Hospital, France
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Lee CY, Chang YF, Lee CL, Wu MC, Ho CL, Chang YC, Chan YJ. Molecular viral epidemiology and clinical characterization of acute febrile respiratory infections in hospitalized children in Taiwan. J Med Virol 2016; 87:1860-6. [PMID: 26089293 PMCID: PMC7166343 DOI: 10.1002/jmv.24258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2015] [Indexed: 12/28/2022]
Abstract
Acute respiratory infection (ARI) is a leading cause of morbidity and hospitalization in children. To profile the viruses causing ARI in children admitted to a community‐based hospital in central Taiwan, a cross‐sectional study was conducted on children under 14 years of age that were hospitalized with febrile ARI. Viral etiology was determined using conventional cell culture and a commercial respiratory virus panel fast assay (xTAG RVP), capable of detecting 19 different respiratory viruses and subtype targets. Demographic, clinical, and laboratory data were recorded and analyzed. The RVP fast assay identified at least one respiratory virus in 130 of the 216 specimens examined (60.2%) and rose to 137 (63.4%) by combining the results of cell culture and RVP fast assay. In order of frequency, the etiological agents identified were, rhinovirus/enterovirus (24.6%), respiratory syncytial virus (13.8%), adenovirus (11.5%), parainfluenza virus (9.2%), influenza B (8.4%), influenza A (5.4%), human metapneumovirus (4.6%), human coronavirus (2%), and human bocavirus (2%). Co‐infection did not result in an increase in clinical severity. The RVP assay detected more positive specimens, but failed to detect 6 viruses identified by culture. The viral detection rate for the RVP assay was affected by how many days after admission the samples were taken (P = 0.03). In conclusion, Rhinovirus/enterovirus, respiratory syncytial virus, and adenovirus were prevalent in this study by adopting RVP assay. The viral detection rate is influenced by sampling time, especially if the tests are performed during the first three days of hospitalization. J. Med. Virol. 87:1860–1866, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Chun-Yi Lee
- Departmentof Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Yu-Fen Chang
- Department of Clinical Laboratory, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Chia-Lin Lee
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Meng-Che Wu
- Departmentof Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Chi-Lin Ho
- Departmentof Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Yu-Chuan Chang
- Departmentof Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Yu-Jiun Chan
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Public Health, National Yang-Ming University, Taipei, Taiwan
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22
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Scotta MC, Chakr VCBG, de Moura A, Becker RG, de Souza APD, Jones MH, Pinto LA, Sarria EE, Pitrez PM, Stein RT, Mattiello R. Respiratory viral coinfection and disease severity in children: A systematic review and meta-analysis. J Clin Virol 2016; 80:45-56. [PMID: 27155055 PMCID: PMC7185664 DOI: 10.1016/j.jcv.2016.04.019] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/16/2016] [Accepted: 04/25/2016] [Indexed: 11/29/2022]
Abstract
Respiratory viral coinfections are common in children. Overall pediatric respiratory viral coinfections have no impact on severity. Prognostic role of specific viral interactions remains unclear.
Background With advent of molecular diagnostic technologies, studies have reported detection of two or more respiratory viruses in about 30% of children with respiratory infections. However, prognostic role of coinfection remains unclear. Objective Evaluate relation between respiratory viral confection and illness severity in children. Study design MEDLINE (through PUBMED), EMBASE, EBSCO, LILACS databases were searched up to March 2015 by two independent reviewers. Studies assessing severity of viral coinfection in patients aged less than 18 years were included. Standardized forms were used for data extraction of population, study design, clinical syndromes, virus combinations compared and severity outcomes. Risk of bias and quality of evidence were assessed through EPHPP and GRADE. Subgroup analysis was performed according to age and viral combinations. Results Of 5218 records screened, 43 were included in analysis. Viral coinfection did not influence risks of all outcomes assessed: length of stay (mean difference in days in coinfection, −0.10 [95% confidence interval: −0.51 to 0.31]), length of supplemental oxygen (−0.42 [−1.05 to 0.20]), need of hospitalization (odds ratio of coinfection, 0.96 [95% confidence interval: 0.61–1.51]), supplemental oxygen (0.94 [0.66 to 1.34]), need of intensive care (0.99 [0.64 to 1.54]), mechanical ventilation (0.81 [0.33 to 2.01]) and death (2.22 [0.83 to 5.95]). Sub-analyses according to age and viral combinations have not shown influence of these factors in outcomes. Conclusions Respiratory viral coinfection did not increase severity in all outcomes assessed. Further studies are necessary to confirm this finding, especially regarding role of specific viral interactions.
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Affiliation(s)
- Marcelo Comerlato Scotta
- Centro Infant, Biomedical Research Institute, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Angela de Moura
- Centro Infant, Biomedical Research Institute, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rafaela Garces Becker
- Centro Infant, Biomedical Research Institute, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana Paula Duarte de Souza
- Centro Infant, Biomedical Research Institute, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marcus Herbert Jones
- Centro Infant, Biomedical Research Institute, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Leonardo Araújo Pinto
- Centro Infant, Biomedical Research Institute, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Edgar Enrique Sarria
- Universidade de Santa Cruz do Sul (UNISC). School of Medicine, Department of Biology and Pharmacy, Brazil
| | - Paulo Marcio Pitrez
- Centro Infant, Biomedical Research Institute, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Renato Tetelbom Stein
- Centro Infant, Biomedical Research Institute, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Rita Mattiello
- Centro Infant, Biomedical Research Institute, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.
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23
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Timmermans A, Melendrez MC, Se Y, Chuang I, Samon N, Uthaimongkol N, Klungthong C, Manasatienkij W, Thaisomboonsuk B, Tyner SD, Rith S, Horm VS, Jarman RG, Bethell D, Chanarat N, Pavlin J, Wongstitwilairoong T, Saingam P, El BS, Fukuda MM, Touch S, Sovann L, Fernandez S, Buchy P, Chanthap L, Saunders D. Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia. PLoS One 2016; 11:e0152529. [PMID: 27028323 PMCID: PMC4814059 DOI: 10.1371/journal.pone.0152529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/15/2016] [Indexed: 01/16/2023] Open
Abstract
Little is known about circulation of influenza and other respiratory viruses in remote populations along the Thai-Cambodia border in western Cambodia. We screened 586 outpatients (median age 5, range 1–77) presenting with influenza-like-illness (ILI) at 4 sentinel sites in western Cambodia between May 2010 and December 2012. Real-time reverse transcriptase (rRT) PCR for influenza was performed on combined nasal and throat specimens followed by viral culture, antigenic analysis, antiviral susceptibility testing and full genome sequencing for phylogenetic analysis. ILI-specimens negative for influenza were cultured, followed by rRT-PCR for enterovirus and rhinovirus (EV/RV) and EV71. Influenza was found in 168 cases (29%) and occurred almost exclusively in the rainy season from June to November. Isolated influenza strains had close antigenic and phylogenetic relationships, matching vaccine and circulating strains found elsewhere in Cambodia. Influenza vaccination coverage was low (<20%). Western Cambodian H1N1(2009) isolate genomes were more closely related to 10 earlier Cambodia isolates (94.4% genome conservation) than to 13 Thai isolates (75.9% genome conservation), despite sharing the majority of the amino acid changes with the Thai references. Most genes showed signatures of purifying selection. Viral culture detected only adenovirus (5.7%) and parainfluenza virus (3.8%), while non-polio enteroviruses (10.3%) were detected among 164 culture-negative samples including coxsackievirus A4, A6, A8, A9, A12, B3, B4 and echovirus E6 and E9 using nested RT-PCR methods. A single specimen of EV71 was found. Despite proximity to Thailand, influenza epidemiology of these western Cambodian isolates followed patterns observed elsewhere in Cambodia, continuing to support current vaccine and treatment recommendations from the Cambodian National Influenza Center. Amino acid mutations at non-epitope sites, particularly hemagglutinin genes, require further investigation in light of an increasingly important role of permissive mutations in influenza virus evolution. Further research about the burden of adenovirus and non-polio enteroviruses as etiologic agents in acute respiratory infections in Cambodia is also needed.
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Affiliation(s)
- Ans Timmermans
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Melanie C. Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- * E-mail:
| | - Youry Se
- Department of Immunology, Armed Forces Research Institute of Medical Sciences, Battambang, Cambodia
| | - Ilin Chuang
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Nou Samon
- Department of Immunology, Armed Forces Research Institute of Medical Sciences, Battambang, Cambodia
| | - Nichapat Uthaimongkol
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Wudtichai Manasatienkij
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stuart D. Tyner
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sareth Rith
- Virology Department, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Viseth Srey Horm
- Virology Department, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Richard G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Delia Bethell
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Nitima Chanarat
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Julie Pavlin
- Deputy Director, Armed Forces Health Surveillance Center, Silver Spring, Maryland, United States of America
| | | | - Piyaporn Saingam
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - But Sam El
- Department of Immunology, Armed Forces Research Institute of Medical Sciences, Battambang, Cambodia
| | - Mark M. Fukuda
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sok Touch
- Communicable Disease Control Department, Ministry of Health, Phnom Penh, Cambodia
| | - Ly Sovann
- Communicable Disease Control Department, Ministry of Health, Phnom Penh, Cambodia
| | - Stefan Fernandez
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Philippe Buchy
- Virology Department, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Lon Chanthap
- Department of Immunology, Armed Forces Research Institute of Medical Sciences, Phnom Penh, Cambodia
| | - David Saunders
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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24
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Naughtin M, Sareth R, Sentilhes AC, Vong S, Joffret ML, Cornillot E, Deubel V, Delpeyroux F, Frutos R, Buchy P. Genetic diversity of human rhinoviruses in Cambodia during a three-year period reveals novel genetic types. INFECTION GENETICS AND EVOLUTION 2015; 35:42-9. [PMID: 26231720 PMCID: PMC7105975 DOI: 10.1016/j.meegid.2015.07.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 11/06/2022]
Abstract
Five novel genotypes are identified based on VP1 sequences. Co-infections with other viruses is demonstrated. The genome of rhinoviruses is saturated. A novel classification system considering amino acid sequences should be developed.
Acute respiratory viral infections are a major cause of morbidity during early childhood in developing countries. Human rhinoviruses are the most frequent cause of upper respiratory tract infections in humans, which can range in severity from asymptomatic to clinically severe disease. In this study we collected 4170 nasopharyngeal swabs from patients hospitalised with influenza-like illness in two Cambodian provincial hospitals between 2007 and 2010. Samples were screened for 18 respiratory viruses using 5 multiplex PCRs. A total of 11.2% of samples tested positive for human rhinoviruses (HRV). VP4/2 and VP1 regions were amplified and sequenced to study the distribution of rhinoviruses genotypes and species in Cambodia during this three-year period. Five novel genotypes, 2 species A, 2 species B and 1 species C were identified based on VP1 sequences. Co-infections with other viruses were demonstrated.
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Affiliation(s)
- Monica Naughtin
- Institut Pasteur in Cambodia, Virology Unit, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia
| | - Rith Sareth
- Institut Pasteur in Cambodia, Virology Unit, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia
| | | | - Sirenda Vong
- Institut Pasteur in Cambodia, Virology Unit, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia
| | - Marie-Line Joffret
- Institut Pasteur, Biologie des Virus Entériques, 25-28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM U994, Institut National de Santé et de La Recherche Médicale, Paris, France
| | - Emmanuel Cornillot
- CEMIPAI, CPBS, UMR 5236, CNRS-UM1-UM2, 1919 route de Mende, 34293 Montpellier Cedex 5, France
| | - Vincent Deubel
- Institut Pasteur in Cambodia, Virology Unit, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia
| | - Francis Delpeyroux
- Institut Pasteur, Biologie des Virus Entériques, 25-28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM U994, Institut National de Santé et de La Recherche Médicale, Paris, France
| | - Roger Frutos
- CEMIPAI, CPBS, UMR 5236, CNRS-UM1-UM2, 1919 route de Mende, 34293 Montpellier Cedex 5, France; Cirad, UMR 17, Cirad-Ird, TA-A17/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France.
| | - Philippe Buchy
- Institut Pasteur in Cambodia, Virology Unit, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia.
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25
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Clinical and epidemiological characteristics of acute respiratory virus infections in Vietnamese children. Epidemiol Infect 2015; 144:527-36. [PMID: 26145204 DOI: 10.1017/s095026881500134x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Information about viral acute respiratory infections (ARIs) is essential for prevention, diagnosis and treatment, but it is limited in tropical developing countries. This study described the clinical and epidemiological characteristics of ARIs in children hospitalized in Vietnam. Nasopharyngeal samples were collected from children with ARIs at Ho Chi Minh City Children's Hospital 2 between April 2010 and May 2011 in order to detect respiratory viruses by polymerase chain reaction. Viruses were found in 64% of 1082 patients, with 12% being co-infections. The leading detected viruses were human rhinovirus (HRV; 30%), respiratory syncytial virus (RSV; 23·8%), and human bocavirus (HBoV; 7·2%). HRV was detected all year round, while RSV epidemics occurred mainly in the rainy season. Influenza A (FluA) was found in both seasons. The other viruses were predominant in the dry season. HRV was identified in children of all age groups. RSV, parainfluenza virus (PIV) 1, PIV3 and HBoV, and FluA were detected predominantly in children aged 24 months, respectively. Significant associations were found between PIV1 with croup (P < 0·005) and RSV with bronchiolitis (P < 0·005). HBoV and HRV were associated with hypoxia (P < 0·05) and RSV with retraction (P < 0·05). HRV, RSV, and HBoV were detected most frequently and they may increase the severity of ARIs in children.
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26
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Adenoviruses and acute respiratory infections in children living in an equatorial area of Brazil. Epidemiol Infect 2015; 144:355-62. [DOI: 10.1017/s0950268815000916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
SUMMARYHuman adenoviruses (HAdVs) are important respiratory pathogens, found in 2–27% of acute respiratory infection (ARI) cases. Few studies have analysed the diversity of species and types of HAdVs associated with ARI in Brazil. The purpose of this study was to determine the circulation patterns of the different HAdV species and respective types associated with ARI in children in the city of Fortaleza, northeastern Brazil. HAdVs were screened by an indirect immunofluorescence assay, and subsequently identified as species and types by PCR and sequencing of the hexon gene (HVR1–HVR6). Between 2001 and 2013, a total of 290 HAdV strains were detected, 190 of which were identified as belonging to the HAdV-B, -C and -E species. Seven types of HAdVs circulated in the studied population during the analysed period, with HAdV-3 being predominant.
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27
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Ly N, Tokarz R, Mishra N, Sameroff S, Jain K, Rachmat A, An US, Newell S, Harrison DJ, Lipkin WI. Multiplex PCR analysis of clusters of unexplained viral respiratory tract infection in Cambodia. Virol J 2014; 11:224. [PMID: 25514971 PMCID: PMC4280028 DOI: 10.1186/s12985-014-0224-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/05/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Fevers of unknown origin constitute a substantial disease burden in Southeast Asia. In majority of the cases, the cause of acute febrile illness is not identified. METHODS We used MassTag PCR, a multiplex assay platform, to test for the presence of 15 viral respiratory agents from 85 patients with unexplained respiratory illness representing six disease clusters that occurred in Cambodia between 2009 and 2012. RESULTS We detected a virus in 37 (44%) of the cases. Human rhinovirus, the virus detected most frequently, was found in both children and adults. The viruses most frequently detected in children and adults, respectively, were respiratory syncytial virus and enterovirus 68. Sequence analysis indicated that two distinct clades of enterovirus 68 were circulating during this time period. CONCLUSIONS This is the first report of enterovirus 68 in Cambodia and contributes to the appreciation of this virus as an important respiratory pathogen.
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Affiliation(s)
- Nary Ly
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
| | - Agus Rachmat
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - Ung Sam An
- National Institute of Public Health, Cambodian Ministry of Health, Phnom Penh, Cambodia.
| | - Steven Newell
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - Dustin J Harrison
- U.S. Naval Medical Research Unit-2 Detachment, Phnom Penh, Cambodia.
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, USA.
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Lanaspa M, Annamalay AA, LeSouëf P, Bassat Q. Epidemiology, etiology, x-ray features, importance of co-infections and clinical features of viral pneumonia in developing countries. Expert Rev Anti Infect Ther 2014; 12:31-47. [PMID: 24410617 PMCID: PMC7103723 DOI: 10.1586/14787210.2014.866517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Pneumonia is still the number one killer of young children globally, accounting for 18% of mortality in children under 5 years of age. An estimated 120 million new cases of pneumonia occur globally each year. In developing countries, management and prevention efforts against pneumonia have traditionally focused on bacterial pathogens. More recently however, viral pathogens have gained attention as a result of improved diagnostic methods, such as polymerase chain reaction, outbreaks of severe disease caused by emerging pathogens, discovery of new respiratory viruses as well as the decrease in bacterial pneumonia as a consequence of the introduction of highly effective conjugate vaccines. Although the epidemiology, etiology and clinical characterization of viral infections are being studied extensively in the developed world, little data are available from low- and middle-income countries. In this paper, we review the epidemiology, etiology, clinical and radiological features of viral pneumonia in developing countries.
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Affiliation(s)
- Miguel Lanaspa
- Barcelona Center for International Health Research, Hospital Clinic, University of Barcelona, Rosello 132, 08036 Barcelona, Spain
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Goka EA, Vallely PJ, Mutton KJ, Klapper PE. Mutations associated with severity of the pandemic influenza A(H1N1)pdm09 in humans: a systematic review and meta-analysis of epidemiological evidence. Arch Virol 2014; 159:3167-83. [PMID: 25078388 DOI: 10.1007/s00705-014-2179-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/12/2014] [Indexed: 10/25/2022]
Abstract
Mutations in the haemagglutinin (HA), non-structural protein 1 (NS1) and polymerase basic protein 2 (PB2) of influenza viruses have been associated with virulence. This study investigated the association between mutations in these genes in influenza A(H1N1)pdm09 virus and the risk of severe or fatal disease. Searches were conducted on the MEDLINE, EMBASE and Web of Science electronic databases and the reference lists of published studies. The PRISMA and STROBE guidelines were followed in assessing the quality of studies and writing-up. Eighteen (18) studies, from all continents, were included in the systematic review (recruiting patients 0 - 77 years old). The mutation D222G was associated with a significant increase in severe disease (pooled RD: 11 %, 95 % CI: 3.0 % - 18.0 %, p = 0.004) and the risk of fatality (RD: 23 %, 95 % CI: 14.0 %-31.0 %, p = < 0.0001). No association was observed between the mutations HA-D222N, D222E, PB2-E627K and NS1-T123V and severe/fatal disease. The results suggest that no virus quasispecies bearing virulence-conferring mutations in the HA, PB2 and NS1 predominated. However issues of sampling bias, and bias due to uncontrolled confounders such as comorbidities, and viral and bacterial coinfection, should be born in mind. Influenza A viruses should continue to be monitored for the occurrence of virulence-conferring mutations in HA, PB2 and NS1. There are suggestions that respiratory virus coinfections also affect virus virulence. Studies investigating the role of genetic mutations on disease outcome should make efforts to also investigate the role of respiratory virus coinfections.
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Affiliation(s)
- E A Goka
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, 1st Floor Stopford building, Oxford Road, Manchester, M13 9PL, UK,
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Goyet S, Barennes H, Libourel T, van Griensven J, Frutos R, Tarantola A. Knowledge translation: a case study on pneumonia research and clinical guidelines in a low- income country. Implement Sci 2014; 9:82. [PMID: 24969242 PMCID: PMC4094455 DOI: 10.1186/1748-5908-9-82] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/23/2014] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The process and effectiveness of knowledge translation (KT) interventions targeting policymakers are rarely reported. In Cambodia, a low-income country (LIC), an intervention aiming to provide evidence-based knowledge on pneumonia to health authorities was developed to help update pediatric and adult national clinical guidelines. Through a case study, we assessed the effectiveness of this KT intervention, with the goal of identifying the barriers to KT and suggest strategies to facilitate KT in similar settings. METHODS An extensive search for all relevant sources of data documenting the processes of updating adult and pediatric pneumonia guidelines was done. Documents included among others, reports, meeting minutes, and email correspondences. The study was conducted in successive phases: an appraisal of the content of both adult and pediatric pneumonia guidelines; an appraisal of the quality of guidelines by independent experts, using the AGREE-II instrument; a description and modeling of the KT process within the guidelines updating system, using the Unified Modeling Language (UML) tools 2.2; and the listing of the barriers and facilitators to KT we identified during the study. RESULTS The first appraisal showed that the integration of the KT key messages in pediatric and adult guidelines varied with a better efficiency in the pediatric guidelines. The overall AGREE-II quality assessments scored 37% and 44% for adult and pediatric guidelines, respectively. Scores were lowest for the domains of 'rigor of development' and 'editorial independence.' The UML analysis highlighted that time frames and constraints of the involved stakeholders greatly differed and that there were several missed opportunities to translate on evidence into the adult pneumonia guideline. Seventeen facilitating factors and 18 potential barriers to KT were identified. Main barriers were related to the absence of a clear mandate from the Ministry of Health for the researchers and to a lack of synchronization between knowledge production and policy-making. CONCLUSIONS Study findings suggest that stakeholders, both researchers and policy makers planning to update clinical guidelines in LIC may need methodological support to overcome the expected barriers.
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Affiliation(s)
- Sophie Goyet
- Epidemiology and Public Health Unit, Institut Pasteur, Phnom Penh, Cambodia
| | - Hubert Barennes
- Agence Nationale de recherche sur le SIDA et les hépatites, Paris, France
- ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, Université de Bordeaux, F-33000 Bordeaux, France
- INSERM, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, F-33000 Bordeaux, France
| | - Therese Libourel
- Université Montpellier 2, UMR Espace Dev, IRD-UM2-UAG-ULR, Montpellier, France
| | - Johan van Griensven
- Sihanouk Hospital Center of HOPE, Phnom Penh, Cambodia
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Roger Frutos
- Université Montpellier 2, CPBS, UMR 5236 CNRS-UM1-UM2, Montpellier, France
- Intertryp, UMR 17, IRD-Cirad, Campus international de Baillarguet, 34398 Montpellier, Cedex 5, France
| | - Arnaud Tarantola
- Epidemiology and Public Health Unit, Institut Pasteur, Phnom Penh, Cambodia
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Asner SA, Science ME, Tran D, Smieja M, Merglen A, Mertz D. Clinical disease severity of respiratory viral co-infection versus single viral infection: a systematic review and meta-analysis. PLoS One 2014; 9:e99392. [PMID: 24932493 PMCID: PMC4059637 DOI: 10.1371/journal.pone.0099392] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 05/14/2014] [Indexed: 01/31/2023] Open
Abstract
Background Results from cohort studies evaluating the severity of respiratory viral co-infections are conflicting. We conducted a systematic review and meta-analysis to assess the clinical severity of viral co-infections as compared to single viral respiratory infections. Methods We searched electronic databases and other sources for studies published up to January 28, 2013. We included observational studies on inpatients with respiratory illnesses comparing the clinical severity of viral co-infections to single viral infections as detected by molecular assays. The primary outcome reflecting clinical disease severity was length of hospital stay (LOS). A random-effects model was used to conduct the meta-analyses. Results Twenty-one studies involving 4,280 patients were included. The overall quality of evidence applying the GRADE approach ranged from moderate for oxygen requirements to low for all other outcomes. No significant differences in length of hospital stay (LOS) (mean difference (MD) −0.20 days, 95% CI −0.94, 0.53, p = 0.59), or mortality (RR 2.44, 95% CI 0.86, 6.91, p = 0.09) were documented in subjects with viral co-infections compared to those with a single viral infection. There was no evidence for differences in effects across age subgroups in post hoc analyses with the exception of the higher mortality in preschool children (RR 9.82, 95% CI 3.09, 31.20, p<0.001) with viral co-infection as compared to other age groups (I2 for subgroup analysis 64%, p = 0.04). Conclusions No differences in clinical disease severity between viral co-infections and single respiratory infections were documented. The suggested increased risk of mortality observed amongst children with viral co-infections requires further investigation.
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Affiliation(s)
- Sandra A. Asner
- Division of Infectious Diseases, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Unit of Paediatric Infectious Diseases, Department of Paediatrics, University Hospital Lausanne, Lausanne, Switzerland
- Division of Infectious Diseases, Department of Medicine, University Hospital Lausanne, Lausanne, Switzerland
| | - Michelle E. Science
- Division of Infectious Diseases, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Dat Tran
- Division of Infectious Diseases, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Marek Smieja
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Health Sciences, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
| | - Arnaud Merglen
- Division of Paediatric Medicine and the Paediatric Outcomes Research Team, The Hospital for Sick Children, University of Toronto, Toronto, Canada
- Division of General Paediatrics, University Hospitals of Geneva and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Dominik Mertz
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Health Sciences, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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Goyet S, Vlieghe E, Kumar V, Newell S, Moore CE, Bousfield R, Leang HC, Chuop S, Thong P, Rammaert B, Hem S, van Griensven J, Rachmat A, Fassier T, Lim K, Tarantola A. Etiologies and resistance profiles of bacterial community-acquired pneumonia in Cambodian and neighboring countries' health care settings: a systematic review (1995 to 2012). PLoS One 2014; 9:e89637. [PMID: 24626053 PMCID: PMC3953073 DOI: 10.1371/journal.pone.0089637] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/21/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Community-acquired pneumonia (CAP) is one of the most important causes of morbidity and mortality worldwide. Etiological data for Cambodia is scarce. We aimed to describe the main etiological agents causing CAP, and their resistance patterns in Cambodia and the greater Mekong region. METHODS A review of bacterial etiologies of CAP and antimicrobial resistance in Cambodia and neighboring countries was conducted via: (1) a systematic review of published literature in all NCBI databases using Pubmed, Google scholar, EMBASE, the World Health Organization and the Cambodian Ministry of Health libraries; (2) a review of unpublished data from Cambodia provided by national and international stakeholders working at different tiers of the healthcare system. RESULTS Twenty three articles and five data sources reported etiologies for 5919 CAP patients diagnosed between May 1995 and December 2012, including 1421 (24.0%), 3571 (60.3%) and 927 (15.7%) from Cambodia, Thailand and Vietnam, respectively. Streptococcus pneumoniae and Haemophilus influenzae were the most common pathogens ranking among the five most prevalent in 12 and 10 studies, respectively. Gram-negative bacteria such as Burkholderia pseudomallei and Klebsiella pneumoniae were also frequently diagnosed, particularly in bacteremic CAP in Thai adults and Cambodian children. In Thailand and Vietnam, Mycoplasma pneumoniae and Chlamydia pneumoniae were frequently identified in settings using indirect laboratory testing. CONCLUSIONS Based on this analysis, CAP data in Cambodia seems to present etiological and resistance profiles comparable to those of neighboring countries. Findings have been shared with the national authorities upon the revision of the national therapeutic guidelines and were disseminated using a specially created website.
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Affiliation(s)
- Sophie Goyet
- Epidemiology unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | | | - Varun Kumar
- Angkor Hospital for Children, Siem Reap, Cambodia
| | | | - Catrin E. Moore
- Angkor Hospital for Children, Siem Reap, Cambodia
- Wellcome Trust Major Overseas Programme, Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Oxford University, Oxford, United Kingdom
| | - Rachel Bousfield
- Angkor Hospital for Children, Siem Reap, Cambodia
- Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Oxford University, Oxford, United Kingdom
| | - Heng C. Leang
- National Institute of Public Health, Phnom Penh, Cambodia
| | - Sokheng Chuop
- National Institute of Public Health, Phnom Penh, Cambodia
| | - Phe Thong
- Sihanouk Hospital Center of HOPE, Phnom Penh, Cambodia
| | - Blandine Rammaert
- Hopital Necker-Enfants malades service des Maladies Infectieuses et Tropicales, APHP, Paris, France
| | - Sopheak Hem
- Epidemiology unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Johan van Griensven
- Institute of Tropical Medicine, Antwerp, Belgium
- Sihanouk Hospital Center of HOPE, Phnom Penh, Cambodia
| | - Agus Rachmat
- Naval Medical Research Unit2, Phnom Penh, Cambodia
| | - Thomas Fassier
- University of Health Sciences, Faculty of Medicine, Phnom Penh, Cambodia
| | - Kruy Lim
- Sihanouk Hospital Center of HOPE, Phnom Penh, Cambodia
| | - Arnaud Tarantola
- Epidemiology unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
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Lu MP, Ma LY, Zheng Q, Dong LL, Chen ZM. Clinical characteristics of adenovirus associated lower respiratory tract infection in children. World J Pediatr 2013; 9:346-9. [PMID: 24235068 DOI: 10.1007/s12519-013-0431-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 06/05/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Acute lower respiratory tract infection (ALRI) due to adenovirus infection is a low frequency event but often causes severe outcome. This study was undertaken to uncover the clinical and epidemiological features of adenovirus infection in children. METHODS Hospitalized children with ALRI were analyzed through continuous monitoring from 2006 to 2012. Nasopharyngeal aspirates were examined by direct immunofluorescence to detect respiratory agents including respiratory syncytial virus, adenovirus, influenza virus types A/B, parainfluenza virus types 1/2/3. Chlamydia pneumonia, Mycoplasma pneumonia and Chlamydia trachomatis were determined by real-time PCR. A retrospective analysis was made of 479 patients with positive infection of adenovirus. RESULTS The positive detection rate of adenovirus was 0.63% in patients with ALRI. The incidence rate of adenovirus-associated acute lower respiratory tract infection peaked at the second six months of life. The morbidity was much higher in winter, spring and summer than in autumn. Patients with pneumonia accounted for 73.90% of the patients. More than one-third of the patients developed severe pneumonia, whereas no death was found. Features of severe adenovirus-associated lower respiratory tract infection included persistent high fever with serious infective symptoms, and hepatic dysfunction was one of the most common complications. Mixed infection of atypical pathogens was common (18.58%) in this study. CONCLUSIONS Adenovirus is a critical pathogen that can cause severe respiratory infections even in immunocompetent children. Coinfection of adenovirus with atypical pathogens is common. Antibiotic treatment with azithromycin or erythromycin is necessary in patients with mixed infection of atypical pathogens.
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Affiliation(s)
- Mei-Ping Lu
- Department of Respiratory, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China,
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Acute lower respiratory infections on lung sequelae in Cambodia, a neglected disease in highly tuberculosis-endemic country. Respir Med 2013; 107:1625-32. [PMID: 23937802 PMCID: PMC7125659 DOI: 10.1016/j.rmed.2013.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 07/08/2013] [Accepted: 07/23/2013] [Indexed: 11/22/2022]
Abstract
Background Little is known about post-infectious pulmonary sequelae in countries like Cambodia where tuberculosis is hyper-endemic and childhood pulmonary infections are highly frequent. We describe the characteristics of hospitalized Cambodian patients presenting with community-acquired acute lower respiratory infections (ALRI) on post-infectious pulmonary sequelae (ALRIPS). Methods Between 2007 and 2010, inpatients ≥15 years with ALRI were prospectively recruited. Clinical, biological, radiological and microbiological data were collected. Chest radiographs were re-interpreted by experts to compare patients with ALRIPS, on previously healthy lungs (ALRIHL) and active pulmonary tuberculosis (TB). Patients without chest radiograph abnormality or with abnormality suggestive as other chronic respiratory diseases were excluded from this analysis. Results Among the 2351 inpatients with community-acquired ALRI, 1800 were eligible: 426 (18%) ALRIPS, 878 (37%) ALRIHL and 496 (21%) TB. ALRIPS patients had less frequent fever than other ALRI (p < 0.001) and more productive cough than ALRIHL (p < 0.001). Streptococcus pneumoniae, Haemophilus influenzae, and Pseudomonas aeruginosa accounted for 83% of ALRIPS group positive cultures. H. influenzae and P. aeruginosa were significantly associated with ALRIPS compared with ALRIHL. Treatment was appropriate in 58% of ALRIPS patients. Finally, 79% of ALRIPS were not recognized by local clinicians. In-hospital mortality was low (1%) but probably underestimated in the ALRIPS group. Conclusion ALRIPS remains often misdiagnosed as TB with inappropriate treatment in low-income countries. Better-targeted training programs would help reduce the morbidity burden and financial costs.
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Mameli C, Zuccotti GV. The impact of viral infections in children with community-acquired pneumonia. Curr Infect Dis Rep 2013; 15:197-202. [PMID: 23549618 PMCID: PMC7088739 DOI: 10.1007/s11908-013-0339-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
For many years viral causes of community-acquired pneumonia were often been given limited attention. The number of published studies on influenza alone increased fivefold from 2001 to 2010. Specifically several studies have underlined that the involvement of viruses in community-acquired pneumonia has been underestimated, and this underestimation has been attributed to a lack of appropriate diagnostic methods. Now, with the advent of modern molecular assays, it is well recognized that viruses account for the largest proportion of community-acquired pneumonia in preschool children in both developed and developing countries. Respiratory syncytial virus, influenza virus, adenovirus, and parainfluenza virus are the major pathogens involved, but the relative importance of additional viruses (rhinoviruses, bocavirus, human metapneumovirus) is increasing and will be better defined by future research.
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Affiliation(s)
- Chiara Mameli
- Department of Pediatrics, L. Sacco Hospital, University of Milan, via G.B. Grassi 74, 20157, Milano, Italy
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