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Amodio E, Belluzzo M, Genovese D, Palermo M, Pisciotta V, Vitale F. What 'case definition' for respiratory syncytial virus infection? Results of a systematic literature review to improve surveillance among the adults. J Public Health (Oxf) 2024:fdae066. [PMID: 38705841 DOI: 10.1093/pubmed/fdae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 02/27/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND Human respiratory syncytial virus (hRSV) is a leading cause of acute lower respiratory tract infection in frail individuals, including children, the elderly and immunocompromised people, with mild to severe symptoms. World Health Organization claims hRSV causes most elderly influenza-like illnesses (ILI) and severe acute respiratory infections (SARI). In this study, different case definitions for hRSV surveillance were examined for accuracy. METHODS The following search query ('Respiratory Syncytial Virus' OR 'RSV' OR 'hRSV' AND 'case definition') was used on PubMed/MEDLINE and Scopus with a 15-year-old baseline age restriction to conduct a systematic literature review. RESULTS Of 12 records, 58% employed the SARI definition, 50% the ILI definition and 42% the acute respiratory infection (ARI) definition, with some overlap. In young adults (18-64 years old), most studies show RSV prevalence between 6.25 and 72.54 cases per 1000 per year, and 19.23 to 98.5 in older adults. The outpatient ARI and hospitalized SARI criteria are particularly sensitive and specific. CONCLUSIONS Disease burden measurement requires a clear case definition; however, current literature is questionable. Currently, hRSV surveillance uses numerous case definitions with debatable accuracy. The epidemiology, clinical characteristics, and disease burden of hRSV are difficult to characterize without a standard surveillance case definition.
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Affiliation(s)
- Emanuele Amodio
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties 'G. D'Alessandro', University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
| | - Miriam Belluzzo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties 'G. D'Alessandro', University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
| | - Dario Genovese
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties 'G. D'Alessandro', University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
| | - Martina Palermo
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties 'G. D'Alessandro', University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
| | - Vincenzo Pisciotta
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties 'G. D'Alessandro', University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
| | - Francesco Vitale
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties 'G. D'Alessandro', University of Palermo, Via del Vespro 133, 90127 Palermo, Italy
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Hassan MZ, Islam MA, Shoshi HR, Hossain MK, Shirin T, Chowdhury F. Characterizing deaths among adult patients with severe acute respiratory infection: during the pre- and COVID-19 pandemic periods in Bangladesh, 2018-2022. Trop Med Health 2023; 51:70. [PMID: 38115037 PMCID: PMC10729565 DOI: 10.1186/s41182-023-00565-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Severe acute respiratory infection (SARI) is a leading cause of mortality globally, peaking during the COVID-19 pandemic. We analyzed SARI-associated deaths during the pre-and-pandemic periods in Bangladesh to identify the contributing factors. METHODS We analyzed data from hospital-based influenza surveillance at nine tertiary-level hospitals in Bangladesh. We considered March 2018-February 2020 as the pre-pandemic period and March 2020-February 2022 as the pandemic period and included adult (≥ 18 years) participants in our study. Surveillance physicians identified WHO-SARI case definition meeting inpatients and collected demographics, clinical characteristics, and outcomes at hospital discharge and 30 days post-discharge. We performed rRT-PCR for influenza and SARS-CoV-2 viruses on collected nasopharyngeal and oropharyngeal swabs. We used multivariable Cox's regression models to calculate the hazard ratio (HR) for factors associated with SARI deaths in these adult patients. RESULTS We enrolled 4392 SARI patients during the pre-pandemic and 3824 SARI patients during the pandemic period. Case fatality ratio was higher during the pandemic: 13.62% (521) [in-hospital: 6.45% (247); post-discharge: 7.17% (274)] compared to pre-pandemic, 6.01% (264) [in-hospital: 2.01% (89), post-discharge: 4% (175)] (p < 0.001). Pre-pandemic, influenza was detected in 14% (37/264) of SARI deaths. Influenza was detected during the pandemic in 2.3% (12/521), SARS-CoV-2 in 41.8% (218/521), and both viruses in only one SARI death. History of smoking and the presence of 1 or more co-morbid conditions independently attributed to SARI deaths in adults in the pre-pandemic period. SARI deaths in such patients were also associated with respiratory difficulties on admission in both pre-pandemic (aHR 2.36; 95% CI:1.65-3.36) and pandemic period (aHR 2.30; 95% CI: 1.57-3.35) after accounting for age, sex, smoking status, presence of 1 or more co-morbid conditions, and detection of influenza and SARS-CoV-2 viruses. CONCLUSIONS During the pandemic, SARI mortality increased; influenza-associated mortality declined, and SARS-CoV-2 caused over a third of SARI deaths. Post-discharge mortality was higher than in-hospital mortality during both periods. Limiting premature discharge and strengthening post-discharge monitoring and nursing services could reduce unexpected deaths. Formative research to better understand post-discharge mortality is essential to reduce SARI deaths.
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Affiliation(s)
- Md Zakiul Hassan
- Programme for Emerging Infections, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (Icddr,b), Mohakhali, Dhaka, Bangladesh.
| | - Md Ariful Islam
- Programme for Emerging Infections, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (Icddr,b), Mohakhali, Dhaka, Bangladesh
| | - Homayra Rahman Shoshi
- Programme for Emerging Infections, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (Icddr,b), Mohakhali, Dhaka, Bangladesh
| | - Md Kamal Hossain
- Programme for Emerging Infections, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (Icddr,b), Mohakhali, Dhaka, Bangladesh
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Fahmida Chowdhury
- Programme for Emerging Infections, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (Icddr,b), Mohakhali, Dhaka, Bangladesh
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Özgen-Top Ö, Aysert-Yıldız P, Özger HS, Güzel-Tunçcan Ö. Evaluation of Hospitalized Patients with Community-Acquired Influenza-Like Illness During Two Influenza Seasons. INFECTIOUS DISEASES & CLINICAL MICROBIOLOGY 2023; 5:323-331. [PMID: 38633854 PMCID: PMC10986686 DOI: 10.36519/idcm.2023.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/02/2023] [Indexed: 04/19/2024]
Abstract
Objective Influenza is among the most important respiratory infections affecting all age groups and can lead to hospitalizations. We aimed to determine the frequency of influenza infections among acute admissions with influenza-like illness (ILI) and evaluate the demographic, clinical findings, and outcomes of patients with influenza. Methods This prospective, active surveillance study was conducted in a university hospital between 2015 and 2017. Patients hospitalized for at least 24 hours in the selected units with community-acquired ILI were screened according to certain influenza-predicting ICD-10 codes. Nasopharyngeal and pharyngeal swab samples were taken from patients who were eligible for the study. Patients tested for influenza with real-time polymerase chain reaction. Univariate and multivariate analyses were performed for data. Results Among 440 patients screened according to influenza-related ICD-10 codes, 112 were included. Influenza positivity was detected in 37 of the 112 patients. Clinical findings were similar between influenza positive and negative groups and also between influenza subtypes, excluding sore throat, which was more common in the H1N1 group. Alanine transaminase (ALT), aspartate transaminase (AST), and creatine kinase (CK) elevations were found to be significantly higher in the influenza-positive group. When influenza-positive patients with and without pneumonia were compared, the rate of vaccination in the same season was higher in patients without pneumonia than in patients with pneumonia (38.8% and 10.5%, respectively; p=0.04). Conclusion Integrating molecular tests detecting both influenza and other respiratory viruses into influenza surveillance programs can increase the efficacy and quality of these programs. The elevation of AST, ALT, and CK in influenza cases can be considered in distinguishing influenza from other ILI cases. Vaccination in the same season can reduce the risk of pneumonia in influenza-positive patients.
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Affiliation(s)
- Özge Özgen-Top
- Department of Infectious Diseases and Clinical Microbiology, Gazi University School of Medicine, Ankara, Türkiye
| | - Pınar Aysert-Yıldız
- Department of Infectious Diseases and Clinical Microbiology, Gazi University School of Medicine, Ankara, Türkiye
| | - Hasan Selçuk Özger
- Department of Infectious Diseases and Clinical Microbiology, Gazi University School of Medicine, Ankara, Türkiye
| | - Özlem Güzel-Tunçcan
- Department of Infectious Diseases and Clinical Microbiology, Gazi University School of Medicine, Ankara, Türkiye
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Denayer S, Dufrasne FE, Monsieurs B, van Eycken R, Houben S, Seyler L, Demuyser T, van Nedervelde E, Bourgeois M, Delaere B, Magerman K, Jouck D, Lissoir B, Sion C, Reynders M, Petit E, Dauby N, Hainaut M, Laenen L, Maes P, Baele G, Dellicour S, Cuypers L, André E, Couvreur S, Brondeel R, Barbezange C, Bossuyt N, van Gucht S. Genomic monitoring of SARS-CoV-2 variants using sentinel SARI hospital surveillance. Influenza Other Respir Viruses 2023; 17:e13202. [PMID: 37840842 PMCID: PMC10570899 DOI: 10.1111/irv.13202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023] Open
Abstract
Background To support the COVID-19 pandemic response, many countries, including Belgium, implemented baseline genomic surveillance (BGS) programs aiming to early detect and characterize new SARS-CoV-2 variants. In parallel, Belgium maintained a sentinel network of six hospitals that samples patients with severe acute respiratory infections (SARI) and integrated SARS-CoV-2 detection within a broader range of respiratory pathogens. We evaluate the ability of the SARI surveillance to monitor general trends and early signals of viral genetic evolution of SARS-CoV-2 and compare it with the BGS as a reference model. Methods Nine-hundred twenty-five SARS-CoV-2 positive samples from patients fulfilling the Belgian SARI definition between January 2020 and December 2022 were sequenced using the ARTIC Network amplicon tiling approach on a MinION platform. Weekly variant of concern (VOC) proportions and types were compared to those that were circulating between 2021 and 2022, using 96,251 sequences of the BGS. Results SARI surveillance allowed timely detection of the Omicron (BA.1, BA.2, BA.4, and BA.5) and Delta (B.1.617.2) VOCs, with no to 2 weeks delay according to the start of their epidemic growth in the Belgian population. First detection of VOCs B.1.351 and P.1 took longer, but these remained minor in Belgium. Omicron BA.3 was never detected in SARI surveillance. Timeliness could not be evaluated for B.1.1.7, being already major at the start of the study period. Conclusions Genomic surveillance of SARS-CoV-2 using SARI sentinel surveillance has proven to accurately reflect VOCs detected in the population and provides a cost-effective solution for long-term genomic monitoring of circulating respiratory viruses.
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Affiliation(s)
- Sarah Denayer
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - François E. Dufrasne
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Bert Monsieurs
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Reinout van Eycken
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Sarah Houben
- Observational Clinical Trials, Scientific Directorate of infectious Diseases in HumansSciensanoUkkelBelgium
| | - Lucie Seyler
- Department of Internal Medicine and Infectiology, Universitair Ziekenhuis Brussel (UZB)Vrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel (UZB)Vrije Universiteit Brussel (VUB)BrusselsBelgium
- AIMS Lab, Center for Neurosciences, Faculty of Medicine and PharmacyVrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Els van Nedervelde
- Department of Internal Medicine and Infectiology, Universitair Ziekenhuis Brussel (UZB)Vrije Universiteit Brussel (VUB)BrusselsBelgium
| | | | | | - Koen Magerman
- Infection Control and Clinical LaboratoryJessa ZiekenhuisHasseltBelgium
- Department of Immunology and InfectionHasselt UniversityHasseltBelgium
| | - Door Jouck
- Infection ControlJessa ZiekenhuisHasseltBelgium
| | | | - Catherine Sion
- Laboratory Site St‐JosephGrand Hôpital de CharleroiGillyBelgium
| | | | - Evelyn Petit
- Laboratory MedicineAZ Sint‐Jan Brugge‐Oostende AVBrugesBelgium
| | - Nicolas Dauby
- Department of Infectious Diseases, Centre Hospitalier Universitaire Saint‐PierreUniversité Libre de Bruxelles (ULB)BrusselsBelgium
- Institute for Medical Immunology, ULB Center for Research in Immunology (U‐CRI)Université Libre de Bruxelles (ULB)BrusselsBelgium
- School of Public HealthUniversité Libre de Bruxelles (ULB)BrusselsBelgium
| | - Marc Hainaut
- Pediatrics Department, CHU Saint‐PierreUniversité Libre de Bruxelles (ULB)BrusselsBelgium
| | - Lies Laenen
- National Reference Center for Respiratory Pathogens, UZ LeuvenUniversity Hospitals LeuvenLeuvenBelgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Rega InstituteKU LeuvenLeuvenBelgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega InstituteKU LeuvenLeuvenBelgium
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega InstituteKU LeuvenLeuvenBelgium
- Spatial Epidemiology Lab (SpELL)Université Libre de BruxellesBrusselsBelgium
| | - Lize Cuypers
- National Reference Center for Respiratory Pathogens, UZ LeuvenUniversity Hospitals LeuvenLeuvenBelgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Emmanuel André
- National Reference Center for Respiratory Pathogens, UZ LeuvenUniversity Hospitals LeuvenLeuvenBelgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Simon Couvreur
- Epidemiology and public Health, Epidemiology of Infectious DiseasesSciensanoBrusselsBelgium
| | - Ruben Brondeel
- Epidemiology and public Health, Epidemiology of Infectious DiseasesSciensanoBrusselsBelgium
| | - Cyril Barbezange
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Nathalie Bossuyt
- Epidemiology and public Health, Epidemiology of Infectious DiseasesSciensanoBrusselsBelgium
| | - Steven van Gucht
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
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Rozenbaum MH, Begier E, Kurosky SK, Whelan J, Bem D, Pouwels KB, Postma M, Bont L. Incidence of Respiratory Syncytial Virus Infection in Older Adults: Limitations of Current Data. Infect Dis Ther 2023:10.1007/s40121-023-00802-4. [PMID: 37310617 DOI: 10.1007/s40121-023-00802-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/30/2023] [Indexed: 06/14/2023] Open
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) is an important cause of severe respiratory illness in older adults and adults with respiratory or cardiovascular comorbidities. Published estimates of its incidence and prevalence in adult groups vary widely. This article reviews the potential limitations affecting RSV epidemiology studies and suggests points to consider when evaluating or designing them. METHODS Studies reporting the incidence or prevalence of RSV infection in adults in high-income Western countries from 2000 onwards were identified via a rapid literature review. Author-reported limitations were recorded, together with presence of other potential limitations. Data were synthesized narratively, with a focus on factors affecting incidence estimates for symptomatic infection in older adults. RESULTS A total of 71 studies met the inclusion criteria, most in populations with medically attended acute respiratory illness (ARI). Only a minority used case definitions and sampling periods tailored specifically to RSV; many used influenza-based or other criteria that are likely to result in RSV cases being missed. The great majority relied solely on polymerase chain reaction (PCR) testing of upper respiratory tract samples, which is likely to miss RSV cases compared with dual site sampling and/or addition of serology. Other common limitations were studying a single season, which has potential for bias due to seasonal variability; failure to stratify results by age, which underestimates the burden of severe disease in older adults; limited generalizability beyond a limited study setting; and absence of measures of uncertainty in the reporting of results. CONCLUSIONS A significant proportion of studies are likely to underestimate the incidence of RSV infection in older adults, although the effect size is unclear and there is also potential for overestimation. Well-designed studies, together with increased testing for RSV in patients with ARI in clinical practice, are required to accurately capture both the burden of RSV and the potential public health impact of vaccines.
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Affiliation(s)
| | | | | | | | | | | | | | - Louis Bont
- University Medical Center Utrecht, Utrecht, The Netherlands
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Mohamed AM, Al Sayyad A, Matar E, Isa HM, Hasan WF, Hashim NSJY, Alajaimi BA, Aldolabi Q. Factors associated with poor outcomes in patients with severe acute respiratory infections in Bahrain. Influenza Other Respir Viruses 2023; 17:e13133. [PMID: 37123813 PMCID: PMC10133729 DOI: 10.1111/irv.13133] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
Background Severe acute respiratory tract infection (SARI) is a major global health threat. This study aimed to examine risk factors associated with poor outcomes in patients with SARI. Methods All patients who met World Health Organization's (WHO) SARI case definition and were admitted to Salmaniya Medical Complex from January 2018 to December 2021 were included. Epidemiological and virological data were obtained and analyzed. Results Of 1159 patients with SARI included, 731 (63.1%) patients were below 50 years, and 357 (30.8%) tested positive for viral pathogens. The most prevalent virus was Flu-A (n = 134, 37.5%), SARS-CoV2 (n = 118, 33%), RSV (n = 51, 14.3%), Flu B (n = 49,13.7%), other viruses (n = 3, 0.8%), and combined infection (n = 2, 0.6%). Six hundred fifty-eight (56.8%) patients had comorbidities, mainly diabetes (n = 284, 43%) and heart disease (n = 217, 33%). 183 (16%) patients were admitted to ICU, 110 (9%) needed mechanical ventilation, and 80 (7%) patients died.The odds of ICU admission were higher for patients with hematological (OR 5.9, 95% CI 3.1-11.1) and lung diseases (OR 2.7, 95% CI 1.6-4.6). The odds of mechanical ventilation were higher among patients with lung disease (OR 3.1, 95% 1.7-5.5). The mortality odds were higher among patients above 50 (OR 2.4, 95% CI 1.4-4.1) and chronic kidney disease (OR 2.5, 95% CI 1.1-5.2). Conclusions Being 50 years or above or having kidney, lung, or heart diseases was associated with worse SARI outcomes. Efforts and actions in developing better strategies to vaccinate individuals at high risk and early diagnosis and treatment should help in reducing the burden of SARI.
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Affiliation(s)
- Afaf Merza Mohamed
- Consultant Family Medicine & Public HealthMinistry of HealthManamaBahrain
| | - Adel Al Sayyad
- Consultant Family Medicine, Epidemiology & Public Health, Chief of Disease Control Section, Ministry of Health. Associate Prof. of Family and Community MedicineCMMS, AGUManamaBahrain
| | - Ebrahim Matar
- Medical Intern, Eastern Health ClusterDammamSaudi Arabia
| | - Hasan M. Isa
- Consultant Pediatric Gastroenterologist, Pediatric DepartmentSalmaniya Medical Complex, Arabian Gulf UniversityManamaBahrain
| | | | | | | | - Qatrmeer Aldolabi
- Public Health Specialist (PHS), Disease Control SectionMinistry of HealthManamaBahrain
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Ogunbayo AE, Mogotsi MT, Sondlane H, Nkwadipo KR, Sabiu S, Nyaga MM. Pathogen Profile of Children Hospitalised with Severe Acute Respiratory Infections during COVID-19 Pandemic in the Free State Province, South Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph191610418. [PMID: 36012053 PMCID: PMC9408356 DOI: 10.3390/ijerph191610418] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 05/30/2023]
Abstract
Severe acute respiratory infections (SARI) contribute to mortality in children ≤5 years. Their microbiological aetiologies are often unknown and may be exacerbated in light of coronavirus disease 19 (COVID-19). This study reports on respiratory pathogens in children ≤5 years (n = 84) admitted with SARI during and between the second and third waves of COVID-19 infection in South Africa. Nasopharyngeal/oropharyngeal swabs collected were subjected to viral detection using QIAstat-Dx® Respiratory SARS-CoV-2 Panel. The results revealed viral positivity and negativity detection rates of 88% (74/84) and 12% (10/84), respectively. Of the 21 targeted pathogens, human rhinovirus/enterovirus (30%), respiratory syncytial virus (RSV; 26%), and severe acute respiratory syndrome coronavirus 2 (24%) were mostly detected, with other viruses being 20% and a co-infection rate of 64.2% (54/84). Generally, RSV-positive samples had lower Ct values, and fewer viruses were detected during the third wave. Changes in the circulation patterns of respiratory viruses with total absence of influenza virus could be attributed to measures against COVID-19 transmission, which may result in waned immunity, thereby increasing susceptibility to severe infections in the following season. High viral co-infection rate, as detected, may complicate diagnosis. Nonetheless, accurate identification of the pathogens may guide treatment decisions and infection control.
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Affiliation(s)
- Ayodeji E. Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Milton T. Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Hlengiwe Sondlane
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Kelebogile R. Nkwadipo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
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Probst V, Rankin DA, Haddadin Z, Hamdan L, Rahman HK, Yanis A, Talj R, Spieker AJ, Howard L, Stewart LS, Guevara C, Yepsen E, Faouri S, Shehabi A, Williams JV, Chappell J, Khuri-Bulos N, Halasa NB. Adenovirus Infection in Hospitalized Children with Acute Respiratory Infection in Jordan. Pediatr Infect Dis J 2022; 41:277-283. [PMID: 35315822 PMCID: PMC8943843 DOI: 10.1097/inf.0000000000003423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND The most common clinical manifestation of adenovirus (AdV) infection is acute respiratory illness (ARI). Specific AdV species associated with ARI hospitalizations are not well defined in the Middle East. METHODS A viral surveillance study was conducted among children <2 years hospitalized in Amman, Jordan, from March 2010 to March 2013. Nasal and throat respiratory specimens were obtained from enrolled children and tested for viruses using a real-time reverse-transcription quantitative polymerase chain reaction. AdV-positive specimens were typed by partial hexon gene sequencing. Demographic and clinical features were compared between AdV detected as single pathogen versus co-detected with other respiratory viruses, and between AdV-B and AdV-C species. RESULTS AdV was detected in 475/3168 (15%) children hospitalized with ARI; of these, 216 (45%) specimens were successfully typed with AdV-C as the most common species detected (140/216; 65%). Children with AdV-single detection (88/475; 19%) had a higher frequency of fever (71% vs. 56%; P=0.015), diarrhea (18% vs. 11%; p=0.048), and/or seizures/abnormal movements (14% vs. 5%; p=0.003). Children with AdV co-detected with other viruses more likely required oxygen support [adjusted odds ratio (aOR) 1.91 (95% CI: 1.08, 3.39), P = 0.027] than those with AdV-single detection. Children with AdV-C had higher odds of co-detections with other viruses compared with those with AdV-B [aOR 4.00 (95% CI: 1.91, 8.44), P < 0.001]. CONCLUSION Clinical differences were identified between AdV-single and AdV co-detected with other viruses, and between AdV-B and AdV-C. Larger studies with AdV typing are needed to determine additional epidemiological and clinical differences between specific AdV species and types.
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Affiliation(s)
- Varvara Probst
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Danielle A. Rankin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Epidemiology PhD Program, Vanderbilt University School of Medicine, Nashville, TN
| | - Zaid Haddadin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Lubna Hamdan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Herdi K. Rahman
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Ahmad Yanis
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Rana Talj
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Andrew J. Spieker
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Leigh Howard
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Laura S. Stewart
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Claudia Guevara
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Erin Yepsen
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Samir Faouri
- Department of Pediatrics, Al Bashir Hospital, Amman, Jordan
| | - Asem Shehabi
- Department of Pediatrics, Jordan University, Amman, Jordan
| | - John V. Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - James Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | | | - Natasha B. Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
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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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10
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Komoyo GF, Yambiyo BM, Manirakiza A, Gody JC, Muller CP, Hübschen JM, Nakoune E, Snoeck CJ. Epidemiology and genetic characterization of respiratory syncytial virus in children with acute respiratory infections: Findings from the influenza sentinel surveillance network in Central African Republic, 2015 to 2018. Health Sci Rep 2021; 4:e298. [PMID: 34013070 PMCID: PMC8112815 DOI: 10.1002/hsr2.298] [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: 08/20/2020] [Revised: 03/21/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND AND AIMS Respiratory syncytial virus (RSV) is one of the main viral pathogens causing acute respiratory infections in children under 5 years of age but has seldom been studied in Central African Republic (CAF). Taking advantage of the national influenza surveillance network in CAF, this study aimed at providing the first insights into RSV prevalence and seasonality over 4 years of surveillance and the clinical manifestations of RSV in this population in CAF. METHODS A total of 3903 children under 5 years matching the influenza-like illness (ILI, 68.5%) or severe acute respiratory infection (SARI, 31.5%) case definitions were recruited from January 2015 to December 2018. The presence of RSV viral RNA in nasopharyngeal samples was assessed by RT-PCR, followed by RSV-A and RSV-B typing and Sanger sequencing on a subset of samples. Phylogenetic analyses were carried on partial G protein sequences. Associations between RSV and demographic or clinical manifestations were investigated by statistical analyses. RESULTS RSV prevalence was significantly higher in infants <6 months (13.4%), in hospitalized children (13.3% vs 5.5%) and in male patients (9.5% vs 6.4%). An overall prevalence of RSV of 8.0% in the period of 2015 to 2018 was shown, with significant annual (6.4%-10.6%) and seasonal (12.7% in rainy season vs 3.0% in dry season) fluctuations. While RSV seasons in 2015, 2016, and 2018 were relatively similar, 2017 showed deviations from the overall patterns with significantly higher RSV circulation and an outbreak peak 3 to 5 months earlier. Concomitant circulation of RSV-A and RSV-B with an alternating predominance of RSV-A and RSV-B strains and temporal RSV-A genotype replacement from NA1 to ON1 was observed. CONCLUSION This study represents the first in-depth epidemiological analysis of RSV in CAF and provides first insights into RSV genetic diversity and seasonality in the country.
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Affiliation(s)
- Giscard F. Komoyo
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
- Ecole Doctorale d'Infectiologie Tropicale de Franceville, GabonFrancevilleGabon
| | - Brice M. Yambiyo
- Service d'épidémiologieInstitut Pasteur de BanguiBanguiCentral African Republic
| | | | - Jean C. Gody
- Complexe pédiatrique de BanguiCentre National Hospitalier Universitaire de BanguiBanguiCentral African Republic
| | - Claude P. Muller
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Judith M. Hübschen
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Emmanuel Nakoune
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
| | - Chantal J. Snoeck
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
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11
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Zhu T, Zhang P, Shen X, Cheng J, Chai J, Feng R, Wang D. Prevalence of respiratory tract infections and influencing factors: A cross-sectional survey in Anhui Province, China. Public Health Nurs 2021; 38:542-554. [PMID: 33655587 DOI: 10.1111/phn.12874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 12/01/2022]
Abstract
OBJECTIVES This study used available data to analyze the prevalence and influencing factors of various Respiratory tract infections (RTIs), to better our understanding of the local and national epidemiology, and to inform future prevention and control programs. DESIGN We used a structured questionnaire to solicit information about social demographics and symptoms of the last RTI administered with stratified clustered randomized sampling. Descriptive analysis was used to investigate the reported symptoms, and multivariate logistic regression models to identify relationships between the prevalence and influencing factors of common RTIs. RESULTS The study documented a prevalence rate of 1.5% for common cold, 0.5% for influenza, and 0.9% for 9-AURTIs (nine acute upper RTIs, including acute pharyngitis, sore throat, acute tonsillitis, acute suppurative tonsillitis, acute laryngitis, acute bronchitis, acute pharyngitis, acute upper RTI, and viral upper RTI), adding up to 3.4% of overall RTIs in the past 2 weeks. Results also revealed a L-shaped trend along age-axis for all the RTIs, and marginal to moderate associations between RTIs and other commonly researched factors (education, body mass index, sex, and annual income), as well as environmental and behavior factors. CONCLUSIONS RTIs in Anhui, China are common and associated with a variety of socio-demographic, behavioral, and environmental factors. RTIs merit better epidemiological understanding and added interventions tailored to efforts in reducing their health and economic burden. These understandings and efforts are especially relevant for public health nurses since most RTI patients are treated in community settings.
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Affiliation(s)
- Ting Zhu
- School of Health Service Management, Anhui Medical University, Hefei, China
| | - Pinglan Zhang
- School of Health Service Management, Anhui Medical University, Hefei, China
| | - Xingrong Shen
- School of Health Service Management, Anhui Medical University, Hefei, China
| | - Jing Cheng
- School of Health Service Management, Anhui Medical University, Hefei, China
| | - Jing Chai
- School of Health Service Management, Anhui Medical University, Hefei, China
| | - Rui Feng
- Anhui Medical University, University Library, Hefei, China
| | - Debin Wang
- School of Health Service Management, Anhui Medical University, Hefei, China
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12
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Coronavirus Surveillance in a Pediatric Population in Jordan From 2010 to 2013: A Prospective Viral Surveillance Study. Pediatr Infect Dis J 2021; 40:e12-e17. [PMID: 33165274 DOI: 10.1097/inf.0000000000002965] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Human coronaviruses (HCoVs) are a significant cause of acute respiratory illness (ARI) in children; however, the role of HCoVs in ARI among hospitalized children in the Middle East is not well defined. METHODS Children under 2 years admitted with fever and/or respiratory symptoms were enrolled from 2010 to 2013 in Amman, Jordan. Nasal/throat swabs were collected and stored for testing. Demographic and clinical characteristics were collected through parent/guardian interviews and medical chart abstractions. Prior stored specimens were tested for HCoVs (HKU1, OC43, 229E and NL63) by qRT-PCR. RESULTS Of the 3168 children enrolled, 6.7% were HCoVs-positive. Among HCoV-positive children, the median age was 3.8 (1.9-8.4) months, 59% were male, 14% were premature, 11% had underlying medical conditions and 76% had viral-codetection. The most common presenting symptoms were cough, fever, wheezing and shortness of breath. HCoVs were detected year-round, peaking in winter-spring months. Overall, 56%, 22%, 13% and 6% were OC43, NL63, HKU1 and 229E, respectively. There was no difference in disease severity between the species, except higher intensive care unit admission frequency in NL63-positive subjects. CONCLUSIONS HCoVs were detected in around 7% of children enrolled in our study. Despite HCoV detection in children with ARI with highest peaks in respiratory seasons, the actual burden and pathogenic role of HCoVs in ARI merits further evaluation given the high frequency of viral codetection.
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13
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Cimolai N. Complicating Infections Associated with Common Endemic Human Respiratory Coronaviruses. Health Secur 2020; 19:195-208. [PMID: 33186086 DOI: 10.1089/hs.2020.0067] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Coronaviruses OC43, 229E, NL63, and HKU1 are endemic human respiratory coronaviruses that typically cause mild to moderate upper respiratory infections, similar to the common cold. They also may cause simple and complicated lower respiratory infections, otitis media, asthma exacerbations, gastroenteritis, and a few systemic complications. These viruses are usually seasonal (with winter dominance) and affect nearly all age groups. The seasonal and annual variation in virus prevalence has implications for understanding the concept of acquired immunity and its persistence or diminution. Coronaviruses generally have outbreak potential in susceptible populations of any age, particularly in patients with comorbidities, who tend to have increased clinical disease. These 4 coronaviruses are often found in the context of what appears to be coinfection with other pathogens, but especially other viruses. If coronaviruses are not specifically tested for, the sole detection of a viral copathogen would suggest the pathogen is the causative agent, when a coronavirus may be culpable, or both. The detection of these viruses in circumstances where respiratory viruses are generally sought in clinical samples is, therefore, justified. These pathogens can be chronically shed from the respiratory tract, which is more likely to occur among immunocompromised and complicated patients. These viruses share the potential for genetic drift. The genome is among the largest of RNA viruses, and the capability of these viruses to further change is likely underestimated. Given the potential disease among humans, it is justified to search for effective antiviral chemotherapy for these viruses and to consider uses in niche situations should effective therapy be defined. Whereas SARS-CoV-2 may follow the epidemiological pattern of SARS-CoV and extinguish slowly over time, there is yet concern that SARS-CoV-2 may establish itself as an endemic human respiratory coronavirus similar to OC43, 2299E, NL63, and HKU1. Until sufficient data are acquired to better understand the potential of SARS-CoV-2, continued work on antiviral therapy and vaccination is imperative.
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Affiliation(s)
- Nevio Cimolai
- Nevio Cimolai, MD, FRCPC, is a Professor, Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia; he is also Medical Staff, Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia; both in Vancouver, Canada
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14
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Shi T, Denouel A, Tietjen AK, Campbell I, Moran E, Li X, Campbell H, Demont C, Nyawanda BO, Chu HY, Stoszek SK, Krishnan A, Openshaw P, Falsey AR, Nair H. Global Disease Burden Estimates of Respiratory Syncytial Virus-Associated Acute Respiratory Infection in Older Adults in 2015: A Systematic Review and Meta-Analysis. J Infect Dis 2020; 222:S577-S583. [PMID: 30880339 DOI: 10.1093/infdis/jiz059] [Citation(s) in RCA: 215] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Respiratory syncytial virus-associated acute respiratory infection (RSV-ARI) constitutes a substantial disease burden in older adults aged ≥65 years. We aimed to identify all studies worldwide investigating the disease burden of RSV-ARI in this population. We estimated the community incidence, hospitalization rate, and in-hospital case-fatality ratio (hCFR) of RSV-ARI in older adults, stratified by industrialized and developing regions, using data from a systematic review of studies published between January 1996 and April 2018 and 8 unpublished population-based studies. We applied these rate estimates to population estimates for 2015 to calculate the global and regional burdens in older adults with RSV-ARI in the community and in hospitals for that year. We estimated the number of in-hospital deaths due to RSV-ARI by combining hCFR data with hospital admission estimates from hospital-based studies. In 2015, there were about 1.5 million episodes (95% confidence interval [CI], .3 million-6.9 million) of RSV-ARI in older adults in industrialized countries (data for developing countries were missing), and of these, approximately 14.5% (214 000 episodes; 95% CI, 100 000-459 000) were admitted to hospitals. The global number of hospital admissions for RSV-ARI in older adults was estimated at 336 000 hospitalizations (uncertainty range [UR], 186 000-614 000). We further estimated about 14 000 in-hospital deaths (UR, 5000-50 000) related to RSV-ARI globally. The hospital admission rate and hCFR were higher for those aged ≥65 years than for those aged 50-64 years. The disease burden of RSV-ARI among older adults is substantial, with limited data from developing countries. Appropriate prevention and management strategies are needed to reduce this burden.
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Affiliation(s)
- Ting Shi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Angeline Denouel
- Global Vaccine Epidemiology and Modeling Department, Sanofi Pasteur, Lyon, France
| | - Anna K Tietjen
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Iain Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Emily Moran
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Xue Li
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Clarisse Demont
- Global Vaccine Epidemiology and Modeling Department, Sanofi Pasteur, Lyon, France
| | | | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle
| | | | - Anand Krishnan
- All India Institute of Medical Sciences, New Delhi, India
| | - Peter Openshaw
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Ann R Falsey
- University of Rochester School of Medicine, New York
- ReSViNET Foundation, Zeist, the Netherlands
| | - Harish Nair
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
- ReSViNET Foundation, Zeist, the Netherlands
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15
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Grunberg M, Sno R, Adhin MR. Epidemiology of respiratory viruses in patients with severe acute respiratory infections and influenza-like illness in Suriname. Influenza Other Respir Viruses 2020; 15:72-80. [PMID: 32881286 PMCID: PMC7767960 DOI: 10.1111/irv.12791] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/12/2020] [Indexed: 12/13/2022] Open
Abstract
Background Influenza has been well studied in developed countries with temperate climates, in contrast to low‐ and middle‐income (LMIC) countries, thus hampering the effort to attain representative global data. Furthermore, data on non‐influenza respiratory infections are also limited. Insight in viral respiratory infections in Suriname, a tropical LMIC in South America, would contribute to improved local preventive measures and a better global understanding of respiratory viruses. Methods From May 2016 through April 2018, all patients (n = 1096) enrolled in the national severe acute respiratory infection and influenza‐like illness surveillance were screened for the presence of 10 respiratory viruses with singleplex RT‐PCR. Results The overall viral‐positive detection rate was 45.3%, specified as RSV (19.4%), influenza (15.5%), hMPV (4.9%), AdV (4.6%), and parainfluenza (3.8%). Co‐infections were detected in 6.2% of the positive cases. Lower overall positivity was observed in the SARI vs ILI surveillance and influenza prevalence was higher in outpatients (45.0% vs 6.7%), while RSV exhibited the reverse (4.8% vs 23.8%). Respiratory infections in general were more common in children than in adults (54.4% vs 29.5%), although children were significantly less affected by influenza (11.5% vs 22.7%). None of the respiratory viruses displayed a clear seasonal pattern, and viral interference was observed between RSV and influenza. Conclusions The comprehensive information presented for Suriname, including first data on non‐influenza respiratory viruses, displayed distinct differences between the viruses, in seasonality, within age groups and between SARI/ILI, accentuating the need, especially for tropical LMIC countries to continue ongoing surveillance and accumulate local data.
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Affiliation(s)
- Meritha Grunberg
- Prof. Dr. Paul C. Flu" Institute for Biomedical Sciences, Paramaribo, Suriname
| | - Rachel Sno
- Prof. Dr. Paul C. Flu" Institute for Biomedical Sciences, Paramaribo, Suriname
| | - Malti R Adhin
- Prof. Dr. Paul C. Flu" Institute for Biomedical Sciences, Paramaribo, Suriname.,Department of Biochemistry, Faculty of Medical Sciences, Anton de Kom Universiteit van Suriname, Paramaribo, Suriname
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16
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Abu Elhassan UE, Mohamed SAA, Rizk MS, Sherif M, El-Harras M. Outcomes of patients with Severe Acute Respiratory Infections (SARI) admitted to the intensive care unit: results from the Egyptian Surveillance Study 2010-2014. Multidiscip Respir Med 2020; 15:465. [PMID: 32607231 PMCID: PMC7296279 DOI: 10.4081/mrm.2020.465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/18/2020] [Indexed: 11/23/2022] Open
Abstract
Background Few data exist about respiratory viral infections in Egyptian patients. Hereby we describe the outcomes of hospitalized Egyptian patients with severe acute respiratory infections (SARI) admitted to the ICU. Methods A prospective study in which all hospitalized patients meeting the WHO case definition for SARI and admitted to the ICU, during the period 2010–2014, were enrolled. Samples were tested using RT-PCR for influenza A, B, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), parainfluenza virus, adenovirus, bocavirus, enterovirus, and rhinovirus. Data were analyzed to study the clinical features of SARI-ICU patients and which pathogens are related to severe outcomes. Associated comorbidities were evaluated using Charlson Age-Comorbidity Index (CACI). Results Out of 1,075 patients with SARI, 219 (20.3%) were admitted to the ICU. The highest rates were reported for RSV (37%). SARI-ICU patients had higher rates of hospital stay, pneumonia, respiratory failure, ARDS, and mortality. Multivariate logistic regression analysis identified associated respiratory disorders (p=0.001), radiological abnormalities (p=0.023), and longer hospital stay (p=0.005) as risk factors for severe outcomes. Conclusions This surveillance study showed that 20% of hospitalized Egyptian patients with viral SARI needed ICU admission. SARI-ICU patients had higher rates of hospital stay, pneumonia, respiratory failure, ARDS, and mortality. Higher comorbidity index scores, radiological abnormalities, and longer hospital stay are risk factors for severe outcomes in SARI-ICU patients in our locality.
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Affiliation(s)
| | - Sherif A A Mohamed
- Department of Chest Diseases and Tuberculosis, Faculty of Medicine, Assiut University, Assiut
| | - Magda S Rizk
- Department of Anesthesia and Intensive Care, Faculty of Medicine, Cairo University, Cairo
| | - Mai Sherif
- Department of Clinical Pathology, Faculty of Medicine, Cairo University, Cairo
| | - Mohamed El-Harras
- Department of Clinical Pathology, Faculty of Medicine, Mansura University, Mansura, Egypt
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17
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Cimolai N. Features of enteric disease from human coronaviruses: Implications for COVID-19. J Med Virol 2020; 92:1834-1844. [PMID: 32462689 PMCID: PMC7283829 DOI: 10.1002/jmv.26066] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/25/2020] [Indexed: 01/19/2023]
Abstract
Coronaviruses have long been studied in both human and veterinary fields. Whereas the initial detection of endemic human respiratory coronaviruses was problematic, detection of these and newly discovered human coronaviruses has been greatly facilitated with major advances in the laboratory. Nevertheless, technological factors can affect the accuracy and timeliness of virus detection. Many human coronaviruses can be variably found in stool samples. All human coronaviruses have been variably associated with symptoms of gastroenteritis. Coronaviruses can occasionally be cultured from enteric specimens, but most detection is accomplished with genetic amplification technologies. Excretion of viral RNA in stool can extend for a prolonged period. Culture‐positive stool samples have been found to exceed a fourteen day period after onset of infection for some coronaviruses. Virus can also sometimes be cultured from patients' respiratory samples during the late incubation period. Relatively asymptomatic patients may excrete virus. Both viable and nonviable virus can be found in the immediate environment of the patient, the health care worker, and less often the public. These lessons from the past study of animal and human coronaviruses can be extended to presumptions for severe acute respiratory syndrome coronavirus 2. Already, the early reports from the coronavirus disease‐2019 pandemic are confirming some concerns. These data have the cumulative potential to cause us to rethink some current and common public health and infection control strategies. coronaviruses are variably found in human enteric samples during the course of infection. abdominal and intestinal illnesses are associated with coronavirus infections. enteric excretion of live virus and viral RNA have been confirmed. occasionally, live virus can be found in stool samples to exceed a fourteen day period after disease onset, and virus can also be cultured from these samples during the late incubation period or from asymptomatic individuals.
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Affiliation(s)
- Nevio Cimolai
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, Children's and Women's Health Centre of British Columbia, The University of British Columbia, Vancouver, British Columbia, Canada
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18
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Zaki MES, Eid AR, Faried OA. Clinico-Pathological Study of Adenovirus Associated with Respiratory Infections in Children. Open Microbiol J 2020. [DOI: 10.2174/1874285802014010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background:
Adenovirus is associated with respiratory tract infections in children worldwide. However, there is insufficient data about adenovirus infections in Egyptian children and the genotypes present in this infection.
Objective:
The aim of the present study was to investigate the prevalence of adenovirus and its genotypes in respiratory tract infection in children by real-time Polymerase Chain Reaction (PCR).
Methods:
The study was a cross-sectional study that included 100 children complaining of respiratory tract infections signs and symptoms. Laboratory investigation for adenovirus included real-time polymerase chain reaction and genotypes detection by Multiplex Polymerase Chain Reaction (PCR).
Results:
Adenovirus was detected by PCR for fiber gene in 11% with genotype 3 in 6 samples (54.5%) and genotype 7 in 5 samples (45.5%) positive for adenovirus by Multiplex PCR. The main presenting symptoms and signs in children with adenovirus detected by PCR were cough, fever, wheezing, and croups (90.9%, 81.1%, 63.6%, and 63.6%, respectively). The diagnosis in children with adenovirus was pneumonia in 72.7% and bronchitis in 27.7%. There were statistically insignificant differences in demographic, clinical, and hematological parameters between children with adenovirus and children negative to adenovirus by PCR.
Conclusion:
The clinical characteristics of respiratory infections with adenovirus vary upon the age of the patients and the immune status. Therefore, there is a requirement for an extensive study of adenovirus in respiratory infections in children with different ages and immune status.
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Cai W, Buda S, Schuler E, Hirve S, Zhang W, Haas W. Risk factors for hospitalized respiratory syncytial virus disease and its severe outcomes. Influenza Other Respir Viruses 2020; 14:658-670. [PMID: 32064773 PMCID: PMC7578333 DOI: 10.1111/irv.12729] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 01/10/2020] [Accepted: 01/24/2020] [Indexed: 11/26/2022] Open
Abstract
Introduction Respiratory syncytial virus (RSV) is a major cause of hospital admission for acute lower respiratory tract infection in young children. Objectives We aimed to identify risk factors for hospitalized RSV disease and its severe outcomes. Methods We conducted a retrospective cohort study analyzing data of a ICD‐10‐code‐based hospital surveillance for severe acute respiratory infections (SARI). Using univariable and multivariable logistic regression analysis, we assessed age‐group, gender, season, and underlying medical conditions as possible risk factors for RSV and its severe outcomes including ICU admission, application of ventilator support, and death, respectively. Results Of the 413 552 patients hospitalized with SARI in the database, 8761 were diagnosed with RSV from week 01/2009 to 20/2018 with 97% (8521) aged <5 years. Among children aged <5 years, age‐groups 0‐5 months (OR: 20.29, 95% CI: 18.37‐22.41) and 6 months‐1 year (OR: 4.59, 95% CI: 4.16‐5.06), and underlying respiratory and cardiovascular disorders specific to the perinatal period (OR: 1.32, 95% CI: 1.11‐1.57) were risk factors for being diagnosed with RSV. Age‐group 0‐5 months (OR: 2.39, 95% CI: 1.45‐3.94), low birth weight (OR: 6.77, 95% CI: 1.28‐35.71), preterm newborn (OR: 6.71, 95% CI: 2.19‐20.61), underlying respiratory and cardiovascular disorders specific to the perinatal period (OR: 4.97, 95% CI: 3.36‐7.34), congenital malformation of the heart (OR: 3.65, 95% CI: 1.90‐7.02), congenital malformation of the great vessels (OR: 3.50, 95% CI: 1.10‐11.18), congenital defect originating in perinatal period (OR: 4.07, 95% CI: 1.71‐9.70), cardiovascular disease (OR: 5.19, 95% CI: 2.77‐9.72), neurological disorders (OR: 6.48, 95% CI: 3.76‐11.18), blood disease (OR: 3.67, 95% CI: 1.98‐6.79), and liver disease (OR: 14.99, 95% CI: 1.49‐150.82) contributed to ICU admission in RSV cases. Conclusions Using ICD‐10‐based surveillance data allows to identify risk factors for hospitalized RSV disease and its severe outcomes, and quantify the risk in different age‐groups.
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Affiliation(s)
- Wei Cai
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany.,Medizinische Fakultät Charité - Universitätsmedizin, Berlin, Germany
| | - Silke Buda
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | | | | | - Wenqing Zhang
- Global Influenza Programme, World Health Organization, Geneva, Switzerland
| | - Walter Haas
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany.,Medizinische Fakultät Charité - Universitätsmedizin, Berlin, Germany
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Abstract
Respiratory syncytial virus (RSV) is the most common pathogen associated with acute lower respiratory tract infections in young children. RSV is also a major viral pathogen causing severe lung disease in the adult population, particularly among the elderly. We conducted a review of adult RSV studies published from January 1970 to February 2017 to determine the burden of disease among adults worldwide. There were no restrictions on health care setting or definition of RSV infection. A total of 1530 published studies were identified, 95 of which were included in this review. The incidence rates of hospitalised RSV acute respiratory tract infection (ARI) in adults >65 years old ranged from 7.3 to 13.0/105 population in Africa and Asia and from 190 to 254/105 population in the USA. Higher incidence rates (195–1790/105 population) were observed in adults ≥50 years old for outpatient or emergency visits in the USA. Of all ARI patients, RSV accounted for 1–10% in adults and 2–14% in patients with chronic diseases or transplantation. Given the limitations in the existing data, significant efforts should be made to generate evidence on the burden of RSV infections in adults and to estimate the potential impact of future preventive interventions.
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Pecego AC, Amâncio RT, Costa DM, Bozza FA, Siqueira MM, Oliveira ML, Cerbino-Neto J, Japiassu A. Etiology, clinical, and epidemiological characteristics of severe respiratory infection in people living with HIV. Int J STD AIDS 2020; 31:100-108. [PMID: 31969059 PMCID: PMC7206327 DOI: 10.1177/0956462419882587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
People living with HIV (PLWH) are more prone to severe respiratory infections. We used the severe acute respiratory infection (SARI) definition to describe the etiology, clinical, and epidemiological characteristics in this population. This was a prospective observational study including PLWH hospitalized with fever and cough. Those with symptom onset up to 10 days were classified as severe acute respiratory infection and 11–30 days as non-severe acute respiratory infection. Blood, urine samples and nasopharyngeal swabs were collected. Data were extracted from patient charts during their hospital stay. Forty-nine patients were included, median CD4 cell count: 80 cells/mm3, median time since HIV diagnosis and hospital admission: 84 months and 80% were antiretroviral therapy exposed. Twenty-seven patients were classified as SARI. Etiology was identified in 69%, 47% were polymicrobial. Respiratory virus (9 SARI vs. 13 non-SARI), bacteria (5 SARI vs. 4 non-SARI), Mycobacterium tuberculosis (6 SARI group vs. 7 non-SARI group), Pneumocystis jirovecii (4 SARI vs. 1 non-SARI), Cryptococcus neoformans (1 SARI vs. 3 non-SARI), and influenza A (1 SARI vs. 2 non-SARI). Dyspnea was statistically more prevalent in SARI (78% vs. 36%, p = 0.011) but the risk of death was higher in the non-SARI (4% vs. 36%, p = 0.0067). In the severely immunocompromised PLWH, severe acute respiratory infection can be caused by multiple pathogens and codetection is a common feature.
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Affiliation(s)
- AC Pecego
- Instituto Nacional de Infectologia – Fundação Oswaldo Cruz (Fiocruz) – Laboratório de Medicina Intensiva, Rio de Janeiro, Brazil
- AC Pecego, Instituto Nacional de Infectologia (INI), FIOCRUZ, Av Brasil 4365, Manguinhos, Rio de Janeiro, RJ, Brazil.
| | - RT Amâncio
- Instituto Nacional de Infectologia – Fundação Oswaldo Cruz (Fiocruz) – Laboratório de Medicina Intensiva, Rio de Janeiro, Brazil
| | - DM Costa
- Instituto Nacional de Infectologia – Fundação Oswaldo Cruz (Fiocruz) – Laboratório de Medicina Intensiva, Rio de Janeiro, Brazil
| | - FA Bozza
- Instituto Nacional de Infectologia – Fundação Oswaldo Cruz (Fiocruz) – Laboratório de Medicina Intensiva, Rio de Janeiro, Brazil
- Instituto D’Or de Pesquisa e Ensino, Rio de Janeiro, Brazil
| | - MM Siqueira
- Instituto Oswaldo Cruz – Fiocruz – Laboratório de Vírus Respiratório, do IOC/FIOCRUZ, Rio de Janeiro, Brazil
| | - ML Oliveira
- Instituto Oswaldo Cruz – Fiocruz – Laboratório de Vírus Respiratório, do IOC/FIOCRUZ, Rio de Janeiro, Brazil
| | - J Cerbino-Neto
- Laboratório de Pesquisa em Imunização e Vigilância em Saúde, Rio de Janeiro, Brazil
| | - A Japiassu
- Instituto Nacional de Infectologia – Fundação Oswaldo Cruz (Fiocruz) – Laboratório de Medicina Intensiva, Rio de Janeiro, Brazil
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Aydın H, Doğan H, Özüçelik DN, Koçak M, Gül OA. Viral prevalence, clinical profiles and comparison of severity scores for predicting the mortality of adults with severe acute respiratory infections. Turk J Med Sci 2019; 49:862-871. [PMID: 31195770 PMCID: PMC7018304 DOI: 10.3906/sag-1807-231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Background/aim The aim of this study was to determine the accuracy of severity scores for predicting the 28-day mortality among adults with severe acute respiratory infection (SARI) admitted to the emergency department. Materials and methods This study included 159 consecutive adult patients with SARI admitted to the emergency department of a tertiary hospital. A standard form was filled out in order to record demographic information, clinical parameters, laboratory tests, and radiographic findings of the patients. CURB-65, PSI, SIRS, qSOFA, SOFA and APACHE II scores were compared between the survivor and nonsurvivor groups. Results Of 159 patients included in the study, 38.4% were positive for respiratory viruses and 28.3% were positive for influenza viruses. 35.8% of the patients were admitted to an intensive care unit (ICU) and the mortality rate was 36.5%. The area under the receiver operating characteristic curve of CURB-65, PSI, SIRS criteria, qSOFA, SOFA and APACHE II scores were 0.717, 0.712, 0.607, 0.683, 0.755, and 0.748, respectively in predicting mortality and 0.759, 0.744, 0.583, 0.728, 0.741, and 0.731, respectively in predicting ICU admission. Conclusion SOFA and APACHE II were more accurate than SIRS in predicting the 28-day mortality among adults with SARI. There was no significant difference among these scores in terms of other multivariate comparisons.
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Affiliation(s)
- Hakan Aydın
- Department of Emergency Medicine, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, İstanbul, Turkey
| | - Halil Doğan
- Department of Emergency Medicine, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, İstanbul, Turkey
| | - Doğaç Niyazi Özüçelik
- Department of Emergency Medicine, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, İstanbul, Turkey
| | - Mehmet Koçak
- Department of Emergency Medicine, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, İstanbul, Turkey
| | - Osman Avşar Gül
- Department of Emergency Medicine, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, İstanbul, Turkey
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Hatem A, Mohamed S, Abu Elhassan UE, Ismael EAM, Rizk MS, El-Kholy A, El-Harras M. Clinical characteristics and outcomes of patients with severe acute respiratory infections (SARI): results from the Egyptian surveillance study 2010-2014. Multidiscip Respir Med 2019; 14:11. [PMID: 30976418 PMCID: PMC6442424 DOI: 10.1186/s40248-019-0174-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/05/2019] [Indexed: 11/10/2022] Open
Abstract
Background Respiratory viral and atypical bacterial infections data in Egyptian patients are sparse. This study describes the clinical features and outcomes of patients with severe acute respiratory infections (SARI) in hospitalized patients in Egypt. Methods SARI surveillance was implemented at Cairo University Hospital (CUH) during the period 2010–2014. All hospitalized patients meeting the WHO case definition for SARI were enrolled. Nasopharyngeal/oropharyngeal (NP/OP) swabs were collected and samples were tested using RT-PCR for influenza A, B, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), parainfluenza virus (PIV 1,2,3,4), adenovirus, bocavirus, coronavirus, enterovirus, rhinovirus, and atypical bacteria. Data were analyzed to calculate positivity rates for viral pathogens and determine which pathogens related to severe outcomes or resulted in death. Results Overall, 1,075/3,207 (33.5%) cases had a viral etiology, with a mean age of 5.74 (±13.87) years. The highest rates were reported for RSV (485 cases, 45.2%), PIV (125, 11.6%), and adenovirus (105, 9.8%). Children had a higher viral rate (981, 91.2%) compared to 94 (8.8%) cases in adults. Patients with identified viruses had significantly lower rates for ICU admission, hospital stay, mechanical ventilation, and overall mortality than those without identified viruses. No infections were independently associated with severe outcomes. Conclusions Viral pathogens were encountered in one-third of hospitalized adult and pediatric Egyptian patients with SARI, while atypical bacteria had a minor role. Highest rates of viral infections were reported for RSV, PIV, and adenovirus. Viral infections had neither negative impacts on clinical features nor outcomes of patients with SARI in our locality.
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Affiliation(s)
- Ashraf Hatem
- 1Department of Chest Diseases, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Sherif Mohamed
- 2Department of Chest Diseases and Tuberculosis, Faculty of Medicine, Assiut University, Assiut, 71516 Egypt
| | - Usama E Abu Elhassan
- 1Department of Chest Diseases, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Eman A M Ismael
- 1Department of Chest Diseases, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Magda S Rizk
- 3Department of Anesthesia and Intensive Care, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Amany El-Kholy
- 4Department of Clinical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed El-Harras
- Department of Clinical Pathology, Faculty of Medicine, Mansura University, Mansura, Egypt
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Human adenovirus load in respiratory tract secretions are predictors for disease severity in children with human adenovirus pneumonia. Virol J 2018; 15:123. [PMID: 30086789 PMCID: PMC6081882 DOI: 10.1186/s12985-018-1037-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 08/02/2018] [Indexed: 12/02/2022] Open
Abstract
Background Pneumonia is a serious public health issue and is concerned around the world. This study is to investigate the association between viral load in children with human adenovirus (HAdV) pneumonia and disease severity. Methods A total of 1313 cases of children hospitalized in Hunan Provincial People’s Hospital due to community acquired pneumonia (CAP) from April 2011 to May 2014 were enrolled in this study. Samples of nasopharyngeal aspirate were collected for the cohort. WHO criteria for CAP grading was emerged for pneumonia severity classification. Real-time fluorescence quantitative PCR (qRT-PCR) was used to detect 12 kinds of respiratory viruses. HAdV types were identified by nested PCR. The relationship between HAdV load and severity of disease was there by analyzed. Results Finally, 174 cases (174/1313, 13.3%) were positive for HAdV, and HAdV type 7 (HAdV-7) was the main serotype (76/174, 43.7%). Among the 174 cases, 70 cases were with HAdV infection alone and 104 cases were accompanied by other viruses. The patients were divided into mild pneumonia group (n = 108 cases) and severe pneumonia group (n = 66 cases). HAdV load of children in severe pneumonia group was higher than that in mild pneumonia group. Similar result was obtained in the 70 cases with HAdV infection alone after subgrouping. Relevant factors analysis results showed that severe pneumonia children presented lower onset age, more prone to fever, longer fever time, and longer hospital stay compared with that of mild pneumonia children. Children with HAdV-7 infection developed more frequently severe pneumonia. Multivariate regression analysis showed that HAdV load, age, and fever time were risk factors for pneumonia severity. Conclusion The severity of HAdV infection is significantly correlated with viral load and serotype.
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Barnes SR, Wansaula Z, Herrick K, Oren E, Ernst K, Olsen SJ, Casal MG. Mortality estimates among adult patients with severe acute respiratory infections from two sentinel hospitals in southern Arizona, United States, 2010-2014. BMC Infect Dis 2018; 18:78. [PMID: 29433471 PMCID: PMC5809880 DOI: 10.1186/s12879-018-2984-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 01/31/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND From October 2010 through February 2016, Arizona conducted surveillance for severe acute respiratory infections (SARI) among adults hospitalized in the Arizona-Mexico border region. There are few accurate mortality estimates in SARI patients, particularly in adults ≥ 65 years old. The purpose of this study was to generate mortality estimates among SARI patients that include deaths occurring shortly after hospital discharge and identify risk factors for mortality. METHODS Patients admitted to two sentinel hospitals between 2010 and 2014 who met the SARI case definition were enrolled. Demographic data were used to link SARI patients to Arizona death certificates. Mortality within 30 days after the date of admission was calculated and risk factors were identified using logistic regression models. RESULTS Among 258 SARI patients, 47% were females, 51% were white, non-Hispanic and 39% were Hispanic. The median age was 63 years (range, 19 to 97 years) and 80% had one or more pre-existing health condition; 9% died in hospital. Mortality increased to 12% (30/258, 30% increase) when electronic vital records and a 30-day post-hospitalization time frame were used. Being age ≥ 65 years (OR = 4.0; 95% CI: 1.6-9.9) and having an intensive care unit admission (OR = 7.4; 95% CI: 3.0-17.9) were independently associated with mortality. CONCLUSION The use of electronic vital records increased SARI-associated mortality estimates by 30%. These findings may help guide prevention and treatment measures, particularly in high-risk persons in this highly fluid border population.
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Affiliation(s)
- Steve R. Barnes
- Arizona Department of Health Services, Border Infectious Disease Surveillance Program, 400 West Congress, Suite 116, Tucson, AZ 85701 USA
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N Martin Ave, Tucson, AZ 85724 USA
| | - Zimy Wansaula
- Arizona Department of Health Services, Border Infectious Disease Surveillance Program, 400 West Congress, Suite 116, Tucson, AZ 85701 USA
| | - Kristen Herrick
- Arizona Department of Health Services, Office of Infectious Disease Services, 150 N 18th Ave Phoenix, Phoenix, AZ 85007 USA
| | - Eyal Oren
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N Martin Ave, Tucson, AZ 85724 USA
| | - Kacey Ernst
- Mel and Enid Zuckerman College of Public Health, University of Arizona, 1295 N Martin Ave, Tucson, AZ 85724 USA
| | - Sonja J. Olsen
- Influenza Division, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30329-4027 USA
| | - Mariana G. Casal
- Arizona Department of Health Services, Border Infectious Disease Surveillance Program, 400 West Congress, Suite 116, Tucson, AZ 85701 USA
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Piralla A, Rovida F, Girello A, Premoli M, Mojoli F, Belliato M, Braschi A, Iotti G, Pariani E, Bubba L, Zanetti AR, Baldanti F. Frequency of respiratory virus infections and next-generation analysis of influenza A/H1N1pdm09 dynamics in the lower respiratory tract of patients admitted to the ICU. PLoS One 2017; 12:e0178926. [PMID: 28591230 PMCID: PMC5462403 DOI: 10.1371/journal.pone.0178926] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/22/2017] [Indexed: 01/07/2023] Open
Abstract
Recent molecular diagnostic methods have significantly improved the diagnosis of viral pneumonia in intensive care units (ICUs). It has been observed that 222G/N changes in the HA gene of H1N1pdm09 are associated with increased lower respiratory tract (LRT) replication and worse clinical outcome. In the present study, the frequency of respiratory viruses was assessed in respiratory samples from 88 patients admitted to 16 ICUs during the 2014–2015 winter-spring season in Lombardy. Sixty-nine out of 88 (78.4%) patients were positive for a respiratory viral infection at admission. Of these, 57/69 (82.6%) were positive for influenza A (41 A/H1N1pdm09 and 15 A/H3N2), 8/69 (11.6%) for HRV, 2/69 (2.9%) for RSV and 2/69 (2.9%) for influenza B. Phylogenetic analysis of influenza A/H1N1pdm09 strains from 28/41 ICU-patients and 21 patients with mild respiratory syndrome not requiring hospitalization, showed the clear predominance of subgroup 6B strains. The median influenza A load in LRT samples of ICU patients was higher than that observed in the upper respiratory tract (URT) (p<0.05). Overall, a greater number of H1N1pdm09 virus variants were observed using next generation sequencing on partial HA sequences (codons 180–286) in clinical samples from the LRT as compared to URT. In addition, 222G/N/A mutations were observed in 30% of LRT samples from ICU patients. Finally, intra-host evolution analysis showed the presence of different dynamics of viral population in LRT of patients hospitalized in ICU with a severe influenza infection.
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Affiliation(s)
- Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Francesca Rovida
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alessia Girello
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Marta Premoli
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Francesco Mojoli
- Section of Surgery and Anesthesiology, Unit of Anesthesia, Intensive Care and Pain Therapy, Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Italy
| | - Mirko Belliato
- Department of Anesthesia and Intensive Care, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Antonio Braschi
- Section of Surgery and Anesthesiology, Unit of Anesthesia, Intensive Care and Pain Therapy, Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Italy
| | - Giorgio Iotti
- Section of Surgery and Anesthesiology, Unit of Anesthesia, Intensive Care and Pain Therapy, Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Italy
- Department of Anesthesia and Intensive Care, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Laura Bubba
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
- * E-mail: ,
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Piralla A, Mariani B, Rovida F, Baldanti F. Frequency of respiratory viruses among patients admitted to 26 Intensive Care Units in seven consecutive winter-spring seasons (2009-2016) in Northern Italy. J Clin Virol 2017; 92:48-51. [PMID: 28527970 PMCID: PMC7172430 DOI: 10.1016/j.jcv.2017.05.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/04/2017] [Accepted: 05/06/2017] [Indexed: 12/29/2022]
Abstract
Viral infections are present in large proportion of ICU-admitted patients with CAP. Influenza and rhinovirus accounted for a significant number of viral CAP episodes. The use of LRT instead of URT samples might be useful in the diagnosis of viral CAP
Background The role of respiratory viruses in the etiology of community-acquired pneumonia (CAP) is still debated. The advent of molecular assays has improved the identification of viruses in patients with CAP and according to published studies, viruses account for 11-55% of adult CAP cases. Objectives and study design In the present study, the frequency of respiratory viruses was evaluated in respiratory samples collected from 414 patients with CAP admitted to 26 ICUs in the Lombardy Region (10 million inhabitants) during seven winter-spring seasons (2009–2016). Results In 226 (54.6%) patients one or more respiratory viruses were identified, while 188 (45.4%) patients were negative. A single virus infection was observed in 214/226 (94.7%) patients; while, in 12/226 (5.3%) at least two respiratory viruses were detected. Influenza A was the most common virus in 140/226 patients (61.9%) followed by rhinoviruses (33/226, 14.6%), respiratory syncytial virus (13/226, 5.8%), influenza B virus (9/226, 4.0%), human coronaviruses (9/226, 4.0%), cytomegalovirus (9/226, 4.0%) and human metapneumovirus (1/226, 0.4%). Conclusions Viral infections are present in a consistent proportion of patients admitted to the ICU for CAP. Influenza A and rhinovirus accounted for three-quarters of all CAP in ICU patients. The use of lower respiratory instead of upper respiratory samples might be useful in the diagnosis of viral CAP.
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Affiliation(s)
- Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Bianca Mariani
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Francesca Rovida
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy.
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Fernandes-Matano L, Monroy-Muñoz IE, Angeles-Martínez J, Sarquiz-Martinez B, Palomec-Nava ID, Pardavé-Alejandre HD, Santos Coy-Arechavaleta A, Santacruz-Tinoco CE, González-Ibarra J, González-Bonilla CR, Muñoz-Medina JE. Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico. PLoS One 2017; 12:e0176298. [PMID: 28467515 PMCID: PMC5415110 DOI: 10.1371/journal.pone.0176298] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/07/2017] [Indexed: 01/10/2023] Open
Abstract
Background Acute respiratory infections are the leading cause of morbidity and mortality worldwide. Although a viral aetiological agent is estimated to be involved in up to 80% of cases, the majority of these agents have never been specifically identified. Since 2009, diagnostic and surveillance efforts for influenza virus have been applied worldwide. However, insufficient epidemiological information is available for the many other respiratory viruses that can cause Acute respiratory infections. Methods This study evaluated the presence of 14 non-influenza respiratory viruses in 872 pharyngeal exudate samples using RT-qPCR. All samples met the operational definition of a probable case of an influenza-like illness or severe acute respiratory infection and had a previous negative result for influenza by RT-qPCR. Results The presence of at least one non-influenza virus was observed in 312 samples (35.8%). The most frequent viruses were rhinovirus (RV; 33.0%), human respiratory syncytial virus (HRSV; 30.8%) and human metapneumovirus (HMPV; 10.6%). A total of 56 cases of co-infection (17.9%) caused by 2, 3, or 4 viruses were identified. Approximately 62.5% of all positive cases were in children under 9 years of age. Conclusion In this study, we identified 13 non-influenza respiratory viruses that could occur in any season of the year. This study provides evidence for the prevalence and seasonality of a wide range of respiratory viruses that circulate in Mexico and constitute a risk for the population. Additionally, our data suggest that including these tests more widely in the diagnostic algorithm for influenza may reduce the use of unnecessary antibiotics, reduce the hospitalisation time, and enrich national epidemiological data with respect to the infections caused by these viruses.
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Affiliation(s)
| | - Irma Eloísa Monroy-Muñoz
- Laboratorio de Genómica, Departamento de Genética y Genómica Humana, Instituto Nacional de Perinatología “Isidro Espinosa de los Reyes”. Ciudad de México, México
| | - Javier Angeles-Martínez
- Laboratorio de Genómica, Departamento de Biología Molecular, Instituto Nacional de Cardiología “Ignacio Chávez”. Ciudad de México, México
| | - Brenda Sarquiz-Martinez
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Iliana Donají Palomec-Nava
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Hector Daniel Pardavé-Alejandre
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Andrea Santos Coy-Arechavaleta
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Clara Esperanza Santacruz-Tinoco
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Joaquín González-Ibarra
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Cesar Raúl González-Bonilla
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - José Esteban Muñoz-Medina
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
- * E-mail:
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Niang MN, Diop NS, Fall A, Kiori DE, Sarr FD, Sy S, Goudiaby D, Barry MA, Fall M, Dia N. Respiratory viruses in patients with influenza-like illness in Senegal: Focus on human respiratory adenoviruses. PLoS One 2017; 12:e0174287. [PMID: 28328944 PMCID: PMC5362214 DOI: 10.1371/journal.pone.0174287] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/06/2017] [Indexed: 12/20/2022] Open
Abstract
Background Human adenoviruses (HAdVs) are highly contagious pathogens that are associated with a wide spectrum of human illnesses involving the respiratory tract. In the present study, we investigate the epidemiologic and viral molecular features of HAdVs circulating in Senegal after 4 consecutive years of sentinel surveillance of influenza-like Illness cases. Methodology and results From January 2012 to December 2015 swabs were collected from consenting ILI outpatients. Adenoviral detection is performed by rRT-PCR with the Anyplex™ II RV16 Detection kit (Seegene) and molecular characterization was performed using a partial hexon gene sequence. 6381 samples were collected. More than half of patients (51.7%; 3297/6381) were children of ≤ 5 years. 1967 (30.8%) were positive for HAdV with 1561 (79.4%) found in co-infection with at least one another respiratory virus. The most common co-detections were with influenza viruses (53.1%; 1045/1967), rhinoviruses (30%; 591/1967), enteroviruses (18.5%; 364/1967) and RSV (13.5%; 266/1967). Children under 5 were the most infected group (62.2%; 1224/1967; p <0.05). We noted that HAdV was detected throughout the year at a high level with detection peaks of different amplitudes without any clear seasonality. Phylogenetic analysis revealed species HAdV-C in majority, species HAdV-B and one HAdV- 4 genome type. The 9 HAdV-B species like strains from Senegal grouped with genome types HAdV-7, HAdV-55 and HAdV-11 as shown by a phylogenetic branch with a high bootstrap value of (88%). Conclusion In conclusion, the results of the present study suggest strong year-round HAdV activity in Senegal, especially in children up to 5 years of age. Molecular studies revealed that the dominant species in circulation in patients with ILI appears to be HAdV-C and HAdV-B species. The circulation of though HAdV-7 and HAdV-55 genome types is of note as these serotypes are recognized causes of more severe and even fatal acute respiratory infections.
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Affiliation(s)
| | - Ndeye Sokhna Diop
- Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal
| | - Amary Fall
- Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal
| | - Davy E. Kiori
- Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal
| | - Fatoumata Diene Sarr
- Institut Pasteur de Dakar, Unité d’Epidémiologie des maladies infectieuses, Dakar, Sénégal
| | - Sara Sy
- Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal
| | - Déborah Goudiaby
- Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal
| | - Mamadou Aliou Barry
- Institut Pasteur de Dakar, Unité d’Epidémiologie des maladies infectieuses, Dakar, Sénégal
| | - Malick Fall
- Département de Biologie Animale Faculté des Sciences et Techniques Université Cheikh Anta DIOP de Dakar, Dakar, Senegal
| | - Ndongo Dia
- Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, Sénégal
- * E-mail:
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Wansaula Z, Olsen SJ, Casal MG, Golenko C, Erhart LM, Kammerer P, Whitfield N, McCotter OZ. Surveillance for severe acute respiratory infections in Southern Arizona, 2010-2014. Influenza Other Respir Viruses 2016; 10:161-9. [PMID: 26590069 PMCID: PMC4814863 DOI: 10.1111/irv.12360] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2015] [Indexed: 11/28/2022] Open
Abstract
Background The Binational Border Infectious Disease Surveillance program began surveillance for severe acute respiratory infections (SARI) on the US–Mexico border in 2009. Here, we describe patients in Southern Arizona. Methods Patients admitted to five acute care hospitals that met the SARI case definition (temperature ≥37·8°C or reported fever or chills with history of cough, sore throat, or shortness of breath in a hospitalized person) were enrolled. Staff completed a standard form and collected a nasopharyngeal swab which was tested for selected respiratory viruses by reverse transcription polymerase chain reaction. Results From October 2010–September 2014, we enrolled 332 SARI patients. Fifty‐two percent were male and 48% were white non‐Hispanic. The median age was 63 years (47% ≥65 years and 5·2% <5 years). During hospitalization, 51 of 230 (22%) patients required intubation, 120 of 297 (40%) were admitted to intensive care unit, and 28 of 278 (10%) died. Influenza vaccination was 56%. Of 309 cases tested, 49 (16%) were positive for influenza viruses, 25 (8·1%) for human metapneumovirus, 20 (6·5%) for parainfluenza viruses, 16 (5·2%) for coronavirus, 11 (3·6%) for respiratory syncytial virus, 10 (3·2%) for rhinovirus, 4 (1·3%) for rhinovirus/enterovirus, 3 (1·0%) for enteroviruses, and 3 (1·0%) for adenovirus. Among the 49 influenza‐positive specimens, 76% were influenza A (19 H3N2, 17 H1N1pdm09, and 1 not subtyped), and 24% were influenza B. Conclusion Influenza viruses were a frequent cause of SARI in hospitalized patients in Southern Arizona. Monitoring respiratory illness in border populations will help better understand the etiologies. Improving influenza vaccination coverage may help prevent some SARI cases.
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Affiliation(s)
- Zimy Wansaula
- Arizona Department of Health Services, Office of Border Health, Tucson, AZ, USA
| | - Sonja J Olsen
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mariana G Casal
- Arizona Department of Health Services, Office of Border Health, Tucson, AZ, USA
| | - Catherine Golenko
- Arizona Department of Health Services, Office of Infectious Disease Services, Phoenix, AZ, USA
| | - Laura M Erhart
- Arizona Department of Health Services, Office of Infectious Disease Services, Phoenix, AZ, USA
| | | | - Natalie Whitfield
- Clinical and Molecular Microbiology, University of Arizona, Tucson, AZ, USA
| | - Orion Z McCotter
- Arizona Department of Health Services, Office of Border Health, Tucson, AZ, USA.,Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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