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Altawalah H, Alfouzan W, Al-Fadalah T, Zalzala MA, Ezzikouri S. Viral etiology of severe lower respiratory tract infections in SARS-CoV-2 negative hospitalized patients during the COVID-19 pandemic in Kuwait. Heliyon 2024; 10:e29855. [PMID: 38681623 PMCID: PMC11046192 DOI: 10.1016/j.heliyon.2024.e29855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Background The prevalence of respiratory infections is largely underexplored in Kuwait. The aim of our study is to determine the etiology of infections from patients who are SARS-CoV-2 negative hospitalized with severe lower respiratory tract infections (LRTIs) in Kuwait during the coronavirus disease 2019 (COVID-19) pandemic. Methods We conducted an observational cross-sectional study among severe LRTI patients between September 2021 and March 2022. Respiratory samples from 545 non-COVID-19 severe LRTIs patients were prospectively evaluated with FTD Respiratory 21 Plus® real-time PCR, targeting 20 different viruses and 1 atypical bacterial pathogen. Results Among all 545 hospitalized cases, 411 (75.4 %) tested positive for at least one respiratory pathogen. The most common were rhinovirus (HRV) (32.7 %), respiratory syncytial virus (RSV) (20.9 %), metapneumovirus (HMPV) (14.1 %), bocavirus (13.2 %), and influenza A (12.7 %). The proportion of pathogens detected was highest in the under-5 age group, while HKU1 (44.4 %) predominated in the elderly (>50 years). Conclusion Our study reveals a high prevalence of respiratory viruses in severe acute lower respiratory tract infections among non-COVID-19 hospitalized patients in Kuwait. HRV remains the main etiology affecting the country, particularly in infants. These results underscore the necessity of employing multiplex PCR for accurate diagnosis and describing the epidemiology of infections among severe lower respiratory tract infections. This will facilitate the use of specific antiviral therapy and help avoid excessive or inappropriate antibiotic therapy.
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Affiliation(s)
- Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
- Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait, Kuwait
| | - Wadha Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
- Laboratory Medicine, Farwania Hospital, Ministry of Health, Farwania, Kuwait
| | - Talal Al-Fadalah
- Qualities and Accreditation Directorate, Ministry of Health, Kuwait, Kuwait
| | - Mariam Ali Zalzala
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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Wang S, Wang XF, Li N, Zhang YX, Chen J, Wang GM. [Distribution of non-bacterial pathogens in 1 788 children with community-acquired pneumonia]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2023; 25:633-638. [PMID: 37382134 DOI: 10.7499/j.issn.1008-8830.2212079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
OBJECTIVES To investigate the distribution characteristics of non-bacterial pathogens in community-acquired pneumonia (CAP) in children. METHODS A total of 1 788 CAP children admitted to Shenyang Children's Hospital from December 2021 to November 2022 were selected. Multiple RT-PCR and capillary electrophoresis were used to detect 10 viral pathogens and 2 atypical pathogens, and serum antibodies of Chlamydial pneumoniae (Ch) and Mycoplasma pneumoniae (MP) were detected. The distribution characteristics of different pathogens were analyzed. RESULTS Among the 1 788 CAP children, 1 295 children were pathogen-positive, with a positive rate of 72.43% (1 295/1 788), including a viral pathogen positive rate of 59.68% (1 067/1 788) and an atypical pathogen positive rate of 22.04% (394/1 788). The positive rates from high to low were MP, respiratory syncytial virus (RSV), influenza B virus (IVB), human metapneumovirus (HMPV), human rhinovirus (HRV), human parainfluenza virus (HPIV), influenza A virus (IVA), bocavirus (BoV), human adenovirus (HADV), Ch, and human coronavirus (HCOV). RSV and MP were the main pathogens in spring; MP had the highest positive rate in summer, followed by IVA; HMPV had the highest positive rate in autumn; IVB and RSV were the main pathogens in winter. The positive rate of MP in girls was higher than that in boys (P<0.05), and there were no significant differences in other pathogens between genders (P>0.05). The positivity rates of certain pathogens differed among age groups (P<0.05): the positivity rate of MP was highest in the >6 year-old group; the positivity rates of RSV and Ch were highest in the <1 year-old group; the positivity rates of HPIV and IVB were highest in the 1 to <3 year-old group. RSV, MP, HRV, and HMPV were the main pathogens in children with severe pneumonia, while MP was the primary pathogen in children with lobar pneumonia, and MP, IVB, HMPV, RSV, and HRV were the top 5 pathogens in acute bronchopneumonia. CONCLUSIONS MP, RSV, IVB, HMPV, and HRV are the main pathogens of CAP in children, and there are certain differences in the positive rates of respiratory pathogens among children of different ages, genders, and seasons.
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Affiliation(s)
- Shuang Wang
- Department of Pediatrics, Affiliated Hospital, Liaoning University of Traditional Chinese Medicine, Shenyang 110032, China
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Regassa BT, Gebrewold LA, Mekuria WT, Kassa NA. Molecular epidemiology of respiratory syncytial virus in children with acute respiratory illnesses in Africa: A systematic review and meta-analysis. J Glob Health 2023; 13:04001. [PMID: 36637855 PMCID: PMC9840062 DOI: 10.7189/jogh.13.04001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Background Globally, the respiratory syncytial virus (RSV) is the most common etiologic agent of acute respiratory illnesses in children. However, its burden has not been well addressed in developing countries. We aimed to estimate the molecular epidemiology of RSV in children less than 18 years of age with acute respiratory infections in Africa by conducting a systematic review and meta-analysis. Methods We systematically searched PubMed, Scopus, CINAHL, and Global Index Medicus databases to identify studies published from January 1, 2002, to April 27, 2022, following the PRISMA 2020 guideline. We assessed the study quality using the Joanna Brigg's Institute (JBI) critical appraisal checklists. We conducted a qualitative synthesis by describing the characteristics of included studies and performed the quantitative synthesis with random effects model using STATA-14. We checked for heterogeneity with Q statistics, quantified by I2, and determined the prediction interval. We performed subgroup analyses to explain the sources of heterogeneity and assessed publication biases by funnel plots augmented with Egger's test. Results Eighty-eight studies with 105 139 participants were included in the review. The overall pooled prevalence of RSV in children <18 years of age was 23% (95% confidence interval (CI) = 20, 25%). Considerable heterogeneity was present across the included studies. The adjusted prediction interval was found to be 19%-27%. Heterogeneities were explained by subgroups analyses. The highest prevalence of RSV was found among inpatients, 28% (95% CI = 25, 31%) compared with inpatients/outpatients and outpatients, with statistically significant differences (P < 0.01). The RSV estimate was also highest among those with acute lower respiratory tract illnesses (ALRTIs), 28% (95% CI = 25, 31%) compared with acute upper respiratory tract illnesses (AURTIs) and both acute upper/lower respiratory manifestations, with statistically different prevalence (P < 0.01). RSV infection estimates in each sub-region of Africa were statistically different (P < 0.01). There were no statistically significant differences in RSV infections by designs, specimen types, and specimen conditions, despite them contributing to heterogeneity. Conclusions We found a high prevalence of RSV in pediatric populations with acute respiratory tract illnesses in Africa, highlighting that the prevention and control of RSV infections in children deserve more attention. Registration PROSPERO CRD42022327054.
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Affiliation(s)
- Belay Tafa Regassa
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Ambo University, Ethiopia
| | - Lami Abebe Gebrewold
- Department of Public Health, College of Medicine and Health Sciences, Ambo University, Ethiopia
| | - Wagi Tosisa Mekuria
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Ambo University, Ethiopia
| | - Nega Assefa Kassa
- School of Public Health, College of Health and Medical Sciences, Haramaya University, Ethiopia
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Razanajatovo NH, Randriambolamanantsoa TH, Rabarison JH, Randrianasolo L, Ankasitrahana MF, Ratsimbazafy A, Raherinandrasana AH, Razafimanjato H, Raharinosy V, Andriamandimby SF, Heraud JM, Dussart P, Lacoste V. Epidemiological Patterns of Seasonal Respiratory Viruses during the COVID-19 Pandemic in Madagascar, March 2020-May 2022. Viruses 2022; 15:12. [PMID: 36680053 PMCID: PMC9864023 DOI: 10.3390/v15010012] [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: 11/09/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Three epidemic waves of coronavirus disease-19 (COVID-19) occurred in Madagascar from March 2020 to May 2022, with a positivity rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) of 21% to 33%. Our study aimed to identify the impact of COVID-19 on the epidemiology of seasonal respiratory viruses (RVs) in Madagascar. We used two different specimen sources (SpS). First, 2987 nasopharyngeal (NP) specimens were randomly selected from symptomatic patients between March 2020 and May 2022 who tested negative for SARS-CoV-2 and were tested for 14 RVs by multiplex real-time PCR. Second, 6297 NP specimens were collected between March 2020 and May 2022 from patients visiting our sentinel sites of the influenza sentinel network. The samples were tested for influenza, respiratory syncytial virus (RSV), and SARS-CoV-2. From SpS-1, 19% (569/2987) of samples tested positive for at least one RV. Rhinovirus (6.3%, 187/2987) was the most frequently detected virus during the first two waves, whereas influenza predominated during the third. From SpS-2, influenza, SARS-CoV-2, and RSV accounted for 5.4%, 24.5%, and 39.4% of the detected viruses, respectively. During the study period, we observed three different RV circulation profiles. Certain viruses circulated sporadically, with increased activity in between waves of SARS-CoV-2. Other viruses continued to circulate regardless of the COVID-19 situation. Certain viruses were severely disrupted by the spread of SARS-CoV-2. Our findings underline the importance and necessity of maintaining an integrated disease surveillance system for the surveillance and monitoring of RVs of public health interest.
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Affiliation(s)
| | | | | | - Laurence Randrianasolo
- Epidemiology and Clinical Research Unit, Institut Pasteur of Madagascar, Antananarivo 101, Madagascar
| | - Miamina Fidy Ankasitrahana
- Direction de la Veille Sanitaire, de la Surveillance Epidémiologique et Ripostes, Ministry of Public Health, Antananarivo 101, Madagascar
| | - Arvé Ratsimbazafy
- National Influenza Center, Virology Unit, Institut Pasteur of Madagascar, Antananarivo 101, Madagascar
| | - Antso Hasina Raherinandrasana
- Direction de la Veille Sanitaire, de la Surveillance Epidémiologique et Ripostes, Ministry of Public Health, Antananarivo 101, Madagascar
| | - Helisoa Razafimanjato
- National Influenza Center, Virology Unit, Institut Pasteur of Madagascar, Antananarivo 101, Madagascar
| | - Vololoniaina Raharinosy
- National Influenza Center, Virology Unit, Institut Pasteur of Madagascar, Antananarivo 101, Madagascar
| | - Soa Fy Andriamandimby
- National Influenza Center, Virology Unit, Institut Pasteur of Madagascar, Antananarivo 101, Madagascar
| | | | - Philippe Dussart
- National Influenza Center, Virology Unit, Institut Pasteur of Madagascar, Antananarivo 101, Madagascar
| | - Vincent Lacoste
- National Influenza Center, Virology Unit, Institut Pasteur of Madagascar, Antananarivo 101, Madagascar
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Garbern SC, Relan P, O’Reilly GM, Bills CB, Schultz M, Trehan I, Kivlehan SM, Becker TK. A systematic review of acute and emergency care interventions for adolescents and adults with severe acute respiratory infections including COVID-19 in low- and middle-income countries. J Glob Health 2022; 12:05039. [DOI: 10.7189/jogh.12.05039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Stephanie Chow Garbern
- Department of Emergency Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Pryanka Relan
- Department of Emergency Medicine, Emory Healthcare Network, Atlanta, Georgia, USA
| | - Gerard M O’Reilly
- Emergency and Trauma Centre, The Alfred, Melbourne, Australia
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Corey B Bills
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Megan Schultz
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Indi Trehan
- Departments of Pediatrics, Global Health, and Epidemiology, University of Washington, Seattle, Washington, USA
| | - Sean M Kivlehan
- Department of Emergency Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Humanitarian Initiative, Cambridge, Massachusetts, USA
| | - Torben K Becker
- Department of Emergency Medicine, University of Florida, Gainesville, Florida, USA
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6
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von Mollendorf C, Berger D, Gwee A, Duke T, Graham SM, Russell FM, Mulholland EK. Aetiology of childhood pneumonia in low- and middle-income countries in the era of vaccination: a systematic review. J Glob Health 2022; 12:10009. [PMID: 35866332 PMCID: PMC9305023 DOI: 10.7189/jogh.12.10009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background This systematic review aimed to describe common aetiologies of severe and non-severe community acquired pneumonia among children aged 1 month to 9 years in low- and middle-income countries. Methods We searched the MEDLINE, EMBASE, and PubMed online databases for studies published from January 2010 to August 30, 2020. We included studies on acute community-acquired pneumonia or acute lower respiratory tract infection with ≥1 year of continuous data collection; clear consistent case definition for pneumonia; >1 specimen type (except empyema studies where only pleural fluid was required); testing for >1 pathogen including both viruses and bacteria. Two researchers reviewed the studies independently. Results were presented as a narrative summary. Quality of evidence was assessed with the Quality Assessment Tool for Quantitative Studies. The study was registered on PROSPERO [CRD42020206830]. Results We screened 5184 records; 1305 duplicates were removed. The remaining 3879 titles and abstracts were screened. Of these, 557 articles were identified for full-text review, and 55 met the inclusion criteria - 10 case-control studies, three post-mortem studies, 11 surveillance studies, eight cohort studies, five cross-sectional studies, 12 studies with another design and six studies that included patients with pleural effusions or empyema. Studies which described disease by severity showed higher bacterial detection (Streptococcus pneumoniae, Staphylococcus aureus) in severe vs non-severe cases. The most common virus causing severe disease was respiratory syncytial virus (RSV). Pathogens varied by age, with RSV and adenovirus more common in younger children. Influenza and atypical bacteria were more common in children 5-14 years than younger children. Malnourished and HIV-infected children had higher rates of pneumonia due to bacteria or tuberculosis. Conclusions Several viral and bacterial pathogens were identified as important targets for prevention and treatment. Bacterial pathogens remain an important cause of moderate to severe disease, particularly in children with comorbidities despite widespread PCV and Hib vaccination.
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Affiliation(s)
- Claire von Mollendorf
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Daria Berger
- Royal Children's Hospital, Parkville, Victoria, Australia
| | - Amanda Gwee
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Royal Children's Hospital, Parkville, Victoria, Australia
| | - Trevor Duke
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Royal Children's Hospital, Parkville, Victoria, Australia
| | - Stephen M Graham
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Royal Children's Hospital, Parkville, Victoria, Australia
| | - Fiona M Russell
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - E Kim Mulholland
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
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Epidemiology and Molecular Analyses of Influenza B Viruses in Senegal from 2010 to 2019. Viruses 2022; 14:v14051063. [PMID: 35632804 PMCID: PMC9143141 DOI: 10.3390/v14051063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/04/2023] Open
Abstract
Influenza virus types A and B are responsible for acute viral infections that affect annually 1 billion people, with 290,000 to 650,000 deaths worldwide. In this study, we investigated the circulation of influenza B viruses over a 10-year period (2010–2019). Specimens from patients suspected of influenza infection were collected. Influenza detection was performed following RNA extraction and real-time RT-PCR. Genes coding for hemagglutinin (HA) and neuraminidase (NA) of influenza B viruses were partially sequenced, and phylogenetic analyses were carried out subsequently. During the study period, we received and tested a total of 15,156 specimens. Influenza B virus was detected in 1322 (8.7%) specimens. The mean age of influenza B positive patients was 10.9 years. When compared to reference viruses, HA genes from Senegalese circulating viruses showed deletions in the HA1 region. Phylogenetic analysis highlighted the co-circulation of B/Victoria and B/Yamagata lineage viruses with reassortant viruses. We also noted a clear seasonal pattern of circulation of influenza B viruses in Senegal.
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de Mangou A, Combe A, Coolen-Allou N, Miltgen G, Traversier N, Belmonte O, Vandroux D, Bohrer M, Cousty J, Caron M, Vidal C, Allyn J, Allou N. Severe community-acquired pneumonia in Reunion Island: Epidemiological, clinical, and microbiological characteristics, 2016–2018. PLoS One 2022; 17:e0267184. [PMID: 35427402 PMCID: PMC9012352 DOI: 10.1371/journal.pone.0267184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/04/2022] [Indexed: 12/17/2022] Open
Abstract
Purpose No data are available on severe community-acquired pneumonia (CAP) in the French overseas department of Reunion Island. This is unfortunate as the microorganisms responsible for the disease are likely to differ from those in temperate regions due to a tropical climate and proximity to other islands of the Indian Ocean region. The aim of this study was to assess the epidemiological, clinical, prognosis, and microbiological characteristics of patients with severe CAP in Reunion Island. Materials and methods This retrospective study evaluated all patients with CAP aged >18 years and hospitalized in one of the two intensive care units of Reunion Island between 2016 and 2018. Microorganisms were identified by culture from blood and respiratory samples, multiplex polymerase chain reaction from respiratory samples, urinary antigen tests, and serology. Results Over the study period, 573 cases of severe CAP were recorded, with a mean incidence of 22 per 100,000 person-years. The most frequently isolated microorganism was influenza (21.9%) followed by Streptococcus pneumoniae (12%). The influenza virus was detected in affected patients all year round. Twenty-four patients with severe CAP came from another island of the Indian Ocean region (4.2%), mainly Madagascar (>50%). Two of these patients presented with melioidosis and 4 were infected with Acinetobacter spp. Conclusions Our findings have major implications for the management of severe CAP in tropical regions. The most frequently isolated microorganism in patients with severe CAP in Reunion Island is influenza followed by S. pneumoniae. Physicians should be aware that influenza is the main cause of severe CAP in patients living in or returning from Reunion Island, where this virus circulates all year round.
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Affiliation(s)
- Axel de Mangou
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Agathe Combe
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Nathalie Coolen-Allou
- Respiratory Disease, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Guillaume Miltgen
- Microbiology, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
- UMR Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM U1187, IRD 249, Université de la Réunion, Saint-Denis, France
| | - Nicolas Traversier
- Microbiology, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Olivier Belmonte
- Microbiology, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - David Vandroux
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Michel Bohrer
- Department of Medical Information, Saint-Denis University Hospital, Saint-Denis, Reunion Island, France
| | - Julien Cousty
- Intensive Care Unit, Centre Hospitalier Universitaire Sud Réunion, Saint-Pierre, France
| | - Margot Caron
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Charles Vidal
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Jérôme Allyn
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
- Clinical Informatic Department, Saint-Denis University Hospital, Saint-Denis, Reunion Island, France
| | - Nicolas Allou
- Intensive Care Unit, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
- Clinical Informatic Department, Saint-Denis University Hospital, Saint-Denis, Reunion Island, France
- * E-mail:
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Assessment of surveillance predictors for suspected respiratory syncytial virus, influenza and Streptococcus pneumoniae infections in children aged <5 years in Madagascar. IJID REGIONS 2022; 2:82-89. [PMID: 35757077 PMCID: PMC9216384 DOI: 10.1016/j.ijregi.2021.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/26/2021] [Accepted: 12/08/2021] [Indexed: 11/20/2022]
Abstract
A sensitive surveillance case definition can be defined based on specific symptoms. Intercostal recession and dyspnoea may be used to identify children with respiratory syncytial virus (RSV) infection. Fever was not necessarily a good predictor of paediatric RSV infection. Headache may be used to identify influenza infection in children. Sweats and productive cough may define infection due to Streptococcus pneumoniae in children.
Background The lack of rapid, sensitive and affordable diagnostic tests that can distinguish a wide variety of respiratory pathogens at the point of care is an obstacle to the rapid implementation of control measures following events and epidemics. In addition, the absence of a standardized case definition to differentiate putative aetiologies is a challenge to assessing the burden of disease. This study aimed to identify the clinical spectrum of respiratory pathogens commonly associated with respiratory tract infections in the context of disease surveillance. Methods Data obtained from prospective hospital-based severe acute respiratory infection surveillance among children aged <5 years from November 2010 to July 2013 were used in this study. Results Intercostal recession and dyspnoea were predictive of respiratory syncytial virus (RSV) infection, whereas headache and chills were more often observed during influenza A infection. Male patients were at a higher risk for RSV infection than female patients. Productive cough, chills, sweating and weight loss were significantly associated with Streptococcus pneumoniae infection. The presence of fever did not necessarily indicate RSV infection. Conclusions Combined with other examinations, this study shows the value of including the syndromic approach in the panel of diagnostic criteria for rapid identification of the risk of infectious diseases in areas where laboratory diagnostics are challenging. Given the current situation with coronavirus disease 2019, this approach may help decision makers to implement appropriate control measures.
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Kettenburg G, Kistler A, Ranaivoson HC, Ahyong V, Andrianiaina A, Andry S, DeRisi JL, Gentles A, Raharinosy V, Randriambolamanantsoa TH, Ravelomanantsoa NAF, Tato CM, Dussart P, Heraud JM, Brook CE. Full Genome Nobecovirus Sequences From Malagasy Fruit Bats Define a Unique Evolutionary History for This Coronavirus Clade. Front Public Health 2022; 10:786060. [PMID: 35223729 PMCID: PMC8873168 DOI: 10.3389/fpubh.2022.786060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/17/2022] [Indexed: 12/02/2022] Open
Abstract
Bats are natural reservoirs for both Alpha- and Betacoronaviruses and the hypothesized original hosts of five of seven known zoonotic coronaviruses. To date, the vast majority of bat coronavirus research has been concentrated in Asia, though coronaviruses are globally distributed; indeed, SARS-CoV and SARS-CoV-2-related Betacoronaviruses in the subgenus Sarbecovirus have been identified circulating in Rhinolophid bats in both Africa and Europe, despite the relative dearth of surveillance in these regions. As part of a long-term study examining the dynamics of potentially zoonotic viruses in three species of endemic Madagascar fruit bat (Pteropus rufus, Eidolon dupreanum, Rousettus madagascariensis), we carried out metagenomic Next Generation Sequencing (mNGS) on urine, throat, and fecal samples obtained from wild-caught individuals. We report detection of RNA derived from Betacoronavirus subgenus Nobecovirus in fecal samples from all three species and describe full genome sequences of novel Nobecoviruses in P. rufus and R. madagascariensis. Phylogenetic analysis indicates the existence of five distinct Nobecovirus clades, one of which is defined by the highly divergent ancestral sequence reported here from P. rufus bats. Madagascar Nobecoviruses derived from P. rufus and R. madagascariensis demonstrate, respectively, Asian and African phylogeographic origins, mirroring those of their fruit bat hosts. Bootscan recombination analysis indicates significant selection has taken place in the spike, nucleocapsid, and NS7 accessory protein regions of the genome for viruses derived from both bat hosts. Madagascar offers a unique phylogeographic nexus of bats and viruses with both Asian and African phylogeographic origins, providing opportunities for unprecedented mixing of viral groups and, potentially, recombination. As fruit bats are handled and consumed widely across Madagascar for subsistence, understanding the landscape of potentially zoonotic coronavirus circulation is essential for mitigation of future zoonotic threats.
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Affiliation(s)
- Gwenddolen Kettenburg
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Hafaliana Christian Ranaivoson
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Angelo Andrianiaina
- Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Santino Andry
- Department of Entomology, University of Antananarivo, Antananarivo, Madagascar
| | | | - Anecia Gentles
- Odum School of Ecology, University of Georgia, Athens, GA, United States
| | | | | | | | | | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jean-Michel Heraud
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cara E. Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
- *Correspondence: Cara E. Brook
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Tempia S, Moyes J, Cohen AL, Walaza S, McMorrow ML, Treurnicht FK, Hellferscee O, Wolter N, von Gottberg A, Dawood H, Variava E, Cohen C. The national burden of influenza-like illness and severe respiratory illness overall and associated with nine respiratory viruses in South Africa, 2013-2015. Influenza Other Respir Viruses 2022; 16:438-451. [PMID: 35150059 PMCID: PMC8983907 DOI: 10.1111/irv.12949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Estimates of the disease burden associated with different respiratory viruses are severely limited in low- and middle-income countries, especially in Africa. METHODS We estimated age-specific numbers and rates of medically and non-medically attended influenza-like illness (ILI) and severe respiratory illness (SRI) that were associated with influenza, respiratory syncytial virus (RSV), rhinovirus, human metapneumovirus, adenovirus, enterovirus and parainfluenza virus types 1-3 after adjusting for the attributable fraction (AF) of virus detection to illness in South Africa during 2013-2015. The base rates were estimated from five surveillance sites and extrapolated nationally. RESULTS The mean annual rates per 100,000 population were 51,383 and 4196 for ILI and SRI, respectively. Of these, 26% (for ILI) and 46% (for SRI) were medically attended. Among outpatients with ILI, rhinovirus had the highest AF-adjusted rate (7221), followed by influenza (6443) and adenovirus (1364); whereas, among inpatients with SRI, rhinovirus had the highest AF-adjusted rate (400), followed by RSV (247) and influenza (130). Rhinovirus (9424) and RSV (2026) had the highest AF-adjusted rates among children aged <5 years with ILI or SRI, respectively, whereas rhinovirus (757) and influenza (306) had the highest AF-adjusted rates among individuals aged ≥65 years with ILI or SRI, respectively. CONCLUSIONS There was a substantial burden of ILI and SRI in South Africa during 2013-2015. Rhinovirus and influenza had a prominent disease burden among patients with ILI. RSV and influenza were the most prominent causes of SRI in children and the elderly, respectively.
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Affiliation(s)
- Stefano Tempia
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa.,Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,MassGenics, Duluth, GA, USA.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adam L Cohen
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.,Global Immunization Monitoring and Surveillance Team, Expanded Programme on Immunization, Department of Immunization, Vaccines and Biological, World Health Organization, Geneva, Switzerland
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Florette K Treurnicht
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Division of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Orienka Hellferscee
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Halima Dawood
- Department of Medicine, Pietermaritzburg Metropolitan Hospital, Pietermaritzburg, South Africa.,Department of Medicine, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Ebrahim Variava
- Department of Medicine, Klerksdorp-Tshepong Hospital Complex, Klerksdorp, South Africa.,Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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12
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Van Goethem N, Robert A, Bossuyt N, Van Poelvoorde LAE, Quoilin S, De Keersmaecker SCJ, Devleesschauwer B, Thomas I, Vanneste K, Roosens NHC, Van Oyen H. Evaluation of the added value of viral genomic information for predicting severity of influenza infection. BMC Infect Dis 2021; 21:785. [PMID: 34376182 PMCID: PMC8353062 DOI: 10.1186/s12879-021-06510-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/18/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The severity of an influenza infection is influenced by both host and viral characteristics. This study aims to assess the relevance of viral genomic data for the prediction of severe influenza A(H3N2) infections among patients hospitalized for severe acute respiratory infection (SARI), in view of risk assessment and patient management. METHODS 160 A(H3N2) influenza positive samples from the 2016-2017 season originating from the Belgian SARI surveillance were selected for whole genome sequencing. Predictor variables for severity were selected using a penalized elastic net logistic regression model from a combined host and genomic dataset, including patient information and nucleotide mutations identified in the viral genome. The goodness-of-fit of the model combining host and genomic data was compared using a likelihood-ratio test with the model including host data only. Internal validation of model discrimination was conducted by calculating the optimism-adjusted area under the Receiver Operating Characteristic curve (AUC) for both models. RESULTS The model including viral mutations in addition to the host characteristics had an improved fit ([Formula: see text]=12.03, df = 3, p = 0.007). The optimism-adjusted AUC increased from 0.671 to 0.732. CONCLUSIONS Adding genomic data (selected season-specific mutations in the viral genome) to the model containing host characteristics improved the prediction of severe influenza infection among hospitalized SARI patients, thereby offering the potential for translation into a prospective strategy to perform early season risk assessment or to guide individual patient management.
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Affiliation(s)
- Nina Van Goethem
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium.
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200, Woluwe-Saint-Lambert, Belgium.
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Clos Chapelle-aux-champs 30, 1200, Woluwe-Saint-Lambert, Belgium
| | - Nathalie Bossuyt
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Laura A E Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Sophie Quoilin
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | | | - Brecht Devleesschauwer
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Department of Veterinary Public Health and Food Safety, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Isabelle Thomas
- National Reference Center Influenza, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Herman Van Oyen
- Scientific Directorate of Epidemiology and Public Health, Sciensano, J. Wytsmanstraat 14, 1050, Brussels, Belgium
- Department of Public Health and Primary Care, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
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13
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Randremanana RV, Andriamandimby S, Rakotondramanga JM, Razanajatovo NH, Mangahasimbola RT, Randriambolamanantsoa TH, Ranaivoson HC, Rabemananjara HA, Razanajatovo I, Razafindratsimandresy R, Rabarison JH, Brook CE, Rakotomanana F, Rabetombosoa RM, Razafimanjato H, Ahyong V, Raharinosy V, Raharimanga V, Raharinantoanina SJ, Randrianarisoa MM, Bernardson B, Randrianasolo L, Randriamampionona LBN, Tato CM, DeRisi JL, Dussart P, Vololoniaina MC, Randriatsarafara FM, Randriamanantany ZA, Heraud J. The COVID-19 epidemic in Madagascar: clinical description and laboratory results of the first wave, march-september 2020. Influenza Other Respir Viruses 2021; 15:457-468. [PMID: 33586912 PMCID: PMC8013501 DOI: 10.1111/irv.12845] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Following the first detection of SARS-CoV-2 in passengers arriving from Europe on 19 March 2020, Madagascar took several mitigation measures to limit the spread of the virus in the country. METHODS Nasopharyngeal and/or oropharyngeal swabs were collected from travellers to Madagascar, suspected SARS-CoV-2 cases and contact of confirmed cases. Swabs were tested at the national reference laboratory using real-time RT-PCR. Data collected from patients were entered in an electronic database for subsequent statistical analysis. All distribution of laboratory-confirmed cases were mapped, and six genomes of viruses were fully sequenced. RESULTS Overall, 26,415 individuals were tested for SARS-CoV-2 between 18 March and 18 September 2020, of whom 21.0% (5,553/26,145) returned positive. Among laboratory-confirmed SARS-CoV-2-positive patients, the median age was 39 years (IQR: 28-52), and 56.6% (3,311/5,553) were asymptomatic at the time of sampling. The probability of testing positive increased with age with the highest adjusted odds ratio of 2.2 [95% CI: 1.9-2.5] for individuals aged 49 years and more. Viral strains sequenced belong to clades 19A, 20A and 20B indicative of several independent introduction of viruses. CONCLUSIONS Our study describes the first wave of the COVID-19 in Madagascar. Despite early strategies in place Madagascar could not avoid the introduction and spread of the virus. More studies are needed to estimate the true burden of disease and make public health recommendations for a better preparation to another wave.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Fanjasoa Rakotomanana
- Epidemiology and Clinical Research UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
| | | | | | | | | | - Vaomalala Raharimanga
- Epidemiology and Clinical Research UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
| | | | | | - Barivola Bernardson
- Epidemiology and Clinical Research UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
| | - Laurence Randrianasolo
- Epidemiology and Clinical Research UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
| | | | | | | | - Philippe Dussart
- Virology UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
| | | | | | | | - Jean‐Michel Heraud
- Virology UnitInstitut Pasteur de MadagascarAntananarivoMadagascar
- Present address:
Virology DepartmentInstitut Pasteur de DakarDakarSenegal
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14
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Chanie MG, Melaku MS, Yalew M, Arefaynie M, Bitew G, Amsalu ET, Kefale B, Muche A, Fentaw Z, Dewau R, Adane B, Damtie Y, Ayele WM, Ewunetie GE, Adane M. Predictors of community acquired childhood pneumonia among 2-59 months old children in the Amhara Region, Ethiopia. BMC Pulm Med 2021; 21:179. [PMID: 34034726 PMCID: PMC8152354 DOI: 10.1186/s12890-021-01548-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
Background Worldwide, pneumonia is the third leading cause of death in under 5 years children. Ethiopia is ranked 4th out of 15 countries having the highest burdens of the death rate among under-five children due to pneumonia. Regardless of this fact, efforts to identify determinants of pneumonia have been limited yet in Amhara region. This study was aimed to identify predictors of community-acquired childhood pneumonia among 2–59 months old children in the Amhara region, Ethiopia. Methods Facility-based case–control study was conducted in the Amhara region from June 4 to July 15, 2018, among 28 health centers distributed across the region. The total sample size used was 888 (296 cases and 592 controls) children whose age were 2–59 months. At first, multistage sampling technique was employed. Data were collected on a face-to-face interview. Epi data v. 4.6 for data entry and statistical packages for social sciences version 23 for data analysis were used. Multivariable logistic regression analyses were used to test the associations between the study variables at P-value < 0.05 with 95% CI. As a result, determinants were identified for CAP. Results Among 888 enrolled children (296 cases and 592 controls), who experienced a community-acquired pneumonia had an increased risk of maternal age of 18–24 years (AOR 0.03, at 95%CI (0.01, 0.14), Government employee (AOR 0.19, at 95% CI (0.07,0.54), lack of separate kitchen (AOR 5.37; at 95% CI (1.65, 17.43), history of diarrhea in the past two weeks (AOR 10.2; at 95% CI (5.13, 20.18), previous respiratory tract infections (AOR 8.3, at 95% CI (3.32, 20.55) and history of parental asthma (AOR 4.9, at 95% CI (2.42, 10.18). Conclusion Maternal age of 18–24 years and government employee, lack of separate kitchen, history of diarrhea in the past two weeks; previous respiratory tract infection and history of parental asthma were found statistically significant. Health personnel’s needs to focus on creating awareness to the community on the merit of the separate kitchen for reduction of Community-acquired childhood pneumonia, and focus on prevention and management of childhood diarrheal and acute respiratory tract infections.
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Affiliation(s)
- Muluken Genetu Chanie
- Department of Health Systems and Policy, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Mequannent Sharew Melaku
- Department of Health Informatics, Institute of Public Health, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Melaku Yalew
- Department of Reproductive Health, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Mastewal Arefaynie
- Department of Reproductive Health, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Gedamnesh Bitew
- Department of Epidemiology and Biostatistics, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Erkihun Tadesse Amsalu
- Department of Epidemiology and Biostatistics, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Bereket Kefale
- Department of Reproductive Health, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Amare Muche
- Department of Epidemiology and Biostatistics, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Zinabu Fentaw
- Department of Epidemiology and Biostatistics, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia.
| | - Reta Dewau
- Department of Epidemiology and Biostatistics, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Bezawit Adane
- Department of Epidemiology and Biostatistics, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Yitayish Damtie
- Department of Reproductive Health, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Wolde Melese Ayele
- Department of Epidemiology and Biostatistics, School of Public Health, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | | | - Metadel Adane
- Department of Environmental Health Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
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15
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Epidemiology and Seasonality of Childhood Respiratory Syncytial Virus Infections in the Tropics. Viruses 2021; 13:v13040696. [PMID: 33923823 PMCID: PMC8074094 DOI: 10.3390/v13040696] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/03/2021] [Accepted: 02/19/2021] [Indexed: 12/19/2022] Open
Abstract
Infections caused by respiratory syncytial virus (RSV) are a major cause of morbidity and mortality in young children worldwide. Understanding seasonal patterns of region-specific RSV activity is important to guide resource allocation for existing and future treatment and prevention strategies. The decades of excellent RSV surveillance data that are available from the developed countries of the world are incredibly instructive in advancing public health initiatives in those regions. With few exceptions, these developed nations are positioned geographically across temperate regions of the world. RSV surveillance across tropical regions of the world has improved in recent years, but remains spotty, and where available, still lacks the necessary longitudinal data to determine the amount of seasonal variation expected over time. However, existing and emerging data collected across tropical regions of the world do indicate that patterns of infection are often quite different from those so well described in temperate areas. Here, we provide a brief summary regarding what is known about general patterns of RSV disease activity across tropical Asia, Africa and South America, then offer additional country-specific details using examples where multiple reports and/or more robust surveillance data have become available.
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16
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Li J, Song CL, Wang T, Ye YL, Du JR, Li SH, Zhu JM. Etiological and epidemiological characteristics of severe acute respiratory infection caused by multiple viruses and Mycoplasma pneumoniae in adult patients in Jinshan, Shanghai: A pilot hospital-based surveillance study. PLoS One 2021; 16:e0248750. [PMID: 33750952 PMCID: PMC7984646 DOI: 10.1371/journal.pone.0248750] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 03/04/2021] [Indexed: 12/21/2022] Open
Abstract
Background Severe acute respiratory infection (SARI) results in a tremendous disease burden worldwide. Available research on active surveillance among hospitalized adult patients suffering from SARI in China is limited. This pilot study aimed to identify associated etiologies and describe the demographic, epidemiological and clinical profiles of hospitalized SARI patients aged over 16 years in Jinshan, Shanghai. Methods Active surveillance was conducted at 1 sentinel hospital in Jinshan district, Shanghai, from April 2017 to March 2018. Hospitalized SARI patients aged over 16 years old were enrolled, and nasopharyngeal swabs were collected within 24 hours of admission and tested for multiple respiratory viruses (including 18 common viruses) and Mycoplasma pneumoniae with real-time polymerase chain reaction. Demographic, epidemiological and clinical information was obtained from case report forms. Results In total, 397 SARI patients were enrolled; the median age was 68 years, and 194 (48.9%) patients were male. A total of 278 (70.0%) patients had at least one underlying chronic medical condition. The most frequent symptoms were cough (99.2%) and sputum production (88.4%). The median duration of hospitalization was 10 days. A total of 250 infection patients (63.0%) were positive for at least one pathogen, of whom 198 (49.9%) were positive for a single pathogen and 52 (13.1%) were positive for multiple pathogens. The pathogens identified most frequently were M. pneumoniae (23.9%, 95/397), followed by adenovirus (AdV) (11.6%, 46/397), influenza virus A/H3N2 (Flu A/H3N2) (11.1%, 44/397), human rhinovirus (HRhV) (8.1%, 32/397), influenza virus B/Yamagata (Flu B/Yamagata) (6.3%, 25/397), pandemic influenza virus A/H1N1 (Flu A/pH1N1) (4.0%, 16/397), parainfluenza virus (PIV) type 1 (2.0%, 8/397), human coronavirus (HCoV) type NL63 (2.0%, 8/397), HCoV 229E (1.5%, 6/397), HCoV HKU1 (1.5%, 6/397), PIV 3 (1.5%, 6/397), human metapneumovirus (HMPV) (1.5%, 6/397), PIV 4 (1.3%, 5/397), HCoV OC43 (1.0%, 4/397), influenza virus B/Victoria (Flu B/Victoria) (0.5%, 2/397), respiratory syncytial virus (RSV) type B (0.5%, 2/397), and human bocavirus (HBoV) (0.3%, 1/397). The seasonality of pathogen-confirmed SARI patients had a bimodal distribution, with the first peak in the summer and the second peak in the winter. Statistically significant differences were observed with respect to the rates of dyspnea, radiographically diagnosed pneumonia and the presence of at least one comorbidity in patients who were infected with only M. pneumoniae, AdV, HRhV, Flu A/H3N2, Flu A /pH1N1 or Flu B/Yamagata. The differences in the positivity rates of the above 6 pathogens among the different age groups were nonsignificant. Conclusions M. pneumoniae, AdV and Flu A/H3N2 were the main pathogens detected in hospitalized SARI patients aged over 16 years old in Jinshan district, Shanghai. Our findings highlight the importance of sustained multipathogen surveillance among SARI patients in sentinel hospitals, which can provide useful information on SARI etiologies, epidemiology, and clinical characteristics.
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Affiliation(s)
- Jian Li
- Clinical Research Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (JL); (JMZ)
| | - Can-Lei Song
- Department of Acute Infectious Diseases Control, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
| | - Tang Wang
- Department of Acute Infectious Diseases Control, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
| | - Yu-Long Ye
- Department of Microbiology, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
| | - Jian-Ru Du
- Department of Microbiology, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
| | - Shu-Hua Li
- Department of Acute Infectious Diseases Control, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
| | - Jian-Min Zhu
- Department of Acute Infectious Diseases Control, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
- * E-mail: (JL); (JMZ)
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17
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Zhu G, Xu D, Zhang Y, Wang T, Zhang L, Gu W, Shen M. Epidemiological characteristics of four common respiratory viral infections in children. Virol J 2021; 18:10. [PMID: 33407659 PMCID: PMC7787583 DOI: 10.1186/s12985-020-01475-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/21/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Viruses are the main infectious agents of acute respiratory infections in children. We aim to describe the epidemiological characteristics of viral pathogens of acute respiratory tract infections in outpatient children. METHODS From April 2018 to March 2019, the results of viral detection using oral pharyngeal swabs from 103,210 children with acute respiratory tract infection in the outpatient department of the Children's Hospital, Zhejiang University School of Medicine, were retrospectively analyzed. Viral antigens, including adenovirus (ADV), influenza A (FLUA), influenza B (FLUB) and respiratory syncytial virus (RSV), were detected by the colloidal gold method. RESULTS At least one virus was detected in 38,355 cases; the positivity rate was 37.2%. A total of 1910 cases of mixed infection with two or more viruses were detected, and the positivity rate of multiple infection was 1.9%. The ADV positivity rate was highest in the 3-6-year-old group (18.7%), the FLUA positivity rate was highest in the > 6-year-old group (21.6%), the FLUB positivity rate was highest in the > 6-year-old group (6.6%), and the RSV positivity rate was highest in the < 1-year-old group (10.6%). There was a significant difference in the positivity rate of viral infection among different age groups (χ2 = 1280.7, P < 0.001). The rate of positive viral infection was highest in winter (47.1%). The ADV infection rate was highest in spring (18.2%). The rates of FLUA and FLUB positivity were highest in winter (28.8% and 3.6%, respectively). The rate of RSV positivity was highest in autumn (17.4%). The rate of positive viral infection in different seasons was significantly different (χ2 = 6459.1, P < 0.001). CONCLUSIONS Viral infection rates in children differ for different ages and seasons. The positivity rate of ADV is highest in the preschool period and that of RSV is highest in infants; that of FLU increases with age. The total positive rate of viral infection in different seasons is highest in winter, as is the rate of FLU positivity.
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Affiliation(s)
- Guohong Zhu
- Department of Pulmonology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333, Binsheng Road, Hangzhou, Zhejiang Province, China
| | - Dan Xu
- Department of Pulmonology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333, Binsheng Road, Hangzhou, Zhejiang Province, China.
| | - Yuanyuan Zhang
- Department of Pulmonology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333, Binsheng Road, Hangzhou, Zhejiang Province, China
| | - Tianlin Wang
- Department of Pulmonology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333, Binsheng Road, Hangzhou, Zhejiang Province, China
| | - Lingyan Zhang
- Department of Internal Medicine, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, China
| | - Weizhong Gu
- Department of Pathology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, China
| | - Meiping Shen
- Nursing Department, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang Province, China
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18
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Lagare A, Rajatonirina S, Testa J, Mamadou S. The epidemiology of seasonal influenza after the 2009 influenza pandemic in Africa: a systematic review. Afr Health Sci 2020; 20:1514-1536. [PMID: 34394213 PMCID: PMC8351825 DOI: 10.4314/ahs.v20i4.5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Influenza infection is a serious public health problem that causes an estimated 3 to 5 million cases and 250,000 deaths worldwide every year. The epidemiology of influenza is well-documented in high- and middle-income countries, however minimal effort had been made to understand the epidemiology, burden and seasonality of influenza in Africa. This study aims to assess the state of knowledge of seasonal influenza epidemiology in Africa and identify potential data gaps for policy formulation following the 2009 pandemic. Method We reviewed articles from Africa published into four databases namely: MEDLINE (PubMed), Google Scholar, Cochrane Library and Scientific Research Publishing from 2010 to 2019. Results We screened titles and abstracts of 2070 studies of which 311 were selected for full content evaluation and 199 studies were considered. Selected articles varied substantially on the basis of the topics they addressed covering the field of influenza surveillance (n=80); influenza risk factors and co-morbidities (n=15); influenza burden (n=37); influenza vaccination (n=40); influenza and other respiratory pathogens (n=22) and influenza diagnosis (n=5). Conclusion Significant progress has been made since the last pandemic in understanding the influenza epidemiology in Africa. However, efforts still remain for most countries to have sufficient data to allow countries to prioritize strategies for influenza prevention and control.
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Affiliation(s)
- Adamou Lagare
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
| | | | - Jean Testa
- Centre de Recherche Médicale et Sanitaire (CERMES), Niamey, Niger
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19
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Aman AT, Wibawa T, Kosasih H, Asdie RH, Safitri I, Intansari US, Mawarti Y, Sudarmono P, Arif M, Puspitasari D, Alisjahbana B, Parwati KTM, Gasem MH, Lokida D, Lukman N, Hartono TS, Mardian Y, Liang CJ, Siddiqui S, Karyana M, Lau CY. Etiologies of severe acute respiratory infection (SARI) and misdiagnosis of influenza in Indonesia, 2013-2016. Influenza Other Respir Viruses 2020; 15:34-44. [PMID: 32666619 PMCID: PMC7405185 DOI: 10.1111/irv.12781] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 03/02/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background Severe acute respiratory infection (SARI) accounts for a large burden of illness in Indonesia. However, epidemiology of SARI in tertiary hospitals in Indonesia is unknown. This study sought to assess the burden, clinical characteristics, and etiologies of SARI and concordance of clinical diagnosis with confirmed etiology. Methods Data and samples were collected from subjects presenting with SARI as part of the acute febrile Illness requiring hospitalization study (AFIRE). In tertiary hospitals, clinical diagnosis was ascertained from chart review. Samples were analyzed to determine the “true” etiology of SARI at hospitals and Indonesia Research Partnership on Infectious Diseases (INA‐RESPOND) laboratory. Distribution and characteristics of SARI by true etiology and accuracy of clinical diagnosis were assessed. Results Four hundred and twenty of 1464 AFIRE subjects presented with SARI; etiology was identified in 242 (57.6%), including 121 (28.8%) viruses and bacteria associated with systemic infections, 70 (16.7%) respiratory bacteria and viruses other than influenza virus, and 51 (12.1%) influenza virus cases. None of these influenza patients were accurately diagnosed as having influenza during hospitalization. Conclusions Influenza was misdiagnosed among all patients presenting with SARI to Indonesian tertiary hospitals in the AFIRE study. Diagnostic approaches and empiric management should be guided by known epidemiology. Public health strategies to address the high burden of influenza should include broad implementation of SARI screening, vaccination programs, clinician education and awareness campaigns, improved diagnostic capacity, and support for effective point‐of‐care tests.
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Affiliation(s)
- Abu Tholib Aman
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada / Dr. Sardjito Hospital, Yogyakarta, Indonesia.,Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada / Dr. Sardjito Hospital, Yogyakarta, Indonesia.,Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia
| | - Herman Kosasih
- Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia
| | - Rizka Humardewayanti Asdie
- Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia.,Department of Internal Medicine, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada / Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Ida Safitri
- Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia.,Department of Pediatric, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada / Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Umi Solekhah Intansari
- Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia.,Department of Clinical Pathology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada / Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Yuli Mawarti
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada / Dr. Sardjito Hospital, Yogyakarta, Indonesia.,Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia
| | - Pratiwi Sudarmono
- Cipto Mangunkusumo Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Mansyur Arif
- Faculty of Medicine, Universitas Hasanudin / Dr. Wahidin Sudirohusodo Hospital, Makassar, Indonesia
| | - Dwiyanti Puspitasari
- Dr. Soetomo Academic General Hospital, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Bachti Alisjahbana
- Faculty of Medicine, Universitas Padjadjaran / Dr. Hasan Sadikin Hospital, Sumedang, Indonesia
| | | | | | - Dewi Lokida
- Tangerang District Hospital, Tangerang, Indonesia
| | - Nurhayati Lukman
- Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia
| | - Teguh Sarry Hartono
- Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia.,Sulianti Saroso Hospital, Jakarta, Indonesia
| | - Yan Mardian
- Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia
| | - C Jason Liang
- National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD, USA
| | - Sophia Siddiqui
- Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia.,National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD, USA
| | - Muhammad Karyana
- Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia.,National Institute of Health Research and Development (NIHRD), Ministry of Health, Jakarta, Indonesia
| | - Chuen-Yen Lau
- Indonesia Research Partnership on Infectious Diseases (INA-RESPOND), Jakarta, Indonesia.,National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Bethesda, MD, USA
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20
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Razanajatovo Rahombanjanahary NH, Rybkina K, Randriambolamanantsoa TH, Razafimanjato H, Heraud JM. Genetic diversity and molecular epidemiology of respiratory syncytial virus circulated in Antananarivo, Madagascar, from 2011 to 2017: Predominance of ON1 and BA9 genotypes. J Clin Virol 2020; 129:104506. [PMID: 32585620 DOI: 10.1016/j.jcv.2020.104506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND Respiratory syncytial virus is the main cause of acute respiratory infections leading to a considerable morbidity and mortality among under-5 years children. A comprehensive scheme of RSV virus evolution is of great value in implementing effective universal RSV vaccine. OBJECTIVE We investigated the clinical spectrum and molecular characteristics of detected RSV over a period of seven years (January 2011 to June 2017) in Antananarivo, the capital city of Madagascar. STUDY DESIGN 671 nasopharyngeal samples taken from children aged less than 5 years suffered from ARI were screened for RSV by real-time PCR. Clinical data were retrieved from case report forms. Genotype identification was performed by reverse-transcription PCR and sequencing of the second hyper variable region (HVR2) of the G glycoprotein. RESULTS Amongst samples tested, 292 (43.5 %) were found positive for RSV. RSV A predominated during the study period which accounted for 62.3 % (182/292) of positive samples while RSV B represented 37.0 % (108/292). Phylogenetic analyses identified NA1 and ON1 genotypes among RSV A. Though NA1 widespread from 2011 to 2013, ON1 became prevalent during the following years. Among RSV B, THB, CB1 and BA9 genotypes were detected. A co-circulation of THB and CB1 strains occurred during the 2011 season that was substituted by the BA9 from 2012. Malagasy ON1 strains carried some characteristic amino acid substitutions that distinguish them from the worldwide ON1 strains. By analyzing clinical spectrum, ON1 and BA genotypes seemed to prevail in mild infections compared to NA1. CONCLUSION Results obtained here will have its implication in predicting temporal evolution of RSV at the local level. Considering the insularity of the country, information obtained should help in comparative analysis with global RSV strains to optimize vaccine efficacy.
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Affiliation(s)
| | - Ksenia Rybkina
- National Influenza Center, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Helisoa Razafimanjato
- National Influenza Center, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jean-Michel Heraud
- National Influenza Center, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
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21
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Ratovoson R, Randremanana R, Rakotomanana F, Andriamandimby SF, Mangahasimbola R, Masquelier B, Richard V, Piola P, Pison G, Baril L. Cohort Profile: Moramanga health survey in urban and rural areas in Madagascar (MHURAM project). Int J Epidemiol 2019; 48:1754-1755i. [PMID: 31665291 DOI: 10.1093/ije/dyz215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 11/15/2022] Open
Affiliation(s)
- Rila Ratovoson
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar.,DemoSud Research Unit, Institut National d'Etudes Démographiques, Paris, France
| | - Rindra Randremanana
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Fanjasoa Rakotomanana
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Reziky Mangahasimbola
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Bruno Masquelier
- DemoSud Research Unit, Institut National d'Etudes Démographiques, Paris, France.,Center for Demographic Research, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Vincent Richard
- Direction of International Affairs, Institut Pasteur, Paris, France
| | - Patrice Piola
- Epidemiology and Public Health Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Gilles Pison
- DemoSud Research Unit, Institut National d'Etudes Démographiques, Paris, France.,Eco-Anthropology Research Unit, National Museum of Natural History, Paris, France
| | - Laurence Baril
- Epidemiology and Clinical Research Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
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