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Diouf FS, Tidjani Alou M, Bassene H, Cortaredona S, Diatta G, Raoult D, Sokhna C, Lagier JC. Seasonal variation of asymptomatic viral and bacterial nasopharyngeal carriage in rural Senegal. J Infect Public Health 2024; 17:922-928. [PMID: 38579539 DOI: 10.1016/j.jiph.2024.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/26/2024] [Accepted: 03/17/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The surveillance of respiratory pathogens in rural areas of West Africa has, to date, largely been focussed on symptoms. In this prospective study conducted prior to the COVID-19 pandemic, we aimed to assess the asymptomatic prevalence of respiratory pathogen carriage in a group of individuals living in a rural area of Senegalese. METHODS Longitudinal follow up was performed through monthly nasopharyngeal swabbing during the dry season and weekly swabbing during the rainy season. We enrolled 15 individuals from the village of Ndiop. A total of 368 nasopharyngeal swabs were collected over a one-year period. We investigated the prevalence of 18 respiratory viruses and eight respiratory bacteria in different age groups using singleplex and multiplex PCR. RESULTS In total, 19.56% of the samples (72/368) were positive for respiratory viruses and 13.60% of the samples (50/368) were positive for respiratory bacteria. Coronaviruses (19/72, 26.39%), adenoviruses (17/72, 23.61%), rhinoviruses (14/72, 19.44%), Streptococcus pneumoniae (17/50, 34%), and Moraxella catarrhalis (15/50, 30%) were the most frequently detected viruses. Interestingly, the carriage of respiratory pathogens was shown to be more frequent during the rainy season, as pluviometry was shown to be positively associated with the occurrence of respiratory viruses such as influenza (P = .0078, r2 =.523) and RSV (P = .0055, r2 =.554). CONCLUSIONS Our results show a non-negligible circulation of respiratory pathogens in a rural area in Senegal (West Africa) with an underestimated proportion of asymptomatic individuals. This study highlights the fact that the circulation of viruses and bacteria in the community has been overlooked.
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Affiliation(s)
- Fatou Samba Diouf
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Maryam Tidjani Alou
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Hubert Bassene
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - Sebastien Cortaredona
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Georges Diatta
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - Didier Raoult
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France.
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Lingani M, Cissé A, Ilboudo AK, Yaméogo I, Tarnagada Z. Patterns of Non-influenza Respiratory Viruses Among Severe Acute Respiratory Infection Cases in Burkina Faso: A Surveillance Study. Influenza Other Respir Viruses 2024; 18:e13271. [PMID: 38501305 PMCID: PMC10949177 DOI: 10.1111/irv.13271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Although influenza viruses cause only one-fifth of severe acute respiratory infections (SARI) in Burkina Faso, the other viral causes of SARI remain poorly investigated to inform clinical and preventive decision making. METHODS Between 2016 and 2019, we prospectively enrolled inpatients meeting the World Health Organization (WHO) case definition of SARI in Burkina Faso. Results of viral etiologies among inpatients tested negative for influenza using the Fast Track Diagnostics Respiratory Kits (FTD-33) were reported. RESULTS Of 1541 specimens tested, at least one respiratory virus was detected in 76.1% of the 1231 specimens negative for influenza virus. Human rhinoviruses (hRVs) were the most detected pathogens (476; 38.7%), followed by human adenoviruses (hAdV) (17.1%, 210/1231), human respiratory syncytial virus (hRSV) (15.4%, 189/1231), enterovirus (EnV) (11.2%, 138/1231), human bocavirus (hBoV) (7.9%, 97/1231), parainfluenza 3 (hPIV3) (6.1%, 75/1231), human metapneumovirus (hMPV) (6.0%,74/1321), parainfluenza 4 (hPIV4) (4.1%, 51/1231), human coronavirus OC43 (hCoV-OC43) (3.4%, 42/1231), human coronavirus HKU1(hCoV-HKU1) (2.7%, 33/1231), human coronavirus NL63 (hCoV-NL63) (2.5%, 31/1231), parainfluenza 1 (hPIV1) (2.0%, 25/1231), parainfluenza 2 (hPIV2) (1.8%, 22/1231), human parechovirus (PeV) (1.1%, 14/1231), and human coronavirus 229E (hCoV-229E) (0.9%, 11/1231). Among SARI cases, infants aged 1-4 years were mostly affected (50.7%; 622/1231), followed by those <1 year of age (35.7%; 438/1231). Most detected pathogens had year-long circulation patterns, with seasonal peaks mainly observed during the cold and dry seasons. CONCLUSION Several non-influenza viruses are cause of SARI in Burkina Faso. The integration of the most common pathogens into the routine influenza surveillance system might be beneficial.
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Affiliation(s)
- Moussa Lingani
- Laboratoire National de Référence‐GrippesInstitut de Recherche en Sciences de la Santé (LNRG‐IRSS)OuagadougouBurkina Faso
- Unité de Recherche Clinique de NanoroInstitut de Recherche en Sciences de la Santé (IRSS‐URCN)NanoroBurkina Faso
| | - Assana Cissé
- Laboratoire National de Référence‐GrippesInstitut de Recherche en Sciences de la Santé (LNRG‐IRSS)OuagadougouBurkina Faso
- One Health Association Burkina FasoOuagadougouBurkina Faso
| | - Abdoul Kader Ilboudo
- Laboratoire National de Référence‐GrippesInstitut de Recherche en Sciences de la Santé (LNRG‐IRSS)OuagadougouBurkina Faso
- One Health Association Burkina FasoOuagadougouBurkina Faso
| | - Issaka Yaméogo
- One Health Association Burkina FasoOuagadougouBurkina Faso
- Service de surveillance épidémiologiqueMinistère de la santé et de l'Hygiène publiqueOuagadougouBurkina Faso
| | - Zekiba Tarnagada
- Laboratoire National de Référence‐GrippesInstitut de Recherche en Sciences de la Santé (LNRG‐IRSS)OuagadougouBurkina Faso
- One Health Association Burkina FasoOuagadougouBurkina Faso
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Tambe LAM, Mathobo P, Munzhedzi M, Bessong PO, Mavhandu-Ramarumo LG. Prevalence and Molecular Epidemiology of Human Coronaviruses in Africa Prior to the SARS-CoV-2 Outbreak: A Systematic Review. Viruses 2023; 15:2146. [PMID: 38005824 PMCID: PMC10675249 DOI: 10.3390/v15112146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Coronaviruses, re-emerging in human populations, cause mild or severe acute respiratory diseases, and occasionally epidemics. This study systematically reviewed human coronavirus (HCoVs) infections in Africa prior to the SARS-CoV-2 outbreak. Forty studies on the prevalence or molecular epidemiology of HCoVs were available from 13/54 African countries (24%). The first published data on HCoV was from South Africa in 2008. Eight studies (20%) reported on HCoV molecular epidemiology. Endemic HCoV prevalence ranged from 0.0% to 18.2%. The prevalence of zoonotic MERS-CoV ranged from 0.0% to 83.5%. Two studies investigated SARS-CoV infection, for which a prevalence of 0.0% was reported. There was heterogeneity in the type of tests used in determining HCoV prevalence. Two studies reported that risk factors for HCoV include exposure to infected animals or humans. The quantity of virologic investigations on HCoV on the African continent was scant, and Africa was not prepared for SARS-CoV-2.
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Affiliation(s)
- Lisa Arrah Mbang Tambe
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Phindulo Mathobo
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mukhethwa Munzhedzi
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Pascal Obong Bessong
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
- Centre for Global Health Equity, School of Medicine, 1400 University Ave, Charlottesville, VA 22903, USA
| | - Lufuno Grace Mavhandu-Ramarumo
- HIV/AIDS & Global Health Research Programme, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa; (L.A.M.T.); (P.M.); (M.M.); (P.O.B.)
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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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Klink T, Rankin DA, Piya B, Spieker AJ, Faouri S, Shehabi A, Williams JV, Khuri-Bulos N, Halasa NB. Evaluating the diagnostic accuracy of the WHO Severe Acute Respiratory Infection (SARI) criteria in Middle Eastern children under two years over three respiratory seasons. PLoS One 2020; 15:e0232188. [PMID: 32353012 PMCID: PMC7192447 DOI: 10.1371/journal.pone.0232188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/08/2020] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVE The World Health Organization created the Severe Acute Respiratory Infection (SARI) criteria in 2011 to monitor influenza (flu)-related hospitalization. Many studies have since used the SARI case definition as inclusion criteria for surveillance studies. We sought to determine the sensitivity, specificity, positive predictive value, and negative predictive value of the SARI criteria for detecting ten different respiratory viruses in a Middle Eastern pediatric cohort. MATERIALS AND METHODS The data for this study comes from a prospective acute respiratory surveillance study of hospitalized children <2 years in Amman, Jordan from March 16, 2010 to March 31, 2013. Participants were recruited if they had a fever and/or respiratory symptoms. Nasal and throat swabs were obtained and tested by real-time RT-PCR for eleven viruses. Subjects meeting SARI criteria were determined post-hoc. Sensitivity, specificity, positive predictive value, and negative predictive value of the SARI case definition for detecting ten different viruses were calculated and results were stratified by age. RESULTS Of the 3,175 patients enrolled, 3,164 were eligible for this study, with a median age of 3.5 months, 60.4% male, and 82% virus-positive (44% RSV and 3.8% flu). The sensitivity and specificity of the SARI criteria for detecting virus-positive patients were 44% and 77.9%, respectively. Sensitivity of SARI criteria for any virus was lowest in children <3 months at 22.4%. Removing fever as a criterion improved the sensitivity by 65.3% for detecting RSV in children <3 months; whereas when cough was removed, the sensitivity improved by 45.5% for detecting flu in same age group. CONCLUSIONS The SARI criteria have poor sensitivity for detecting RSV, flu, and other respiratory viruses-particularly in children <3 months. Researchers and policy makers should use caution if using the criteria to estimate burden of disease in children.
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Affiliation(s)
- Thomas Klink
- Medicine and Pediatric Residency Program, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Danielle A. Rankin
- Vanderbilt Epidemiology PhD Program, Vanderbilt University School of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Bhinnata Piya
- Vanderbilt Institute for Clinical and Translational Research, Nashville, Tennessee, United States of America
| | - Andrew J. Spieker
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - 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, United States of America
| | | | - Natasha B. Halasa
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, United States of America
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Knobbe RB, Diallo A, Fall A, Gueye AD, Dieng A, van Immerzeel TD, Ba A, Diop A, Diop A, Niang M, Boye CS. Pathogens Causing Respiratory Tract Infections in Children Less Than 5 Years of Age in Senegal. Microbiol Insights 2019; 12:1178636119890885. [PMID: 31908474 PMCID: PMC6937528 DOI: 10.1177/1178636119890885] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/03/2019] [Indexed: 12/28/2022] Open
Abstract
Introduction: While acute respiratory tract infections are the main cause of paediatric mortality and morbidity worldwide, pathogen patterns shift due to factors such as hygiene, vaccinations, and antibiotic resistance. Knowledge about current cause of respiratory infections is lacking, particularly in low- and middle-income countries. The aim of this study was to identity the various respiratory pathogens causing acute respiratory tract infections in children below 5 years of age visiting a sub-urban primary care clinic in Senegal. Methods: A case-control study was performed in September and October 2018. Oropharyngeal swabs were collected from cases; infants with fever and respiratory symptoms, and controls; children involved in the vaccination programme. Viral identification was conducted by polymerase chain reaction for 21 different viruses; bacteria were identified by culture studies. Associations between microorganisms, acute respiratory infection and severity of disease were calculated by multivariate regression adjusting for confounders such as age, sex, and living area. Results: Overall, 102 cases and 96 controls were included. Microorganisms were detected in 90.1% of cases and 53.7% of controls (P < .001). Influenza virus A (including H1N1), influenza virus B, respiratory syncytial virus (RSV), and Streptococcus pneumoniae were independently associated with acute respiratory tract infections. Co-detection of two or more pathogens was present in 49.5% of cases; 31.7% of cases had a pneumonia and 90.2% was treated with antibiotics. Conclusions: This case-control study in a primary care setting in sub-Saharan Africa found influenza virus A and B, RSV, and S pneumoniae to be the main causes of acute respiratory tract infections in children below 5 years of age. We recommend evaluation of antibiotics prescription behaviour in this setting.
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Affiliation(s)
- Rebecca B Knobbe
- Laboratory of Bacteriology and Virology, Aristide Le Dantec Teaching Hospital, Dakar, Senegal.,Paediatric Infectious Disease and Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Abdallah Diallo
- Paediatric Medical Care Unit, Institut de Pédiatrie Sociale de Pikine, Dakar, Senegal
| | - Amary Fall
- Medical Virology Unit, Pasteur Institute, Dakar, Senegal
| | - Aida D Gueye
- Laboratory of Bacteriology and Virology, Aristide Le Dantec Teaching Hospital, Dakar, Senegal
| | - Assane Dieng
- Laboratory of Bacteriology and Virology, Aristide Le Dantec Teaching Hospital, Dakar, Senegal
| | | | - Abou Ba
- Paediatric Unit, Albert Royer Hospital, Dakar, Senegal
| | - Amadou Diop
- Laboratory of Bacteriology and Virology, Aristide Le Dantec Teaching Hospital, Dakar, Senegal
| | - Abdoulaye Diop
- Laboratory of Bacteriology and Virology, Aristide Le Dantec Teaching Hospital, Dakar, Senegal
| | - Mbayame Niang
- Medical Virology Unit, Pasteur Institute, Dakar, Senegal
| | - Cheikh Sb Boye
- Laboratory of Bacteriology and Virology, Aristide Le Dantec Teaching Hospital, Dakar, Senegal
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