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Wada FW, Desta AF, Gebre M, Mihret W, Seyoum T, Melaku K, Alemu A, Howe R, Mulu A, Mihret A. Pneumococcal colonization and coinfecting respiratory viruses in children under 5 years in Addis Ababa, Ethiopia: a prospective case-control study. Sci Rep 2024; 14:4174. [PMID: 38378681 PMCID: PMC10879120 DOI: 10.1038/s41598-024-54256-w] [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: 10/18/2023] [Accepted: 02/10/2024] [Indexed: 02/22/2024] Open
Abstract
A comprehensive understanding of the dynamics of Streptococcus pneumoniae colonization in conjunction with respiratory virus infections is essential for enhancing our knowledge of the pathogenesis and advancing the development of effective preventive strategies. Therefore, a case-control study was carried out in Addis Ababa, Ethiopia to investigate the colonization rate of S. pneumoniae and its coinfection dynamics with respiratory viruses among children under the age of 5 years. Samples from the nasopharyngeal and/or oropharyngeal, along with socio-demographic and clinical information, were collected from 420 children under 5 years old (210 cases with lower respiratory tract infections and 210 controls with conditions other than respiratory infections.). A one-step Multiplex real-time PCR using the Allplex Respiratory Panel Assays 1-4 was performed to identify respiratory viruses and bacteria. Data analysis was conducted using STATA software version 17. The overall colonization rate of S. pneumoniae in children aged less than 5 years was 51.2% (215/420). The colonization rates in cases and controls were 54.8% (115/210) and 47.6% (100/210), respectively (p = 0.14). Colonization rates were observed to commence at an early age in children, with a colonization rate of 48.9% and 52.7% among infants younger than 6 months controls and cases, respectively. The prevalence of AdV (OR, 3.11; 95% CI [1.31-8.19]), RSV B (OR, 2.53; 95% CI [1.01-6.78]) and HRV (OR, 1.7; 95% CI [1.04-2.78]) tends to be higher in children who tested positive for S. pneumoniae compared to those who tested negative for S. pneumoniae. Further longitudinal research is needed to understand and determine interaction mechanisms between pneumococci and viral pathogens and the clinical implications of this coinfection dynamics.
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Affiliation(s)
- Fiseha Wadilo Wada
- Armauer Hansen Research Institute, Ministry of Health, Addis Ababa, Ethiopia.
- Department of Biomedical Sciences, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
- Department of Medical Laboratory Sciences, College of Health Sciences and Medicine, Wolaita Sodo University, Wolaita Soddo, Ethiopia.
| | - Adey Feleke Desta
- Department of Biomedical Sciences, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Meseret Gebre
- Armauer Hansen Research Institute, Ministry of Health, Addis Ababa, Ethiopia
| | - Wude Mihret
- Armauer Hansen Research Institute, Ministry of Health, Addis Ababa, Ethiopia
| | - Tamrayehu Seyoum
- Armauer Hansen Research Institute, Ministry of Health, Addis Ababa, Ethiopia
| | - Kalkidan Melaku
- Armauer Hansen Research Institute, Ministry of Health, Addis Ababa, Ethiopia
| | - Ashenafi Alemu
- Armauer Hansen Research Institute, Ministry of Health, Addis Ababa, Ethiopia
| | - Rawleigh Howe
- Armauer Hansen Research Institute, Ministry of Health, Addis Ababa, Ethiopia
| | - Andargachew Mulu
- Armauer Hansen Research Institute, Ministry of Health, Addis Ababa, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Ministry of Health, Addis Ababa, Ethiopia
- Department of Microbiology, Immunology, and Parasitology, School of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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Goh M, Joy C, Gillespie AN, Soh QR, He F, Sung V. Asymptomatic viruses detectable in saliva in the first year of life: a narrative review. Pediatr Res 2024; 95:508-531. [PMID: 38135726 DOI: 10.1038/s41390-023-02952-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023]
Abstract
Viral infections are common in children. Many can be asymptomatic or have delayed health consequences. In view of increasing availability of point-of-care viral detection technologies, with possible application in newborn screening, this review aimed to (1) identify potentially asymptomatic viruses detectable in infants under one year old, via saliva/nasopharyngeal swab, and (2) describe associations between viruses and long-term health conditions. We systematically searched Embase(Ovid), Medline(Ovid) and PubMed, then further searched the literature in a tiered approach. From the 143 articles included, 28 potentially asymptomatic viruses were identified. Our second search revealed associations with a range of delayed health conditions, with most related to the severity of initial symptoms. Many respiratory viruses were linked with development of recurrent wheeze or asthma. Of note, some potentially asymptomatic viruses are linked with later non-communicable diseases: adenovirus serotype 36 and obesity, Enterovirus-A71 associated Hand, Foot, Mouth Disease and Attention-Deficit Hyperactivity Disorder, Ebstein Barr Virus (EBV) and malignancy, EBV and multiple sclerosis, HHV-6 and epilepsy, HBoV-1 and lung fibrosis and Norovirus and functional gastrointestinal disorders. Our review identified many potentially asymptomatic viruses, detectable in early life with potential delayed health consequences, that could be important to screen for in the future using rapid point-of-care viral detection methods. IMPACT: Novel point-of-care viral detection technologies enable rapid detection of viruses, both old and emerging. In view of increasing capability to screen for viruses, this is the first review to explore which potentially asymptomatic viruses, that are detectable using saliva and/or nasopharyngeal swabs in infants less than one year of age, are associated with delayed adverse health conditions. Further research into detecting such viruses in early life and their delayed health outcomes may pave new ways to prevent non-communicable diseases in the future.
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Affiliation(s)
- Melody Goh
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
- Prevention Innovation, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Charissa Joy
- Prevention Innovation, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Monash Children's Hospital Clayton, Clayton, VIC, Australia
| | - Alanna N Gillespie
- Prevention Innovation, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Centre for Community Child Health, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Qi Rui Soh
- Prevention Innovation, Murdoch Children's Research Institute, Parkville, VIC, Australia
- The University of Melbourne, Faculty of Medicine Dentistry and Health Sciences Melbourne, Melbourne, VIC, Australia
| | - Fan He
- Prevention Innovation, Murdoch Children's Research Institute, Parkville, VIC, Australia
- John Richards Centre for Rural Ageing Research, La Trobe University, Wodonga, VIC, Australia
| | - Valerie Sung
- Prevention Innovation, Murdoch Children's Research Institute, Parkville, VIC, Australia.
- Monash Children's Hospital Clayton, Clayton, VIC, Australia.
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.
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Brown JA, Hauser A, Abela IA, Pasin C, Epp S, Mohloanyane T, Nsakala BL, Trkola A, Labhardt ND, Kouyos RD, Günthard HF. Seroprofiling of Antibodies Against Endemic Human Coronaviruses and Severe Acute Respiratory Syndrome Coronavirus 2 in a Human Immunodeficiency Virus Cohort in Lesotho: Correlates of Antibody Response and Seropositivity. J Infect Dis 2023; 228:1042-1054. [PMID: 37261930 PMCID: PMC10582919 DOI: 10.1093/infdis/jiad197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/18/2023] [Accepted: 05/27/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Serological data on endemic human coronaviruses (HCoVs) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in southern Africa are scarce. Here, we report on (1) endemic HCoV seasonality, (2) SARS-CoV-2 seroprevalence, and (3) correlates of SARS-CoV-2 seropositivity and strength of SARS-CoV-2 and endemic HCoV serological responses among adults living with human immunodeficiency virus (HIV). METHODS Plasma samples were collected from February 2020 to July 2021 within an HIV cohort in Lesotho. We used the AntiBody CORonavirus Assay (ABCORA) multiplex immunoassay to measure antibody responses to endemic HCoV (OC43, HKU1, NL63, and 229E) and SARS-CoV-2 antigens. RESULTS Results for 3173 samples from 1403 adults were included. Serological responses against endemic HCoVs increased over time and peaked in winter and spring. SARS-CoV-2 seropositivity reached >35% among samples collected in early 2021 and was associated with female sex, obesity, working outside the home, and recent tiredness or fever. Positive correlations were observed between the strength of response to endemic HCoVs and to SARS-CoV-2 and between older age or obesity and the immunoglobulin G response to SARS-CoV-2. CONCLUSIONS These results add to our understanding of the impact of biological, clinical, and social/behavioral factors on serological responses to coronaviruses in southern Africa.
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Affiliation(s)
- Jennifer A Brown
- Division of Clinical Epidemiology, Department of Clinical Research, University Hospital Basel, Basel, Switzerland
- Division of Clinical Epidemiology, Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Anthony Hauser
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Irene A Abela
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chloé Pasin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Selina Epp
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | | | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Niklaus D Labhardt
- Division of Clinical Epidemiology, Department of Clinical Research, University Hospital Basel, Basel, Switzerland
- Division of Clinical Epidemiology, Department of Clinical Research, University of Basel, Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Han S, Xu B, Feng Q, Feng Z, Zhu Y, Ai J, Deng L, Li C, Cao L, Sun Y, Fu Z, Jin R, Shang Y, Chen Z, Xu L, Xie Z, Shen K. Multicenter analysis of epidemiological and clinical features of pediatric acute lower respiratory tract infections associated with common human coronaviruses in China, 2014-2019. Virol J 2023; 20:229. [PMID: 37817170 PMCID: PMC10566024 DOI: 10.1186/s12985-023-02198-6] [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: 04/20/2023] [Accepted: 10/02/2023] [Indexed: 10/12/2023] Open
Abstract
The common human coronaviruses (HCoVs) HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 which are members of the coronavirus family are long co-existed with humans and widely distributed globally. Common HCoVs usually cause mild, self-limited upper respiratory tract infections (URTI), and also associated with lower respiratory tract infections (LRTI), especially in children. However, there are little multicentre studies have been conducted in children of several different areas in China, and the epidemic potential of common HCoVs remains unclear. Understanding of the common HCoVs is valuable for clinical and public health. Herein, we retrospectively analysed the medical records of children with acute lower respiratory tract infection admitted to 9 hospitals from different regions in China from 2014 to 2019. Of the 124 patients who tested positive for coronaviruses, OC43 was the predominant type, accounting for 36.3% (45/124) of the detections. Children aged ≤ 6 months and 12-23 months had the highest detection rate of common HCoVs, and the detection rate gradually declined after 2 years old. These four HCoVs could be detected all year round. Among the areas of our study, the overall positive rate was higher in southern China, especially in Guangzhou (29/124, 23.4%). Moreover, common HCoV-positive patients were codetected with 9 other common respiratory pathogens. 229E (11/13, 84.6%) was the most frequently associated with codetection, with EV/RhV was the most frequently codetected virus. Cough (113/124, 91.1%) and fever (73/124, 58.9%) were the most common symptoms of common HCoVs infection.
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Affiliation(s)
- Shuaibing Han
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Beijing, 100045, China
| | - Baoping Xu
- Department of Respiratory Diseases I, Beijing Children's Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, 100045, China
| | - Qianyu Feng
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Beijing, 100045, China
| | - Ziheng Feng
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Beijing, 100045, China
| | - Yun Zhu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Beijing, 100045, China
| | - Junhong Ai
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Beijing, 100045, China
| | - Li Deng
- Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Changchong Li
- The 2nd Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Ling Cao
- Children's Hospital, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yun Sun
- Yinchuan Maternal and Child Health Hospital, Yinchuan, 750000, China
| | - Zhou Fu
- Children's Hospital of Chongqing Medical University, Chongqing, 400015, China
| | - Rong Jin
- Guiyang Women and Children Healthcare Hospital, Guiyang, 550003, China
| | - Yunxiao Shang
- Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Zhiming Chen
- The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310005, China
| | - Lili Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Beijing, 100045, China.
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
- Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Beijing, 100045, China.
| | - Kunling Shen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
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5
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Faye MN, Barry MA, Jallow MM, Wade SF, Mendy MP, Sy S, Fall A, Kiori DE, Ndiaye NK, Goudiaby D, Diamanka A, Niang MN, Dia N. Epidemiology of Non-SARS-CoV2 Human Coronaviruses (HCoVs) in People Presenting with Influenza-like Illness (ILI) or Severe Acute Respiratory Infections (SARI) in Senegal from 2012 to 2020. Viruses 2022; 15:20. [PMID: 36680061 PMCID: PMC9864203 DOI: 10.3390/v15010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/03/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
In addition to emerging coronaviruses (SARS-CoV, MERS, SARS-CoV-2), there are seasonal human coronaviruses (HCoVs): HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1. With a wide distribution around the world, HCoVs are usually associated with mild respiratory disease. In the elderly, young children and immunocompromised patients, more severe or even fatal respiratory infections may be observed. In Africa, data on seasonal HCoV are scarce. This retrospective study investigated the epidemiology and genetic diversity of seasonal HCoVs during nine consecutive years of influenza-like illness surveillance in Senegal. Nasopharyngeal swabs were collected from ILI outpatients or from SARI hospitalized patients. HCoVs were diagnosed by qRT-PCR and the positive samples were selected for molecular characterization. Among 9337 samples tested for HCoV, 406 (4.3%) were positive: 235 (57.9%) OC43, 102 (25.1%) NL63, 58 (14.3%) 229E and 17 (4.2%) HKU1. The four types circulated during the study period and a peak was noted between November and January. Children under five were the most affected. Co-infections were observed between HCoV types (1.2%) or with other viruses (76.1%). Genetically, HCoVs types showed diversity. The results highlighted that the impact of HCoVs must be taken into account in public health; monitoring them is therefore particularly necessary both in the most sensitive populations and in animals.
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Affiliation(s)
- Modeste Name Faye
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Mamadou Malado Jallow
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Serigne Fallou Wade
- Ecole Supérieure des Sciences Agricoles et de l’Alimentation (ES2A), Université Amadou Makhtar MBOW de Dakar (UAM), Dakar 12900, Senegal
| | - Marie Pedapa Mendy
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Sara Sy
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Amary Fall
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Davy Evrard Kiori
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | | | - Deborah Goudiaby
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Arfang Diamanka
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | | | - Ndongo Dia
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
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