1
|
Kovacs D, Mambule I, Read JM, Kiran A, Chilombe M, Bvumbwe T, Aston S, Menyere M, Masina M, Kamzati M, Ganiza TN, Iuliano D, McMorrow M, Bar-Zeev N, Everett D, French N, Ho A. Epidemiology of Human Seasonal Coronaviruses Among People With Mild and Severe Acute Respiratory Illness in Blantyre, Malawi, 2011-2017. J Infect Dis 2024; 230:e363-e373. [PMID: 38365443 PMCID: PMC11322416 DOI: 10.1093/infdis/jiad587] [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: 07/10/2023] [Accepted: 12/18/2023] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND The aim of this study was to characterize the epidemiology of human seasonal coronaviruses (HCoVs) in southern Malawi. METHODS We tested for HCoVs 229E, OC43, NL63, and HKU1 using real-time polymerase chain reaction (PCR) on upper respiratory specimens from asymptomatic controls and individuals of all ages recruited through severe acute respiratory illness (SARI) surveillance at Queen Elizabeth Central Hospital, Blantyre, and a prospective influenza-like illness (ILI) observational study between 2011 and 2017. We modeled the probability of having a positive PCR for each HCoV using negative binomial models, and calculated pathogen-attributable fractions (PAFs). RESULTS Overall, 8.8% (539/6107) of specimens were positive for ≥1 HCoV. OC43 was the most frequently detected HCoV (3.1% [191/6107]). NL63 was more frequently detected in ILI patients (adjusted incidence rate ratio [aIRR], 9.60 [95% confidence interval {CI}, 3.25-28.30]), while 229E (aIRR, 8.99 [95% CI, 1.81-44.70]) was more frequent in SARI patients than asymptomatic controls. In adults, 229E and OC43 were associated with SARI (PAF, 86.5% and 89.4%, respectively), while NL63 was associated with ILI (PAF, 85.1%). The prevalence of HCoVs was similar between children with SARI and controls. All HCoVs had bimodal peaks but distinct seasonality. CONCLUSIONS OC43 was the most prevalent HCoV in acute respiratory illness of all ages. Individual HCoVs had distinct seasonality that differed from temperate settings.
Collapse
Affiliation(s)
- Dory Kovacs
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Ivan Mambule
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Research Department, Joint Clinical Research Centre, Kampala, Uganda
| | - Jonathan M. Read
- Centre for Health Information Computation and Statistics, Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
| | - Anmol Kiran
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Moses Chilombe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Malaria Alert Centre, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Thandiwe Bvumbwe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Blantyre Malaria Project, Blantyre, Malawi
| | - Stephen Aston
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Mavis Menyere
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Mazuba Masina
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Moses Kamzati
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Thokozani Namale Ganiza
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Danielle Iuliano
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Meredith McMorrow
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Naor Bar-Zeev
- International Vaccine Access Center, Department of international Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States
| | - Dean Everett
- Department of Pathology and Infectious Diseases, College of Medicine and Health Sciences, Abu Dhabi, United Arab Emirates
- Infection Research Unit, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Neil French
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Antonia Ho
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Medical Research Council-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
2
|
Wilson R, Kovacs D, Crosby M, Ho A. Global Epidemiology and Seasonality of Human Seasonal Coronaviruses: A Systematic Review. Open Forum Infect Dis 2024; 11:ofae418. [PMID: 39113828 PMCID: PMC11304597 DOI: 10.1093/ofid/ofae418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024] Open
Abstract
Background We characterized the global epidemiology and seasonality of human coronaviruses (HCoVs) OC43, NL63, 229E, and HKU1. Methods In this systematic review, we searched MEDLINE, EMBASE, Web of Science, SCOPUS, CINAHL, and backward citations for studies published until 1 September 2023. We included studies with ≥12 months of consecutive data and tested for ≥1 HCoV species. Case reports, review articles, animal studies, studies focusing on SARS-CoV-1, SARS-CoV-2, and/or Middle East respiratory syndrome, and those including <100 cases were excluded. Study quality and risk of bias were assessed using Joanna Briggs Institute Critical Appraisal Checklist tools. We reported the prevalence of all HCoVs and individual species. Seasonality was reported for studies that included ≥100 HCoVs annually. This study is registered with PROSPERO, CRD42022330902. Results A total of 201 studies (1 819 320 samples) from 68 countries were included. A high proportion were from China (19.4%; n = 39), whereas the Southern Hemisphere was underrepresented. Most were case series (77.1%, n = 155) with samples from secondary care (74.1%, n = 149). Seventeen (8.5%) studies included asymptomatic controls, whereas 76 (37.8%) reported results for all 4 HCoV species. Overall, OC43 was the most prevalent HCoV. Median test positivity of OC43 and NL63 was higher in children, and 229E and HKU1 in adults. Among 18 studies that described seasonality (17 from the Northern Hemisphere), circulation of all HCoVs mostly peaked during cold months. Conclusions In our comprehensive review, few studies reported the prevalence of individual HCoVs or seasonality. Further research on the burden and circulation of HCoVs is needed, particularly from Africa, South Asia, and Central/South America.
Collapse
Affiliation(s)
- Rory Wilson
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Dory Kovacs
- College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, UK
| | - Mairi Crosby
- College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, UK
| | - Antonia Ho
- Medical Research Council-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| |
Collapse
|
3
|
Marafungana N, Naidoo KL, Gounder L, Masekela R. Severe lower respiratory tract infections are associated with human adenovirus in hospitalised children in a high HIV prevalence area. Afr J Thorac Crit Care Med 2024; 30:e1208. [PMID: 39171152 PMCID: PMC11334900 DOI: 10.7196/ajtccm.2024.v30i2.1208] [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: 06/22/2023] [Accepted: 03/25/2024] [Indexed: 08/23/2024] Open
Abstract
Background Viral causes of lower respiratory tract infections (LRTIs) are associated with increased mortality in children aged <5 years (U5). Human adenovirus (HAdV) has been associated with severe LRTI; however, its relationship with HIV and malnutrition in South Africa (SA) is not understood. Objectives To identify the prevalence of and factors associated with HAdV LRTIs in hospitalised U5 childen. Methods Clinical and viral data on U5 children hospitalised with severe LRTI from January 2018 to June 2020 at King Edward VIII Hospital, Durban, SA, including results of a multiplex polymerase chain reaction (PCR) panel assay for respiratory viruses, were retrieved from inpatient files and laboratory databases and retrospectively analysed. Standard descriptive statistics and Pearson's χ², Fisher's exact and Mann-Whitney tests were used to determine significant associations with HAdV LRTI. Results Among the 206 viral assays analysed (15.6% of all LRTI admissions), HAdV was the most common virus identified. The cohort had a median (interquartile range) age of 5 (2 - 13) months, 47.3% had perinatal HIV exposure, and 34.5% had severe acute malnutrition (SAM). No seasonal pattern with HAdV could be demonstrated. SAM and prematurity were significant risk factors for readmission, and perinatal HIV exposure was a significant risk factor for presence of multiple viruses on analysis of a respiratory specimen. Detection of HAdV was not associated with an increased risk of requiring oxygen or ventilatory support. Conclusion HAdV was the most common virus found on analysis of multiplex PCR panel results in children hospitalised with severe LRTI in SA, where high rates of HIV exposure may result in increased susceptibility to viral co-infections. The role of HAdV as a cause of severe LRTI in SA infants, who have high rates of HIV exposure, requires greater scrutiny. Study synopsis What the study adds. This study provides retrospective data identifying human adenovirus (HAdV) as the most common cause of severe lower respiratory tract infection (LRTI) in children aged <5 years (U5). The impact of respiratory syncytial virus as a common pathogen in children is well established. The study confirms anecdotal evidence that HAdV is an important disease-causing pathogen associated with LRTI. Children with perinatal HIV exposure and severe acute malnutrition (SAM) may be particularly susceptible.Implications of the findings. HAdV must be considered a major cause of severe LRTI in U5 children. Children with LRTI who had perinatal HIV exposure and those with SAM need to be tested for HAdV and to be monitored for severe disease.
Collapse
Affiliation(s)
- N Marafungana
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban,
South Africa
- King Edward VIII Hospital, Durban, South Africa
| | - K L Naidoo
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban,
South Africa
- King Edward VIII Hospital, Durban, South Africa
| | - L Gounder
- Department of Virology, National Health Laboratory Service, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - R Masekela
- Department of Paediatrics and Child Health, School of Clinical Medicine, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban,
South Africa
| |
Collapse
|
4
|
Herrera AL, Potts R, Huber VC, Chaussee MS. Influenza enhances host susceptibility to non-pulmonary invasive Streptococcus pyogenes infections. Virulence 2023; 14:2265063. [PMID: 37772916 PMCID: PMC10566429 DOI: 10.1080/21505594.2023.2265063] [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: 03/31/2023] [Accepted: 09/25/2023] [Indexed: 09/30/2023] Open
Abstract
Streptococcus pyogenes (group A streptococcus; GAS) causes a variety of invasive diseases (iGAS) such as bacteremia, toxic shock syndrome, and pneumonia, which are associated with high mortality despite the susceptibility of the bacteria to penicillin ex vivo. Epidemiologic studies indicate that respiratory influenza virus infection is associated with an increase in the frequency of iGAS diseases, including those not directly involving the lung. We modified a murine model of influenza A (IAV)-GAS superinfection to determine if viral pneumonia increased the susceptibility of mice subsequently infected with GAS in the peritoneum. The results showed that respiratory IAV infection increased the morbidity (weight loss) of mice infected intraperitoneally (i.p.) with GAS 3, 5, and 10 d after the initial viral infection. Mortality was also significantly increased when mice were infected with GAS 3 and 5 d after pulmonary IAV infection. Increased mortality among mice infected with virus 5 d prior to bacterial infection correlated with increased dissemination of GAS from the peritoneum to the blood, spleen, and lungs. The interval was also associated with a significant increase in the pro-inflammatory cytokines IFN-γ, IL-12, TNF-α, MCP-1 and IL-27 in sera. We conclude, using a murine model, that respiratory influenza virus infection increases the likelihood and severity of systemic iGAS disease, even when GAS infection does not originate in the respiratory tract.
Collapse
Affiliation(s)
- Andrea L. Herrera
- Division of Basic Biomedical Sciences, The Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA
| | - Rashaun Potts
- Division of Basic Biomedical Sciences, The Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA
| | - Victor C. Huber
- Division of Basic Biomedical Sciences, The Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA
| | - Michael S. Chaussee
- Division of Basic Biomedical Sciences, The Sanford School of Medicine of the University of South Dakota, Vermillion, SD, USA
| |
Collapse
|
5
|
Luka MM, Otieno JR, Kamau E, Morobe JM, Murunga N, Adema I, Nyiro JU, Macharia PM, Bigogo G, Otieno NA, Nyawanda BO, Rabaa MA, Emukule GO, Onyango C, Munywoki PK, Agoti CN, Nokes DJ. Rhinovirus dynamics across different social structures. NPJ VIRUSES 2023; 1:6. [PMID: 38665239 PMCID: PMC11041716 DOI: 10.1038/s44298-023-00008-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/30/2023] [Indexed: 04/28/2024]
Abstract
Rhinoviruses (RV), common human respiratory viruses, exhibit significant antigenic diversity, yet their dynamics across distinct social structures remain poorly understood. Our study delves into RV dynamics within Kenya by analysing VP4/2 sequences across four different social structures: households, a public primary school, outpatient clinics in the Kilifi Health and Demographics Surveillance System (HDSS), and countrywide hospital admissions and outpatients. The study revealed the greatest diversity of RV infections at the countrywide level (114 types), followed by the Kilifi HDSS (78 types), the school (47 types), and households (40 types), cumulatively representing >90% of all known RV types. Notably, RV diversity correlated directly with the size of the population under observation, and several RV type variants occasionally fuelled RV infection waves. Our findings highlight the critical role of social structures in shaping RV dynamics, information that can be leveraged to enhance public health strategies. Future research should incorporate whole-genome analysis to understand fine-scale evolution across various social structures.
Collapse
Affiliation(s)
- Martha M. Luka
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Present Address: School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ UK
| | - James R. Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - John Mwita Morobe
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Irene Adema
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Joyce Uchi Nyiro
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Peter M. Macharia
- Population & Health Impact Surveillance Group, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Health Informatics, Computing, and Statistics, Lancaster Medical School, Lancaster University, Lancaster, UK
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | | | - Maia A. Rabaa
- Coronavirus and Other Respiratory Viruses Division (CORVD), National Center for Immunization and Respiratory Diseases (NCIRD), U.S. Centers of Disease Control and Prevention (CDC), Atlanta, GA USA
| | - Gideon O. Emukule
- U.S. Centers of Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Clayton Onyango
- U.S. Centers of Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Patrick K. Munywoki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- U.S. Centers of Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Charles N. Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- Department of Public Health, Pwani University, Kilifi, Kenya
| | - D. James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| |
Collapse
|
6
|
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.
Collapse
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.)
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Habgood-Coote D, Wilson C, Shimizu C, Barendregt AM, Philipsen R, Galassini R, Calle IR, Workman L, Agyeman PKA, Ferwerda G, Anderson ST, van den Berg JM, Emonts M, Carrol ED, Fink CG, de Groot R, Hibberd ML, Kanegaye J, Nicol MP, Paulus S, Pollard AJ, Salas A, Secka F, Schlapbach LJ, Tremoulet AH, Walther M, Zenz W, Van der Flier M, Zar HJ, Kuijpers T, Burns JC, Martinón-Torres F, Wright VJ, Coin LJM, Cunnington AJ, Herberg JA, Levin M, Kaforou M. Diagnosis of childhood febrile illness using a multi-class blood RNA molecular signature. MED 2023; 4:635-654.e5. [PMID: 37597512 DOI: 10.1016/j.medj.2023.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/08/2023] [Accepted: 06/19/2023] [Indexed: 08/21/2023]
Abstract
BACKGROUND Appropriate treatment and management of children presenting with fever depend on accurate and timely diagnosis, but current diagnostic tests lack sensitivity and specificity and are frequently too slow to inform initial treatment. As an alternative to pathogen detection, host gene expression signatures in blood have shown promise in discriminating several infectious and inflammatory diseases in a dichotomous manner. However, differential diagnosis requires simultaneous consideration of multiple diseases. Here, we show that diverse infectious and inflammatory diseases can be discriminated by the expression levels of a single panel of genes in blood. METHODS A multi-class supervised machine-learning approach, incorporating clinical consequence of misdiagnosis as a "cost" weighting, was applied to a whole-blood transcriptomic microarray dataset, incorporating 12 publicly available datasets, including 1,212 children with 18 infectious or inflammatory diseases. The transcriptional panel identified was further validated in a new RNA sequencing dataset comprising 411 febrile children. FINDINGS We identified 161 transcripts that classified patients into 18 disease categories, reflecting individual causative pathogen and specific disease, as well as reliable prediction of broad classes comprising bacterial infection, viral infection, malaria, tuberculosis, or inflammatory disease. The transcriptional panel was validated in an independent cohort and benchmarked against existing dichotomous RNA signatures. CONCLUSIONS Our data suggest that classification of febrile illness can be achieved with a single blood sample and opens the way for a new approach for clinical diagnosis. FUNDING European Union's Seventh Framework no. 279185; Horizon2020 no. 668303 PERFORM; Wellcome Trust (206508/Z/17/Z); Medical Research Foundation (MRF-160-0008-ELP-KAFO-C0801); NIHR Imperial BRC.
Collapse
Affiliation(s)
- Dominic Habgood-Coote
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Clare Wilson
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Chisato Shimizu
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Anouk M Barendregt
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Ria Philipsen
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Rachel Galassini
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Irene Rivero Calle
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Lesley Workman
- Department of Paediatrics & Child Health, Red Cross Childrens Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Philipp K A Agyeman
- Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Gerben Ferwerda
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Suzanne T Anderson
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - J Merlijn van den Berg
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Marieke Emonts
- Great North Children's Hospital, Department of Paediatric Immunology, Infectious Diseases & Allergy and NIHR Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Enitan D Carrol
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, UK
| | - Colin G Fink
- Micropathology Ltd Research and Diagnosis, Coventry, UK; University of Warwick, Coventry, UK
| | - Ronald de Groot
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Laboratory Medicine, Nijmegen, the Netherlands
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - John Kanegaye
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Mark P Nicol
- Marshall Centre, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Stéphane Paulus
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Antonio Salas
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), 15706 Galicia, Spain
| | - Fatou Secka
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - Luregn J Schlapbach
- Pediatric and Neonatal Intensive Care Unit, and Children`s Research Center, University Children's Hospital Zurich, Zurich, Switzerland; Child Health Research Centre, The University of Queensland, and Paediatric Intensive Care Unit, Queensland Children's Hospital, Brisbane, QLD, Australia
| | - Adriana H Tremoulet
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Michael Walther
- Medical Research Council Unit, Fajara, The Gambia at the London School of Hygiene and Tropical Medicine, MRCG at LSHTM Fajara, Banjul, The Gambia
| | - Werner Zenz
- University Clinic of Paediatrics and Adolescent Medicine, Department of General Paediatrics, Medical University of Graz, Graz, Austria
| | - Michiel Van der Flier
- Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands; Paediatric Infectious Diseases and Immunology Amalia Children's Hospital, Radboudumc, Nijmegen, the Netherlands
| | - Heather J Zar
- Department of Paediatrics & Child Health, Red Cross Childrens Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Taco Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Amsterdam, the Netherlands; Department of Blood Cell Research, Sanquin Blood Supply, Division Research and Landsteiner Laboratory of Amsterdam UMC (AUMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Jane C Burns
- Department of Pediatrics, Rady Children's Hospital San Diego/University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Federico Martinón-Torres
- Pediatrics Department, Translational Pediatrics and Infectious Diseases Section, Santiago de Compostela, Spain; Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group GENVIP, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Victoria J Wright
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Aubrey J Cunnington
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Jethro A Herberg
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Michael Levin
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease and Centre for Paediatrics & Child Health, Department of Infectious Disease, Imperial College London, London, UK.
| |
Collapse
|
9
|
Wadilo F, Feleke A, Gebre M, Mihret W, Seyoum T, Melaku K, Howe R, Mulu A, Mihret A. Viral etiologies of lower respiratory tract infections in children < 5 years of age in Addis Ababa, Ethiopia: a prospective case-control study. Virol J 2023; 20:163. [PMID: 37481644 PMCID: PMC10363322 DOI: 10.1186/s12985-023-02131-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Lower respiratory tract infections (LRTIs) are a major cause of morbidity and mortality in children worldwide and disproportionally affect Sub-Saharan Africa. Despite the heaviest burden of LRIs in Ethiopia, to date, no published studies have reported a comprehensive viral etiology of LRTIs among children in Ethiopia. The objective of this study was to determine and estimate the etiological contribution of respiratory viruses to LRTIs in < 5 years children in Ethiopia. METHODS A prospective case-control study was conducted from September 2019 to May 2022 in two major governmental hospitals, St. Paul Hospital Millennium Medical College and ALERT Hospital in Addis Ababa, Ethiopia. Nasopharyngeal/oropharyngeal samples and socio-demographic and clinical information were collected from children under 5 years. A one-step Multiplex real-time PCR (Allplex™ Respiratory Panel Assays 1-3) was done to detect respiratory viruses. STATA software version 17 was used for the data analysis. We computed the odds ratio (OR), the attributable fraction among exposed (AFE) and the population attributable fraction (PAF) to measure the association of the detected viruses with LRTIs. RESULTS Overall, 210 LRTIs cases and 210 non-LRTI controls were included in the study. The likelihood of detecting one or more viruses from NP/OP was higher among cases than controls (83.8% vs. 50.3%, p = 0.004). The multivariate logistic regression showed a significantly higher detection rate for RSV A (OR: 14.6, 95% CI 4.1-52.3), RSV B (OR: 8.1, 95% CI 2.3-29.1), influenza A virus (OR: 5.8, 95% CI 1.5-22.9), and PIV 1 (OR: 4.3, 95% CI 1.1-16.4), among cases when compared with controls. The overall AFE and PAF for RSV A were (93.2% and 17.3%), RSV B (87.7% and 10.4%) and Influenza A virus (82.8% and 6.3%), respectively. The mean CT values were significantly lower for only RSV B detected in the case groups as compared with the mean CT values of RSV B detected in the control group (p = 0.01). CONCLUSIONS RSV, Influenza A and PIV 1 viruses were significantly associated with LRTIs in < 5 years children in Addis Ababa, Ethiopia. Therefore, we underscore the importance of developing prevention strategies for these viruses in Ethiopia and support the importance of developing and introducing an effective vaccine against these viruses.
Collapse
Affiliation(s)
- Fiseha Wadilo
- 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 Sodo, Ethiopia.
| | - Adey Feleke
- 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
| | - Rawliegh 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
| |
Collapse
|
10
|
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.
Collapse
Affiliation(s)
- Shuang Wang
- Department of Pediatrics, Affiliated Hospital, Liaoning University of Traditional Chinese Medicine, Shenyang 110032, China
| | | | | | | | | | | |
Collapse
|
11
|
Hill V, Githinji G, Vogels CBF, Bento AI, Chaguza C, Carrington CVF, Grubaugh ND. Toward a global virus genomic surveillance network. Cell Host Microbe 2023; 31:861-873. [PMID: 36921604 PMCID: PMC9986120 DOI: 10.1016/j.chom.2023.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The COVID-19 pandemic galvanized the field of virus genomic surveillance, demonstrating its utility for public health. Now, we must harness the momentum that led to increased infrastructure, training, and political will to build a sustainable global genomic surveillance network for other epidemic and endemic viruses. We suggest a generalizable modular sequencing framework wherein users can easily switch between virus targets to maximize cost-effectiveness and maintain readiness for new threats. We also highlight challenges associated with genomic surveillance and when global inequalities persist. We propose solutions to mitigate some of these issues, including training and multilateral partnerships. Exploring alternatives to clinical sequencing can also reduce the cost of surveillance programs. Finally, we discuss how establishing genomic surveillance would aid control programs and potentially provide a warning system for outbreaks, using a global respiratory virus (RSV), an arbovirus (dengue virus), and a regional zoonotic virus (Lassa virus) as examples.
Collapse
Affiliation(s)
- Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Ana I Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA; The Rockefeller Foundation, New York, NY, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Christine V F Carrington
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
| |
Collapse
|
12
|
Krockow EM, Patel S, Roland D. Decision Challenges for Managing Acute Paediatric Infections: Implications for Antimicrobial Resistance. Antibiotics (Basel) 2023; 12:antibiotics12050828. [PMID: 37237731 DOI: 10.3390/antibiotics12050828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Overprescribing of antibiotics in paediatrics accounts for a significant proportion of inappropriate antibiotic use in human healthcare, thereby contributing to the global health emergency of antimicrobial resistance. Antimicrobial stewardship efforts are complicated by the unique social dynamics in paediatric healthcare, with a specific challenge being the prominent role of parents and carers who act as intermediaries between prescribers and paediatric patients. In this Perspective article concentrating on healthcare of the United Kingdom, we describe this complicated interplay of different decision stakeholders (patients, parents and prescribers), outline four dimensions of decision challenges (social, psychological, systemic and specific diagnostic and treatment challenges) and provide a number of theory-based strategies for supporting different stakeholders during the decision process, ultimately with the aim of improving antimicrobial stewardship. Key decision challenges for patients and carers include limited knowledge and experience of managing infections, which were exacerbated during the COVID-19 pandemic and frequently result in health anxiety and inappropriate health-seeking behaviours. Challenges for medical prescribers span societal pressures from prominent patient litigation cases, cognitive biases, and system pressures to specific diagnostic problems (e.g., age limitations of current clinical scoring systems). Strategies for mitigating decision challenges in paediatric infection management will need to include a range of context- and stakeholder-specific actions, including improvements of integrated care and public health education as well as better clinical decision tools and access to evidence-based guidelines.
Collapse
Affiliation(s)
- Eva M Krockow
- School of Psychology and Vison Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Sanjay Patel
- Department of Paediatric Infectious Diseases and Immunology, Southampton Children's Hospital, Southampton SO16 6YD, UK
| | - Damian Roland
- Paediatric Emergency Medicine Leicester Academic (PEMLA) Group, Children's Emergency Department, Leicester Royal Infirmary, Leicester LE1 5WW, UK
- SAPPHIRE Group, Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| |
Collapse
|
13
|
Nyawanda BO, Murunga N, Otieno NA, Bigogo G, Nyiro JU, Vodicka E, Bulterys M, Nokes DJ, Munywoki PK, Emukule GO. Estimates of the national burden of respiratory syncytial virus in Kenyan children aged under 5 years, 2010-2018. BMC Med 2023; 21:122. [PMID: 37004034 PMCID: PMC10067313 DOI: 10.1186/s12916-023-02787-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/15/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is among the leading childhood causes of viral pneumonia worldwide. Establishing RSV-associated morbidity and mortality is important in informing the development, delivery strategies, and evaluation of interventions. METHODS Using data collected during 2010-2018 from base regions (population-based surveillance studies in western Kenya and the Kilifi Health and Demographic Surveillance Study), we estimated age-specific rates of acute respiratory illness (ARI), severe acute respiratory illness (SARI-defined as hospitalization with cough or difficulty breathing with onset within the past 10 days), and SARI-associated deaths. We extrapolated the rates from the base regions to other regions of Kenya, while adjusting for risk factors of ARI and healthcare seeking behavior, and finally applied the proportions of RSV-positive cases identified from various sentinel and study facilities to the rates to obtain regional age-specific rates of RSV-associated outpatient and non-medically attended ARI and hospitalized SARI and severe ARI that was not hospitalized (non-hospitalized SARI). We applied age-specific RSV case fatality ratios to SARI to obtain estimates of RSV-associated in- and out-of-hospital deaths. RESULTS Among Kenyan children aged < 5 years, the estimated annual incidence of outpatient and non-medically attended RSV-associated ARI was 206 (95% credible interval, CI; 186-229) and 226 (95% CI; 204-252) per 1000 children, respectively. The estimated annual rates of hospitalized and non-hospitalized RSV-associated SARI were 349 (95% CI; 303-404) and 1077 (95% CI; 934-1247) per 100,000 children respectively. The estimated annual number of in- and out-of-hospital deaths associated with RSV infection in Kenya were 539 (95% CI; 420-779) and 1921 (95% CI; 1495-2774), respectively. Children aged < 6 months had the highest burden of RSV-associated severe disease: 2075 (95% CI; 1818-2394) and 44 (95% CI 25-71) cases per 100,000 children for hospitalized SARI and in-hospital deaths, respectively. CONCLUSIONS Our findings suggest a substantial disease burden due to RSV infection, particularly among younger children. Prioritizing development and use of maternal vaccines and affordable long-lasting monoclonal antibodies could help reduce this burden.
Collapse
Affiliation(s)
- Bryan O Nyawanda
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya.
| | - Nickson Murunga
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nancy A Otieno
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Godfrey Bigogo
- Kenya Medical Research Institute, Centre for Global Health Research, Kisumu, Kenya
| | - Joyce U Nyiro
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Marc Bulterys
- US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - D James Nokes
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | | |
Collapse
|
14
|
Wilkes C, Bava M, Graham HR, Duke T. What are the risk factors for death among children with pneumonia in low- and middle-income countries? A systematic review. J Glob Health 2023; 13:05003. [PMID: 36825608 PMCID: PMC9951126 DOI: 10.7189/jogh.13.05003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Background Knowledge of the risk factors for and causes of treatment failure and mortality in childhood pneumonia is important for prevention, diagnosis, and treatment at an individual and population level. This review aimed to identify the most important risk factors for mortality among children aged under ten years with pneumonia. Methods We systematically searched MEDLINE, EMBASE, and PubMed for observational and interventional studies reporting risk factors for mortality in children (aged two months to nine years) in low- and middle-income countries (LMICs). We screened articles according to specified inclusion and exclusion criteria, assessed risk of bias using the EPHPP framework, and extracted data on demographic, clinical, and laboratory risk factors for death. We synthesized data descriptively and using Forest plots and did not attempt meta-analysis due to the heterogeneity in study design, definitions, and populations. Findings We included 143 studies in this review. Hypoxaemia (low blood oxygen level), decreased conscious state, severe acute malnutrition, and the presence of an underlying chronic condition were the risk factors most strongly and consistently associated with increased mortality in children with pneumonia. Additional important clinical factors that were associated with mortality in the majority of studies included particular clinical signs (cyanosis, pallor, tachypnoea, chest indrawing, convulsions, diarrhoea), chronic comorbidities (anaemia, HIV infection, congenital heart disease, heart failure), as well as other non-severe forms of malnutrition. Important demographic factors associated with mortality in the majority of studies included age <12 months and inadequate immunisation. Important laboratory and investigation findings associated with mortality in the majority of studies included: confirmed Pneumocystis jirovecii pneumonia (PJP), consolidation on chest x-ray, pleural effusion on chest x-ray, and leukopenia. Several other demographic, clinical and laboratory findings were associated with mortality less consistently or in a small numbers of studies. Conclusions Risk assessment for children with pneumonia should include routine evaluation for hypoxaemia (pulse oximetry), decreased conscious state (e.g. AVPU), malnutrition (severe, moderate, and stunting), and the presence of an underlying chronic condition as these are strongly and consistently associated with increased mortality. Other potentially useful risk factors include the presence of pallor or anaemia, chest indrawing, young age (<12 months), inadequate immunisation, and leukopenia.
Collapse
Affiliation(s)
- Chris Wilkes
- Murdoch Children’s Research Institution, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Mohamed Bava
- Murdoch Children’s Research Institution, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Hamish R Graham
- Murdoch Children’s Research Institution, Royal Children’s Hospital, Parkville, Victoria, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Trevor Duke
- Murdoch Children’s Research Institution, Royal Children’s Hospital, Parkville, Victoria, Australia,Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, Victoria, Australia
| | | |
Collapse
|
15
|
Krumkamp R, Kohsar M, Nolte K, Hogan B, Eibach D, Jaeger A, Akenten CW, Drosten C, Boahen KG, Sarpong N, Eckerle I, Binger T, Owusu-Dabo E, May J, Kreuels B. Pathogens associated with hospitalization due to acute lower respiratory tract infections in children in rural Ghana: a case-control study. Sci Rep 2023; 13:2443. [PMID: 36765075 PMCID: PMC9916495 DOI: 10.1038/s41598-023-29410-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Respiratory infections are one of the most common causes of death among children under the age of five years. Data on prevalence and relevance of specific organisms in African children are still lacking. This case-control-study investigated prevalence and relevance of specific organisms in Ghanaian children admitted to hospital with symptoms of lower respiratory tract infection (LRTI). Pharyngeal swabs were taken and tested by PCR for 19 respiratory isolates. Adjusted odds ratios (aORs) were calculated to estimate associations between isolates and admission with LRTI. Population attributable fractions (PAFs) were calculated to assess the proportion of LRTI cases due to a particular pathogen. The study included 327 cases and 562 controls. We found associations between detection and admission for LRTI for influenza (aOR 98.6; 95% confidence interval (CI) 20.0-1789.6), respiratory syncytial virus (aOR 40.2; 95% CI 7.2-758.6), H. influenzae (aOR 4.1; 95% CI 2.2-7.9) and S. pneumoniae (aOR 2.4; 95% CI 1.7-3.4). PAFs ≥ 10% were observed for S. pneumoniae (30%; 95% CI 26-42), H. influenzae (10%; 95% CI 2-19) and influenza (10%; 95% CI 2-18). This study highlights the need for heightened surveillance and development of effective vaccines for respiratory pathogens other than SARS-CoV-2 in the future.
Collapse
Affiliation(s)
- Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany
| | - Matin Kohsar
- Division for Tropical Medicine, I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Kolja Nolte
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Benedikt Hogan
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Deutsche Gesellschaft Für Internationale Zusammenarbeit (GIZ GmbH), Berlin, Germany
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Anna Jaeger
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany
| | | | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Kennedy Gyau Boahen
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Nimako Sarpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Isabella Eckerle
- Department of Medicine, University of Geneva, Geneva, Switzerland
| | - Tabea Binger
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kumasi, Ghana
| | - Ellis Owusu-Dabo
- Global and International Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany
- Tropical Medicine II, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Benno Kreuels
- German Center for Infection Research (DZIF), Partner Site Hamburg - Lübeck - Borstel - Riems, Hamburg, Germany.
- Division for Tropical Medicine, I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
- Research Group Snakebite Envenoming, Department of Implementation Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Murunga N, Nyawanda B, Nyiro JU, Otieno GP, Kamau E, Agoti CN, Lewa C, Gichuki A, Mutunga M, Otieno N, Mayieka L, Ochieng M, Kikwai G, Hunsperger E, Onyango C, Emukule G, Bigogo G, Verani JR, Chaves SS, Nokes DJ, Munywoki PK. Surveillance of respiratory viruses at health facilities from across Kenya, 2014. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17908.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Acute respiratory illnesses (ARI) are a major cause of morbidity and mortality globally. With (re)emergence of novel viruses and increased access to childhood bacterial vaccines, viruses have assumed greater importance in the aetiology of ARI. There are now promising candidate vaccines against some of the most common endemic respiratory viruses. Optimal delivery strategies for these vaccines, and the need for interventions against other respiratory viruses, requires geographically diverse data capturing temporal variations in virus circulation. Methods: We leveraged three health facility-based respiratory illness surveillance platforms operating in 11 sites across Kenya. Nasopharyngeal (NP) and/or oropharyngeal (OP) specimens, patient demographic, and clinical characteristics were collected in 2014 from individuals of various ages presenting with respiratory symptoms at the surveillance facilities. Real time multiplex polymerase chain reaction was used to detect rhinoviruses, respiratory syncytial virus (RSV), influenza virus, human coronaviruses (hCoV), and adenoviruses. Results: From 11 sites, 5451 NP/OP specimens were collected and tested from patients. Of these, 40.2% were positive for at least one of the targeted respiratory viruses. The most frequently detected were rhinoviruses (17.0%) and RSV A/B (10.5%), followed by influenza A (6.2%), adenovirus (6.0%) and hCoV (4.2%). RSV was most prevalent among infants aged <12 months old (18.9%), adenovirus among children aged 12–23 months old (11.0%), influenza A among children aged 24–59 months (9.3%), and rhinovirus across all age groups (range, 12.7–19.0%). The overall percent virus positivity varied by surveillance site, health facility type and case definition used in surveillance. Conclusions: We identify rhinoviruses, RSV, and influenza A as the most prevalent respiratory viruses. Higher RSV positivity in inpatient settings compared to outpatient clinics strengthen the case for RSV vaccination. To inform the design and delivery of public health interventions, long-term surveillance is required to establish regional heterogeneities in respiratory virus circulation and seasonality.
Collapse
|
18
|
Murunga N, Nyawanda B, Nyiro JU, Otieno GP, Kamau E, Agoti CN, Lewa C, Gichuki A, Mutunga M, Otieno N, Mayieka L, Ochieng M, Kikwai G, Hunsperger E, Onyango C, Emukule G, Bigogo G, Verani JR, Chaves SS, Nokes DJ, Munywoki PK. Surveillance of respiratory viruses at health facilities from across Kenya, 2014. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17908.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Acute respiratory illnesses (ARI) are a major cause of morbidity and mortality globally. With (re)emergence of novel viruses and increased access to childhood bacterial vaccines, viruses have assumed greater importance in the aetiology of ARI. There are now promising candidate vaccines against some of the most common endemic respiratory viruses. Optimal delivery strategies for these vaccines, and the need for interventions against other respiratory viruses, requires geographically diverse data capturing temporal variations in virus circulation. Methods: We leveraged three health facility-based respiratory illness surveillance platforms operating in 11 sites across Kenya. Nasopharyngeal (NP) and/or oropharyngeal (OP) specimens, patient demographic, and clinical characteristics were collected in 2014 from individuals of various ages presenting with respiratory symptoms at the surveillance facilities. Real time multiplex polymerase chain reaction was used to detect rhinoviruses, respiratory syncytial virus (RSV), influenza virus, human coronaviruses (hCoV), and adenoviruses. Results: From 11 sites, 5451 NP/OP specimens were collected and tested from patients. Of these, 40.2% were positive for at least one of the targeted respiratory viruses. The most frequently detected were rhinoviruses (17.0%) and RSV A/B (10.5%), followed by influenza A (6.2%), adenovirus (6.0%) and hCoV (4.2%). RSV was most prevalent among infants aged <12 months old (18.9%), adenovirus among children aged 12–23 months old (11.0%), influenza A among children aged 24–59 months (9.3%), and rhinovirus across all age groups (range, 12.7–19.0%). The overall percent virus positivity varied by surveillance site, health facility type and case definition used in surveillance. Conclusions: We identify rhinoviruses, RSV, and influenza A as the most prevalent respiratory viruses. Higher RSV positivity in inpatient settings compared to outpatient clinics strengthen the case for RSV vaccination. To inform the design and delivery of public health interventions, long-term surveillance is required to establish regional heterogeneities in respiratory virus circulation and seasonality.
Collapse
|
19
|
von Mollendorf C, Berger D, Gwee A, Duke T, Graham SM, Russell FM, Mulholland EK. Aetiology of childhood pneumonia in low- and middle-income countries in the era of vaccination: a systematic review. J Glob Health 2022; 12:10009. [PMID: 35866332 PMCID: PMC9305023 DOI: 10.7189/jogh.12.10009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background This systematic review aimed to describe common aetiologies of severe and non-severe community acquired pneumonia among children aged 1 month to 9 years in low- and middle-income countries. Methods We searched the MEDLINE, EMBASE, and PubMed online databases for studies published from January 2010 to August 30, 2020. We included studies on acute community-acquired pneumonia or acute lower respiratory tract infection with ≥1 year of continuous data collection; clear consistent case definition for pneumonia; >1 specimen type (except empyema studies where only pleural fluid was required); testing for >1 pathogen including both viruses and bacteria. Two researchers reviewed the studies independently. Results were presented as a narrative summary. Quality of evidence was assessed with the Quality Assessment Tool for Quantitative Studies. The study was registered on PROSPERO [CRD42020206830]. Results We screened 5184 records; 1305 duplicates were removed. The remaining 3879 titles and abstracts were screened. Of these, 557 articles were identified for full-text review, and 55 met the inclusion criteria - 10 case-control studies, three post-mortem studies, 11 surveillance studies, eight cohort studies, five cross-sectional studies, 12 studies with another design and six studies that included patients with pleural effusions or empyema. Studies which described disease by severity showed higher bacterial detection (Streptococcus pneumoniae, Staphylococcus aureus) in severe vs non-severe cases. The most common virus causing severe disease was respiratory syncytial virus (RSV). Pathogens varied by age, with RSV and adenovirus more common in younger children. Influenza and atypical bacteria were more common in children 5-14 years than younger children. Malnourished and HIV-infected children had higher rates of pneumonia due to bacteria or tuberculosis. Conclusions Several viral and bacterial pathogens were identified as important targets for prevention and treatment. Bacterial pathogens remain an important cause of moderate to severe disease, particularly in children with comorbidities despite widespread PCV and Hib vaccination.
Collapse
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
| | | |
Collapse
|
20
|
Ojuawo OB, Iroh Tam PY. Childhood Pneumonia Diagnostics in Sub-Saharan Africa: A Systematic Review. J Trop Pediatr 2022; 68:6604072. [PMID: 35674266 DOI: 10.1093/tropej/fmac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND The prompt and accurate aetiological diagnosis of childhood pneumonia remains a challenge, especially in sub-Saharan Africa (SSA) because of limited resources for disease management. OBJECTIVE To review existing diagnostics for childhood pneumonia and potential modalities available to differentiate between bacterial and viral aetiologies in SSA. METHODS Online databases were searched for relevant articles published between January 2010 and December 2020 regarding childhood pneumonia diagnosis, conducted in SSA in children less than 18 years of age. The 2020 PRISMA checklist was utilized in appraising the selected studies and the QUADAS-2 tool was employed to assess the risk of bias in each of the studies selected. RESULTS A total of 1542 study titles and abstracts were screened following which 45 studies (39 on childhood pneumonia diagnostics and 6 on discriminating between bacterial and viral childhood pneumonia) were selected for review. Microbiological investigations (79.7%) constituted the most utilized index tests with blood-related specimen (32.8%) being the most utilized specimen. The most performed index diagnostic modality was polymerase chain reaction (PCR) (53.1%). The commonest reference gold standard technique was based on clinical diagnosis of the disease (46.2%). Only six studies in SSA attempted at using serum biomarkers, either singly or in combination to distinguish between aetiologies with use of combined biomarkers showing promise. CONCLUSION Microbiological investigations are the most employed diagnostic methods for childhood pneumonia in SSA. More studies are required to evaluate the potential use of serum biomarkers; either singly or in combination with the goal of discriminating bacterial and viral childhood pneumonia.
Collapse
Affiliation(s)
| | - Pui-Ying Iroh Tam
- Respiratory Department, Sandwell and West Birmingham Hospitals NHS Trust, Dudley Road, Birmingham B187QH, UK.,Department of Paediatrics and Child Health, Kamuzu University of Health Sciences, Blantyre, Malawi.,Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| |
Collapse
|
21
|
Rhedin S, Eklundh A, Ryd-Rinder M, Peltola V, Waris M, Gantelius J, Lindh M, Andersson M, Gaudenzi G, Mårtensson A, Naucler P, Alfvén T. Myxovirus resistance protein A for discriminating between viral and bacterial lower respiratory tract infections in children - The TREND study. Clin Microbiol Infect 2022; 28:1251-1257. [PMID: 35597507 DOI: 10.1016/j.cmi.2022.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Discriminating between viral and bacterial lower respiratory tract infection (LRTI) in children is challenging, leading to an excessive use of antibiotics. Myxovirus resistance protein A (MxA) is a promising biomarker for viral infections. The primary aim of the study was to assess differences in blood MxA levels between children with viral and bacterial LRTI. Secondary aims were to assess differences in blood MxA levels between children with viral LRTI and asymptomatic controls and to assess MxA levels in relation to different respiratory viruses. METHODS Children with LRTI were enrolled as cases at Sachs' Children and Youth Hospital, Stockholm, Sweden. Nasopharyngeal aspirates and blood samples for analysis of viral PCR, MxA and CRP were systematically collected from all study subjects in addition to standard laboratory/radiology assessment. Aetiology was defined according to an algorithm based on laboratory and radiological findings. Asymptomatic children with minor surgical disease were enrolled as controls. RESULTS MxA levels were higher in children with viral LRTI (n=242) as compared to both bacterial (n=5) LRTI (p<0.01, area under the curve (AUC) 0.90, 95% confidence interval (CI):0.81-0.99) and controls (AUC 0.92, 95% CI:0.88-0.95). In the subgroup of children with pneumonia diagnosis, a cut-off of MxA 430μg/l discriminated between viral (n=29) and bacterial (n=4) aetiology with 93% (95% CI: 78%-99%) sensitivity and 100% (95% CI: 51%-100%) specificity (AUC 0.98, 95% CI: 0.94-1.00). The highest MxA levels were seen in cases PCR positive for influenza (median MxA 1699μg/l, interquartile range (IQR): 732-2996) and respiratory syncytial virus (median MxA 1115μg/l, IQR: 679-2489). CONCLUSION MxA accurately discriminated between viral and bacterial aetiology in children with LRTI, particularly in the group of children with pneumonia diagnosis, but the number of children with bacterial LRTI was low.
Collapse
Affiliation(s)
- Samuel Rhedin
- Pediatric Emergency Unit, Sachs' Children and Youth Hospital, Stockholm, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
| | - Annika Eklundh
- Pediatric Emergency Unit, Sachs' Children and Youth Hospital, Stockholm, Sweden; Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Malin Ryd-Rinder
- Pediatric Emergency Department, Astrid Lindgren Children's Hospital, Karolinska university Hospital, Stockholm, Sweden; Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Ville Peltola
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital, University of Turku, Finland
| | - Matti Waris
- Institute of Biomedicine, University of Turku and Clinical Microbiology, Turku University Hospital, Finland
| | - Jesper Gantelius
- Department of Protein Science, Division of Nanobiotechnology, KTH Royal Institute of Technology, SciLifeLab, Solna, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Maria Andersson
- Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Giulia Gaudenzi
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden; Department of Protein Science, Division of Nanobiotechnology, KTH Royal Institute of Technology, SciLifeLab, Solna, Sweden
| | - Andreas Mårtensson
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Sweden
| | - Pontus Naucler
- Division of Infectious Diseases, Department of Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Solna, Sweden
| | - Tobias Alfvén
- Pediatric Emergency Unit, Sachs' Children and Youth Hospital, Stockholm, Sweden; Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
22
|
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.
Collapse
|
23
|
Giacomelli Cao R, Christian L, Xu Z, Jaramillo L, Smith B, Karlsson EA, Schultz-Cherry S, Mejias A, Ramilo O. Early Changes in Interferon Gene Expression and Antibody Responses Following Influenza Vaccination in Pregnant Women. J Infect Dis 2022; 225:341-351. [PMID: 34197595 PMCID: PMC8915434 DOI: 10.1093/infdis/jiab345] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/29/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Influenza immunization during pregnancy provides protection to the mother and the infant. Studies in adults and children with inactivated influenza vaccine have identified changes in immune gene expression that were correlated with antibody responses. The current study was performed to define baseline blood transcriptional profiles and changes induced by inactivated influenza vaccine in pregnant women and to identify correlates with antibody responses. METHODS Pregnant women were immunized with inactivated influenza vaccine during the 2013-2014 and 2014-2015 seasons. Blood samples were collected on day 0 (before vaccination) and on days 1 and 7 after vaccination for transcriptional profile analyses, and on days 0 and 30, along with delivery and cord blood samples, to measure antibody titers. RESULTS Transcriptional analysis demonstrated overexpression of interferon-stimulated genes (ISGs) on day 1 and of plasma cell genes on day 7. Prevaccination ISG expression and ISGs overexpressed on day 1 were significantly correlated with increased H3N2, B Yamagata, and B Victoria antibody titers. Plasma cell gene expression on day 7 was correlated with increased B Yamagata and B Victoria antibody titers. Compared with women who were vaccinated during the previous influenza season, those who were not showed more frequent significant correlations between ISGs and antibody titers. CONCLUSIONS Influenza vaccination in pregnant women resulted in enhanced expression of ISGs and plasma cell genes correlated with antibody responses. Brief summary: This study identified gene expression profiles of interferon-stimulated genes and plasma cells before vaccination and early after vaccination that were correlated with antibody responses in pregnant women vaccinated for influenza.
Collapse
Affiliation(s)
- Raquel Giacomelli Cao
- Center for Vaccines and Immunity, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Lisa Christian
- Institute for Behavioral Medical Research, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Department of Psychiatry, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Zhaohui Xu
- Center for Vaccines and Immunity, Nationwide Children’s Hospital, Columbus, Ohio, USA
- The Ohio State University, Columbus, Ohio, USA
| | - Lisa Jaramillo
- Center for Vaccines and Immunity, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Bennett Smith
- Center for Vaccines and Immunity, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Erik A Karlsson
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Current affiliation: Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Asuncion Mejias
- Center for Vaccines and Immunity, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Division of Infectious Diseases, Nationwide Children’s Hospital, Columbus, Ohio, USA
- The Ohio State University, Columbus, Ohio, USA
| | - Octavio Ramilo
- Center for Vaccines and Immunity, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Division of Infectious Diseases, Nationwide Children’s Hospital, Columbus, Ohio, USA
- The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
24
|
Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya. Sci Rep 2022; 12:202. [PMID: 34997042 PMCID: PMC8742071 DOI: 10.1038/s41598-021-03987-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/02/2021] [Indexed: 01/30/2023] Open
Abstract
Pneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus diagnostics in Kilifi, Kenya, using random-primed viral next generation sequencing (viral NGS) on respiratory samples which tested negative for the common viral respiratory pathogens by a local standard diagnostic panel. Among 95 hospitalised pneumonia patients and 95 household-cohort individuals, analysis of viral NGS identified at least one respiratory-associated virus in 35 (37%) and 23 (24%) samples, respectively. The majority (66%; 42/64) belonged to the Picornaviridae family. The NGS data analysis identified a number of viruses that were missed by the diagnostic panel (rhinovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus), and these failures could be attributed to PCR primer/probe binding site mismatches. Unexpected viruses identified included parvovirus B19, enterovirus D68, coxsackievirus A16 and A24 and rubella virus. The regular application of such viral NGS could help evaluate assay performance, identify molecular causes of missed diagnoses and reveal gaps in the respiratory virus set used for local screening assays. The results can provide actionable information to improve the local pneumonia diagnostics and reveal locally important viral pathogens.
Collapse
|
25
|
Mwita Morobe J, Kamau E, Murunga N, Gatua W, Luka MM, Lewa C, Cheruiyot R, Mutunga M, Odundo C, James Nokes D, Agoti CN. Trends and Intensity of Rhinovirus Invasions in Kilifi, Coastal Kenya, Over a 12-Year Period, 2007-2018. Open Forum Infect Dis 2021; 8:ofab571. [PMID: 34988244 PMCID: PMC8694214 DOI: 10.1093/ofid/ofab571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/11/2021] [Indexed: 12/05/2022] Open
Abstract
Background Rhinoviruses (RVs) are ubiquitous pathogens and the principal etiological agents of common cold. Despite the high frequency of RV infections, data describing their long-term epidemiological patterns in a defined population remain limited. Methods Here, we analyzed 1070 VP4/VP2 genomic region sequences sampled at Kilifi County Hospital on the Kenya coast. The samples were collected between 2007 and 2018 from hospitalized pediatric patients (<60 months of age) with acute respiratory illness. Results Of 7231 children enrolled, RV was detected in 1497 (20.7%) and VP4/VP2 sequences were recovered from 1070 samples (71.5%). A total of 144 different RV types were identified (67 Rhinovirus A, 18 Rhinovirus B, and 59 Rhinovirus C) and at any month, several types co-circulated with alternating predominance. Within types, multiple genetically divergent variants were observed. Ongoing RV infections through time appeared to be a combination of (1) persistent types (observed up to 7 consecutive months), (2) reintroduced genetically distinct variants, and (3) new invasions (average of 8 new types annually). Conclusions Sustained RV presence in the Kilifi community is mainly due to frequent invasion by new types and variants rather than continuous transmission of locally established types/variants.
Collapse
Affiliation(s)
- John Mwita Morobe
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nickson Murunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Winfred Gatua
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Martha M Luka
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Clement Lewa
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Robinson Cheruiyot
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Martin Mutunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Calleb Odundo
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
| |
Collapse
|
26
|
Cimolai N. Co-detections versus coinfections in the context of SARS-CoV-2 diagnostics. J Antimicrob Chemother 2021; 77:542. [PMID: 34695212 DOI: 10.1093/jac/dkab391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nevio Cimolai
- Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada.,Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
27
|
A Multicenter Study of Viral Aetiology of Community-Acquired Pneumonia in Hospitalized Children in Chinese Mainland. Virol Sin 2021; 36:1543-1553. [PMID: 34523109 PMCID: PMC8440149 DOI: 10.1007/s12250-021-00437-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/18/2021] [Indexed: 12/25/2022] Open
Abstract
Community-acquired pneumonia (CAP) is one of the leading causes of morbidity and mortality in children worldwide. In this study, we aimed to describe the aetiology of viral infection of pediatric CAP in Chinese mainland. During November 2014 to June 2016, the prospective study was conducted in 13 hospitals. The hospitalized children under 18 years old who met the criteria for CAP were enrolled. The throat swabs or nasopharyngeal aspirates (NPAs) were collected which were then screened 18 respiratory viruses using multiplex PCR assay. Viral pathogens were present in 56.6% (1539/2721) of the enrolled cases, with the detection rate of single virus in 39.8% of the cases and multiple viruses in 16.8% of the cases. The most frequently detected virus was respiratory syncytial virus (RSV) (15.2%, 414/2721). The highest detection rate of virus was in < 6-month-age group (70.7%, 292/413). RSV, human metapneumovirus (HMPV), human parainfluenza viruses (HPIVs) and influenza B virus (Flu B) showed the similar prevalence patterns both in north and south China, but HPIVs, Flu A, human bocavirus (HBoV), human adenovirus (HAdV) and human coronaviruses (HCoVs) showed the distinct circulating patterns in north and south China. Human enterovirus/human rhinovirus (HEV/HRV) (27.6%, 27/98), HBoV (18.4%, 18/98), RSV (16.3%, 16/98) and HMPV (14.3%, 14/98) were the most commonly detected viruses in severe pneumonia cases with single virus infection. In conclusion, viral pathogens are frequently detected in pediatric CAP cases and may therefore play a vital role in the aetiology of CAP. RSV was the most important virus in hospitalized children with CAP in Chinese mainland.
Collapse
|
28
|
Caballero MT, Satav A, Gill CJ, Omer SB, Pieciak RC, Kazi AM, Simões EA, Polack FP. Challenges of Assessing Community Mortality Due to Respiratory Viruses in Children Aged Less Than 5 Years. Clin Infect Dis 2021; 73:S248-S254. [PMID: 34472573 PMCID: PMC8411250 DOI: 10.1093/cid/ciab487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background Estimating the real impact of respiratory syncytial virus (RSV) disease is key for the development of vaccines and treatments. Ascertaining the burden of community mortality due to RSV is challenging due to the lack of primary data. Therefore, conducting observational studies to determine the factors associated with community mortality due to the virus in developing countries is important. Objective Our aim in this study was to describe the obstacles, gaps, and challenges that investigators face in low-income, vulnerable regions in 4 developing countries on 3 continents. Results The main obstacles and challenges of ascertaining community mortality due to RSV were defining strategies to consent families for testing before burial, sampling individuals at the household level, supporting bereaved parents with different cultural and religious backgrounds, establishing tailored strategies for studies in challenging settings, and integrating RSV mortality data from nasopharyngeal samples. Conclusion Detailed logistical planning based on population sociodemographic information, grief counseling, staff training, and a multidisciplinary approach with adequate laboratory infrastructure is critical to successful observational community-based RSV studies.
Collapse
Affiliation(s)
- Mauricio T Caballero
- Fundacion INFANT, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, (CONICET), Buenos Aires, Argentina
| | - Ashish Satav
- Meditation, AIDS, Health, Addiction & Nutrition (MAHAN) (MAHAN) Trust, Mahatma Gandhi Tribal Hospital Karmagram, Utavali, Tahsil, Dharni, Amravati, India
| | - Christopher J Gill
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Saad B Omer
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA.,Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, USA.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA.,Yale School of Nursing, Yale University, New Haven, Connecticut, USA
| | - Rachel C Pieciak
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Abdul Momin Kazi
- Department of Pediatrics, The Aga Khan University, Karachi, Pakistan
| | - Eric Af Simões
- Department of Pediatrics, Section of Infectious Diseases, University of Colorado School of Medicine, and Children's Hospital Colorado, Aurora, Colorado, USA.,Department of Epidemiology, Center for Global Health Colorado School of Public Health, Aurora, Colorado, USA
| | | |
Collapse
|
29
|
Awori JO, Kamau A, Morpeth S, Kazungu S, Silaba M, Sande J, Karani A, Nyongesa S, Mwarumba S, Musyimi R, Bett A, Wande S, Shebe M, Ngama M, Munywoki PK, Muturi N, Nokes DJ, Feikin DR, Murdoch DR, Prosperi C, O’Brien KL, Deloria Knoll M, Hammitt LL, Scott JAG. The Etiology of Pneumonia in HIV-uninfected Children in Kilifi, Kenya: Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study. Pediatr Infect Dis J 2021; 40:S29-S39. [PMID: 34448742 PMCID: PMC8448399 DOI: 10.1097/inf.0000000000002653] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND In the 1980s, Streptococcus pneumoniae and Haemophilus influenzae were identified as the principal causes of severe pneumonia in children. We investigated the etiology of severe childhood pneumonia in Kenya after introduction of conjugate vaccines against H. influenzae type b, in 2001, and S. pneumoniae, in 2011. METHODS We conducted a case-control study between August 2011 and November 2013 among residents of the Kilifi Health and Demographic Surveillance System 28 days to 59 months of age. Cases were hospitalized at Kilifi County Hospital with severe or very severe pneumonia according to the 2005 World Health Organization definition. Controls were randomly selected from the community and frequency matched to cases on age and season. We tested nasal and oropharyngeal samples, sputum, pleural fluid, and blood specimens and used the Pneumonia Etiology Research for Child Health Integrated Analysis, combining latent class analysis and Bayesian methods, to attribute etiology. RESULTS We enrolled 630 and 863 HIV-uninfected cases and controls, respectively. Among the cases, 282 (44%) had abnormal chest radiographs (CXR positive), 33 (5%) died in hospital, and 177 (28%) had diagnoses other than pneumonia at discharge. Among CXR-positive pneumonia cases, viruses and bacteria accounted for 77% (95% CrI: 67%-85%) and 16% (95% CrI: 10%-26%) of pneumonia attribution, respectively. Respiratory syncytial virus, S. pneumoniae and H. influenza, accounted for 37% (95% CrI: 31%-44%), 5% (95% CrI: 3%-9%), and 6% (95% CrI: 2%-11%), respectively. CONCLUSIONS Respiratory syncytial virus was the main cause of CXR-positive pneumonia. The small contribution of H. influenzae type b and pneumococcus to pneumonia may reflect the impact of vaccine introductions in this population.
Collapse
Affiliation(s)
- Juliet O. Awori
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Alice Kamau
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Susan Morpeth
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Sidi Kazungu
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Micah Silaba
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | | | - Angela Karani
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Sammy Nyongesa
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Salim Mwarumba
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Robert Musyimi
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Anne Bett
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Siti Wande
- Clinical Sciences Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Mohammed Shebe
- Clinical Sciences Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Mwanajuma Ngama
- Clinical Sciences Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Patrick K. Munywoki
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - Neema Muturi
- Clinical Sciences Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
| | - D. James Nokes
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
- School of Life Sciences and WIDER, University of Warwick, Coventry, United Kingdom
| | - Daniel R. Feikin
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David R. Murdoch
- Department of Pathology, University of Otago, Christchurch, New Zealand
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Christine Prosperi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Katherine L. O’Brien
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Maria Deloria Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Laura L. Hammitt
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - J. Anthony G. Scott
- From the Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, CGMR-Coast, Kilifi, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Nuffield Department of Tropical Medicine, Oxford University, Oxford, United Kingdom
| |
Collapse
|
30
|
El-Nawawy A, Antonios MA, Meheissen MA, Fahim MM. Respiratory viruses associated with severe mechanically ventilated pneumonia in children. J Med Virol 2021; 94:461-468. [PMID: 34415627 PMCID: PMC8426888 DOI: 10.1002/jmv.27284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/18/2021] [Indexed: 12/11/2022]
Abstract
The burden of pneumonia, especially that caused by respiratory viruses, is markedly high in the pediatric age group. This study aimed to assess viral agents causing severe pneumonia among mechanically ventilated patients. Nonbronchoscopic bronchoalveolar lavage was performed for pediatric patients having severe pneumonia indicated for mechanical ventilation to be tested with a multiplex PCR immediate diagnosis of their etiologic pathogen. Among the 75 patients recruited, viral agents were detected in 73.4% of cases. Rhinovirus and respiratory syncytial virus (RSV) were the most common viruses detected in 32.1% and 29.5%, respectively. The rate of viral infection showed a clear increased incidence in the winter season. The mortality rate among viral‐associated severe pneumonia reached 56.36%. Odds of mortality increased threefolds in presence of comorbid conditions and 10‐folds with congenital heart disease. The study demonstrated the neglected importance of rhinovirus besides RSV in causing severe critical pneumonia in the pediatric age.
Collapse
Affiliation(s)
- Ahmed El-Nawawy
- Department of Pediatrics, Faculty of Medicine, El-Shatby Children's Hospital Alexandria, Alexandria University, Alexandria, Egypt
| | - Manal Am Antonios
- Department of Pediatrics, Faculty of Medicine, El-Shatby Children's Hospital Alexandria, Alexandria University, Alexandria, Egypt
| | - Marwa A Meheissen
- Department of Medical Microbiology and Immuology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Marwan M Fahim
- Department of Pediatrics, Faculty of Medicine, El-Shatby Children's Hospital Alexandria, Alexandria University, Alexandria, Egypt
| |
Collapse
|
31
|
Roguski KM, Rolfes MA, Reich JS, Owens Z, Patel N, Fitzner J, Cozza V, Lafond KE, Azziz-Baumgartner E, Iuliano AD. Variability in published rates of influenza-associated hospitalizations: A systematic review, 2007-2018. J Glob Health 2021; 10:020430. [PMID: 33274066 PMCID: PMC7699004 DOI: 10.7189/jogh.10.020430] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background Influenza burden estimates help provide evidence to support influenza prevention and control programs at local and international levels. Methods Through a systematic review, we aimed to identify all published articles estimating rates of influenza-associated hospitalizations, describe methods and data sources used, and identify regions of the world where estimates are still lacking. We evaluated study heterogeneity to determine if we could pool published rates to generate global estimates of influenza-associated hospitalization. Results We identified 98 published articles estimating influenza-associated hospitalization rates from 2007-2018. Most articles (65%) identified were from high-income countries, with 34 of those (53%) presenting estimates from the United States. While we identified fewer publications (18%) from low- and lower-middle-income countries, 50% of those were published from 2015-2018, suggesting an increase in publications from lower-income countries in recent years. Eighty percent (n = 78) used a multiplier approach. Regression modelling techniques were only used with data from upper-middle or high-income countries where hospital administrative data was available. We identified variability in the methods, case definitions, and data sources used, including 91 different age groups and 11 different categories of case definitions. Due to the high observed heterogeneity across articles (I2>99%), we were unable to pool published estimates. Conclusions The variety of methods, data sources, and case definitions adapted locally suggests that the current literature cannot be synthesized to generate global estimates of influenza-associated hospitalization burden.
Collapse
Affiliation(s)
| | - Melissa A Rolfes
- US Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Jeremy S Reich
- US Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Zachary Owens
- Emory University, Rollins School of Public Health, Department of Epidemiology, Atlanta, Georgia, USA
| | - Neha Patel
- US Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Julia Fitzner
- World Health Organization, Global Influenza Programme, Geneva, Switzerland
| | - Vanessa Cozza
- World Health Organization, Global Influenza Programme, Geneva, Switzerland
| | - Kathryn E Lafond
- US Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | | | - A Danielle Iuliano
- US Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| |
Collapse
|
32
|
Design and Evaluation of Multiplex One-Step Reverse Transcription PCR-Dipstick Chromatography Method for the Analysis of Seven Respiratory Pathogens. Curr Microbiol 2021; 78:3656-3666. [PMID: 34338833 PMCID: PMC8326646 DOI: 10.1007/s00284-021-02621-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022]
Abstract
Influenza A, influenza B, severe acute respiratory syndrome coronavirus 2, adenovirus, respiratory syncytial virus, Mycoplasma pneumoniae, and Chlamydophila pneumoniae are common pathogens that can cause severe pneumonia and other symptoms, resulting in acute lower respiratory tract infections. The objective of this study was to design and evaluate a sensitive and specific multiplex one-step reverse transcription PCR (RT-PCR)–dipstick chromatography method for simultaneous rapid detection of these seven pathogens. Streptavidin-coated blue latex particles were used to read out a positive signal. Based on the DNA–DNA hybridization of oligonucleotide sequences (Tag) for forward primer with the complementary oligonucleotide sequence (cTag) on the dipstick and biotin–streptavidin interactions, PCR products were able to be illuminated visually on the dipstick. The specificity and the limit of detection (LOD) were also evaluated. Moreover, the clinical performance of this method was compared with Sanger sequencing for 896 samples. No cross reaction with other pathogens was found, confirming the high specificity of this method. The LOD was 10 copies/µL for each of the tested pathogens, and the whole procedure took less than 40 min. Using 896 samples, the sensitivity and specificity were shown to be no lower than 94.5%. The positive predictive value was higher than 82.1%, and the negative predictive value was higher than 99.5%. The kappa value between the PCR–dipstick chromatography method and Sanger sequencing ranged from 0.869 to 0.940. In summary, our one-step RT-PCR–dipstick chromatography method is a sensitive and specific tool for rapidly detecting multiplex respiratory pathogens.
Collapse
|
33
|
Epidemiology of Human Metapneumovirus-associated Lower Respiratory Tract Infections in African Children: Systematic Review and Meta-analysis. Pediatr Infect Dis J 2021; 40:479-485. [PMID: 33480663 DOI: 10.1097/inf.0000000000003041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Human metapneumovirus (hMPV) has been associated with upper and lower respiratory tract infections (LRTI) in children and adults. This systematic review evaluated the epidemiology of hMPV-associated LRTI, including severe acute respiratory infection (SARI) hospitalization or clinically diagnosed severe pneumonia, in African children under 5 years of age. METHODS We searched Science Direct, PubMed, Cochrane Central, Scopus, and WHO regional databases using the terms "("Human metapneumovirus" AND "Africa") OR ("hMPV" AND "Africa")" up to September 17, 2020. Other sources included ClinicalTrials.gov to obtain unpublished data. Studies were included if children were less than 5 years of age and hospitalized with hMPV-associated LRTI, SARI or if clinically diagnosed with severe pneumonia in the community. The main outcomes were prevalence of hMPV identified among children with hospitalized LRTI or SARI. We further calculated odds ratios for hMPV in cases with LRTI compared with non-LRTI controls. Pooled results were calculated using a random-effects model. RESULTS Thirty studies were eligible for inclusion in the review. The prevalence of hMPV-LRTI/SARI among hospitalized and severe pneumonia cases was 4.7% [95% confidence interval (CI): 3.9-5.6, I2 = 95.0]. The case-control studies indicated that hMPV was 2.0-fold (95% CI: 0.9-4.4) more likely to be identified in LRTI cases (10.3%) than controls (6.0%). Three of 5 studies reported hMPV-associated LRTI case fatality risk, with a pooled estimate of 1.3% (95% CI: 0.3-2.9; I2 = 49). CONCLUSIONS hMPV was associated with approximately 5% of LRTI/SARI hospitalizations or severe pneumonia cases in Africa.
Collapse
|
34
|
Umuhoza T, Bulimo WD, Oyugi J, Musabyimana JP, Kinengyere AA, Mancuso JD. Prevalence of human respiratory syncytial virus, parainfluenza and adenoviruses in East Africa Community partner states of Kenya, Tanzania, and Uganda: A systematic review and meta-analysis (2007-2020). PLoS One 2021; 16:e0249992. [PMID: 33905425 PMCID: PMC8078816 DOI: 10.1371/journal.pone.0249992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 03/29/2021] [Indexed: 01/19/2023] Open
Abstract
Background Viruses are responsible for a large proportion of acute respiratory tract infections (ARTIs). Human influenza, parainfluenza, respiratory-syncytial-virus, and adenoviruses are among the leading cause of ARTIs. Epidemiological evidence of those respiratory viruses is limited in the East Africa Community (EAC) region. This review sought to identify the prevalence of respiratory syncytial virus, parainfluenza, and adenoviruses among cases of ARTI in the EAC from 2007 to 2020. Methods A literature search was conducted in Medline, Global Index Medicus, and the grey literature from public health institutions and programs in the EAC. Two independent reviewers performed data extraction. We used a random effects model to pool the prevalence estimate across studies. We assessed heterogeneity with the I2 statistic, and Cochran’s Q test, and further we did subgroup analysis. This review was registered with PROSPERO under registration number CRD42018110186. Results A total of 12 studies met the eligibility criteria for the studies documented from 2007 to 2020. The overall pooled prevalence of adenoviruses was 13% (95% confidence interval [CI]: 6–21, N = 28829), respiratory syncytial virus 11% (95% CI: 7–15, N = 22627), and parainfluenza was 9% (95% CI: 7–11, N = 28363). Pooled prevalence of reported ARTIs, all ages, and locality varied in the included studies. Studies among participants with severe acute respiratory disease had a higher pooled prevalence of all the three viruses. Considerable heterogeneity was noted overall and in subgroup analysis. Conclusion Our findings indicate that human adenoviruses, respiratory syncytial virus and parainfluenza virus are prevalent in Kenya, Tanzania, and Uganda. These three respiratory viruses contribute substantially to ARTIs in the EAC, particularly among those with severe disease and those aged five and above.
Collapse
Affiliation(s)
- Therese Umuhoza
- Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Wallace D. Bulimo
- Department of Emerging Infectious Diseases, United States Army Medical Directorate – Africa, Nairobi, Kenya
- School of Medicine, University of Nairobi, Nairobi, Kenya
- * E-mail:
| | - Julius Oyugi
- Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | | | - Alison A. Kinengyere
- Sir Albert Cook Library, College of Health Sciences, University Makerere, Kampala, Uganda
| | - James D. Mancuso
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| |
Collapse
|
35
|
Abstract
The current frequency of COVID-19 in a pandemic era ensures that co-infections with a variety of co-pathogens will occur. Generally, there is a low rate of bonafide co-infections in early COVID-19 pulmonary infection as currently appreciated. Reports of high co-infection rates must be tempered by limitations in current diagnostic methods since amplification technologies do not necessarily confirm live pathogen and may be subject to considerable laboratory variation. Some laboratory methods may not exclude commensal microbes. Concurrent serodiagnoses have long been of concern for accuracy in these contexts. Presumed virus co-infections are not specific to COVID-19. The association of influenza viruses and SARS-CoV-2 in co-infection has been considerably variable during influenza season. Other respiratory virus co-infections have generally occurred in less than 10% of COVID-19 patients. Early COVID-19 disease is more commonly associated with bacterial co-pathogens that typically represent usual respiratory micro-organisms. Late infections, especially among severe clinical presentations, are more likely to be associated with nosocomial or opportunistic pathogens given the influence of treatments that can include antibiotics, antivirals, immunomodulating agents, blood products, immunotherapy, steroids, and invasive procedures. As anticipated, hospital care carries risk for multi-resistant bacteria. Overall, co-pathogen identification is linked with longer hospital stay, greater patient complexity, and adverse outcomes. As for other viral infections, a general reduction in the use of empiric antibiotic treatment is warranted. Further insight into co-infections with COVID-19 will contribute overall to effective antimicrobial therapies and disease control.
Collapse
Affiliation(s)
- Nevio Cimolai
- Faculty of Medicine, The University of British Columbia, Vancouver, Canada.,Children's and Women's Health Centre of British Columbia, 4480 Oak Street, Vancouver, B.C. V6H3V4 Canada
| |
Collapse
|
36
|
Yu X, Ma Y, Gao Y, You H. Epidemiology of Adenovirus Pneumonia and Risk Factors for Bronchiolitis Obliterans in Children During an Outbreak in Jilin, China. Front Pediatr 2021; 9:722885. [PMID: 34650942 PMCID: PMC8506152 DOI: 10.3389/fped.2021.722885] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/02/2021] [Indexed: 01/13/2023] Open
Abstract
Background: Jilin Province, located in northeastern China, recently experienced a human adenovirus (HAdV) epidemic. Few studies involving hospitalized pediatric patients with pneumonia caused by HAdV in our region exist. HAdV pneumonia can lead to severe long-term respiratory sequelae, such as post-infectious bronchiolitis obliterans (PIBO), which has a poor prognosis and greatly influences the quality of life of pediatric patients. However, studies on the risk factors for PIBO are limited. Objective: To describe the HAdV pneumonia prevalence and determine potential risk factors for PIBO development among hospitalized children in Jilin Province, China. Methods: The data of 187 children with HAdV pneumonia (10 months-12 years old) admitted to the First Hospital of Jilin University during an outbreak between October 2018 and January 2020 were retrospectively studied. We analyzed the epidemiological characteristics of HAdV pneumonia, focusing on severe HAdV pneumonia (66 cases). The risk factors for BO development were determined by comparing the demographic and clinical data of the BO and non-BO groups. Results: The largest number of HAdV pneumonia cases occurred in January 2019 (severe n = 18, general n = 21), followed by December 2018 (severe n = 14, general n = 11), June 2019 (general n = 17), July 2019 (general, n = 14), and May 2019 (general, n = 13). In total, 91.98% of the children with HAdV pneumonia were <6 years old (172/187), and 50% of the pediatric patients with severe HAdV pneumonia were <2 years old (33/66). We found that 30.3% of the severe cohort developed BO (20/66), and the strongest independent risk factors for PIBO were persistent wheezing (OR 181.776, 95% CI, 3.385-9,761.543) and acute respiratory failure (OR 51.288, 95% CI, 1.858-1,415.441) during a severe pneumonia episode. Conclusions: The largest number of HAdV pneumonia cases, especially severe cases, occurred in winter in Northeast China, followed by summer. The majority of children admitted with HAdV pneumonia were <6 years old, and half of severe HAdV pneumonia patients were <2 years old. Children who had persistent wheezing or acute respiratory failure during the acute phase of severe HAdV pneumonia were prone to the development of BO.
Collapse
Affiliation(s)
- Xiuhua Yu
- Department of Pediatrics, First Hospital of Jilin University, Changchun, China
| | - Yucong Ma
- Department of Pediatrics, First Hospital of Jilin University, Changchun, China
| | - Yang Gao
- Department of Pediatrics, First Hospital of Jilin University, Changchun, China
| | - Hailong You
- Department of Pediatrics, First Hospital of Jilin University, Changchun, China
| |
Collapse
|
37
|
Rose EB, Nyawanda BO, Munywoki PK, Murunga N, Bigogo GM, Otieno NA, Onyango C, Chaves SS, Verani JR, Emukule GO, Widdowson MA, Nokes DJ, Gerber SI, Langley GE. Respiratory syncytial virus seasonality in three epidemiological zones of Kenya. Influenza Other Respir Viruses 2020; 15:195-201. [PMID: 33305543 PMCID: PMC7902254 DOI: 10.1111/irv.12810] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/31/2020] [Accepted: 09/06/2020] [Indexed: 11/30/2022] Open
Abstract
Understanding respiratory syncytial virus (RSV) circulation patterns is necessary to guide the timing of limited‐duration interventions such as vaccines. We describe RSV circulation over multiple seasons in three distinct counties of Kenya during 2006‐2018. Kilifi and Siaya counties each had consistent but distinct RSV seasonality, lasting on average 18‐22 weeks. Based on data from available years, RSV did not have a clear pattern of circulation in Nairobi. This information can help guide the timing of vaccines and immunoprophylaxis products that are under development.
Collapse
Affiliation(s)
- Erica Billig Rose
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bryan O Nyawanda
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Patrick K Munywoki
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Nickson Murunga
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Godfrey M Bigogo
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Nancy A Otieno
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Clayton Onyango
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Sandra S Chaves
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.,Influenza Program, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Jennifer R Verani
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Gideon O Emukule
- Influenza Program, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Marc-Alain Widdowson
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya.,Institute of Tropical Medicine, Antwerp, Belgium
| | - D James Nokes
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK
| | - Susan I Gerber
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Gayle E Langley
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
38
|
Kamau E, Otieno JR, Lewa CS, Mwema A, Murunga N, Nokes DJ, Agoti CN. Evolution of respiratory syncytial virus genotype BA in Kilifi, Kenya, 15 years on. Sci Rep 2020; 10:21176. [PMID: 33273687 PMCID: PMC7712891 DOI: 10.1038/s41598-020-78234-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/20/2020] [Indexed: 01/12/2023] Open
Abstract
Respiratory syncytial virus (RSV) is recognised as a leading cause of severe acute respiratory disease and deaths among infants and vulnerable adults. Clinical RSV isolates can be divided into several known genotypes. RSV genotype BA, characterised by a 60-nucleotide duplication in the G glycoprotein gene, emerged in 1999 and quickly disseminated globally replacing other RSV group B genotypes. Continual molecular epidemiology is critical to understand the evolutionary processes maintaining the success of the BA viruses. We analysed 735 G gene sequences from samples collected from paediatric patients in Kilifi, Kenya, between 2003 and 2017. The virus population comprised of several genetically distinct variants (n = 56) co-circulating within and between epidemics. In addition, there was consistent seasonal fluctuations in relative genetic diversity. Amino acid changes increasingly accumulated over the surveillance period including two residues (N178S and Q180R) that mapped to monoclonal antibody 2D10 epitopes, as well as addition of putative N-glycosylation sequons. Further, switching and toggling of amino acids within and between epidemics was observed. On a global phylogeny, the BA viruses from different countries form geographically isolated clusters suggesting substantial localized variants. This study offers insights into longitudinal population dynamics of a globally endemic RSV genotype within a discrete location.
Collapse
Affiliation(s)
- Everlyn Kamau
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - James R Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
- Fogarty International Center, NIH, Bethesda, MD, USA
| | - Clement S Lewa
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anthony Mwema
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK
| | - Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| |
Collapse
|
39
|
Shi T, Chen C, Huang L, Fan H, Lu G, Yang D, Zhao C, Zhang D. Risk factors for mortality from severe community-acquired pneumonia in hospitalized children transferred to the pediatric intensive care unit. Pediatr Neonatol 2020; 61:577-583. [PMID: 32651007 DOI: 10.1016/j.pedneo.2020.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/15/2020] [Accepted: 06/15/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Some children hospitalized due to severe community-acquired pneumonia (CAP) require to the pediatric intensive care unit (PICU) because of severe complications. The purpose of this study was to identify the risk factors for mortality in this patient population. METHODS This study evaluated the medical records of 113 hospitalized children with severe CAP, who were transferred to the PICU within 48 h of admission at the Guangzhou Women and Children's Medical Center between 2013 and 2017. RESULTS The study group consisted of 87 boys (77%) and 26 girls (33%), aged between 1 month and 9 years; 72.6% (82/113) of patients were aged <12 months. The mortality rate was 12.3% (14/113). The most common viral and bacterial pathogens isolated were adenovirus (17.7%, 20/113) and Haemophilus influenzae (8.8%, 10/113). Wheezing, cyanosis, oxygen saturation <90%, Pediatric Early Warning Score (PEWS) >3 on admission, not receiving corticosteroid therapy prior to admission, the need for mechanical ventilation, septic shock, multi-organ dysfunction (MODS), and acute renal failure (ARF) occurring prior to transfer to the PICU, increased alanine aminotransferase (ALT) and aspartate transaminase (AST) levels, and decreased hemoglobin and albumin (ALB) levels were associated with mortality (P < 0.05). Non-survivors were more likely to have an oxygen saturation <90% on admission and lower levels of ALB prior to transfer to the PICU than survivors (P < 0.05). CONCLUSIONS Our results showed that hospitalized children with severe CAP who were transferred to the PICU within 48 h of hospital admission were mainly aged <1 year. Additionally, an oxygen saturation <90% and decreased ALB levels were early prognostic variables independently associated with death.
Collapse
Affiliation(s)
- Tingting Shi
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, China.
| | - Chen Chen
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, China.
| | - Li Huang
- Pediatric Intensive Care Unit, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, China.
| | - Huifeng Fan
- Pediatric Intensive Care Unit, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, China.
| | - Gen Lu
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, China.
| | - Diyuan Yang
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, China.
| | - Changan Zhao
- Emergency Department of Guangdong Maternal and Children's Hospital, Guangzhou, 510010, China.
| | - Dongwei Zhang
- Department of Respiratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510120, China.
| |
Collapse
|
40
|
Nyiro JU, Bukusi E, Mwaengo D, Walumbe D, Nyaguara A, Nyawanda B, Otieno N, Berkley JA, Munywoki P, Nokes DJ. Implications of gestational age at antenatal care attendance on the successful implementation of a maternal respiratory syncytial virus (RSV) vaccine program in coastal Kenya. BMC Public Health 2020; 20:1723. [PMID: 33198696 PMCID: PMC7670712 DOI: 10.1186/s12889-020-09841-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/04/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Maternal immunisation to boost respiratory syncytial virus (RSV) specific antibodies in pregnant women is a strategy to enhance infant protection. The timing of maternal vaccination during pregnancy may be critical for its effectiveness. However, Kenya has no documented published data on gestational age distribution of pregnant women attending antenatal care (ANC), or the proportion of women attending ANC during the proposed window period for vaccination, to inform appropriate timing for delivery or estimate potential uptake of this vaccine. METHODS A cross-sectional survey was conducted within the Kilifi Health and Demographic Surveillance System (KHDSS), coastal Kenya. A simple random sample of 1000 women who had registered pregnant in 2017 to 2018 and with a birth outcome by the time of data collection was taken. The selected women were followed at their homes, and individually written informed consent was obtained. Records of their antenatal attendance during pregnancy were abstracted from their ANC booklet. The proportion of all pregnant women from KHDSS (55%) who attended for one or more ANC in 2018 was used to estimate vaccine coverage. RESULTS Of the 1000 women selected, 935 were traced with 607/935 (64.9%) available for interview, among whom 470/607 (77.4%) had antenatal care booklets. The median maternal age during pregnancy was 28.6 years. The median (interquartile range) gestational age in weeks at the first to fifth ANC attendance was 26 (21-28), 29 (26-32), 32 (28-34), 34 (32-36) and 36 (34-38), respectively. The proportion of women attending for ANC during a gestational age window for vaccination of 28-32 weeks (recommended), 26-33 weeks and 24-36 weeks was 76.6% (360/470), 84.5% (397/470) and 96.2% (452/470), respectively. Estimated vaccine coverage was 42.1, 46.5 and 52.9% within the narrow, wide and wider gestational age windows, respectively. CONCLUSIONS In a random sample of pregnant women from Kilifi HDSS, Coastal Kenya with card-confirmed ANC clinic attendance, 76.6% would be reached for maternal RSV vaccination within the gestational age window of 28-32 weeks. Widening the vaccination window (26-33 weeks) or (24-36 weeks) would not dramatically increase vaccine coverage and would require consideration of antibody kinetics data that could affect vaccine efficacy.
Collapse
Affiliation(s)
- Joyce U Nyiro
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, P.O Box 230-80108, Kilifi, Kenya.
| | - Elizabeth Bukusi
- Kenya Medical Research Institute (KEMRI), Centre for Microbiology Research, Nairobi, Kenya
- University of Nairobi, Institute of Tropical and Infectious Diseases, Nairobi, Kenya
| | - Dufton Mwaengo
- University of Nairobi, Institute of Tropical and Infectious Diseases, Nairobi, Kenya
| | - David Walumbe
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, P.O Box 230-80108, Kilifi, Kenya
| | - Amek Nyaguara
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, P.O Box 230-80108, Kilifi, Kenya
| | - Bryan Nyawanda
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research, Kisumu, Kenya
| | - Nancy Otieno
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research, Kisumu, Kenya
| | - James A Berkley
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, P.O Box 230-80108, Kilifi, Kenya
| | - Patrick Munywoki
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, P.O Box 230-80108, Kilifi, Kenya
| | - D James Nokes
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, P.O Box 230-80108, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK
| |
Collapse
|
41
|
Cimolai N. Complicating Infections Associated with Common Endemic Human Respiratory Coronaviruses. Health Secur 2020; 19:195-208. [PMID: 33186086 DOI: 10.1089/hs.2020.0067] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Coronaviruses OC43, 229E, NL63, and HKU1 are endemic human respiratory coronaviruses that typically cause mild to moderate upper respiratory infections, similar to the common cold. They also may cause simple and complicated lower respiratory infections, otitis media, asthma exacerbations, gastroenteritis, and a few systemic complications. These viruses are usually seasonal (with winter dominance) and affect nearly all age groups. The seasonal and annual variation in virus prevalence has implications for understanding the concept of acquired immunity and its persistence or diminution. Coronaviruses generally have outbreak potential in susceptible populations of any age, particularly in patients with comorbidities, who tend to have increased clinical disease. These 4 coronaviruses are often found in the context of what appears to be coinfection with other pathogens, but especially other viruses. If coronaviruses are not specifically tested for, the sole detection of a viral copathogen would suggest the pathogen is the causative agent, when a coronavirus may be culpable, or both. The detection of these viruses in circumstances where respiratory viruses are generally sought in clinical samples is, therefore, justified. These pathogens can be chronically shed from the respiratory tract, which is more likely to occur among immunocompromised and complicated patients. These viruses share the potential for genetic drift. The genome is among the largest of RNA viruses, and the capability of these viruses to further change is likely underestimated. Given the potential disease among humans, it is justified to search for effective antiviral chemotherapy for these viruses and to consider uses in niche situations should effective therapy be defined. Whereas SARS-CoV-2 may follow the epidemiological pattern of SARS-CoV and extinguish slowly over time, there is yet concern that SARS-CoV-2 may establish itself as an endemic human respiratory coronavirus similar to OC43, 2299E, NL63, and HKU1. Until sufficient data are acquired to better understand the potential of SARS-CoV-2, continued work on antiviral therapy and vaccination is imperative.
Collapse
Affiliation(s)
- Nevio Cimolai
- Nevio Cimolai, MD, FRCPC, is a Professor, Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia; he is also Medical Staff, Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia; both in Vancouver, Canada
| |
Collapse
|
42
|
Jarju S, Greenhalgh K, Wathuo M, Banda M, Camara B, Mendy S, Sowe G, Dahaba PO, Jammeh L, Bajinka Y, Sanneh P, Jallow E, Yates A, Lindsey BB, Owens S, Kampmann B, Forrest K, Clarke E, de Silva T. Viral Etiology, Clinical Features and Antibiotic Use in Children <5 Years of Age in the Gambia Presenting With Influenza-like Illness. Pediatr Infect Dis J 2020; 39:925-930. [PMID: 32453201 DOI: 10.1097/inf.0000000000002761] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Knowledge regarding the prevalence, clinical features and etiology of pediatric influenza-like illness (ILI) remains limited in African settings. Furthermore, it is likely that many children presenting with ILI receive antibiotics unnecessarily. More data are required to develop antimicrobial stewardship practice and guide effective vaccine strategies. We undertook a 1-year prospective study of ILI in the Gambia. METHODS Children <5 years of age presenting with ILI from March 2018 to March 2019 were recruited. Clinical and antibiotic prescribing data were collected. Nasopharyngeal swabs were collected and analyzed for 12 respiratory viruses using a multiplex polymerase chain reaction. RESULTS From a total of 735 ILI episodes, 530 (72.1%) nasopharyngeal swabs were positive for ≥1 virus. Of these, 36.7% were positive for rhinovirus, 14.7% for respiratory syncytial virus, 8.4% for influenza and 7.2% for human metapneumovirus. Compared with children <6 months of age, influenza was more common in 6- to 23-month-old children [odd ratio (OR): 5.68; 95% confidence interval (CI): 1.72-18.76; P = 0.004]. Respiratory syncytial virus and human metapneumovirus were associated with low peripheral oxygen saturations (OR: 2.13; 95% CI: 1.23-3.69; P = 0.007; and OR: 2.44; 95% CI: 1.13-5.27; P = 0.023, respectively). Antibiotics were prescribed in 78.3% of all ILI cases. CONCLUSIONS A broad range of viruses are responsible for pediatric ILI in the Gambia. Refined treatment guidelines, improved diagnostic capacity and vaccines to prevent respiratory viruses will all play a role in reducing antimicrobial use for these cases.
Collapse
Affiliation(s)
- Sheikh Jarju
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | | | | | - Mustapha Banda
- Department of Clinical Services, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Bakary Camara
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Simon Mendy
- Department of Clinical Services, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Ghata Sowe
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Pa Omar Dahaba
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Lamin Jammeh
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Yaya Bajinka
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Papis Sanneh
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Edrissa Jallow
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Alexandra Yates
- Sheffield Teaching Hospitals, NHS Foundation, Royal Hallamshire Hospital, Sheffield
| | - Benjamin B Lindsey
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Stephen Owens
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Beate Kampmann
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
- The Vaccine Centre, London School of Hygiene and Tropical Medicine, London
| | - Karen Forrest
- Department of Clinical Services, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Ed Clarke
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
| | - Thushan de Silva
- From the Department of Vaccines & Immunity Theme, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia
- The Florey Institute and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
43
|
Adema IW, Kamau E, Uchi Nyiro J, Otieno GP, Lewa C, Munywoki PK, Nokes DJ. Surveillance of respiratory viruses among children attending a primary school in rural coastal Kenya. Wellcome Open Res 2020; 5:63. [PMID: 33102784 PMCID: PMC7569485 DOI: 10.12688/wellcomeopenres.15703.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2020] [Indexed: 01/07/2023] Open
Abstract
Background: Respiratory viruses are primary agents of respiratory tract diseases. Knowledge on the types and frequency of respiratory viruses affecting school-children is important in determining the role of schools in transmission in the community and identifying targets for interventions. Methods: We conducted a one-year (term-time) surveillance of respiratory viruses in a rural primary school in Kilifi County, coastal Kenya between May 2017 and April 2018. A sample of 60 students with symptoms of ARI were targeted for nasopharyngeal swab (NPS) collection weekly. Swabs were screened for 15 respiratory virus targets using real time PCR diagnostics. Data from respiratory virus surveillance at the local primary healthcare facility was used for comparison. Results: Overall, 469 students aged 2-19 years were followed up for 220 days. A total of 1726 samples were collected from 325 symptomatic students; median age of 7 years (IQR 5-11). At least one virus target was detected in 384 (22%) of the samples with a frequency of 288 (16.7%) for rhinovirus, 47 (2.7%) parainfluenza virus, 35 (2.0%) coronavirus, 15 (0.9%) adenovirus, 11 (0.6%) respiratory syncytial virus (RSV) and 5 (0.3%) influenza virus. The proportion of virus positive samples was higher among lower grades compared to upper grades (25.9% vs 17.5% respectively; χ 2 = 17.2, P -value <0.001). Individual virus target frequencies did not differ by age, sex, grade, school term or class size. Rhinovirus was predominant in both the school and outpatient setting. Conclusion: Multiple respiratory viruses circulated in this rural school population. Rhinovirus was dominant in both the school and outpatient setting and RSV was of notably low frequency in the school. The role of school children in transmitting viruses to the household setting is still unclear and further studies linking molecular data to contact patterns between the school children and their households are required.
Collapse
Affiliation(s)
- Irene Wangwa Adema
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Joyce Uchi Nyiro
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Grieven P. Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Clement Lewa
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Patrick K. Munywoki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - D. James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, Coventry, CV4 7AL, UK
| |
Collapse
|
44
|
Otieno GP, Murunga N, Agoti CN, Gallagher KE, Awori JO, Nokes DJ. Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya. Wellcome Open Res 2020; 5:150. [PMID: 32995556 PMCID: PMC7512035 DOI: 10.12688/wellcomeopenres.16037.2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 12/31/2022] Open
Abstract
Introduction: Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation. We describe the long-term patterns of paediatric disease associated with three of these viruses, HCoV-NL63, OC43 and 229E, in coastal Kenya. Methods: Continuous surveillance of pneumonia admissions was conducted at the Kilifi county hospital (KCH) located in the northern coastal region of Kenya. Children aged <5 years admitted to KCH with clinically defined syndromic severe or very severe pneumonia were recruited. Respiratory samples were taken and tested for 15 virus targets, using real-time polymerase chain reaction. Unadjusted odds ratios were used to estimate the association between demographic and clinical characteristics and HCoV positivity. Results: From 2007 to 2019, we observed 11,445 pneumonia admissions, of which 314 (3.9%) tested positive for at least one of the HCoV types surveyed in the study. There were 129 (41.1%) OC43, 99 (31.5%) 229E, 74 (23.6%) NL63 positive cases and 12 (3.8%) cases of HCoV to HCoV coinfection. Among HCoV positive cases, 47% (n=147) were coinfected with other respiratory virus pathogens. The majority of HCoV cases were among children aged <1 year (66%, n=208), though there was was no change in the proportion infected by age. HCoV-OC43 was predominant of the three HCoV types throughout the surveillance period. Evidence for seasonality was not identified. Conclusions: Overall, 4% of paediatric pneumonia admissions were associated with three endemic HCoVs, with a high proportion of cases co-occurring with another respiratory virus, no clear seasonal pattern, and with the age-distribution of cases following that of pneumonia admissions (i.e. highest in infants). These observations suggest, at most, a small severe disease contribution of endemic HCoVs in this tropical setting and offer insight into their potential future burden and epidemiological characteristics.
Collapse
Affiliation(s)
- Grieven P. Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N. Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Katherine E. Gallagher
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- London School of Hygiene and Tropical Medicine,, London, UK
| | - Juliet O. Awori
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - D. James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| |
Collapse
|
45
|
Li X, Zhang W, Yao S, Zha H, Huang B, Liu D, Wu K. Prevalence and clinical significance of common respiratory pathogens in the upper respiratory tract of children with community-acquired pneumonia in Zunyi, China. Pediatr Pulmonol 2020; 55:2437-2443. [PMID: 32579285 DOI: 10.1002/ppul.24922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/07/2020] [Accepted: 06/13/2020] [Indexed: 11/11/2022]
Abstract
PURPOSE To estimate the prevalence of common respiratory pathogens among children with community-acquired pneumonia (CAP) in Zunyi City, Guizhou, China, and to assess whether the presence of common respiratory pathogens in patients is associated with disease severity. PATIENTS AND METHODS This retrospective study assessed the prevalence of common respiratory viruses and bacteria in the upper respiratory tract of among infants and children aged 1 month to 5 years hospitalized with radiologically confirmed CAP between April 2017 and March 2018. Direct immunofluorescence assay and bacterial culture were used to identify viruses and bacteria in the upper airway specimens, respectively. The association between severe CAP and the presence of pathogens was determined using multivariate logistic regression models. RESULTS Of the 685 patients enrolled, 583 cases had viral and/or bacterial pathogens detected, which included the presence of only viral pathogens, only bacterial pathogens, and mixed viral and bacterial pathogens in 34.3%, 29.7%, and 36.0% of cases, respectively. Respiratory syncytial virus (RSV) was the most common viral pathogen, with a prevalence rate of 39.9% (273/685). Haemophilus influenzae was the most commonly detected bacterial pathogen, with a prevalence rate of 15.3% (105/685). The presence of RSV (adjusted odds ratio [aOR], 1.9; 95% confidence interval [CI], 1.3-2.8) and Staphylococcus aureus (aOR, 13.7; 95% CI, 5.5-33.9) in children with CAP was associated with severe pneumonia. CONCLUSIONS In a cohort of Zunyi infants and children hospitalized with CAP, RSV was the most common pathogen.
Collapse
Affiliation(s)
- Xinmiao Li
- Department of Laboratory Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi City), Zunyi, Guizhou, China
| | - Weiwei Zhang
- Department of Pediatrics, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi City), Zunyi, Guizhou, China
| | - Shifei Yao
- Department of Laboratory Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi City), Zunyi, Guizhou, China
| | - He Zha
- Department of Laboratory Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi City), Zunyi, Guizhou, China
| | - Bo Huang
- Department of Pediatrics, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi City), Zunyi, Guizhou, China
| | - Daishun Liu
- Department of Respiratory Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi City), Zunyi, Guizhou, China
| | - Kaifeng Wu
- Department of Laboratory Medicine, The Third Affiliated Hospital of Zunyi Medical University (The First People's Hospital of Zunyi City), Zunyi, Guizhou, China
| |
Collapse
|
46
|
Luka MM, Kamau E, Adema I, Munywoki PK, Otieno GP, Gicheru E, Gichuki A, Kibinge N, Agoti CN, Nokes DJ. Molecular Epidemiology of Human Rhinovirus From 1-Year Surveillance Within a School Setting in Rural Coastal Kenya. Open Forum Infect Dis 2020; 7:ofaa385. [PMID: 33094115 PMCID: PMC7568438 DOI: 10.1093/ofid/ofaa385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/21/2020] [Indexed: 01/12/2023] Open
Abstract
Background Human rhinovirus (HRV) is the most common cause of the common cold but may also lead to more severe respiratory illness in vulnerable populations. The epidemiology and genetic diversity of HRV within a school setting have not been previously described. The objective of this study was to characterize HRV molecular epidemiology in a primary school in a rural location of Kenya. Methods Between May 2017 and April 2018, over 3 school terms, we collected 1859 nasopharyngeal swabs (NPS) from pupils and teachers with symptoms of acute respiratory infection in a public primary school in Kilifi County, coastal Kenya. The samples were tested for HRV using real-time reverse transcription polymerase chain reaction. HRV-positive samples were sequenced in the VP4/VP2 coding region for species and genotype classification. Results A total of 307 NPS (16.4%) from 164 individuals were HRV positive, and 253 (82.4%) were successfully sequenced. The proportion of HRV in the lower primary classes was higher (19.8%) than upper primary classes (12.2%; P < .001). HRV-A was the most common species (134/253; 53.0%), followed by HRV-C (73/253; 28.9%) and HRV-B (46/253; 18.2%). Phylogenetic analysis identified 47 HRV genotypes. The most common genotypes were A2 and B70. Numerous (up to 22 in 1 school term) genotypes circulated simultaneously, there was no individual re-infection with the same genotype, and no genotype was detected in all 3 school terms. Conclusions HRV was frequently detected among school-going children with mild acute respiratory illness symptoms, particularly in the younger age groups (<5-year-olds). Multiple HRV introductions were observed that were characterized by considerable genotype diversity.
Collapse
Affiliation(s)
- Martha M Luka
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Irene Adema
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Patrick K Munywoki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Grieven P Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Elijah Gicheru
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Alex Gichuki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Nelson Kibinge
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| |
Collapse
|
47
|
Evaluation of Risk Factors for Exacerbations in Children with Adenoviral Pneumonia. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4878635. [PMID: 32802848 PMCID: PMC7415082 DOI: 10.1155/2020/4878635] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/17/2020] [Accepted: 07/10/2020] [Indexed: 12/18/2022]
Abstract
Purpose The aim of this work was to analyze clinical features and laboratory findings of children with adenovirus pneumonia and guide clinical diagnosis, treatment, and assessment of disease severity. Material and Methods. Retrospective analysis of clinical data of 285 children with adenoviral pneumonia who were hospitalized in Wuhan Children's Hospital from December 2018 to October 2019. According to the assessment criteria for severe pneumonia, it was divided into the severe group (92 cases) and the nonsevere group (193 cases). Collected clinical manifestations, complications, and laboratory test indicators in two groups of children and conducted all statistical analyses. Results The risk of fever and wheezing was significantly higher in the severe group than in the nonsevere group. The difference was statistically significant (P < 0.05). The risk of complications in the severe group was significantly higher than that in the nonsevere group. The difference was statistically significant (P < 0.05). The levels of AST, LDH-L, PCT, ferritin, and D-dimer in the severe group were significantly higher than those in the nonsevere group. The difference was statistically significant (P < 0.05). Conclusion Children with severe adenovirus pneumonia have severe clinical manifestations and many complications. AST, LDH-L, PCT, ferritin, and D-dimer levels have important clinical implications for assessing disease severity.
Collapse
|
48
|
Mweu MM, Murunga N, Otieno JW, Nokes DJ. Accuracy of diagnostic tests for respiratory syncytial virus infection within a paediatric hospital population in Kilifi County, Kenya. Wellcome Open Res 2020; 5:155. [PMID: 32984548 PMCID: PMC7499398 DOI: 10.12688/wellcomeopenres.16067.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2020] [Indexed: 11/20/2022] Open
Abstract
Background: Respiratory syncytial virus (RSV)-induced lower respiratory tract disease is a prominent cause of hospitalisation among children aged <5 years in developing countries. Accurate and rapid diagnostic tests are central to informing effective patient management and surveillance efforts geared towards quantifying RSV disease burden. This study sought to estimate the sensitivity (Se), specificity (Sp) (along with the associated factors) and predictive values of a direct immunofluorescence test (IFAT), and two real-time reverse transcription polymerase chain reaction (rRT-PCR) assays for RSV infection within a paediatric hospital population: a multiplex rRT-PCR (MPX) and Fast-Track Diagnostics ® (FTD) Respiratory Pathogens 33 (Resp-33) rRT-PCR. Methods: The study enlisted 1458 paediatrics aged ≤59 months admitted with acute respiratory illness at the Kilifi County Hospital between August 2011 and December 2013. A Bayesian latent class modelling framework was employed to infer the tests' estimates based on the patients' diagnostic data from the three tests. Results: The tests posted statistically similar Se estimates: IFAT (93.7%, [90.7; 95.0]), FTD (97.8%, [94.6; 99.4]) and MPX (97.5%, [94.2; 99.3]). As for Sp, FTD registered a lower estimate (97.4%, [96.2; 98.2]) than MPX (99.7%, [99.0; 100.0]) but similar to IFAT (99.0%, [98.2; 99.6]). The negative and positive predictive values were strong (>91%) and closely mimicked the pattern given by the Se and Sp values respectively. None of the examined covariates (age, sex and pneumonia status) significantly influenced the accuracy of the tests. Conclusions: The evaluation found little to choose between the three diagnostic tests. Nonetheless, with its relative affordability, the conventional IFAT continues to hold promise for use in patient care and surveillance activities for RSV infection within settings where children are hospitalised with severe acute respiratory illness.
Collapse
Affiliation(s)
- Marshal M. Mweu
- School of Public Health, College of Health Sciences, University of Nairobi, Nairobi, Kenya
| | | | | | - D. James Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences, University of Warwick, Coventry, UK
| |
Collapse
|
49
|
Otieno GP, Murunga N, Agoti CN, Gallagher KE, Awori JO, Nokes DJ. Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with pneumonia in Kilifi, Kenya. Wellcome Open Res 2020; 5:150. [PMID: 32995556 PMCID: PMC7512035 DOI: 10.12688/wellcomeopenres.16037.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 03/30/2024] Open
Abstract
Introduction: Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation. We describe the long-term patterns of paediatric disease associated with three of these viruses, HCoV-NL63, OC43 and 229E, in coastal Kenya. Methods: Continuous surveillance of pneumonia admissions was conducted at the Kilifi county hospital (KCH) located in the northern coastal region of Kenya. Children aged <5 years admitted to KCH with clinically defined syndromic severe or very severe pneumonia were recruited. Respiratory samples were taken and tested for 15 virus targets, using real-time polymerase chain reaction. Unadjusted odds ratios were used to estimate the association between demographic and clinical characteristics and HCoV positivity. Results: From 2007 to 2019, we observed 11,445 pneumonia admissions, of which 314 (3.9%) tested positive for at least one HCoV type. There were 129 (41.1%) OC43, 99 (31.5%) 229E, 74 (23.6%) NL63 positive cases and 12 (3.8%) cases of HCoV to HCoV coinfection. Among HCoV positive cases, 47% (n=147) were coinfected with other respiratory virus pathogens. The majority of HCoV cases were among children aged <1 year (66%, n=208), though there was no age-dependence in the proportion testing positive. HCoV-OC43 was predominant of the three HCoV types throughout the surveillance period. Evidence for seasonality was not identified. Conclusions: Overall, 4% of paediatric pneumonia admissions were associated with three endemic HCoVs, with a high proportion of cases co-occurring with another respiratory virus, with no clear seasonal pattern, and with the age-distribution of cases following that of pneumonia admissions (i.e. highest in infants). These observations suggest, at most, a small severe disease contribution of endemic HCoVs in this tropical setting and offer insight into the potential future burden and epidemiological characteristics of SARS-CoV-2.
Collapse
Affiliation(s)
- Grieven P. Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N. Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Katherine E. Gallagher
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- London School of Hygiene and Tropical Medicine,, London, UK
| | - Juliet O. Awori
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - D. James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| |
Collapse
|
50
|
Abidha CA, Nyiro J, Kamau E, Abdullahi O, Nokes DJ, Agoti CN. Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015-16. Virus Evol 2020; 6:veaa031. [PMID: 32523779 PMCID: PMC7266483 DOI: 10.1093/ve/veaa031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Human coronavirus OC43 (HCoV-OC43) is a major contributor to seasonal outbreaks of acute respiratory illness (ARI). The origins of locally circulating HCoV-OC43 strains and characteristics of their genetic diversity are unknown for most settings despite significance to effective HCoV control strategies. Between December 2015 and June 2016, we undertook ARI surveillance in coastal Kenya in nine outpatients and one inpatient health facility (HF). Ninety-two patient samples tested HCoV-OC43 positive and forty (43.5%) were successfully sequenced in spike (S) gene region (2,864 long, ∼70%). Phylogenetic analysis confirmed co-circulation of two distinct HCoV-OC43 clades that closely clustered with genotype G (n = 34, 85%) and genotype H (n = 6, 15%) reference strains. Local viruses within the same clade displayed low genetic diversity yielding identical sequences in multiple HF. Furthermore, the newly sequenced Kenyan viruses showed close phylogenetic relationship to other contemporaneous sampled strains (2015-16) including those originating from distant places (e.g. USA and China). Using a genetic similarity threshold of 99.1 per cent at nucleotide level, the HCoV-OC43 strains sampled globally between 1967 and 2019 fell into nine sequence clusters. Notably, some of these clusters appeared to have become extinct, or occurred only sporadically in a few geographical areas while others persisted globally for multiple years. In conclusion, we found that HCoV-OC43 strains spread rapidly both locally and across the globe with limited genetic evolution in the spike gene. Full-genome sequences that are spatio-temporally representative are required to advance understanding of the transmission pathways of this important human respiratory pathogen.
Collapse
Affiliation(s)
- Carol A Abidha
- Department of Public Health, School of Health and Human Sciences, Pwani University, P.O. Box 195, Kilifi-80108, Kenya.,Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya.,Faculty of Medicine, Heidelberg Institute of Global Health (HIGH), University of Heidelberg, Germany, Im Neuenheimer Feld 324 - 69120 Heidelberg, Germany
| | - Joyce Nyiro
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya
| | - Osman Abdullahi
- Department of Public Health, School of Health and Human Sciences, Pwani University, P.O. Box 195, Kilifi-80108, Kenya.,Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya
| | - David James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, CV4, 7AL UK
| | - Charles N Agoti
- Department of Public Health, School of Health and Human Sciences, Pwani University, P.O. Box 195, Kilifi-80108, Kenya.,Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, Kilifi-80108, Kenya
| |
Collapse
|