Otieno, Grieven P; Murunga, Nickson; Agoti, Charles N; Gallagher, Katherine E; Awori, Juliet O; Nokes, D James; (2020) Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with pneumonia in Kilifi, Kenya. Wellcome Open Research, 5. p. 150. DOI: https://doi.org/10.12688/wellcomeopenres.16037.1
Permanent Identifier
Use this Digital Object Identifier when citing or linking to this resource.
Abstract
<ns4:p><ns4:bold>Introduction: </ns4:bold>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.</ns4:p><ns4:p> <ns4:bold>Methods:</ns4:bold> 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.</ns4:p><ns4:p> <ns4:bold>Results:</ns4:bold> 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.</ns4:p><ns4:p> <ns4:bold>Conclusions:</ns4:bold> 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.</ns4:p>
Item Type | Article |
---|---|
Faculty and Department | Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology (-2023) |
Research Centre | Centre for Epidemic Preparedness and Response |
Elements ID | 149155 |
Download
Filename: 54d0a41a-89ac-4ce1-b7df-ad92847de40c_16037_-_grieven_otieno-2.pdf
Licence: Creative Commons: Attribution 3.0
Download