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Data for Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with pneumonia in Kilifi, Kenya
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Otieno, Grieven P., Murunga, Nickson, Agoti, Charles N., Gallagher, Katherine E., Awori, Juliet O. and Nokes, D. James (2021) Data for Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with pneumonia in Kilifi, Kenya. [Dataset]
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Official URL: https://doi.org/10.7910/DVN/ZQ1DJY
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.
| Item Type: | Dataset | |||||||||||||||
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| Subjects: | Q Science > QR Microbiology > QR355 Virology | |||||||||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | |||||||||||||||
| Type of Data: | Observational data | |||||||||||||||
| Library of Congress Subject Headings (LCSH): | Coronaviruses, Pneumonia in children -- Kenya, Pneumonia | |||||||||||||||
| Publisher: | University of Warwick, School of Life Sciences | |||||||||||||||
| Official Date: | 8 March 2021 | |||||||||||||||
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| Status: | Not Peer Reviewed | |||||||||||||||
| Publication Status: | Published | |||||||||||||||
| Media of Output (format): | .do tabular data | |||||||||||||||
| Access rights to Published version: | Open Access | |||||||||||||||
| Copyright Holders: | University of Warwick | |||||||||||||||
| Description: | Data record consists of 4 do files, 2 sets of tabular data, and an accompanying readme file. |
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