Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya
Open accessAbstract
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.
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The study did not identify evidence of cross-reactive antibodies to endemic coronaviruses in the validation study.
“Despite our prior work showing that HCoVs circulate in Kenya (24), we did not identify evidence of cross-reactive antibodies to endemic coronaviruses in our validation study.”
From Seroprevalence of anti–SARS-CoV-2 IgG antibodies in Kenyan blood donors (2021) · cites this paper as [24]
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Seroprevalence of anti–SARS-CoV-2 IgG antibodies in Kenyan blood donors
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- Authors
- Otieno, G. P., Murunga, N., Agoti, C. N., Gallagher, K. E., Awori, J. O., & Nokes, D. J.
- Affiliations
- University of the Witwatersrand (ZA)
- Corresponding author
- Otieno, Grieven P.
- ORCID
- Venue
- Wellcome Open Research
- Publisher
- F1000 Research Ltd
- Published
- 2020-09-22
- Volume
- 5
- Pages
- 150
- ISSN
- 2398-502X (ISSN-L)
- PMC
- PMC7512035
- OpenAlex
- W3037062122
- Cited by
- 20
- References
- 23
- Citations by year
- 2024: 2 · 2023: 5 · 2022: 7 · 2021: 5 · 2020: 1
- FWCI
- 3.23
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Wellcome Open Research (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Warwick Research Archive Portal (University of Warwick) (acceptedVersion)
- LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Greater South Information System
- Funders
- Bill and Melinda Gates Foundation (48968)
- Wellcome Trust (102975, 220985)
- Topics
- Health Sciences › Medicine › Epidemiology › Respiratory viral infections research
- Health Sciences › Medicine › Epidemiology › Pneumonia and Respiratory Infections
- Health Sciences › Medicine › Pediatrics, Perinatology and Child Health › Literature Analysis and Criticism
- Keywords
- human coronaviruses, HCoV-NL63, HCoV-OC43, HCoV-229E, pediatric pneumonia, seasonal variation, age distribution, Kilifi, Kenya
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