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. 2020 Sep 22:5:150.
doi: 10.12688/wellcomeopenres.16037.2. eCollection 2020.

Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya

Grieven P Otieno  1 , Nickson Murunga  1 , Charles N Agoti  1 , Katherine E Gallagher  1   2 , Juliet O Awori  1 , D James Nokes  1   3
Affiliations

Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya

Grieven P Otieno et al. Wellcome Open Res. .

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.

Keywords: 229E; Human coronavirus; NL63; OC43.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Frequency distribution of discharge diagnosis for mortality cases admitted to Kilifi County Hospital, Kilifi, Kenya 2007–2019, by HCoV type.
LRTI=lower respiratory tract infection, CHD=congenital heart disease, TB=Tuberculosis, GE=Gastroenteritis.
Figure 2.
Figure 2.. Percentage distribution of coinfections between HCoVs and other viral pathogens for pneumonia cases admitted to Kilifi County Hospital, Kilifi, Kenya 2007–2019.
RSV=respiratory syncytial virus (A and B), HRV=human rhinovirus, PIV=parainfluenza, FLU=influenza (A, B and C), hMPV= human metapneumovirus.
Figure 3.
Figure 3.. Monthly prevalence (%) pneumonia admissions at Kilifi County Hospital, Kilifi, Kenya 2007–2019 by HCoV type.
The panel shows proportions for all HCoVs ( a), NL63 ( b), OC43 ( c) and 229E ( d).
Figure 4.
Figure 4.. Proportion of monthly positive cases observed at Kilifi County Hospital, Kilifi, Kenya by HCoV type over a period of 13 years (2007–2019).
The primary y-axis denotes the proportion of samples positive for HCoV the average monthly maximum temperature in °C and relative humidity (%) while the secondary y-axis denotes the average monthly rainfall in millimetres.
Figure 5.
Figure 5.. Plot of time series model residuals against month separated by HCoV type using pneumonia surveillance data at Kilifi County Hospital, Kilifi, Kenya 2007–2019.
See Methods for statistical details.
See this image and copyright information in PMC

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