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

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.<br><br>Data record consists of 4 do files, 2 sets of tabular data, and an accompanying readme file.

These data is part of the long-term continuous respiratory virus surveillance among pneumonia admissions to Kilifi County Hospital (KCH) study.It contains results of specimens collected between January 2007 and December 2019 which were were processed and screened for 3 HCoVs (OC43, NL63 and 229E) and at least 12 other respiratory viral pathogens using real-time polymerase chain reaction (RT-PCR). Aside from that, it also contains the patients’ sociodemographic characteristics (sex and age) and presenting symptoms.

The data is used to describe the long-term patterns of paediatric disease associated with three viruses, HCoV-NL63, OC43 and 229E, in coastal Kenya.