Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with pneumonia in Kilifi, Kenya [version 1;peer review: awaiting peer review]

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 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 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, 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