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.
Highlights
Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation
Endemic HCoV types are detected in a small but non-negligible proportion of respiratory tract infections; mild cases occur across a wide age-range and severe disease is predominant in young children and the elderly[5,6,7,8]
The variables extracted from the hospital surveillance database include; Demographic characteristics, presence/ absence of clinical features, laboratory test results for respiratory syncytial virus (RSV) (A and B), rhinovirus, HCoVs (NL63, OC43, 229E), influenza (A, B and C), parainfluenza virus (1–4), adenovirus, and human metapneumovirus, and hospitalisation outcomes
Summary
Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation. 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. Our study aims to describe the circulation patterns of HCoVs (OC43, 229E, and NL63) over time using data from a long-term surveillance programme in a rural coastal setting in Kenya, 3° south of the equator
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