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

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.

Sero-surveillance for IgG to SARS-CoV-2 at antenatal care clinics in two Kenyan referral hospitals

“…We also lack local data on the rate of antibody waning, which is important to estimate cumulative incidence of infection from snapshot seroprevalence estimates 29,30 . This is especially important in populations, like those reported here, where ongoing transmission may cause 'natural boosting' and where circulation of other human coronaviruses may modify immunological responses to SARS-CoV-2 29,31,32 .…”

Epidemiological and clinical characteristics of infections with seasonal human coronavirus and respiratory syncytial virus in hospitalized children immediately before the coronavirus disease 2019 pandemic

“…Although it depends on the virus detection methods, the virus detection rate by a PCR test in children hospitalized for respiratory tract infections was reported to be approximately 40–85% [ [25] , [26] , [27] , [28] ]. The RSV and seasonal HCoV detection rates in children hospitalized for respiratory tract infections were between 10–40% [ 25 , [27] , [28] , [29] , [30] , [31] , [32] ] and 2.5–9.0% [ 25 , 26 , [28] , [29] , [30] , [32] , [33] , [34] , [35] , [36] ], respectively. Furthermore, previous reports have shown that the co-detection rate of seasonal HCoV and other respiratory viruses was 35–80% [ 25 , 26 , [28] , [29] , [30] , [33] , [34] , [35] , 37 ], of which the co-detection rate with RSV and seasonal HCoV was 10–49% [ 25 , 26 , [28] , [29] , [30] , [33] , [34] , [35] , 37 ].…”

“…The RSV and seasonal HCoV detection rates in children hospitalized for respiratory tract infections were between 10–40% [ 25 , [27] , [28] , [29] , [30] , [31] , [32] ] and 2.5–9.0% [ 25 , 26 , [28] , [29] , [30] , [32] , [33] , [34] , [35] , [36] ], respectively. Furthermore, previous reports have shown that the co-detection rate of seasonal HCoV and other respiratory viruses was 35–80% [ 25 , 26 , [28] , [29] , [30] , [33] , [34] , [35] , 37 ], of which the co-detection rate with RSV and seasonal HCoV was 10–49% [ 25 , 26 , [28] , [29] , [30] , [33] , [34] , [35] , 37 ]. In this study, the co-detection rate between seasonal HCoV and other respiratory viruses was 58.3%, of which the co-detection rate with RSV was 25.0%.…”

Trends and Intensity of Rhinovirus Invasions in Kilifi, Coastal Kenya, Over a 12-Year Period, 2007–2018

“…KCH, located on the coast of Kenya, is a referral hospital serving the wider Kilifi County, which has a population of 1453787 and covers an area of approximately 12254 km 2 . Details of study design, participant recruitment, and sampling procedures have been described elsewhere [ 25 , 29 ]. In brief, upon presentation to the pediatric ward, a detailed medical review was undertaken by the clinician and the decision to admit was made.…”