The burden of human coronavirus infection in children hospitalised with lower respiratory tract infection in Cape Town, South Africa

IntroductionHuman coronaviruses (HCoV) NL63, HKU, OC43 and 229E are known to cause various respiratory infections including croup, pneumonia, and bronchitis in young children. The role of these four HCoV strains in the aetiology of pneumonia is little described in South Africa. MethodsWe used data collected between September 2012 - September 2013 from children aged <13 years with lower respiratory illness at Red Cross War Memorial Childrens Hospital. Respiratory samples including a nasopharyngeal swab (NP) and induced sputum (IS) were taken and tested for the four strains of coronaviruses using FTD33 multiplex real-time PCR. ResultsA total of 460 respiratory samples were analysed. Of these, 258 (56.0%) were male and 19 (4.1%) HIV infected. The median age of the children was 8 (IQR 4-18) months. Nasopharyngeal (NP) samples were obtained from 460 children while induced sputum (IS) was not available for six children due to sample loss prior to analysis, leaving 454 available for analysis. A total of 42 (9.1%, 95% CI 6.7-12.1%) participants tested positive for HCoV in at least one of the two specimens. PCR was able to detect a total of 35 (7.7%) cases from the 454 tested IS specimens compared to 23 (5.0%) detected out of 460 NP samples. The commonest detected HCoVs were coronavirus OC43 with 20 (4.3%) detected from either specimen followed by coronavirus NL63 or coronavirus HKU detected in 14 (3.0%) and 10 (2.2%) of positive test samples, respectively. The least common virus detected HCoV was coronavirus 229E detected in both positive test samples of one participant. Overall HCoVs were detected in 23 (8.9%) of boys compared to 19 (9.1%) of the girls who returned a positive test; p=0.856. The overall age distribution of children with PCR detected HCoVs was similar to that of children with a negative result with median age of 10 (IQR 5-16) months and median of 8 (IQR 4-19) months, respectively; p=0.535. Prevalence of HCoV was 11/192 (5.7%), 23/153 (15.0%) and 8/115 (7.0%) in children <6 months old, 6-18 months and over 18 months respectively; p=0.008. ConclusionChildren aged 6 to 18 months had double the risk of other age groups.