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Background: South Africa reported a notable increase in COVID-19 cases from mid-November, 2021, onwards, starting in Tshwane District, which coincided with the rapid community spread of the SARS-CoV-2 omicron (B.1.1.529) variant. This increased infection rate coincided with a rapid increase in paediatric COVID-19-associated admissions to hospital (hereafter referred to as hospitalisations). Methods: The Tshwane Maternal-Child COVID-19 study is a multicentre observational study in which we investigated the clinical manifestations and outcomes of paediatric patients (aged ≤19 years) who had tested positive for SARS-CoV-2 and were admitted to hospital for any reason in Tshwane District during a 6-week period at the beginning of the fourth wave of the COVID-19 epidemic in South Africa. We used five data sources, which were: (1) COVID-19 line lists; (2) collated SARS-CoV-2 testing data; (3) SARS-CoV-2 genomic sequencing data; (4) COVID-19 hospitalisation surveillance; and (5) clinical data of public sector COVID-19-associated hospitalisations among children aged 13 years and younger. Findings: Between Oct 31 and Dec 11, 2021, 6287 children and adolescents in Tshwane District were recorded as having COVID-19. During this period, 2550 people with COVID-19 were hospitalised, of whom 462 (18%) were aged 19 years or younger. The number of paediatric cases was higher than in the three previous SARS-CoV-2 waves, uncharacteristically increasing ahead of adult hospitalisations. 75 viral samples from adults and children in the district were sequenced, of which 74 (99%) were of the omicron variant. Detailed clinical notes were available for 138 (75%) of 183 children aged ≤13 years with COVID-19 who were hospitalised. 87 (63%) of 138 children were aged 0–4 years. In 61 (44%) of 138 cases COVID-19 was the primary diagnosis, among whom symptoms included fever (37 [61%] of 61), cough (35 [57%]), shortness of breath (19 [31%]), seizures (19 [31%]), vomiting (16 [26%]), and diarrhoea (15 [25%]). Median length of hospital stay was 2 days [IQR 1–3]). 122 (88%) of 138 children with available data needed standard ward care and 27 (20%) needed oxygen therapy. Seven (5%) of 138 children were ventilated and four (3%) died during the study period, all related to complex underlying copathologies. All children and 77 (92%) of 84 parents or guardians with available data were unvaccinated to COVID-19. Interpretation: Rapid increases in paediatric COVID-19 cases and hospitalisations mirror high community transmission of the SARS-CoV-2 omicron variant in Tshwane District, South Africa. Continued monitoring is needed to understand the long-term effect of the omicron variant on children and adolescents. Funding: South African Medical Research Council, South African Department of Science & Innovation, G7 Global Health Fund.
In this multicentre observational study (The Tshwane Maternal-Child COVID-19 study), we collated paediatric COVID-19-related data (ie, for children aged ≤19 years) during the early stages of the fourth COVID-19 wave in South Africa. Our key population of interest was children aged ≤13 years who had been admitted to any of 38 hospitals in Tshwane District during this period. We also collected data for adolescents aged 14 to 19 years, and adults older than 19 years, for comparison. The Tshwane Maternal-Child COVID-19 research study received permission from the ethics committees of both Health Sciences Faculties in Tshwane (University of Pretoria [reference number 822/2020] and Sefako Makgatho Health Sciences University [reference number SMUREC/M/54/2021:IR]), together with the Tshwane District Research Committee. Additionally, three large public sector hospitals (Steve Biko Academic Hospital, Kalafong Academic Hospital, and George Mukhari Academic Hospital) are part of the SA COVID KIDS study and have received ethics approval from the South African Medical Research Council (reference number EC048-11/2020). Ethics approval was also obtained for sequencing of COVID-19 samples (University of Pretoria Ethics Committee, reference number 101/2017). Individual patient consent was not needed for the genome samples at is part of ongoing routine surveilance. We extracted data relevant to the Tshwane District from the following sources: district-based COVID-19 line lists for contact tracing activities (totals, with age breakdowns); SARS-CoV-2 testing data collated by the National Institute for Communicable Diseases (NICD); SARS-CoV-2 genomic sequencing data from samples obtained within the district through the Zoonotic Arbo and Respiratory Virus Research Group (ZARV) at the Department of Medical Virology, National Health Laboratory Services (NHLS), University of Pretoria (Pretoria, South Africa) and from the NGS-SA from the global reference database for SARS-CoV-2 viral genomes, Global Initiative on Sharing Avian Influenza Data (GISAID); COVID-19 hospitalisation data (DATCOV hospital surveillance system, collated by the NICD); and clinical data of public sector paediatric (ie, aged ≤13 years) hospitalisations due to COVID-19, collected for the SA COVID Kids study and for local planning of paediatric clinical services. SARS-CoV-2 testing data were extracted from the NICD for adults, adolescents, and children for the period March 1, 2020, to Dec 5, 2020. A laboratory-confirmed COVID-19 case was defined as any person who tested positive for SARS-CoV-2 on either a real-time RT-PCR (rRT-PCR) or an antigen test using samples obtained from nasopharyngeal or oropharyngeal swabs, with testing done at NHLS laboratories located in four public sector hospitals in the Tshwane District. Access to SARS-CoV-2 testing was not substantially constrained; increased access to rapid antigen testing for enhanced speed of diagnosis was the most important change in COVID-19 testing practices since Oct 5, 2021. For genomic sequencing, we used clinical samples from adults and children from public sector clinics and hospitals in Tshwane District submitted to NHLS for SARS-CoV-2 rRT-PCR testing. Positive cases among adult and paediatric patients from Nov 7 to 29, 2021 (epidemiological weeks 45–48), were collected by ZARV staff for genome sequencing. SARS-CoV-2-positive samples with crossing point threshold values (ct) of 30 or less were sent for next-generation sequencing at the Research Innovation and Sequencing Platform at the University of KwaZulu-Natal (Durban, South Africa), as part of the NGS-SA initiative. Sequences were submitted to GISAID and assigned to lineages. Regarding the DATCOV surveillance system, 38 hospitals in Tshwane District were submitting hospitalisation data during our study period, including all nine public sector hospitals and 25 private sector hospitals (as of Dec 11, 2021). Due to restructuring during the COVID-19 pandemic, one public sector district hospital was closely linked to its adjacent public sector central hospital and subsequently counted as one academic hospital complex for the purposes of this study. The dataset includes information on patient numbers, age groups, sex, level of hospital care, length of stay, and patient outcomes. Although the DATCOV system provides overall disease surveillance, it does not provide detailed clinical data. Therefore, we collated clinical data from treating clinicians and hospital files to supplement and verify the DATCOV data, including clinical presentation, diagnoses, management, and outcomes. Symptoms were analysed in a subgroup of children (aged ≤13 years) with primary SARS-CoV-2 infection. A COVID-19-associated hospitalisation was defined by DATCOV as any person who tested positive for SARS-CoV-2 and was admitted to hospital, regardless of the reason for hospitalisation. Hospitals in the South African public health sector are divided into different levels of care; however, for geographical reasons, care is often first accessed at the closest hospital and not necessarily linked to disease severity. For descriptive purposes, we grouped public sector hospitals into central and academic hospitals (n=3) and regional and district hospitals (n=5) with high care and intensive care services available at central and academic hospitals, and with standard inpatient care (including oxygen therapy, fluid management, and antibiotics) available at all levels. Children who were referred from another hospital were classed as being at the higher level hospital, irrespective of the reason for referral, to avoid being included twice in the dataset. The DATCOV surveillance system reports on children and adolescents aged 19 years and younger. We used descriptive statistics, including mean (SD), ranges, median (IQR), and counts and proportions to describe demographic characteristics for tests, cases, and hospitalisations, and further stratified these data by age group (<1 year; 1–4 years; 5–9 years; 10–14 years; 15–19 years). We calculated the crude admission rate as the number of admissions in different age groups as a proportion of the population (as per Statistics South Africa mid-year population estimates for 2020),19 and present these data as admissions per 1 000 000 people, by age and week of admission. For our in-depth analysis of clinical features, we assessed data for all paediatric patients (aged ≤13 years) admitted to public sector hospitals who had detailed clinical notes from their treated physician. We also did subgroup analyses within this population by primary diagnosis on admission. The funders did not have a role in the study design, data collection, data analysis, data interpretation, or writing of the report.
