Rapid rise in paediatric COVID-19 hospitalisations during the early stages of the Omicron wave, Tshwane District, South Africa

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Abstract Background South Africa reported a notable increase in COVID-19 cases from mid-November 2021 onwards, starting in Tshwane District, linked to rapid community spread of the Omicron variant. This coincided with a rapid rise in paediatric COVID-19-associated hospitalisations. Methods We synthesized data from five sources to describe the impact of Omicron on clinical manifestations and outcomes of hospitalized children (≤19 years) with positive SARS-CoV-2 tests in Tshwane District from 31 October to 11 December 2021, including: 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 paediatric (≤13 years) COVID-19 hospitalisations. Findings During the six-week period 6,287 paediatric (≤19 years) COVID-19 cases were recorded in Tshwane District, of these 462 (7.2%) were hospitalized in 42 hospitals (18% of overall admissions). The number of paediatric cases was higher than in the prior 3 waves, uncharacteristically preceding adult hospitalisations. Of the 75 viral specimens sequenced from the district, 99% were Omicron. Detailed clinical information obtained from 139 of 183 (76%) admitted children (≤13 years; including all public sector hospitalisations) indicated that young children (0-4 years) were most affected (62%). Symptoms included fever (47%), cough (40%), vomiting (24%), difficulty breathing (23%), diarrhoea (20%) and convulsions (20%). Length of hospital stay was short (mean 3.2 days), and in 44% COVID-19 was the primary diagnosis. Most children received standard ward care (92%), with 31 (25%) receiving oxygen therapy. Seven children (6%) were ventilated; four children died, all related to complex underlying co-pathologies. All children and majority of parents for whom data were available were unvaccinated. Interpretation Rapid increases in paediatric COVID-19 cases and hospitalisations mirror high community transmission of SARS-CoV-2 (Omicron variant) in Tshwane District, South Africa. Continued monitoring is needed to understand the long-term impact of the Omicron variant on children. Research in context Evidence before the study The announcement of the new Omicron (B.1.1.529) variant of the SARS-CoV-2 virus was made on 24 November 2021. Clinical characteristics, and disease profiles of children with COVID-19 before the arrival of Omicron have been described in the literature. Added value of the study This study describes the rapid rise in paediatric COVID-19-associated hospitalisations in Tshwane District in the Gauteng Province of South Africa – one of the first known epicentres of the new Omicron variant of the SARS-CoV-2 virus. The clinical picture as well as the steep increase in paediatric positivity rates and hospitalizations are described in detail from the perspective of a large South African health district, providing a broad overview on how the Omicron variant affects the paediatric population. Implication of all available evidence This study describes the clinical picture and outcomes in children in the current wave of SARS-CoV-2 Omicron variant infections by incorporating data from 42 hospitals at all levels of care in a large district within the South African health system. This provides novel paediatric data to assist global preparation for the impact of the Omicron variant in the paediatric setting.

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