Severity of COVID-19 in hospitalised children in Espírito Santo, Brazil: a comparative analysis of pre- and post-Omicron periods

BACKGROUND Children experience Coronavirus disease 2019 (COVID-19) often with milder symptoms but severe outcomes. OBJECTIVES To compare clinical, epidemiological and viral load profiles of hospitalised paediatric COVID-19 cases before and after the emergence of the Omicron variant in Espírito Santo, Brazil, and to explore factors associated with hospitalisation duration. METHODS This cross-sectional observational study included 54 hospitalised children with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, grouped according to epidemiological period: G1 (2020-2021) and G2 (2022). Viral load was quantified by reverse transcription real-time polymerase chain reaction (RT-qPCR), and whole-genome sequencing was performed using Nanopore technology. Group comparisons used chi-square/Fisher's exact tests and Mann-Whitney U tests. Cox regression was applied in an exploratory manner to identify factors associated with hospitalisation duration. FINDINGS The median age was 19.5 months and 68.5% were male. Comorbidities were present in 65% of the cohort, with no significant differences between groups. Children in G1 were more often hospitalised for respiratory syndromes, while G2 had a longer intensive care unit (ICU) stay. More than half of the patients required oxygen support, and those needing oxygen at admission were younger. Viral load was higher in G1 than in G2. In the multivariable Cox model, comorbidities [aHR = 0.47; 95% confidence interval (CI): 0.26-0.86] and male sex (aHR = 0.47; 95% CI: 0.25-0.89) were associated with prolonged hospitalisation. Sequencing identified five SARS-CoV-2 lineages (P.1., B.1.1., BA.1*, BQ.1.1, and BE.9), reflecting the transition from pre-Omicron to Omicron periods. MAIN CONCLUSIONS The pre-Omicron period was marked by higher viral loads and distinct clinical patterns compared with the Omicron period. Comorbidities and male sex were associated with prolonged hospitalisation. These findings should be interpreted as exploratory and hypothesis-generating given the limited cohort size.