BA.5 sub-lineages associated with higher severity of COVID-19 infection: A cross-sectional study in Indonesia

•BA.1 and BA.2 were the sub-lineages of Omicron with milder symptoms.•BA.5 sub-lineages were associated with more severe symptoms.•Booster vaccinations reduced poor outcomes in Omicron infections.•People with multiple comorbidities had the highest risk of contracting severe COVID-19. We aimed to compare the clinical severity and outcome among laboratory-confirmed Omicron variant cases admitted between January and December 2022. This is a cross-sectional study conducted in Hasan Sadikin General Hospital between January and December 2022. We enrolled patients aged ≥18 years with laboratory-confirmed Omicron infection. Data were collected from clinical records and a whole genome sequencing database. We compared the risk of severe symptoms and mortality using a logistic regression analysis adjusted for sex, age, comorbidities, and vaccination status. We enrolled 255 patients and the main sub-lineages were BA.1 (16.1%), BA.2 (11.4%), BA.5 (35.7%), XBB (22.7%), and BQ.1 (14.1%). Compared with BA.1/BA.2, BA.5 sub-lineages were associated with severe symptoms (adjusted odds ratio of 2.9, 95% confidence interval 1.1-8.2, P