Fig. 1.

Study flow diagram. Inclusion and exclusion criteria in the cohort stratified by SARS-CoV-2 variant and restricted to BNT162b2 vaccine. Of the 546 SARS-CoV-2 positive individuals with known/inferred Delta variant, 90 were vaccinated with two-dose BNT162b2, 456 unvaccinated cases. There were 372 SARS-CoV-2 positive individuals with known/inferred Omicron variant: 182 vaccinated with three-dose BNT162b2, and 185 unvaccinated cases. Of the 935 SARS-CoV-2 negative individuals admitted during the Delta time period, 608 were vaccinated with two-dose BNT162b2 and 327 were unvaccinated cases. In the Omicron time period, 721 SARS-CoV-2 negative individuals were admitted: 410 vaccinated with three-dose BNT162b2 and 311 unvaccinated patients. ∗ During the Delta period, the controls include 51 individuals with 2 respiratory hospitalisations; 6 individuals who were admitted with three separate respiratory admissions, and one individual with 4 separate respiratory admissions. 93.8% of the controls (877/935) had only one respiratory hospitalisation. † In the Omicron period, the controls include 94 individuals with two respiratory admissions, 30 individuals with three separate respiratory admissions, 8 individuals with four separate respiratory admissions and 4 individuals with more than four separate respiratory admissions. 81.1% of the controls (585/721) had only one respiratory hospitalisation. Details of adults hospitalised with SARS-CoV-2 infection are provided in Supplementary Fig. S1. VOC, variant of concern.