Post-vaccination COVID-19: A case-control study and genomic analysis of 119 breakthrough infections in partially vaccinated individuals

Background Post-vaccination infections challenge the control of the COVID-19 pandemic. Methods We matched 119 cases of post-vaccination SARS-CoV-2 infection with BNT162b2 mRNA, or ChAdOx1 nCOV-19, to 476 unvaccinated patients with COVID-19 (Sept 2020-March 2021), according to age and sex. Differences in 60-day all-cause mortality, hospital admission, and hospital length of stay were evaluated. Phylogenetic, single nucleotide polymorphism (SNP) and minority variant allele (MVA) full genome sequencing analysis was performed. Results 116/119 cases developed COVID-19 post first vaccination dose (median 14 days, IQR 9 – 24 days). Overall, 13/119 (10∙9%) cases and 158/476 (33∙2%) controls died (p