SummaryBackgroundEvidence is accumulating that the effectiveness of covid-19 vaccines against infection wanes, reaching relatively low values after 6 months. Published studies demonstrating this effect based their findings on a limited range of vaccines or subset of populations, and did not include booster vaccine doses or immunity obtained due to covid-19 infection. Here we evaluate effectiveness of covid-19 vaccines, booster doses or previous infection against covid-19 infection, hospital admission or death for the whole population in the Czech Republic.MethodsData used in this study cover the whole population of the Czech Republic reported as infected and/or vaccinated between the first detected case on March 1, 2020 and November 20, 2021 (for reinfections), or December 26, 2020 and November 20, 2021 (for vaccinations), including hospital admissions and deaths. Vaccinations by all vaccines approved in the EU were included in this study. Anonymous, individual-level data including dates of vaccination, infection, hospital admission and death were provided by the the Institute of Health Information and Statistics of the Czech Republic. The risks of reinfection, breakthrough infection after vaccination, hospital admission and death were calculated using hazard ratios from a Cox regression adjusted for sex, age, vaccine type and vaccination status.FindingsThe vaccine effectiveness against any PCR-confirmed infection declined from 87% (95% CI 86-87) at 0-2 months after the second dose to 53% (95% CI 52-54) at 7-8 months for Comirnaty, from 90% (95% CI 89-91) at 0-2 monthsto 65% (95% CI 63-67) at 7-8 months for Spikevax, and from 83% (95% CI 80-85) at 0-2 months to 55% at (95% CI 54-56) 5-6 months for the Vaxzevria. For Janssen Covid-19 Vaccine we found no significant decline but the estimates are less certain. The vaccine effectiveness against hospital admissions and deaths decayed at a significantly lower rate with about 15%, resp. 10% decline during the first 6-8 months. The administration of a booster dose returns the protection to or above the estimates in the first two months after dose 2. In unvaccinated but previously SARS-CoV-2-positive individuals the protection against PCR-confirmed SARS-CoV-2 infection declined from close to 97% (95% CI 97-97) after 2 months through 90% at 6 months down to 72% (95% CI 65-78) at 18 months.InterpretationOur results confirm the waning of vaccination-induced immunity against infection and a smaller decline in the protection against hospital admission and death. A booster dose is shown to restore the vaccine effectiveness back to the levels seen soon after the completion of the basic vaccination schedule. The post-infection immunity decreases over time, too.FundingNo external funding was used to conduct this study.Research in contextEvidence before this studyAccumulating evidence from several countries indicates that the effectiveness of covid-19 vaccines against infection declines in time, from about 80-90% shortly after completing the vaccination to about 50-60% and even less after 6 months. Published studies also suggest a significant boosting in vaccine effectiveness against infection about one week after the third vaccine dose. However, these observations come from different and often limited data sets. Moreover, the existing studies do not compare the decline in vaccine effectiveness with a decline in infection-based immunity in unvaccinated individuals.Added value of this studyIn our study, we bring together data on infections, vaccinations (including booster doses), hospital admissions and deaths to estimate how the protection due to vaccination or previous SARS-CoV-2 infection declines with time, for the whole population of the Czech Republic. Our findings show an overall decrease in vaccine effectiveness over time and a large increase after the administration of a booster dose. At the same time we show a fairly stable and high post-infection immunity over the study period. We hope this evidence will contribute to a better understanding of the changing impact of vaccines and previous infection in complex, real-world environments, which is crucial for the development of more effective and more easily communicated public health policies.Implications of all the available evidenceOur results strongly support a timely and widespread application of booster vaccine doses since their application appears to restore the vaccine-induced protection to the levels attained soon after completing the original vaccination scheme, including the high protection against mild disease or asymptomatic infection.