The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid
turnover of genetic clades. New variants show intrinsic changes, notably
increased transmissibility, as well as antigenic changes that reduce the
cross-immunity induced by previous infections or vaccinations. How this
functional variation shapes the global evolutionary dynamics has remained
unclear. Here we show that selection induced by vaccination impacts on the
recent antigenic evolution of SARS-CoV-2; other relevant forces include
intrinsic selection and antigenic selection induced by previous infections. We
obtain these results from a fitness model with intrinsic and antigenic fitness
components. To infer model parameters, we combine time-resolved sequence data,
epidemiological records, and cross-neutralisation assays. This model accurately
captures the large-scale evolutionary dynamics of SARS-CoV-2 in multiple
geographical regions. In particular, it quantifies how recent vaccinations and
infections affect the speed of frequency shifts between viral variants. Our
results show that timely neutralisation data can be harvested to identify
hotspots of antigenic selection and to predict the impact of vaccination on
viral evolution