Vaccination shapes evolutionary trajectories of SARS-CoV-2

TL;DR

This study models how vaccination influences the evolution of SARS-CoV-2, revealing that vaccination-driven selection affects variant dynamics and can be monitored through neutralisation data to predict viral evolutionary trends.

Contribution

It introduces a fitness model integrating intrinsic and antigenic factors, linking vaccination and infection history to SARS-CoV-2 evolution.

Findings

Vaccination impacts the rate of variant frequency shifts.

Neutralisation data can identify antigenic selection hotspots.

The model accurately predicts SARS-CoV-2 evolutionary dynamics across regions.

Abstract

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.