Background The molecular epidemiology of respiratory pathogens provides insights into virulence factors, transmission dynamics, and immune escape mechanisms. The SARS-CoV-2 pandemic has showed how viral variant replacement impacts disease severity, transmissibility, and population immunity. Aim This project aims to map the molecular epidemiology of coronaviruses. We will generate longitiunial data for Stockholm Region to analyze temporal and demographic distribution patterns and immunity for seasonal coronavirus and perform in-depth analysis of coronavirus sequences. Methods We will sequence biobanked material from clinical respiratory specimens where these viruses have been detected in routine diagnostics. Using phylogenetic software and custom pipelines we will analyse the virus evolution and perform in-depth sequence analysis of coronavirus sequences. Results This project will deliver a detailed characterization of circulating coronavirus variants and population immunity, and significantly expand number of public seasonal coronaviruses genomes. Relevance The project will provide comprehensive longitudinal data long-term coronavirus evolution and immunity, providning insights for further projections of the SARS-CoV-2 pandemic.