Impact of vaccination on intra-host genetic diversity of patients infected with SARS-CoV-2 Gamma lineage

To better understand the intra-host diversity of SARS-CoV-2 after vaccination in Brazil in early 2021, we investigated 118 whole viral genomes from unvaccinated and vaccinated patients who were diagnosed with COVID-19 from April to July 2021 in São José do Rio Preto and surrounding cities in the state of São Paulo, Brazil. Patients were divided into two equal groups, as follows: (1) unvaccinated individuals (infected with SARS-CoV-2 who did not receive any dose of vaccine); and (2) vaccinated individuals (infected with SARS-CoV-2 14 or more days after having received their second dose of the CoronaVac vaccine—breakthrough infections). We found that the CoronaVac vaccine favored negative selection in different regions of the SARS-CoV-2 genomes, thus reducing genetic diversity at the intra-host level. This outcome reinforces the importance of vaccination as a tool to prevent the emergence of new variants that may enhance virus fitness and affect the progression of COVID-19 worldwide.