Impact of timely vaccination and genomic surveillance on controlling consecutive waves of SARS-CoV-2 variants

Background. During the global COVID-19 pandemic, different SARS-CoV-2 variants of concern (VOCs) emerged, causing massive transmission waves that affected infection outcomes, economies and public health. From January to July 2021 in Uruguay, the transmission wave was primarily driven by the Gamma VOC, in a context of high prevalence of immunologically naive individuals. Following the implementation of a nationwide vaccination campaign, the detection of Delta VOC in July 2021 did not trigger a significant contagion wave, even in the face of increased mobility during the winter holidays.Methods. We present a comprehensive analysis of the dynamics of SARS-CoV-2 in Uruguay until September 2021. By analysing 1,792 viral genomes, we integrate genomic data with vaccination records, variant surveillance and epidemiological information at both regional and global scales.Findings. Our results suggested that the early detection and monitoring systems and an effective vaccination campaign contributed to prevent a second wave of infection in Uruguay following the introduction of the Delta VOC, despite the increased mobility of the populationInterpretation. This study demonstrates how timely vaccination campaigns combined with real-time genomic surveillance can effectively contain the spread of new SARS-CoV-2 variants, even in a population initially naive to the virus. The Uruguayan experience highlights the impact of integrating genomic data into public health strategies, ultimately preventing large outbreaks despite the presence of transmissible VOCs and increased population mobility.Funding: FOCEM COF 03/11, G4 program, Institut Pasteur de Montevideo funded by the BSE of Uruguay, Fondo de Solidaridad para Proyectos Innovadores, Sociedad Civil, Francofonía y Desarrollo Humano, Ambassade de France, Centro Latinoamericano de Biotecnología, Agencia Nacional de Investigación e Innovación, International Programme, British Embassy Montevideo, Uruguay.