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

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 amidst a largely immunologically naive population. Following the implementation of a nationwide vaccination campaign, the detection of the Delta VOC in July 2021 did not trigger a significant transmission wave, even in the face of increased mobility during the winter holidays (late June to mid-July). We present a comprehensive analysis of the dynamics of SARS-CoV-2 in Uruguay until September 2021. By analysing 1792 viral genomes, we integrate genomic data with vaccination records, variant surveillance and epidemiological information at both regional and global scales. Our study highlights the role of timely vaccination combined with real-time genomic surveillance programmes in effectively monitoring and mitigating critical phases of the COVID-19 epidemic.