The emergence of SARS-CoV-2 variants of concern endangers the long-term control of COVID-19, especially in countries with limited genomic surveillance. In this work, we explored genomic drivers of contagion in Chile. We sequenced 3443 SARS-CoV-2 genomes collected between January and July 2021, where the Gamma (P.1), Lambda (C.37), Alpha (B.1.1.7), B.1.1.348, and B.1.1 lineages were predominant. Using a Bayesian model tailored for limited genomic surveillance, we found that Lambda and Gamma variants' reproduction numbers were about 5% and 16% larger than Alpha's, respectively. We observed an overabundance of mutations in the Spike gene, strongly correlated with the variant's transmissibility. Furthermore, the variants' mutational signatures featured a breakpoint concurrent with the beginning of vaccination (mostly CoronaVac, an inactivated virus vaccine), indicating an additional putative selective pressure. Thus, our work provides a reliable method for quantifying novel variants' transmissibility under subsampling (as newly-reported Delta, B.1.617.2) and highlights the importance of continuous genomic surveillance.