The COVID-19 pandemic has already reached approximately 110 million people and it is associated with 2.5 million deaths worldwide. Brazil is the third worst-hit country, with approximately 10.2 million cases and 250 thousand deaths. Unprecedented international efforts have been established in order to share information about epidemiology, viral evolution and transmission dynamics. However, sequencing facilities and research investments are very heterogeneous across different regions and countries across the globe. The understanding of the SARS-CoV-2 biology is a vital part for the development of effective strategies for public health care and disease management. This work aims to analyze the available genomes sequenced in Brazil between February 2020 and February 2021, in order to identify mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages in the Brazilian territory by using phylogenetics and phylodynamics analyses from high-quality genomes. We describe heterogeneous and episodic sequencing efforts, the progression of the different lineages along time, evaluating mutational spectra and frequency oscillations derived from the prevalence of novel and specific lineages across different Brazilian regions. We found at least seven major (1-7) and two minor clades (4.2 and 5.3) related to the six most prevalent Brazilian lineages and described its distribution across the Brazilian territory. The emergence and recent frequency shift of lineages (P.1 and P.2) containing mutations of concern in the spike protein (e. g., E484K, N501Y) draws attention due to their association with immune evasion and enhanced receptor binding affinity. Improvements in genomic surveillance are of paramount importance and should be extended in Brazil to better inform policy makers and enable precise evidence-based decisions to fight the COVID-19 pandemic.