The COVID-19 pandemic has already reached more than 110 million people and 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. International efforts have been established to share information about Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemiology and evolution to support the development of effective strategies for public health and disease management. We aimed to analyze the high-quality genome sequences from Brazil from February 2020-2021 to identify mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages by using phylogenetics and phylodynamics analyses. We describe heterogeneous sequencing efforts, the progression of the different lineages along time, evaluating mutational spectra and frequency oscillations derived from the prevalence of specific lineages across different Brazilian regions. We found at least seven major (1–7) and two minor clades related to the six most prevalent lineages in the country and described its spatial distribution and dynamics. The emergence and recent frequency shift of lineages (P.1 and P.2) carrying 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 about better decisions to fight the COVID-19 pandemic.

COVID-19 大流行已影响到全球超过 1.1 亿人，并导致 250 万人死亡。巴西是第三个受灾最严重的国家，约有 1020 万例病例和 25 万人死亡。国际社会已努力分享有关严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 流行病学和进化的信息，以支持制定有效的公共卫生和疾病管理策略。我们的目的是分析 2020 年 2 月至 2021 年巴西的高质量基因组序列，通过系统发生学和系统动力学分析来确定 SARS-CoV-2 谱系的突变热点、地理和时间分布。我们描述了异质测序工作、不同谱系随时间的进展、评估源自巴西不同地区特定谱系流行情况的突变谱和频率振荡。我们发现了至少七个主要（1-7）和两个次要分支与该国六个最流行的谱系相关，并描述了其空间分布和动态。携带刺突蛋白（例如 E484K、N501Y）相关突变的谱系（P.1 和 P.2）的出现和最近的频率变化引起了人们的关注，因为它们与免疫逃避和增强的受体结合亲和力有关。基因组监测的改进至关重要，应该在巴西推广，以便更好地向决策者通报如何做出更好的决策来抗击 COVID-19 大流行。