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On December 9th, the Brazilian Ministry of Health (MoH) recognised the first case of reinfection in the country. A 37-years-old healthcare worker resident in Northeast Brazil presented two clinical episodes of COVID-19 in June and October 2020, that were confirmed by RT-PCR in samples collected 116 days apart. Whole-genome sequencing revealed that the two infections were caused, respectively, by the two most prevalent SARS-CoV-2 Brazilian lineages B. 1.1. 33 (primo-infection) and B. 1.1. 28 (reinfection). Bayesian analysis indicates that the reinfection probably occurred between September 14th to October 11th, a few days before the second confirmed clinical episode of COVID-19, thus excluding the possibility of viral co-infection followed by long-term viral persistence. Notably, the B. 1.1. 28 virus detected at reinfection corresponds to a new emergent Brazilian viral lineage, initially detected in the Rio de Janeiro state, containing the mutation E484K in the Spike protein. We found this new viral variant, hereafter designated B. 1.1. 28 (E484K), in several states from the South, Northeast, and North Brazilian regions and date its origin at August 27th, 2020 (July 14th-September 18th). These findings documented a classical SARS-CoV-2 reinfection case with the emerging Brazilian lineage B. 1.1. 28 (E484K). Additionally, we provide evidence of this emerging Brazilian clade’s geographic dissemination outside the Rio de Janeiro state.