In summary, our study confirms that endemic transmission of SARS-CoV-2 after the second COVID-19 epidemic wave in the Amazonas state has been associated with the continuous evolution of the VOC gamma through the acquisition of either Spike mutations at the S1/S2 junction (N679K or P681H) or NTD deletions that probably increased viral infectivity or resistance against antiviral immunity. Here, CHMP5 is linked to COVID-19.