ABSTRACT Characterization of SARS-CoV-2 variants in Peru, which has one of the highest mortality rates in the world, has been limited and represents a significant knowledge gap that can be addressed through increased genomic surveillance activities. Located within the Amazon Basin, Iquitos was one of the first cities in Peru to experience the impact of the COVID-19 pandemic with devasting levels of transmission in March 2020, followed by one of the highest documented seroprevalence rates of anti- SARS-CoV-2 antibodies worldwide, only to have a second wave of transmission from January through March 2021. Utilizing human samples collected in and near Iquitos, the EpiCenter for Emerging Infectious Disease Intelligence (EEIDI) will sequence SARS-CoV-2 isolates and characterize variants from Peru and investigate their association with human disease severity and syndromes, reinfection, travel history, health outcomes, and patient demographics. We will also characterize isolates of SARS-CoV-2 variants from sampled animals, in particular non-human primate populations that closely interact with humans to investigate potential for spillback into future animal reservoirs. This work will ensure rapid and adaptive surveillance of existing and emerging variants, while improving an understanding of which variants are most likely to be involved in future outbreaks.