Genomic Characterization of SARS-CoV-2 from an Indigenous Reserve in Mato Grosso do Sul, Brazil

Background: The COVID-19 pandemic had a major impact on indigenous populations. Understanding the viral dynamics within this population is essential to create targeted protection measures.Methods: A total of 204 SARS-CoV-2 positive samples collected between May 2020 and November 2021 from an indigenous area in Mato Grosso do Sul (MS), Midwestern Brazil, were screened. Samples were submitted to whole genome sequencing using the Nanopore sequencing platform. Clinical, demographic, and phylogenetic data were analyzed.Result: We found the co-circulation of six main SARS-CoV-2 lineages in the indigenous population, with the Zeta lineage being the most prevalent, followed by B.1.1 (an ancestral strain), Gamma and Delta. The estimated indigenous population mortality rate was 1.47%.Discussion. Our results revealed that multiple independent SARS-CoV-2 introduction events had occurred through time, probably due to indigenous mobility since the villages studied here are close to urban areas in MS, and people are in constant movement between both areas. The mortality rate was slightly below of the estimation for the state in the period studied, which we believe could be related to the low number of samples evaluated, the underreporting of cases and deaths among the indigenous population, and the inconsistency of secondary data available for this study.Conclusion: In this study, we showed the circulation of multiple SARS-CoV-2 variants in the indigenous population, which should be isolated and protected as they belong to the most fragile group due to their socioeconomic and cultural disparities. We reinforce the need for constant genomic surveillance in order to monitor and prevent the spread of new emerging viruses and to better understand the viral dynamics in these populations, making it possible to direct specific actions.Funding: This work was partially funded by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq grants 4.502.250), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Governo do Estado de Mato Grosso do Sul, Secretaria do Estado de Saúde and Universidade Federal da Grande Dourados (UFGD) and by the National Institutes of Health USA grant U01 AI151698 for the United World Antiviral Research Network (UWARN). L. A. O., and S.S. received a research grant from CNPq. Sponsors didn’t take part in data collection, analysis and interpretation nor in manuscript writing. MG is funded by PON “Ricerca e Innovazione” 2014-2020.Declaration of Interest: We declare no conflicts of interest.Ethical Approval: This study was approved by The National Research Ethics Committee (CONEP) with identification number 4.584.624.