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https://www.arca.fiocruz.br/handle/icict/62281
GENOMIC CHARACTERIZATION OF SARS-COV-2 FROM AN INDIGENOUS RESERVE IN MATO GROSSO DO SUL, BRAZIL.
Author
Oliveira, Laís Albuquerque de
Rezende, Izabela Mauricio de
Navarini, Vinicius João
Marchioro, Silvana Beutinger
Torres, Alex José Leite
Croda, Julio
Croda, Mariana Garcia
Gonçalves, Crhistinne Cavalheiro Maymone
Xavier, Joilson
Castro, Emerson de
Lima, Mauricio
Iani, Felipe
Adelino, Talita
Aburjaile, Flávia
Demarchi, Luiz Henrique Ferraz
Taira, Deborah Ledesma
Zardin, Marina Castilhos Souza Umaki
Fonseca, Vagner
Giovanetti, Marta
Andrews, Jason
Alcantara, Luiz Carlos Junior
Simionatto, Simone
Rezende, Izabela Mauricio de
Navarini, Vinicius João
Marchioro, Silvana Beutinger
Torres, Alex José Leite
Croda, Julio
Croda, Mariana Garcia
Gonçalves, Crhistinne Cavalheiro Maymone
Xavier, Joilson
Castro, Emerson de
Lima, Mauricio
Iani, Felipe
Adelino, Talita
Aburjaile, Flávia
Demarchi, Luiz Henrique Ferraz
Taira, Deborah Ledesma
Zardin, Marina Castilhos Souza Umaki
Fonseca, Vagner
Giovanetti, Marta
Andrews, Jason
Alcantara, Luiz Carlos Junior
Simionatto, Simone
Affilliation
Health Sciences Research Laboratory. Federal University of Grande Dourados. Dourados, MS, Brazil
Stanford Pandemic Preparedness Hub. Department of Medicine. Division of Infectious Diseases and Geographic Medicine. Stanford University School of Medicine. Stanford, CA, United States
Health Sciences Research Laboratory. Federal University of Grande Dourados. Dourados, MS, Brazil
Laboratory of Immunology and Molecular Biology. Institute of Health Sciences. Federal University of Bahia. Salvador, BA, Brazil
Laboratory of Immunology and Molecular Biology. Institute of Health Sciences. Federal University of Bahia. Salvador, BA, Brazil
Oswaldo Cruz Foundation. Campo Grande, MS, Brazil/Faculdade de Medicina. Universidade Federal do Mato Grosso do Sul. Campo Grande, MS, Brazil
Universidade Federal do Mato Grosso do Sul. Faculdade de Medicina. Campo Grande, MS, Brazil
School of Medicine. Federal University of Mato Grosso do Sul. Campo Grande, MS, Brazil/ State Secretariat of Health of Mato Grosso do Sul. Campo Grande. MS, Brazil
Federal University of Minas Gerais. Belo Horizonte, MG, Brazil
Ezequiel Dias Foundation. Belo Horizonte, MG, Brazil
Ezequiel Dias Foundation. Belo Horizonte, MG, Brazil
Ezequiel Dias Foundation. Belo Horizonte, MG, Brazil
Ezequiel Dias Foundation. Belo Horizonte, MG, Brazil
Preventive Veterinary Medicine Departament. Veterinary School. Universidade Federal de Minas Gerais. Belo Horizonte, MG, Brazil
Central Public Health Laboratory. Campo Grande, MS, Brazil
Central Public Health Laboratory. Campo Grande, MS, Brazil
Central Public Health Laboratory. Campo Grande, MS, Brazil
Pan American Health Organization. Brasília, DF, Brazil
Fundação Oswaldo Cruz. Rene Rachou. Belo Horizonte, MG, Brazil/Sciences and Technologies for Sustainable Development and One Health. Università Campus Bio-Medico di Roma. Rome, Italy/Climate-Amplified Diseases and Epidemics. Rio de Janeiro, RJ, Brazil
Stanford Pandemic Preparedness Hub. Department of Medicine. Division of Infectious Diseases and Geographic Medicine. Stanford University School of Medicine. Stanford, CA, United States
Fundação Oswaldo Cruz. Rene Rachou. Belo Horizonte, MG, Brazil/Climate-Amplified Diseases and Epidemics. Rio de Janeiro, RJ, Brazil
Health Sciences Research Laboratory. Federal University of Grande Dourados. Dourados, MS, Brazil
Stanford Pandemic Preparedness Hub. Department of Medicine. Division of Infectious Diseases and Geographic Medicine. Stanford University School of Medicine. Stanford, CA, United States
Health Sciences Research Laboratory. Federal University of Grande Dourados. Dourados, MS, Brazil
Laboratory of Immunology and Molecular Biology. Institute of Health Sciences. Federal University of Bahia. Salvador, BA, Brazil
Laboratory of Immunology and Molecular Biology. Institute of Health Sciences. Federal University of Bahia. Salvador, BA, Brazil
Oswaldo Cruz Foundation. Campo Grande, MS, Brazil/Faculdade de Medicina. Universidade Federal do Mato Grosso do Sul. Campo Grande, MS, Brazil
Universidade Federal do Mato Grosso do Sul. Faculdade de Medicina. Campo Grande, MS, Brazil
School of Medicine. Federal University of Mato Grosso do Sul. Campo Grande, MS, Brazil/ State Secretariat of Health of Mato Grosso do Sul. Campo Grande. MS, Brazil
Federal University of Minas Gerais. Belo Horizonte, MG, Brazil
Ezequiel Dias Foundation. Belo Horizonte, MG, Brazil
Ezequiel Dias Foundation. Belo Horizonte, MG, Brazil
Ezequiel Dias Foundation. Belo Horizonte, MG, Brazil
Ezequiel Dias Foundation. Belo Horizonte, MG, Brazil
Preventive Veterinary Medicine Departament. Veterinary School. Universidade Federal de Minas Gerais. Belo Horizonte, MG, Brazil
Central Public Health Laboratory. Campo Grande, MS, Brazil
Central Public Health Laboratory. Campo Grande, MS, Brazil
Central Public Health Laboratory. Campo Grande, MS, Brazil
Pan American Health Organization. Brasília, DF, Brazil
Fundação Oswaldo Cruz. Rene Rachou. Belo Horizonte, MG, Brazil/Sciences and Technologies for Sustainable Development and One Health. Università Campus Bio-Medico di Roma. Rome, Italy/Climate-Amplified Diseases and Epidemics. Rio de Janeiro, RJ, Brazil
Stanford Pandemic Preparedness Hub. Department of Medicine. Division of Infectious Diseases and Geographic Medicine. Stanford University School of Medicine. Stanford, CA, United States
Fundação Oswaldo Cruz. Rene Rachou. Belo Horizonte, MG, Brazil/Climate-Amplified Diseases and Epidemics. Rio de Janeiro, RJ, Brazil
Health Sciences Research Laboratory. Federal University of Grande Dourados. Dourados, MS, Brazil
Abstract
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.
Results; We found the co-circulation of six main SARS-CoV-2 lineages in the indigenous population, with the Zeta lineage being the most prevalent (27.66%), followed by B.1.1 (an ancestral strain) (20.21%), Gamma (14.36%) and Delta (13.83%). Other lineages represent 45.74% of the total. Our phylogenetic reconstruction indicates that multiple introduction events of different SARS-CoV-2 lineages occurred in the indigenous villages in MS. The estimated indigenous population mortality rate was 1.47%. Regarding the ethnicity of our cohort, 64.82% belong to the Guarani ethnicity, while 33.16% belong to the Terena ethnicity, with a slightly higher prevalence of males (53.43%) among females. Other ethnicities represent 2.01%. We also observed that almost all patients (89.55%) presented signs and symptoms related to COVID-19, being the most prevalent cough, fever, sore throat, and headache.
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. The mortality rate was slightly below of the estimation for the state in the period studied, which we believe could be related to the small number of samples evaluated, the underreporting of cases and deaths among this 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 this 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 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
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