Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil
BackgroundThe COVID-19 pandemic had a major impact on indigenous populations. Understanding the viral dynamics within this population is essential to create targeted protection measures.MethodsA total of 204 SARS-CoV-2 positive samples collected between May 2020 and November 2021 from an indigenous...
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Frontiers Media S.A.
2023-10-01
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| Series: | Frontiers in Public Health |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpubh.2023.1195779/full |
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| author | Laís Albuquerque de Oliveira Izabela Mauricio de Rezende Vinicius João Navarini Silvana Beutinger Marchioro Alex José Leite Torres Julio Croda Julio Croda Mariana Garcia Croda Crhistinne Cavalheiro Maymone Gonçalves Crhistinne Cavalheiro Maymone Gonçalves Joilson Xavier Emerson de Castro Mauricio Lima Felipe Iani Talita Adelino Flávia Aburjaile Luiz Henrique Ferraz Demarchi Deborah Ledesma Taira Marina Castilhos Souza Umaki Zardin Vagner Fonseca Marta Giovanetti Marta Giovanetti Marta Giovanetti Jason Andrews Luiz Carlos Junior Alcantara Luiz Carlos Junior Alcantara Simone Simionatto |
| author_facet | Laís Albuquerque de Oliveira Izabela Mauricio de Rezende Vinicius João Navarini Silvana Beutinger Marchioro Alex José Leite Torres Julio Croda Julio Croda Mariana Garcia Croda Crhistinne Cavalheiro Maymone Gonçalves Crhistinne Cavalheiro Maymone Gonçalves Joilson Xavier Emerson de Castro Mauricio Lima Felipe Iani Talita Adelino Flávia Aburjaile Luiz Henrique Ferraz Demarchi Deborah Ledesma Taira Marina Castilhos Souza Umaki Zardin Vagner Fonseca Marta Giovanetti Marta Giovanetti Marta Giovanetti Jason Andrews Luiz Carlos Junior Alcantara Luiz Carlos Junior Alcantara Simone Simionatto |
| author_sort | Laís Albuquerque de Oliveira |
| collection | DOAJ |
| description | BackgroundThe COVID-19 pandemic had a major impact on indigenous populations. Understanding the viral dynamics within this population is essential to create targeted protection measures.MethodsA 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.ResultsWe 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.DiscussionOur 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.ConclusionIn 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. |
| first_indexed | 2024-03-11T15:31:25Z |
| format | Article |
| id | doaj.art-ac34af6c1eb14eca8488beea835c19d3 |
| institution | Directory Open Access Journal |
| issn | 2296-2565 |
| language | English |
| last_indexed | 2024-03-11T15:31:25Z |
| publishDate | 2023-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Public Health |
| spelling | doaj.art-ac34af6c1eb14eca8488beea835c19d32023-10-27T04:15:51ZengFrontiers Media S.A.Frontiers in Public Health2296-25652023-10-011110.3389/fpubh.2023.11957791195779Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, BrazilLaís Albuquerque de Oliveira0Izabela Mauricio de Rezende1Vinicius João Navarini2Silvana Beutinger Marchioro3Alex José Leite Torres4Julio Croda5Julio Croda6Mariana Garcia Croda7Crhistinne Cavalheiro Maymone Gonçalves8Crhistinne Cavalheiro Maymone Gonçalves9Joilson Xavier10Emerson de Castro11Mauricio Lima12Felipe Iani13Talita Adelino14Flávia Aburjaile15Luiz Henrique Ferraz Demarchi16Deborah Ledesma Taira17Marina Castilhos Souza Umaki Zardin18Vagner Fonseca19Marta Giovanetti20Marta Giovanetti21Marta Giovanetti22Jason Andrews23Luiz Carlos Junior Alcantara24Luiz Carlos Junior Alcantara25Simone Simionatto26Health Sciences Research Laboratory, Federal University of Grande Dourados, Dourados, Mato Grosso do Sul, BrazilStanford Pandemic Preparedness Hub, Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United StatesHealth Sciences Research Laboratory, Federal University of Grande Dourados, Dourados, Mato Grosso do Sul, BrazilLaboratory of Immunology and Molecular Biology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, BrazilLaboratory of Immunology and Molecular Biology, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, BrazilOswaldo Cruz Foundation, Campo Grande, Mato Grosso do Sul, BrazilFaculdade de Medicina (FAMED), Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, BrazilFaculdade de Medicina (FAMED), Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, BrazilSchool of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, BrazilState Secretariat of Health of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, BrazilFederal University of Minas Gerais, Belo Horizonte, Minas Gerais, BrazilEzequiel Dias Foundation (FUNED), Belo Horizonte, Minas Gerais, BrazilEzequiel Dias Foundation (FUNED), Belo Horizonte, Minas Gerais, BrazilEzequiel Dias Foundation (FUNED), Belo Horizonte, Minas Gerais, BrazilEzequiel Dias Foundation (FUNED), Belo Horizonte, Minas Gerais, Brazil0Preventive Veterinary Medicine Departament, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil1Central Public Health Laboratory (Lacen), Campo Grande, Mato Grosso do Sul, BrazilState Secretariat of Health of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil1Central Public Health Laboratory (Lacen), Campo Grande, Mato Grosso do Sul, Brazil2Pan American Health Organization - PAHO, Brasília, Distrito Federal, Brazil3Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil4Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, Rome, Italy5Climate-Amplified Diseases and Epidemics (CLIMADE) Rio de Janeiro, Rio de Janeiro, BrazilStanford Pandemic Preparedness Hub, Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States3Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil5Climate-Amplified Diseases and Epidemics (CLIMADE) Rio de Janeiro, Rio de Janeiro, BrazilHealth Sciences Research Laboratory, Federal University of Grande Dourados, Dourados, Mato Grosso do Sul, BrazilBackgroundThe COVID-19 pandemic had a major impact on indigenous populations. Understanding the viral dynamics within this population is essential to create targeted protection measures.MethodsA 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.ResultsWe 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.DiscussionOur 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.ConclusionIn 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.https://www.frontiersin.org/articles/10.3389/fpubh.2023.1195779/fullSARS-CoV-2COVID-19indigenous populationVoIVOCpandemic |
| spellingShingle | Laís Albuquerque de Oliveira Izabela Mauricio de Rezende Vinicius João Navarini Silvana Beutinger Marchioro Alex José Leite Torres Julio Croda Julio Croda Mariana Garcia Croda Crhistinne Cavalheiro Maymone Gonçalves Crhistinne Cavalheiro Maymone Gonçalves Joilson Xavier Emerson de Castro Mauricio Lima Felipe Iani Talita Adelino Flávia Aburjaile Luiz Henrique Ferraz Demarchi Deborah Ledesma Taira Marina Castilhos Souza Umaki Zardin Vagner Fonseca Marta Giovanetti Marta Giovanetti Marta Giovanetti Jason Andrews Luiz Carlos Junior Alcantara Luiz Carlos Junior Alcantara Simone Simionatto Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil Frontiers in Public Health SARS-CoV-2 COVID-19 indigenous population VoI VOC pandemic |
| title | Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil |
| title_full | Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil |
| title_fullStr | Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil |
| title_full_unstemmed | Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil |
| title_short | Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil |
| title_sort | genomic characterization of sars cov 2 from an indigenous reserve in mato grosso do sul brazil |
| topic | SARS-CoV-2 COVID-19 indigenous population VoI VOC pandemic |
| url | https://www.frontiersin.org/articles/10.3389/fpubh.2023.1195779/full |
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