{"doi":"10.3389/fpubh.2023.1195779","title":"Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, 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.","journal":"Frontiers in Public Health","year":2023,"id":386940,"datarank":0.1141935237205277,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.010221446636535883,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.010221446636535883,"corpus_percentile":28.111704185039066,"corpus_rank":9294,"citation_count":1,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6928,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":50.0,"fair_percentile":62.702537450321,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":917476,"name":"Izabela Maurício de Rezende","orcid":"0000-0003-2616-6300","position":1,"is_corresponding":false},{"id":1156198,"name":"Vinícius João Navarini","orcid":null,"position":2,"is_corresponding":false},{"id":1155777,"name":"Silvana Beutinger Marchioro","orcid":"0000-0003-4282-5871","position":3,"is_corresponding":false},{"id":1001824,"name":"Alex Torres","orcid":"0000-0002-0167-4619","position":4,"is_corresponding":false},{"id":60898,"name":"Julio Croda","orcid":"0000-0002-6665-6825","position":5,"is_corresponding":false},{"id":756327,"name":"Mariana Garcia Croda","orcid":"0000-0003-1436-9717","position":6,"is_corresponding":false},{"id":323784,"name":"Crhistinne Cavalheiro Maymone Gonçalves","orcid":"0000-0001-6953-4965","position":7,"is_corresponding":false},{"id":575888,"name":"Joilson Xavier","orcid":"0000-0003-3916-2018","position":8,"is_corresponding":false},{"id":1056288,"name":"Emerson Castro","orcid":"0000-0002-3210-7342","position":9,"is_corresponding":false},{"id":649177,"name":"Maurício Lima","orcid":null,"position":10,"is_corresponding":false},{"id":575895,"name":"Felipe Campos de Melo Iani","orcid":"0000-0002-3629-8529","position":11,"is_corresponding":false},{"id":575887,"name":"Talita Adelino","orcid":"0000-0002-1471-0084","position":12,"is_corresponding":false},{"id":702224,"name":"Flávia Figueira Aburjaile","orcid":"0000-0002-1067-1882","position":13,"is_corresponding":false},{"id":575891,"name":"Luiz Henrique Ferraz Demarchi","orcid":"0000-0001-8693-7897","position":14,"is_corresponding":false},{"id":1156199,"name":"Deborah Ledesma Taira","orcid":null,"position":15,"is_corresponding":false},{"id":576603,"name":"Marina Castilhos Souza Umaki Zardin","orcid":null,"position":16,"is_corresponding":false},{"id":282144,"name":"Vagner Fonseca","orcid":"0000-0001-5521-6448","position":17,"is_corresponding":false},{"id":282145,"name":"Marta Giovanetti","orcid":"0000-0002-5849-7326","position":18,"is_corresponding":false},{"id":231886,"name":"Jason R. Andrews","orcid":"0000-0002-5967-251X","position":19,"is_corresponding":false},{"id":283627,"name":"Luiz Carlos Junior Alcantara","orcid":null,"position":20,"is_corresponding":false},{"id":1155778,"name":"Simone Simionatto","orcid":"0000-0003-2367-0915","position":21,"is_corresponding":false},{"id":1155776,"name":"Laís Albuquerque de Oliveira","orcid":"0000-0002-8571-3178","position":0,"is_corresponding":true}],"reference_count":19,"raw_metadata":null,"created_at":"2026-07-19T01:18:04.706547Z","pmid":"37965526","pmcid":"PMC10641392","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":38.8889,"fair_a":62.5,"fair_i":40.0,"fair_r":33.3333,"fair_zscore":0.6155,"fair_rationale":{"fair_score":50.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":38.89,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No specific identifier string from a PID scheme appears in the paper text; GISAID IDs are mentioned but not quoted.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"All sequences generated and used in the present study are listed in Supplementary Table 1, along with their GISAID sequence IDs","grounded":true,"rationale":"GISAID is a named repository (class 1). 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Cite the clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All sequences generated and used in the present study are listed in Supplementary Table 1, along with their GISAID sequence IDs","why":"The identifiers appear only in the body text (Supplementary Table 1), not as a reference-list entry. [majority verdict 'partial' (3/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). 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A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier for any external resource is given; references to GISAID are bare names.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No sentence addresses the timing or persistence of the data. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. 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