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In this study, 9493 genome sequences, including 241 local SARS-CoV-2 samples (collected from 21 December 2020, to 16 December 2021, and sequenced in the MinION platform) were analyzed with the following aims: (i) identify the relative prevalence of SARS-CoV-2 lineages in the state of Tocantins; (ii) analyze them phylogenetically against global SARS-CoV-2 sequences; and (iii) hypothesize the viral dispersal routes of the two most abundant lineages found in our study using phylogenetic and phylogeographic approaches. The performed analysis demonstrated that the majority of the strains sequenced during the period belong to the Gamma P.1.7 (32.4%) lineage, followed by Delta AY.99.2 (27.8%), with the first detection of VOC Omicron. As expected, there was mainly a dispersion of P.1.7 from the state of S\u00e3o Paulo to Tocantins, with evidence of secondary spreads from Tocantins to Goi\u00e1s, Mato Grosso, Amap\u00e1, and Par\u00e1. Rio de Janeiro was found to be the source of AY.99.2 and from then, multiple cluster transmission was observed across Brazilian states, especially S\u00e3o Paulo, Paraiba, Federal District, and Tocantins. These data show the importance of trade routes as pathways for the transportation of the virus from Southeast to Northern Brazil.<\/jats:p>","DOI":"10.3390\/v14040659","type":"journal-article","created":{"date-parts":[[2022,3,23]],"date-time":"2022-03-23T22:08:06Z","timestamp":1648073286000},"page":"659","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1442-4771","authenticated-orcid":false,"given":"Ueric Jos\u00e9 Borges","family":"de Souza","sequence":"first","affiliation":[{"name":"Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3388-890X","authenticated-orcid":false,"given":"Ra\u00edssa Nunes","family":"dos Santos","sequence":"additional","affiliation":[{"name":"Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9591-0239","authenticated-orcid":false,"given":"Fernando Lucas","family":"de Melo","sequence":"additional","affiliation":[{"name":"Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Bras\u00edlia 70910-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aline","family":"Belmok","sequence":"additional","affiliation":[{"name":"Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Bras\u00edlia 70910-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jucim\u00e1ria Dantas","family":"Galv\u00e3o","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratory of the State of Tocantins, Palmas 77054-970, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tereza Cristina Vieira","family":"de Rezende","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratory of the State of Tocantins, Palmas 77054-970, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0559-3082","authenticated-orcid":false,"given":"Franciano Dias Pereira","family":"Cardoso","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratory of the State of Tocantins, Palmas 77054-970, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0643-8914","authenticated-orcid":false,"given":"Rog\u00e9rio Fernandes","family":"Carvalho","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Federal University of North Tocantins, Aragua\u00edna 77804-970, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9039-5832","authenticated-orcid":false,"given":"Monike","family":"da Silva Oliveira","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Federal University of North Tocantins, Aragua\u00edna 77804-970, Brazil"},{"name":"Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Goi\u00e1s, Goi\u00e2nia 74001-970, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3272-4375","authenticated-orcid":false,"given":"Jose Carlos","family":"Ribeiro Junior","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology, Federal University of North Tocantins, Aragua\u00edna 77804-970, 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