Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil
Ueric José Borges de Souza,
Raíssa Nunes dos Santos,
Fernando Lucas de Melo,
Aline Belmok,
Jucimária Dantas Galvão,
Tereza Cristina Vieira de Rezende,
Franciano Dias Pereira Cardoso,
Rogério Fernandes Carvalho,
Monike da Silva Oliveira,
Jose Carlos Ribeiro Junior,
Evgeni Evgeniev Gabev,
Ester Cerdeira Sabino,
Clarice Weis Arns,
Bergmann Morais Ribeiro,
Fernando Rosado Spilki,
Fabrício Souza Campos
Affiliations
Ueric José Borges de Souza
Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, Brazil
Raíssa Nunes dos Santos
Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, Brazil
Fernando Lucas de Melo
Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, Brazil
Aline Belmok
Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, Brazil
Jucimária Dantas Galvão
Central Public Health Laboratory of the State of Tocantins, Palmas 77054-970, Brazil
Tereza Cristina Vieira de Rezende
Central Public Health Laboratory of the State of Tocantins, Palmas 77054-970, Brazil
Franciano Dias Pereira Cardoso
Central Public Health Laboratory of the State of Tocantins, Palmas 77054-970, Brazil
Rogério Fernandes Carvalho
Laboratory of Microbiology, Federal University of North Tocantins, Araguaína 77804-970, Brazil
Monike da Silva Oliveira
Laboratory of Microbiology, Federal University of North Tocantins, Araguaína 77804-970, Brazil
Jose Carlos Ribeiro Junior
Laboratory of Microbiology, Federal University of North Tocantins, Araguaína 77804-970, Brazil
Evgeni Evgeniev Gabev
Department of Physiology and Pathophysiology, Medical University of Sofia, 1431 Sofia, Bulgaria
Ester Cerdeira Sabino
Department of Infectious and Parasitic Diseases, Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo 05403-000, Brazil
Clarice Weis Arns
Laboratory of Animal Virology, Institute of Biology, University of Campinas, Campinas 13083-862, Brazil
Bergmann Morais Ribeiro
Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, Brazil
Fernando Rosado Spilki
Molecular Microbiology Laboratory, Feevale University, Novo Hamburgo 93525-075, Brazil
Fabrício Souza Campos
Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, Brazil
Tocantins is a state in the cross-section between the Central-West, North and Northeast regions of Brazilian territory; it is a gathering point for travelers and transportation from the whole country. 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 São Paulo to Tocantins, with evidence of secondary spreads from Tocantins to Goiás, Mato Grosso, Amapá, and Pará. 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 São 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.
