Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in 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 Dec...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-03-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/4/659 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Ueric José Borges de Souza |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T04:09:00Z |
| format | Article |
| id | doaj.art-c257f4e7fa0d49d39a42fa4c3237c0f7 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T04:09:00Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-c257f4e7fa0d49d39a42fa4c3237c0f72023-12-03T14:02:49ZengMDPI AGViruses1999-49152022-03-0114465910.3390/v14040659Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in BrazilUeric José Borges de Souza0Raíssa Nunes dos Santos1Fernando Lucas de Melo2Aline Belmok3Jucimária Dantas Galvão4Tereza Cristina Vieira de Rezende5Franciano Dias Pereira Cardoso6Rogério Fernandes Carvalho7Monike da Silva Oliveira8Jose Carlos Ribeiro Junior9Evgeni Evgeniev Gabev10Ester Cerdeira Sabino11Clarice Weis Arns12Bergmann Morais Ribeiro13Fernando Rosado Spilki14Fabrício Souza Campos15Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, BrazilBioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, BrazilBaculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, BrazilBaculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, BrazilCentral Public Health Laboratory of the State of Tocantins, Palmas 77054-970, BrazilCentral Public Health Laboratory of the State of Tocantins, Palmas 77054-970, BrazilCentral Public Health Laboratory of the State of Tocantins, Palmas 77054-970, BrazilLaboratory of Microbiology, Federal University of North Tocantins, Araguaína 77804-970, BrazilLaboratory of Microbiology, Federal University of North Tocantins, Araguaína 77804-970, BrazilLaboratory of Microbiology, Federal University of North Tocantins, Araguaína 77804-970, BrazilDepartment of Physiology and Pathophysiology, Medical University of Sofia, 1431 Sofia, BulgariaDepartment of Infectious and Parasitic Diseases, Institute of Tropical Medicine, Faculty of Medicine, University of São Paulo, São Paulo 05403-000, BrazilLaboratory of Animal Virology, Institute of Biology, University of Campinas, Campinas 13083-862, BrazilBaculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília 70910-900, BrazilMolecular Microbiology Laboratory, Feevale University, Novo Hamburgo 93525-075, BrazilBioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi 77410-570, BrazilTocantins 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.https://www.mdpi.com/1999-4915/14/4/659SARS-CoV-2variants of concerngenome analysisviral evolutionviral trajectory |
| spellingShingle | 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 Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil Viruses SARS-CoV-2 variants of concern genome analysis viral evolution viral trajectory |
| title | Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil |
| title_full | Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil |
| title_fullStr | Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil |
| title_full_unstemmed | Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil |
| title_short | Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil |
| title_sort | genomic epidemiology of sars cov 2 in tocantins state and the diffusion of p 1 7 and ay 99 2 lineages in brazil |
| topic | SARS-CoV-2 variants of concern genome analysis viral evolution viral trajectory |
| url | https://www.mdpi.com/1999-4915/14/4/659 |
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