Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil
In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cit...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-10-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/10/2013 |
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| author | Ronaldo da Silva Francisco Junior Alessandra P Lamarca Luiz G P de Almeida Liliane Cavalcante Douglas Terra Machado Yasmmin Martins Otávio Brustolini Alexandra L Gerber Ana Paula de C Guimarães Reinaldo Bellini Gonçalves Cassia Alves Diana Mariani Thais Felix Cruz Isabelle Vasconcellos de Souza Erika Martins de Carvalho Mario Sergio Ribeiro Silvia Carvalho Flávio Dias da Silva Márcio Henrique de Oliveira Garcia Leandro Magalhães de Souza Cristiane Gomes da Silva Caio Luiz Pereira Ribeiro Andréa Cony Cavalcanti Claudia Maria Braga de Mello Cláudio J. Struchiner Amilcar Tanuri Ana Tereza R de Vasconcelos |
| author_facet | Ronaldo da Silva Francisco Junior Alessandra P Lamarca Luiz G P de Almeida Liliane Cavalcante Douglas Terra Machado Yasmmin Martins Otávio Brustolini Alexandra L Gerber Ana Paula de C Guimarães Reinaldo Bellini Gonçalves Cassia Alves Diana Mariani Thais Felix Cruz Isabelle Vasconcellos de Souza Erika Martins de Carvalho Mario Sergio Ribeiro Silvia Carvalho Flávio Dias da Silva Márcio Henrique de Oliveira Garcia Leandro Magalhães de Souza Cristiane Gomes da Silva Caio Luiz Pereira Ribeiro Andréa Cony Cavalcanti Claudia Maria Braga de Mello Cláudio J. Struchiner Amilcar Tanuri Ana Tereza R de Vasconcelos |
| author_sort | Ronaldo da Silva Francisco Junior |
| collection | DOAJ |
| description | In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pandemic was characterized by three different phases driven by a successive replacement of lineages. Interestingly, we noticed that viral supercarriers accounted for the overwhelming majority of the circulating virus (>90%) among symptomatic individuals in the state. Moreover, SARS-CoV-2 genomic surveillance also revealed the emergence and spread of two new variants (P.5 and P.1.2), firstly reported in this study. Our findings provided important lessons learned from the different epidemiological aspects of the SARS-CoV-2 dynamic in Rio de Janeiro. Altogether, this might have a strong potential to shape future decisions aiming to improve public health management and understanding mechanisms underlying virus dispersion. |
| first_indexed | 2024-03-10T06:08:38Z |
| format | Article |
| id | doaj.art-933eaa089797448b8aea8344f7e554a9 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T06:08:38Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-933eaa089797448b8aea8344f7e554a92023-11-22T20:19:27ZengMDPI AGViruses1999-49152021-10-011310201310.3390/v13102013Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, BrazilRonaldo da Silva Francisco Junior0Alessandra P Lamarca1Luiz G P de Almeida2Liliane Cavalcante3Douglas Terra Machado4Yasmmin Martins5Otávio Brustolini6Alexandra L Gerber7Ana Paula de C Guimarães8Reinaldo Bellini Gonçalves9Cassia Alves10Diana Mariani11Thais Felix Cruz12Isabelle Vasconcellos de Souza13Erika Martins de Carvalho14Mario Sergio Ribeiro15Silvia Carvalho16Flávio Dias da Silva17Márcio Henrique de Oliveira Garcia18Leandro Magalhães de Souza19Cristiane Gomes da Silva20Caio Luiz Pereira Ribeiro21Andréa Cony Cavalcanti22Claudia Maria Braga de Mello23Cláudio J. Struchiner24Amilcar Tanuri25Ana Tereza R de Vasconcelos26Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, BrazilLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, BrazilLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, BrazilLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, BrazilLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, BrazilLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, BrazilLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, BrazilLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, BrazilLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, BrazilLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, BrazilDepartamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, BrazilDepartamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, BrazilDepartamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, BrazilUnidades de Apoio ao Diagnóstico da COVID-19, Rio de Janeiro 21040-900, BrazilUnidades de Apoio ao Diagnóstico da COVID-19, Rio de Janeiro 21040-900, BrazilSecretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, BrazilSecretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, BrazilSecretaria Municipal de Saúde Rio de Janeiro, Rio de Janeiro 20211-901, BrazilSecretaria Municipal de Saúde Rio de Janeiro, Rio de Janeiro 20211-901, BrazilLaboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, BrazilLaboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, BrazilSecretaria Municipal de Saúde Rio de Janeiro, Rio de Janeiro 20211-901, BrazilLaboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro 20231-092, BrazilSecretaria Estadual de Saúde do Rio de Janeiro, Rio de Janeiro 20031-142, BrazilFundação Getúlio Vargas, Rio de Janeiro 22250-900, BrazilDepartamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-570, BrazilLaboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis 25651-076, BrazilIn the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pandemic was characterized by three different phases driven by a successive replacement of lineages. Interestingly, we noticed that viral supercarriers accounted for the overwhelming majority of the circulating virus (>90%) among symptomatic individuals in the state. Moreover, SARS-CoV-2 genomic surveillance also revealed the emergence and spread of two new variants (P.5 and P.1.2), firstly reported in this study. Our findings provided important lessons learned from the different epidemiological aspects of the SARS-CoV-2 dynamic in Rio de Janeiro. Altogether, this might have a strong potential to shape future decisions aiming to improve public health management and understanding mechanisms underlying virus dispersion.https://www.mdpi.com/1999-4915/13/10/2013surveillanceP.1.2P.5COVID-19supercarrierslineage replacement |
| spellingShingle | Ronaldo da Silva Francisco Junior Alessandra P Lamarca Luiz G P de Almeida Liliane Cavalcante Douglas Terra Machado Yasmmin Martins Otávio Brustolini Alexandra L Gerber Ana Paula de C Guimarães Reinaldo Bellini Gonçalves Cassia Alves Diana Mariani Thais Felix Cruz Isabelle Vasconcellos de Souza Erika Martins de Carvalho Mario Sergio Ribeiro Silvia Carvalho Flávio Dias da Silva Márcio Henrique de Oliveira Garcia Leandro Magalhães de Souza Cristiane Gomes da Silva Caio Luiz Pereira Ribeiro Andréa Cony Cavalcanti Claudia Maria Braga de Mello Cláudio J. Struchiner Amilcar Tanuri Ana Tereza R de Vasconcelos Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil Viruses surveillance P.1.2 P.5 COVID-19 supercarriers lineage replacement |
| title | Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil |
| title_full | Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil |
| title_fullStr | Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil |
| title_full_unstemmed | Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil |
| title_short | Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil |
| title_sort | turnover of sars cov 2 lineages shaped the pandemic and enabled the emergence of new variants in the state of rio de janeiro brazil |
| topic | surveillance P.1.2 P.5 COVID-19 supercarriers lineage replacement |
| url | https://www.mdpi.com/1999-4915/13/10/2013 |
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