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Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants
During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyse more than 1 600 genomic...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Microbiology Society
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9676039/ https://www.ncbi.nlm.nih.gov/pubmed/36106981 http://dx.doi.org/10.1099/mgen.0.000859 |
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author | Lamarca, Alessandra Pavan de Almeida, Luiz G. P. Francisco, Ronaldo da Silva Cavalcante, Liliane Brustolini, Otávio Gerber, Alexandra L. Guimarães, Ana Paula de C. de Oliveira, Thiago Henrique dos Santos Nascimento, Érica Ramos Policarpo, Cintia de Souza, Isabelle Vasconcellos de Carvalho, Erika Martins Ribeiro, Mario Sergio Carvalho, Silvia Dias da Silva, Flávio de Oliveira Garcia, Marcio Henrique de Souza, Leandro Magalhães Da Silva, Cristiane Gomes Ribeiro, Caio Luiz Pereira Cavalcanti, Andréa Cony de Mello, Claudia Maria Braga Tanuri, Amilcar de Vasconcelos, Ana Tereza R. |
author_facet | Lamarca, Alessandra Pavan de Almeida, Luiz G. P. Francisco, Ronaldo da Silva Cavalcante, Liliane Brustolini, Otávio Gerber, Alexandra L. Guimarães, Ana Paula de C. de Oliveira, Thiago Henrique dos Santos Nascimento, Érica Ramos Policarpo, Cintia de Souza, Isabelle Vasconcellos de Carvalho, Erika Martins Ribeiro, Mario Sergio Carvalho, Silvia Dias da Silva, Flávio de Oliveira Garcia, Marcio Henrique de Souza, Leandro Magalhães Da Silva, Cristiane Gomes Ribeiro, Caio Luiz Pereira Cavalcanti, Andréa Cony de Mello, Claudia Maria Braga Tanuri, Amilcar de Vasconcelos, Ana Tereza R. |
author_sort | Lamarca, Alessandra Pavan |
collection | PubMed |
description | During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyse more than 1 600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has initially spread mostly in the homonymous city of Rio de Janeiro, the most populous of the state. In a second stage, dispersal occurred to mid- and long-range cities, which acted as new close-range hubs for spread. We observed that the substitution of Gamma by Delta was possibly caused by its higher viral load, a proxy for transmissibility. This variant turnover prompted a new surge in cases, but with lower lethality than was observed during the peak caused by Gamma. We reason that high vaccination rates in the state of Rio de Janeiro were possibly what prevented a higher number of deaths. |
format | Online Article Text |
id | pubmed-9676039 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-96760392022-11-21 Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants Lamarca, Alessandra Pavan de Almeida, Luiz G. P. Francisco, Ronaldo da Silva Cavalcante, Liliane Brustolini, Otávio Gerber, Alexandra L. Guimarães, Ana Paula de C. de Oliveira, Thiago Henrique dos Santos Nascimento, Érica Ramos Policarpo, Cintia de Souza, Isabelle Vasconcellos de Carvalho, Erika Martins Ribeiro, Mario Sergio Carvalho, Silvia Dias da Silva, Flávio de Oliveira Garcia, Marcio Henrique de Souza, Leandro Magalhães Da Silva, Cristiane Gomes Ribeiro, Caio Luiz Pereira Cavalcanti, Andréa Cony de Mello, Claudia Maria Braga Tanuri, Amilcar de Vasconcelos, Ana Tereza R. Microb Genom Short Communications During the first semester of 2021, all of Brazil has suffered an intense wave of COVID-19 associated with the Gamma variant. In July, the first cases of Delta variant were detected in the state of Rio de Janeiro. In this work, we have employed phylodynamic methods to analyse more than 1 600 genomic sequences of Delta variant collected until September in Rio de Janeiro to reconstruct how this variant has surpassed Gamma and dispersed throughout the state. After the introduction of Delta, it has initially spread mostly in the homonymous city of Rio de Janeiro, the most populous of the state. In a second stage, dispersal occurred to mid- and long-range cities, which acted as new close-range hubs for spread. We observed that the substitution of Gamma by Delta was possibly caused by its higher viral load, a proxy for transmissibility. This variant turnover prompted a new surge in cases, but with lower lethality than was observed during the peak caused by Gamma. We reason that high vaccination rates in the state of Rio de Janeiro were possibly what prevented a higher number of deaths. Microbiology Society 2022-09-15 /pmc/articles/PMC9676039/ /pubmed/36106981 http://dx.doi.org/10.1099/mgen.0.000859 Text en © 2022 The Authors https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. |
spellingShingle | Short Communications Lamarca, Alessandra Pavan de Almeida, Luiz G. P. Francisco, Ronaldo da Silva Cavalcante, Liliane Brustolini, Otávio Gerber, Alexandra L. Guimarães, Ana Paula de C. de Oliveira, Thiago Henrique dos Santos Nascimento, Érica Ramos Policarpo, Cintia de Souza, Isabelle Vasconcellos de Carvalho, Erika Martins Ribeiro, Mario Sergio Carvalho, Silvia Dias da Silva, Flávio de Oliveira Garcia, Marcio Henrique de Souza, Leandro Magalhães Da Silva, Cristiane Gomes Ribeiro, Caio Luiz Pereira Cavalcanti, Andréa Cony de Mello, Claudia Maria Braga Tanuri, Amilcar de Vasconcelos, Ana Tereza R. Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants |
title | Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants |
title_full | Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants |
title_fullStr | Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants |
title_full_unstemmed | Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants |
title_short | Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants |
title_sort | phylodynamic analysis of sars-cov-2 spread in rio de janeiro, brazil, highlights how metropolitan areas act as dispersal hubs for new variants |
topic | Short Communications |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9676039/ https://www.ncbi.nlm.nih.gov/pubmed/36106981 http://dx.doi.org/10.1099/mgen.0.000859 |
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