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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...

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Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2022
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.
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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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