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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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Detalles Bibliográficos
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
Descripción
Sumario: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.