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Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil

2021; Multidisciplinary Digital Publishing Institute; Volume: 13; Issue: 10 Linguagem: Inglês

10.3390/v13102013

1999-4915

Ronaldo da Silva Francisco, Alessandra P. Lamarca, Luiz Gonzaga Paula de Almeida, Liliane Cavalcante, Douglas Terra Machado, Yasmmin Martins, Otávio J. B. Brustolini, Alexandra Lehmkuhl Gerber, Ana Paula de Campos Guimarães, Reinaldo Bellini Gonçalves, Cassia Alves, Diana Mariani, Thais Felix Cordeiro da Cruz, Isabelle Vasconcellos de Souza, Erika Martins de Carvalho, Mário Sérgio 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, Amílcar Tanuri, Ana Tereza Ribeiro de Vasconcelos,

Viral Infections and Outbreaks Research

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.