Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil.
Ronaldo da Silva Francisco JuniorAlessandra P LamarcaLuiz Gonzaga Paula de AlmeidaLiliane CavalcanteDouglas Terra MachadoYasmmin Côrtes MartinsOtávio BrustoliniAlexandra L GerberAna Paula de C GuimarãesReinaldo Bellini GonçalvesCassia AlvesDiana MarianiThais Felix CruzIsabelle Vasconcellos de SouzaErika Martins de CarvalhoMario Sergio RibeiroSilvia CarvalhoFlávio Dias da SilvaMárcio Henrique de Oliveira GarciaLeandro Magalhães de SouzaCristiane Gomes da SilvaCaio Luiz Pereira RibeiroAndréa Cony CavalcantiClaudia Maria Braga de MelloClaudio Jose StruchinerAmilcar TanuriAna Tereza Ribeiro de VasconcelosPublished in: Viruses (2021)
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.