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COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

2021; Nature Portfolio; Volume: 27; Issue: 7 Linguagem: Inglês

10.1038/s41591-021-01378-7

1546-170X

Felipe Gomes Naveca, Valdinete Alves do Nascimento, Victor Costa de Souza, André de Lima Guerra Corado, Fernanda Nascimento, George Silva, Ágatha Costa, Débora Duarte, Karina Pessoa, Matilde Mejía, Maria Júlia Brandão, Michele Silva de Jesus, Luciana Gonçalves, Cristiano Fernandes da Costa, Vanderson de Souza Sampaio, Daniel Ribeiro de Barros, Marineide Silva, Tirza Mattos, Gemilson Soares Pontes, Lígia Fernandes Abdalla, João Hugo Abdalla Santos, Ighor Arantes, Filipe Zimmer Dezordi, Marilda Mendonça Siqueira, Gabriel Luz Wallau, Paola Cristina Resende, Edson Delatorre, Tiago Gräf, Gonzalo Bello,

Virology and Viral Diseases

The northern state of Amazonas is among the regions in Brazil most heavily affected by the COVID-19 epidemic and has experienced two exponentially growing waves, in early and late 2020. Through a genomic epidemiology study based on 250 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from different Amazonas municipalities sampled between March 2020 and January 2021, we reveal that the first exponential growth phase was driven mostly by the dissemination of lineage B.1.195, which was gradually replaced by lineage B.1.1.28 between May and June 2020. The second wave coincides with the emergence of the variant of concern (VOC) P.1, which evolved from a local B.1.1.28 clade in late November 2020 and replaced the parental lineage in <2 months. Our findings support the conclusion that successive lineage replacements in Amazonas were driven by a complex combination of variable levels of social distancing measures and the emergence of a more transmissible VOC P.1 virus. These data provide insights to understanding the mechanisms underlying the COVID-19 epidemic waves and the risk of dissemination of SARS-CoV-2 VOC P.1 in Brazil and, potentially, worldwide.