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

May 25, 2021

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

Nature Med

Researchers in the Brazilian state Amazonas investigated how the progression of COVID-19 outbreaks in the state were driven by different lineages of the SARS-CoV-2 virus. Between March 16, 2020 and January 13, 2021, the authors created 250 SARS-CoV-2 whole genome sequences from different patient samples in the region. Five lineages were identified; during the first peak in early May 2020, the B.1.195 lineage dominated the prevalence of viral strains. This strain was gradually replaced by lineage B.1.1.28 over the summer, and quickly replaced by P.1, a CDC-classified variant of concern, in December 2020. Between December 2020 and January 2021, P.1 exponentially grew to become the most prevalent strain in Amazonas. The authors suggest a relationship between the different SARS-CoV-2 clades and social distancing protocols in Amazonas. They concluded that the rise of Re values in different clades correlated with more relaxed social distancing regulations. They also predicted that the population of Manaus, the capital city of Amazonas, reached herd immunity from natural infection in October 2020, suggesting that the P.1 variant that caused the December 2020 outbreak and collapse of the Manaus health system successfully evaded immunity gained from prior infection with different SARS-CoV-2 lineages. The authors recognize that their modelling may have overestimated the SARS-CoV-2 attack rate in Manaus, and therefore possibly overestimating the natural immunity in Manaus in late 2020.

Naveca FG, Nascimento V, de Souza VC, et al. COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence. Nat Med 2021; : 1–9.

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