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

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

doi:10.1038/s41591-021-01378-7

Abstract

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.

Highlights

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
To acquire a more in-depth understanding of the genetic diversity of SARS-CoV-2 variants circulating in Amazonas state since the early epidemic, we generated 250 SARS-CoV-2 high-quality, whole-genome sequences from individuals living in 25 municipalities, between 16 March 2020 and 13 January 2021 (Fig. 1a,b)

Summary

Introduction

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. 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. The precise relationship between circulating SARS-CoV-2 variants and epidemic dynamics in Amazonas remains unclear due to the paucity of viral sequences sampled in this Brazilian state before December 2020

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Conclusion