A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil

Paola Cristina Resende; Tiago Gräf; Anna Carolina Dias Paixão; Luciana Appolinario; Renata Serrano Lopes; Ana Carolina da Fonseca Mendonça; Alice Sampaio Barreto da Rocha; Fernando Couto Motta; Lidio Gonçalves Lima Neto; Ricardo Khouri; Camila I. de Oliveira; Pedro Santos-Muccillo; João Felipe Bezerra; Dalane Loudal Florentino Teixeira; Irina Riediger; Maria do Carmo Debur; Rodrigo Ribeiro-Rodrigues; Anderson Brandao Leite; Cliomar Alves do Santos; Tatiana Schäffer Gregianini; Sandra Bianchini Fernandes; André Felipe Leal Bernardes; Andrea Cony Cavalcanti; Fábio Miyajima; Claudio Sachhi; Tirza Mattos; Cristiano Fernandes da Costa; Edson Delatorre; Gabriel L. Wallau; Felipe G. Naveca; Gonzalo Bello; Marilda Mendonça Siqueira

A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil

2021

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in Brazil was dominated by two lineages designated as B.1.1.28 and B.1.1.33. The two SARS-CoV-2 variants harboring mutations at the receptor-binding domain of the Spike (S) protein, designated as lineages P.1 and P.2, evolved from lineage B.1.1.28 and are rapidly spreading in Brazil. Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K, N501Y), while lineage P.2 only harbors mutation S:E484K and is considered a Variant of Interest (VOI). On the other hand, epidemiologically relevant B.1.1.33 deriving lineages have not been described so far. Here we report the identification of a new SARS-CoV-2 VOI within lineage B.1.1.33 that also harbors mutation S:E484K and was detected in Brazil between November 2020 and February 2021. This VOI displayed four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NS7b:E33A) and was designated as lineage N.9. The VOI N.9 probably emerged in August 2020 and has spread across different Brazilian states from the Southeast, South, North, and Northeast regions.

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