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

• Published in: Viruses Vol. 13; no. 5; p. 724
• Main Authors: Resende, Paola Cristina, Gräf, Tiago, Paixão, Anna Carolina Dias, Appolinario, Luciana, Lopes, Renata Serrano, Mendonça, Ana Carolina da Fonseca, da Rocha, Alice Sampaio Barreto, Motta, Fernando Couto, Neto, Lidio Gonçalves Lima, Khouri, Ricardo, de Oliveira, Camila I, Santos-Muccillo, Pedro, Bezerra, João Felipe, Teixeira, Dalane Loudal Florentino, Riediger, Irina, Debur, Maria do Carmo, Ribeiro-Rodrigues, Rodrigo, Leite, Anderson Brandao, do Santos, Cliomar Alves, Gregianini, Tatiana Schäffer, Fernandes, Sandra Bianchini, Bernardes, André Felipe Leal, Cavalcanti, Andrea Cony, Miyajima, Fábio, Sachhi, Claudio, Mattos, Tirza, da Costa, Cristiano Fernandes, Delatorre, Edson, Wallau, Gabriel L, Naveca, Felipe G, Bello, Gonzalo, Siqueira, Marilda Mendonça
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 21.04.2021; MDPI
• Subjects: Binding sites; Brazil; Communication; Coronaviruses; COVID-19; Disease transmission; E484K; Epidemiology; Genomes; genomic epidemiology; Markov analysis; Mutation; Phylogenetics; Proteins; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Spike protein; variant of Interest; Brazil; Brazil; variant of Interest; SARS-CoV-2; E484K; genomic epidemiology
• DOI: 10.3390/v13050724
• ISSN: 1999-4915

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.