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,Alice Sampaio Barreto Da Rocha,Cristiano Fernandes Da Costa,Fernando Couto Motta,João Felipe Bezerra,Tiago Gräf,Claudio Sachhi,Cliomar Alves Do Santos,Dalane Loudal Florentino Teixeira,Gonzalo Bello,André Felipe Leal Bernardes,Ricardo Khouri,Maria Do Carmo Debur,Luciana Appolinario,Camila I De Oliveira,Edson Delatorre,Fábio Miyajima,Ana Carolina Da Fonseca Mendonça,Sandra Bianchini Fernandes,Marilda Mendonça Siqueira,Tirza Mattos,Renata Serrano Lopes,Tatiana Schäffer Gregianini,Irina Nastassja Riediger ,Anderson Brandão Leite ,Lídio Gonçãlves Lima Neto ,Gabriel Luz Wallau ,Felipe Gomes Naveca ,Pedro Santos‐Muccillo ,Rodrigo Ribeiro‐Rodrigues ,Andréa Cony Cavalcanti ,Ariane Gomes Paixão

doi:10.3390/v13050724

Abstract

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.

Highlights

The SARS-CoV-2 epidemic in Brazil was mainly driven by lineages B.1.1.28 andB.1.1.33 that probably emerged in February 2020 and were the most prevalent variants in most country regions until October 2020 [1,2]
In this study we identified the emergence of a new Variant of Interest (VOI) (S:E484K) within lineage B.1.1.33 circulating in Brazil
The VOI N.9 displayed a low prevalence (~3%) among all Brazilian SARS-CoV-2 samples analyzed between November 2020 and February 2021, but it is already widely dispersed in the country and comprises a high fraction (35%) of the B.1.1.33 sequences detected in that period

Summary

Introduction

The SARS-CoV-2 epidemic in Brazil was mainly driven by lineages B.1.1.28 andB.1.1.33 that probably emerged in February 2020 and were the most prevalent variants in most country regions until October 2020 [1,2]. The SARS-CoV-2 epidemic in Brazil was mainly driven by lineages B.1.1.28 and. Recent genomic studies bring attention to the emergence of new SARS-CoV-2 variants in Brazil harboring mutations at the receptor-binding site (RBD) of the Spike (S) protein that might impact viral fitness and transmissibility. The VOC P.1, first described in January 2021 [3], displayed an unusual number of lineage-defining mutations in the S protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I) and its emergence was associated with a second COVID-19 epidemic wave in the Amazonas state [4,5]. The VOI P.2, first described in samples from October 2020 in the state of Rio de Janeiro, was distinguished by the presence of the S:E484K mutation in RBD and other four lineage-defining mutations outside the S protein [6]. The P.2 lineage has been detected as the most prevalent variant in several states across the country in late 2020 and early 2021 (https://www.genomahcov.fiocruz.br, accessed on 1 March 2021)

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