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
Open Access
- 21 April 2021
- Vol. 13 (5), 724
- https://doi.org/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.Keywords
Funding Information
- Fundação de Amparo à Pesquisa do Estado do Amazonas (005/2020)
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (402457/2020-0)
- Ministério da Ciência, Tecnologia, Inovações e Comunicações (403276/2020-9)
- Ministério da Saúde (403276/2020-9)
- Fundação Oswaldo Cruz (VPPCB-007-FIO-18-2-30, VPPCB-005-FIO-20-2-87)
- Instituto Nacional de Ciência e Tecnologia de Fluidos Complexos (465259/2014-6)
This publication has 21 references indexed in Scilit:
- Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodiesScience, 2020
- A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiologyNature Microbiology, 2020
- SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platformsPublished by Cold Spring Harbor Laboratory ,2020
- IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic EraMolecular Biology and Evolution, 2020
- Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10Virus Evolution, 2018
- ModelFinder: fast model selection for accurate phylogenetic estimatesNature Methods, 2017
- Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)Virus Evolution, 2016
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and UsabilityMolecular Biology and Evolution, 2013
- Bayesian Phylogeography Finds Its RootsPLoS Computational Biology, 2009