Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics

The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. We report on the occurren...

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Bibliographic Details
Published in:Viruses 2021-05, Vol.13 (5), p.883
Main Authors: González-Puelma, Jorge, Aldridge, Jacqueline, Montes de Oca, Marco, Pinto, Mónica, Uribe-Paredes, Roberto, Fernández-Goycoolea, José, Alvarez-Saravia, Diego, Álvarez, Hermy, Encina, Gonzalo, Weitzel, Thomas, Muñoz, Rodrigo, Olivera-Nappa, Álvaro, Pantano, Sergio, Navarrete, Marcelo A.
Format: Article
Language:English
Subjects:
Coronaviruses
COVID-19
Covid19
Disease transmission
Genomes
Haplotypes
Infectivity
Laboratories
Molecular modelling
Mutation
Pandemics
Phylogenetics
Pipelines
Principal components analysis
Proteins
SARS-CoV2
Severe acute respiratory syndrome coronavirus 2
Simulation
Spike protein
variant
Virulence
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Summary:The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. We report on the occurrence of a SARS-CoV-2 haplotype with nine mutations including D614G/T307I double-mutation of the spike. This variant expanded and completely replaced previous lineages within a short period in the subantarctic Magallanes Region, southern Chile. The rapid lineage shift was accompanied by a significant increase of cases, resulting in one of the highest incidence rates worldwide. Comparative coarse-grained molecular dynamic simulations indicated that T307I and D614G belong to a previously unrecognized dynamic domain, interfering with the mobility of the receptor binding domain of the spike. The T307I mutation showed a synergistic effect with the D614G. Continuous surveillance of new mutations and molecular analyses of such variations are important tools to understand the molecular mechanisms defining infectivity and virulence of current and future SARS-CoV-2 strains.
ISSN:1999-4915
1999-4915
DOI:10.3390/v13050883