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Article

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

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Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile
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Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
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Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile
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Enfermedades Infecciosas, Hospital Clínico de Magallanes, Punta Arenas 6210005, Chile
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Departamento de Matemática y Física, Universidad de Magallanes, Punta Arenas 6210427, Chile
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Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile
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Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile
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Instituto de Ciencias e Innovación en Medicina (ICIM), Universidad del Desarrollo, Santiago 7610658, Chile
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Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago 8370456, Chile
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Facultad de Ciencias, Físicas y Matemáticas, Universidad de Chile, Santiago 8370456, Chile
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Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
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Authors to whom correspondence should be addressed.
Academic Editor: Corinne Ronfort
Viruses 2021, 13(5), 883; https://doi.org/10.3390/v13050883
Received: 26 March 2021 / Revised: 1 May 2021 / Accepted: 7 May 2021 / Published: 11 May 2021
(This article belongs to the Special Issue Emergence and Evolution of the SARS-CoV-2 and Other Coronaviruses)
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. View Full-Text
Keywords: SARS-CoV2; variant; Covid19 SARS-CoV2; variant; Covid19
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    Link: https://catg.cl/lab/docs/jgonzalez-subantarctic-sarscov2/supplementary-movies/
    Description: Table S1: De novo assembled genomes including sample date, location and corresponding GSAID submission numbers, Figure S1: Comprehensive view of the location of recently reported spike mutations, Video S1 and S2: Upper and side views of the motion between initial and final structures of the double mutated spike protein, Video S3: Projection of the principal component of the motion of the segment S1 for the three spike variants, Video S4: Morphing between initial and final conformations of the spike protein mutated on T307I-D614G.
MDPI and ACS Style

González-Puelma, J.; Aldridge, J.; Montes de Oca, M.; Pinto, M.; Uribe-Paredes, R.; Fernández-Goycoolea, J.; Alvarez-Saravia, D.; Álvarez, H.; Encina, G.; Weitzel, T.; Muñoz, R.; Olivera-Nappa, Á.; Pantano, S.; Navarrete, M.A. Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics. Viruses 2021, 13, 883. https://doi.org/10.3390/v13050883

AMA Style

González-Puelma J, Aldridge J, Montes de Oca M, Pinto M, Uribe-Paredes R, Fernández-Goycoolea J, Alvarez-Saravia D, Álvarez H, Encina G, Weitzel T, Muñoz R, Olivera-Nappa Á, Pantano S, Navarrete MA. Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics. Viruses. 2021; 13(5):883. https://doi.org/10.3390/v13050883

Chicago/Turabian Style

González-Puelma, Jorge, Jacqueline Aldridge, Marco Montes de Oca, Mónica Pinto, Roberto Uribe-Paredes, José Fernández-Goycoolea, Diego Alvarez-Saravia, Hermy Álvarez, Gonzalo Encina, Thomas Weitzel, Rodrigo Muñoz, Álvaro Olivera-Nappa, Sergio Pantano, and Marcelo A. Navarrete 2021. "Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics" Viruses 13, no. 5: 883. https://doi.org/10.3390/v13050883

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