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...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-05-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/5/883 |
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| author | Jorge González-Puelma 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 Marcelo A. Navarrete |
| author_facet | Jorge González-Puelma 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 Marcelo A. Navarrete |
| author_sort | Jorge González-Puelma |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T11:32:01Z |
| format | Article |
| id | doaj.art-b17d05a0a0e84e958c9b919f2aac15ec |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T11:32:01Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-b17d05a0a0e84e958c9b919f2aac15ec2023-11-21T19:12:35ZengMDPI AGViruses1999-49152021-05-0113588310.3390/v13050883Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s DynamicsJorge González-Puelma0Jacqueline Aldridge1Marco Montes de Oca2Mónica Pinto3Roberto Uribe-Paredes4José Fernández-Goycoolea5Diego Alvarez-Saravia6Hermy Álvarez7Gonzalo Encina8Thomas Weitzel9Rodrigo Muñoz10Álvaro Olivera-Nappa11Sergio Pantano12Marcelo A. Navarrete13Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, ChileDepartamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, ChileDepartamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, ChileEscuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, ChileDepartamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, ChileDepartamento de Matemática y Física, Universidad de Magallanes, Punta Arenas 6210427, ChileEscuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, ChileEscuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, ChileCentro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, ChileLaboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, ChileEscuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, ChileCentre for Biotechnology and Bioengineering, Universidad de Chile, Santiago 8370456, ChileBiomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, UruguayEscuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, ChileThe 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.https://www.mdpi.com/1999-4915/13/5/883SARS-CoV2variantCovid19 |
| spellingShingle | Jorge González-Puelma 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 Marcelo A. Navarrete Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics Viruses SARS-CoV2 variant Covid19 |
| title | Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics |
| title_full | Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics |
| title_fullStr | Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics |
| title_full_unstemmed | Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics |
| title_short | Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike’s Dynamics |
| title_sort | mutation in a sars cov 2 haplotype from sub antarctic chile reveals new insights into the spike s dynamics |
| topic | SARS-CoV2 variant Covid19 |
| url | https://www.mdpi.com/1999-4915/13/5/883 |
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