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

• Published in: Viruses
• Main Authors: 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
• Format: Article in Journal/Newspaper
• Language: English
• Published: MDPI AG 2021
• Subjects: SARS-CoV2; variant; Covid19; Microbiology; QR1-502; Antarctic; Magallanes; The Spike; Antarc*
• Online Access: https://doi.org/10.3390/v13050883; https://doaj.org/article/b17d05a0a0e84e958c9b919f2aac15ec

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.