Analysis of the D614G mutation in whole genome sequence of SARS-Cov-2 in El Salvador

Abstract

Introduction. The genome sequencing of indigenous samples of SARS-Cov-2 was carry out in October 2020. Objective. To analyze in silico the detected mutation in the isolated sequencies in El Salvador. Methodology. The sequencies were analyzed using the SOPHiA-DDM-V5.7.10 bioinformatic platform; the platform Nexclade beta v0.8.1 was used for the determination of variants due to missense mutation; the indigenous protein S (D614: PDB ID: 6VXX), was visualized and compared as well as the one from the mutant variant (D614G: PDB ID: 6XS6); Pymol-v1.7.2.3. was used in modeling and imaging generation of the proteins’ molecular details. Results. The analysis of the wild protein S crystals and the mutant ones, show differences at molecular level, including the loss of interactions between the residue G614 of the S1 domain and the threonine 859 of the S2 domain, favoring in such manner, the open configuration of the protein S, which is necessary for the interaction between S with the ACE2 receptor.  Conclusion. The global dominance of the D614G and the bioinformatic and laboratory evidences published up to date, show a possible higher infectivity and transmissibility conferred by the variant D614G detected in the sequence of SARS-Cov-2 in El Salvador.