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

Journal
Viruses
ISSN
1999-4915
Date Issued
2021
Author(s)
Jorge González-Puelma
Jacqueline Aldridge
Marco Montes de Oca
Mónica Pinto
Roberto Uribe-Paredes
José Fernández-Goycoolea
Diego Alvarez-Saravia
Hermy Álvarez
Gonzalo Encina
Rodrigo Muñoz
Álvaro Olivera-Nappa
Sergio Pantano
Marcelo A. Navarrete
Type
Resource Types::text::journal::journal article
Scopus ID
2-s2.0-85107181442
WoS ID
WOS:000654714600001
DOI
URL
URL Institutional Repository
Abstract
<jats:p>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.</jats:p>
Cite this document
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. (2021). Mutation in a sars-cov-2 haplotype from sub-antarctic chile reveals new insights into the spike’s dynamics. Viruses, 13(5), 883. https://doi.org/10.3390/v13050883
Subjects
sars-cov2

; 

variant

; 

covid19

; 

antarctic regions

; 

antibodies, neutralizing

; 

antibodies, viral

; 

chile

; 

covid-19

; 

haplotypes

; 

humans

; 

mutant proteins

; 

mutation

; 

protein binding

; 

sars-cov-2

; 

spike glycoprotein, coronavirus

; 

coronavirus spike glycoprotein

; 

mutant protein

; 

neutralizing antibody

; 

protein binding

; 

spike protein, sars-cov-2

; 

virus antibody

; 

article

; 

binding site

; 

bioinformatics

; 

capillary electrophoresis

; 

coronavirus disease 2019

; 

gene frequency

; 

gene mutation

; 

genetic variability

; 

haplotype

; 

high throughput sequencing

; 

home quarantine

; 

human

; 

incidence

; 

lockdown

; 

molecular dynamics

; 

multiplex polymerase chain reaction

; 

nasopharyngeal swab

; 

nucleotide sequence

; 

phylogeny

; 

principal component analysis

; 

receptor binding

; 

sars-cov-2 variant 501y.v1

; 

sars-cov-2 variant 501y.v2

; 

sequence alignment

; 

sequence analysis

; 

severe acute respiratory syndrome coronavirus 2

; 

social distancing

; 

synergistic effect

; 

virus detection

; 

virus genome

; 

virus infectivity

; 

virus transmission

; 

virus virulence

; 

antarctica

; 

chile

; 

epidemiology

; 

genetics

; 

haplotype

; 

metabolism

; 

mutation

; 

pathogenicity

; 

ultrastructure