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

Viruses
Jorge González-PuelmaMarcelo A Navarrete

Abstract

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.

References

Feb 8, 2005·Proceedings of the National Academy of Sciences of the United States of America·Huai-Dong SongGuo-Ping Zhao
Mar 26, 2005·The EMBO Journal·Wenhui LiMichael Farzan
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
Jan 17, 2016·Bioinformatics·Matías R Machado, Sergio Pantano
Jan 18, 2018·Virus Evolution·Pavel SagulenkoRichard A Neher
Jan 23, 2018·Viral Immunology·Meghan O AltmanJonathan W Yewdell
May 23, 2018·Nucleic Acids Research·Andrew WaterhouseTorsten Schwede
May 24, 2018·Bioinformatics·James HadfieldRichard A Neher
Jan 10, 2017·Global Challenges·Stefan Elbe, Gemma Buckland-Merrett
Jan 31, 2020·Journal of Chemical Theory and Computation·Matías R Machado, Sergio Pantano
Feb 23, 2020·Science·Daniel WrappJason S McLellan
Mar 4, 2020·Nature Microbiology·UNKNOWN Coronaviridae Study Group of the International Committee on Taxonomy of Viruses
Mar 31, 2020·Journal of Medical Virology·Gianguglielmo ZehenderMassimo Galli
Mar 31, 2020·Journal of Medical Virology·Andrés E CastilloJorge Fernández
Jul 23, 2020·Science·Yongfei CaiBing Chen
Jul 24, 2020·Nature Structural & Molecular Biology·Rory HendersonPriyamvada Acharya
Aug 28, 2020·Molecular Cell·Fran RobsonWai-Lung Ng
Aug 29, 2020·Nature Communications·Wayne VuongM Joanne Lemieux
Sep 2, 2020·BioRxiv : the Preprint Server for Biology·Bryan A JohnsonVineet D Menachery
Oct 28, 2020·Nature·Jessica A PlantePei-Yong Shi
Nov 4, 2020·Cell Research·Imre Berger, Christiane Schaffitzel
Nov 16, 2020·Biophysical Journal·Emilia P BarrosRommie E Amaro
Nov 28, 2020·Nature Communications·Lizhou ZhangHyeryun Choe
Dec 4, 2020·MedRxiv : the Preprint Server for Health Sciences·Emma B HodcroftRichard A Neher
Feb 11, 2021·Emerging Infectious Diseases·Fabrizio MaggiGianni Bonelli
Apr 16, 2021·The Journal of General Virology·Thomas P PeacockWendy S Barclay

❮ Previous
Next ❯

Software Mentioned

CGconv
Swiss
SIRAH Tools
Treetime
GISAID
Blender
Python
Nextstrain
MEGA
PyMOL

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.