Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1)

Altered host protease determinants for SARS-CoV-2 Omicron

(2023) Jasper Fuk-Woo Chan et al.   Science Advances

Tracking SARS-CoV-2 variants and resources

(2023) Bas B. Oude Munnink et al.   NATURE METHODS

Resistance of Omicron subvariants BA.2.75.2, BA.4.6, and BQ.1.1 to neutralizing antibodies

(2023) Delphine Planas et al.   Nature Communications

Delta-Omicron recombinant escapes therapeutic antibody neutralization

(2023) Ralf Duerr et al.   iScience

SARS-CoV-2 omicron variants harbor spike protein mutations responsible for their attenuated fusogenic phenotype

(2023) Seung Bum Park et al.   Communications Biology

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

(2022) Wanwisa Dejnirattisai et al.   CELL

Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity

(2022) Bo Meng et al.   NATURE

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

(2022) Elisabetta Cameroni et al.   NATURE

Attenuated replication and pathogenicity of SARS-CoV-2 B.1.1.529 Omicron

(2022) Huiping Shuai et al.   NATURE

Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization

(2022) Sandile Cele et al.   NATURE

Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant

(2022) Rigel Suzuki et al.   NATURE

Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies

(2022) Yunlong Cao et al.   NATURE

Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2

(2022) Lihong Liu et al.   NATURE

SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein–ACE2 complex

(2022) Dhiraj Mannar et al.   SCIENCE

Structures of the Omicron Spike trimer with ACE2 and an anti-Omicron antibody

(2022) Wanchao Yin et al.   SCIENCE

Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies

(2022) Yifan Wang et al.   Nature Communications

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

(2022) Alexander J. Pak et al.   Nature Communications

SARS-COV-2 Variants: Differences and Potential of Immune Evasion

(2022) Sandro M. Hirabara et al.   Frontiers in Cellular and Infection Microbiology

The Omicron (B.1.1.529) variant of SARS-CoV-2 binds to the hACE2 receptor more strongly and escapes the antibody response: Insights from structural and simulation data

(2022) Abbas Khan et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Distinctive Roles of Furin and TMPRSS2 in SARS-CoV-2 Infectivity

(2022) Rachid Essalmani et al.   JOURNAL OF VIROLOGY

Structural diversity of the SARS-CoV-2 Omicron spike

(2022) Sophie M.-C. Gobeil et al.   MOLECULAR CELL

Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains

(2022) Anacleto Silva de Souza et al.   Viruses-Basel

Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain

(2022) Gang Ye et al.   Nature Communications

Structures of Omicron spike complexes and implications for neutralizing antibody development

(2022) Hangtian Guo et al.   Cell Reports

Platform for isolation and characterization of SARS-CoV-2 variants enables rapid characterization of Omicron in Australia

(2022) Anupriya Aggarwal et al.   Nature Microbiology

Increased resistance of SARS-CoV-2 Omicron variant to neutralization by vaccine-elicited and therapeutic antibodies

(2022) Takuya Tada et al.   EBioMedicine

SARS‐CoV‐2 Omicron variant: Why global communities should take it seriously?

(2022) Shayan Rahmani et al.   Immunity Inflammation and Disease

Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum

(2022) Aekkachai Tuekprakhon et al.   CELL

Omicron variant receptor-binding domain phylogenetics and molecular dynamics

(2022) Mahmoud Kandeel et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Structural Evolution of Delta (B.1.617.2) and Omicron (BA.1) Spike Glycoproteins

(2022) Ingrid Guarnetti Prandi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer

(2022) Wuqiang Zhan et al.   JOURNAL OF VIROLOGY

What Omicron’s BA.4 and BA.5 variants mean for the pandemic

(2022) Ewen Callaway   NATURE

BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection

(2022) Yunlong Cao et al.   NATURE

SARS-CoV-2 spike N-terminal domain modulates TMPRSS2-dependent viral entry and fusogenicity

(2022) Bo Meng et al.   Cell Reports

Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike

(2022) Victoria Stalls et al.   Cell Reports

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

(2022) Brian J. Willett et al.   Nature Microbiology

Novel cleavage sites identified in SARS-CoV-2 spike protein reveal mechanism for cathepsin L-facilitated viral infection and treatment strategies

(2022) Miao-Miao Zhao et al.   Cell Discovery

Rapid Selection of Sotrovimab Escape Variants in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron-Infected Immunocompromised Patients

(2022) Smaranda Gliga et al.   CLINICAL INFECTIOUS DISEASES

Molecular dynamics simulations highlight the altered binding landscape at the spike-ACE2 interface between the Delta and Omicron variants compared to the SARS-CoV-2 original strain

(2022) Eleni Pitsillou et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Exploring the Binding Affinity and Mechanism between ACE2 and the Trimers of Delta and Omicron Spike Proteins by Molecular Dynamics Simulation and Bioassay

(2022) Liping Zhou et al.   Journal of Chemical Information and Modeling

Differences in incidence and fatality of COVID‐19 by SARS‐CoV‐2 Omicron variant versus Delta variant in relation to vaccine coverage: A world‐wide review

(2022) Chao Wang et al.   JOURNAL OF MEDICAL VIROLOGY

SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies

(2022) MacGregor Cox et al.   NATURE REVIEWS MICROBIOLOGY

Temperature Influences the Interaction between SARS-CoV-2 Spike from Omicron Subvariants and Human ACE2

(2022) Shang Yu Gong et al.   Viruses-Basel

Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape

(2022) Zhennan Zhao et al.   Nature Communications

Spike mutations contributing to the altered entry preference of SARS-CoV-2 omicron BA.1 and BA.2

(2022) Bingjie Hu et al.   Emerging Microbes & Infections

SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope

(2022) Ping He et al.   Nature Microbiology

Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody

(2022) Sanjeev Kumar et al.   Science Advances

SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern

(2022) Anupriya Aggarwal et al.   EBioMedicine

Molecular Dynamics Analysis of Fast-Spreading Severe Acute Respiratory Syndrome Coronavirus 2 Variants and Their Effects on the Interaction with Human Angiotensin-Converting Enzyme 2

(2022) Anacleto Silva de Souza et al.   ACS Omega

Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2

(2022) Panke Qu et al.   Cell Host & Microbe

Intrinsic D614G and P681R/H mutations in SARS-CoV-2 VoCs Alpha, Delta, Omicron and viruses with D614G plus key signature mutations in spike protein alters fusogenicity and infectivity

(2022) Ritika Khatri et al.   MEDICAL MICROBIOLOGY AND IMMUNOLOGY

Elucidating Interactions Between SARS-CoV-2 Trimeric Spike Protein and ACE2 Using Homology Modeling and Molecular Dynamics Simulations

(2021) Sugunadevi Sakkiah et al.   Frontiers in Chemistry

The antigenic anatomy of SARS-CoV-2 receptor binding domain

(2021) Wanwisa Dejnirattisai et al.   CELL

SARS-CoV-2 spike D614G change enhances replication and transmission

(2021) Bin Zhou et al.   NATURE

Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7

(2021) Pengfei Wang et al.   NATURE

The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2

(2021) Donald J. Benton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity

(2021) Seiya Ozono et al.   Nature Communications

SARS-CoV-2 variants and convalescent plasma: reality, fallacies, and opportunities

(2021) Arturo Casadevall et al.   JOURNAL OF CLINICAL INVESTIGATION

Structural impact on SARS-CoV-2 spike protein by D614G substitution

(2021) Jun Zhang et al.   SCIENCE

Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide

(2021) Eileen Socher et al.   Biomedicines

SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity

(2021) Chihiro Motozono et al.   Cell Host & Microbe

Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2

(2021) Jérémie Prévost et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion

(2021) Isabella A T M Ferreira et al.   JOURNAL OF INFECTIOUS DISEASES

Molecular biology of the SARs‐CoV‐2 spike protein: A review of current knowledge

(2021) Chaogeng Zhu et al.   JOURNAL OF MEDICAL VIROLOGY

SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

(2021) Maxwell I. Zimmerman et al.   Nature Chemistry

Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants

(2021) Yongfei Cai et al.   SCIENCE

Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants

(2021) Natália Teruel et al.   PLoS Computational Biology

N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2

(2021) Fang Tian et al.   eLife

Mutation-induced changes in the receptor-binding interface of the SARS-CoV-2 Delta variant B.1.617.2 and implications for immune evasion

(2021) Prabin Baral et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Mechanisms of SARS-CoV-2 entry into cells

(2021) Cody B. Jackson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2

(2021) Chen Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A second functional furin site in the SARS-CoV-2 spike protein

(2021) Yue Zhang et al.   Emerging Microbes & Infections

Relative Reproduction Number of SARS-CoV-2 Omicron (B.1.1.529) Compared with Delta Variant in South Africa

(2021) Hiroshi Nishiura et al.   Journal of Clinical Medicine

The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour

(2021) A. Sofia F. Oliveira et al.   Computational and Structural Biotechnology Journal

Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike

(2021) Bailey Lubinski et al.   iScience

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

(2020) Markus Hoffmann et al.   CELL

SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective

(2020) Manuela Sironi et al.   INFECTION GENETICS AND EVOLUTION

A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

(2020) Meng Yuan et al.   SCIENCE

TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes

(2020) Ruochen Zang et al.   Science Immunology

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

(2020) Bette Korber et al.   CELL

Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike

(2020) Jiandong Huo et al.   Cell Host & Microbe

Structural basis of a shared antibody response to SARS-CoV-2

(2020) Meng Yuan et al.   SCIENCE

Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

(2020) Leonid Yurkovetskiy et al.   CELL

Interaction of Human ACE2 to Membrane-Bound SARS-CoV-1 and SARS-CoV-2 S Glycoproteins

(2020) Sai Priya Anand et al.   Viruses-Basel

Molecular Dynamics Reveals Complex Compensatory Effects of Ionic Strength on the Severe Acute Respiratory Syndrome Coronavirus 2 Spike/Human Angiotensin-Converting Enzyme 2 Interaction

(2020) Anacleto Silva de Souza et al.   Journal of Physical Chemistry Letters

Furin cleavage sites naturally occur in coronaviruses

(2020) Yiran Wu et al.   Stem Cell Research

SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity

(2020) Lizhou Zhang et al.   Nature Communications

D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction

(2020) Sophie M.-C. Gobeil et al.   Cell Reports

De novo design of tunable, pH-driven conformational changes

(2019) Scott E. Boyken et al.   SCIENCE

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Revisiting OPLS Force Field Parameters for Ionic Liquid Simulations

(2017) Brian Doherty et al.   Journal of Chemical Theory and Computation

Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology

(2017) Martino Bertoni et al.   Scientific Reports

The SWISS-MODEL Repository—new features and functionality

(2016) Stefan Bienert et al.   NUCLEIC ACIDS RESEARCH

Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

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GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Cathepsin L Functionally Cleaves the Severe Acute Respiratory Syndrome Coronavirus Class I Fusion Protein Upstream of Rather than Adjacent to the Fusion Peptide

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