Autophagy and evasion of the immune system by SARS-CoV-2. Structural features of the non-structural protein 6 from wild type and Omicron viral strains interacting with a model lipid bilayer

Review Infectious Diseases

Comparing COVID-19 vaccines for their characteristics, efficacy and effectiveness against SARS-CoV-2 and variants of concern: a narrative review

Thibault Fiolet et al.

Summary: Overall, COVID-19 vaccines have high efficacy against the original strain and variants of concern, with rare serious adverse events. However, prices vary significantly for different vaccines.

CLINICAL MICROBIOLOGY AND INFECTION (2022)

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Review Virology

OMICRON (B.1.1.529): A new SARS-CoV-2 variant of concern mounting worldwide fear

Vikram Thakur et al.

Summary: The emergence of the OMICRON variant of SARS-CoV-2 has become a global concern, spreading to over 77 countries and sparking hypotheses about its origins and infectivity. The detection of mutations in the Spike protein's RBD region is concerning, as it may surpass vaccine immunity.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Article Virology

Sequence analysis of the emerging SARS-CoV-2 variant Omicron in South Africa

Lulan Wang et al.

Summary: The discovery of the Omicron variant has sparked global concerns about its mutations, transmission, and immune escape properties. Current research suggests that the variant may impact viral infectivity and host immunity, and it may evolve from clade 20B.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Article Virology

Characterization of the novel SARS-CoV-2 Omicron (B.1.1.529) variant of concern and its global perspective

Shailendra K. Saxena et al.

Summary: Omicron is the latest variant of concern of SARS-CoV-2, with more mutations compared to the previous Delta variant. Fifteen of these mutations are located in the receptor-binding domain of the spike glycoprotein, which may affect transmissibility, infectivity, antibody neutralization, and vaccine efficacy. The study provides insights into the mutational hotspots of Omicron and its global impact on transmission, testing, and immunity.

JOURNAL OF MEDICAL VIROLOGY (2022)

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Article Medicine, General & Internal

Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study

Nicole Wolter et al.

Summary: According to data analysis from South Africa, individuals infected with the omicron variant have a lower likelihood of hospitalization compared to those infected with non-omicron variants. Furthermore, individuals infected with the omicron variant have a lower odds of severe disease compared to individuals infected with the earlier delta variant.

LANCET (2022)

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Editorial Material Medicine, General & Internal

Covid-19 mRNA Vaccines - Six of One, Half a Dozen of the Other

Eric J. Rubin et al.

NEW ENGLAND JOURNAL OF MEDICINE (2022)

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Article Immunology

The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron

Youchun Wang et al.

Summary: The Omicron variant shows greater potential for immune escape compared to other variants, suggesting a significant impact on immunity from previous infections and vaccines.

EMERGING MICROBES & INFECTIONS (2022)

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Letter Infectious Diseases

SARS-CoV-2 viral dynamics in infections with Alpha and Beta variants of concern in the French community

Gina Cosentino et al.

JOURNAL OF INFECTION (2022)

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Editorial Material Infectious Diseases

SARS-CoV-2 delta variant: a persistent threat to the effectiveness of vaccines

Ramachandra Thiruvengadamt et al.

LANCET INFECTIOUS DISEASES (2022)

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Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase in 2021

Alex Bateman et al.

Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.

NUCLEIC ACIDS RESEARCH (2021)

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Editorial Material Medicine, General & Internal

Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic

Salim S. Abdool Karim et al.

LANCET (2021)

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Editorial Material Cell Biology

Autophagosome maturation stymied by SARS-CoV-2

Willa Wen-You Yim et al.

Summary: The study reveals that the SARS-CoV-2 protein ORF3a disrupts autophagy by interfering with the fusion between autophagosomes and lysosomes, through dysregulation of the HOPS complex.

DEVELOPMENTAL CELL (2021)

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Article Immunology

Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions

Amit Kumar et al.

Summary: The NSP6 protein of SARS-CoV-2 is a transmembrane protein with helical structures, while specific regions show different conformational changes in various biological conditions. The 200ns simulation study revealed loss of beta-sheet structures but intact helical regions in comparison to its structural model.

MICROBIAL PATHOGENESIS (2021)

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Article Multidisciplinary Sciences

Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants

Melanie Koehler et al.

Summary: The study utilized atomic force microscopy and molecular dynamics to investigate the impact of SARS-CoV-2 variants on the kinetic, thermodynamic, and structural properties of RBD-ACE2 complex formation. The research found a significant increase in complex stability for several variants of concern.

NATURE COMMUNICATIONS (2021)

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Editorial Material Medicine, General & Internal

Alpha variant SARS-CoV-2 infection: How it all starts

Pere Domingo et al.

EBIOMEDICINE (2021)

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Review Biochemistry & Molecular Biology

COVID-19 mRNA vaccines

Qinrui Huang et al.

Summary: The ongoing COVID-19 pandemic has accelerated the development of mRNA vaccines, with positive results reported and future challenges ahead.

JOURNAL OF GENETICS AND GENOMICS (2021)

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Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

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Review Immunology

Distinguishing features of current COVID-19 vaccines: knowns and unknowns of antigen presentation and modes of action

Franz X. Heinz et al.

Summary: COVID-19 vaccines have been rapidly developed using different technologies, including mRNA, adenoviral vectors, and inactivated vaccines. They all rely on the viral spike protein of SARS-CoV-2 to induce neutralizing antibodies, but the presentation of this key antigen to the immune system varies between different vaccine categories.

NPJ VACCINES (2021)

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Article Medicine, Research & Experimental

SARS-CoV-2 Omicron variant: Characteristics and prevention

Xuemei He et al.

Summary: The new SARS-CoV-2 variant B.1.1.529 named Omicron, reported in South Africa, has raised global concerns after being designated as a variant of concern by the WHO. With a high number of mutations, including 15 in the spike receptor-binding domain, the Omicron variant shares similarities with previous VOCs, sparking worries about its transmissibility and immune evasion.

MEDCOMM (2021)

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Article Health Care Sciences & Services

Impact of original, B.1.1.7, and B.1.351/P.1 SARS-CoV-2 lineages on vaccine effectiveness of two doses of COVID-19 mRNA vaccines: Results from a nationwide case-control study in France

Tiffany Charmet et al.

Summary: The study found that in real-life settings, two doses of mRNA vaccines were effective against COVID-19 with the original virus, B.1.1.7 lineage, and B.1.351/P.1 lineages.

LANCET REGIONAL HEALTH-EUROPE (2021)

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Article Immunology

Immunological mechanisms of vaccine-induced protection against COVID-19 in humans

Manish Sadarangani et al.

Summary: Most COVID-19 vaccines aim to induce immune responses, particularly neutralizing antibodies (NAbs), against the spike protein of the virus. mRNA vaccines have shown efficacy after just one dose, while adenovirus vaccines elicit polyfunctional antibodies and strong T cell responses. These findings suggest that protection may not solely rely on NAbs but also involve other immune effector mechanisms.

NATURE REVIEWS IMMUNOLOGY (2021)

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Article Biophysics

Molecular Insights from Conformational Ensembles via Machine Learning

Oliver Fleetwood et al.

BIOPHYSICAL JOURNAL (2020)

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Improved protein structure prediction using potentials from deep learning

Andrew W. Senior et al.

NATURE (2020)

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Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2

Renhong Yan et al.

SCIENCE (2020)

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Article Multidisciplinary Sciences

On the origin and continuing evolution of SARS-CoV-2

Xiaolu Tang et al.

NATIONAL SCIENCE REVIEW (2020)

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Article Infectious Diseases

Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy

Domenico Benvenuto et al.

JOURNAL OF INFECTION (2020)

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Article Chemistry, Physical

Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? Insights from All-Atom Simulations

Angelo Spinello et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2020)

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Article Chemistry, Physical

Comparing the Binding Interactions in the Receptor Binding Domains of SARS-CoV-2 and SARS-CoV

Muhamed Amin et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2020)

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Chemistry and Biology of SARS-CoV-2

Alexander Domling et al.

CHEM (2020)

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Structure of replicating SARS-CoV-2 polymerase

Hauke S. Hillen et al.

NATURE (2020)

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Article Multidisciplinary Sciences

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

Jun Lan et al.

NATURE (2020)

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Review Biochemistry & Molecular Biology

COVID-19: The first documented coronavirus pandemic in history

Yen-Chin Liu et al.

BIOMEDICAL JOURNAL (2020)

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Scalable molecular dynamics on CPU and GPU architectures with NAMD

James C. Phillips et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

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Article Chemistry, Physical

Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses

Cecilia Hognon et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2020)

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Review Biochemistry & Molecular Biology

Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach

Ahmad Abu Turab Naqvi et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2020)

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Influence of airborne transmission of SARS-CoV-2 on COVID-19 pandemic. A review

Jose L. Domingo et al.

ENVIRONMENTAL RESEARCH (2020)

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Thermodynamics of the Interaction between the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus-2 and the Receptor of Human Angiotensin-Converting Enzyme 2. Effects of Possible Ligands

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Article Chemistry, Physical

Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale Methods

Carlos A. Ramos-Guzman et al.

ACS CATALYSIS (2020)

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Evasion of Type I Interferon by SARS-CoV-2

Hongjie Xia et al.

CELL REPORTS (2020)

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Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein

Lorenzo Casalino et al.

ACS CENTRAL SCIENCE (2020)

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Correction Biochemistry & Molecular Biology

Coronavirus RNA Proofreading: Molecular Basis and Therapeutic Targeting (vol 79, pg 710, 2020)

Fran Robson et al.

MOLECULAR CELL (2020)

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Review Biochemical Research Methods

Molecular Basis of SARS-CoV-2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches

Antonio Frances-Monerris et al.

JOURNAL OF PROTEOME RESEARCH (2020)

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Article Chemistry, Multidisciplinary

Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 Mpro by QM/MM computational methods

Katarzyna Swiderek et al.

CHEMICAL SCIENCE (2020)

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Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response

Indwiani Astuti et al.

DIABETES & METABOLIC SYNDROME-CLINICAL RESEARCH & REVIEWS (2020)

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Induced Night Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin

Marco Marazzi et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2019)

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Article Chemistry, Physical

Triggering Tautomerization of Curcumin by Confinement into Liposomes

Maxime Girardon et al.

CHEMPHOTOCHEM (2019)

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Review Microbiology

Autophagy during viral infection - a double-edged sword

Younho Choi et al.

NATURE REVIEWS MICROBIOLOGY (2018)

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PtdIns(4,5) P2 signaling regulates ATG14 and autophagy

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

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Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

Chad W. Hopkins et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

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Coronavirus NSP6 restricts autophagosome expansion

Eleanor M. Cottam et al.

AUTOPHAGY (2014)

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Electronic Structure Investigation and Parametrization of Biologically Relevant Iron-Sulfur Clusters

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Lipid14: The Amber Lipid Force Field

Callum J. Dickson et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

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Langevin thermostat for rigid body dynamics

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JOURNAL OF CHEMICAL PHYSICS (2009)

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Software news and updates - CHARNIM-GUI: A web-based grraphical user interface for CHARMM

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JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

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The SARS-unique domain (SUD) of SARS coronavirus is an oligo(G)-binding protein

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BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2007)

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Scalable molecular dynamics with NAMD

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A molecular docking model of SARS-CoV S1 protein in complex with its receptor, human ACE2

Y Zhang et al.

COMPUTATIONAL BIOLOGY AND CHEMISTRY (2005)

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The SARS Coronavirus S Glycoprotein Receptor Binding Domain: Fine Mapping and Functional Characterization

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VIROLOGY JOURNAL (2005)

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Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K

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JOURNAL OF PHYSICAL CHEMISTRY A (2001)

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Autophagy and evasion of the immune system by SARS-CoV-2. Structural features of the non-structural protein 6 from wild type and Omicron viral strains interacting with a model lipid bilayer

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