Structures and functions of coronavirus replication–transcription complexes and their relevance for SARS-CoV-2 drug design

Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

(2021) Nicholas C. Huston et al.   MOLECULAR CELL

Coronavirus replication–transcription complex: Vital and selective NMPylation of a conserved site in nsp9 by the NiRAN-RdRp subunit

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

Mechanism of SARS-CoV-2 polymerase stalling by remdesivir

(2021) Goran Kokic et al.   Nature Communications

New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3’‐5’ exoribonucleolytic activity on SARS‐CoV‐2

(2021) Margarida Saramago et al.   FEBS Journal

The SARS-CoV-2 subgenome landscape and its novel regulatory features

(2021) Dehe Wang et al.   MOLECULAR CELL

De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

(2021) Ramya Rangan et al.   NUCLEIC ACIDS RESEARCH

Coronavirus entry: how we arrived at SARS-CoV-2

(2021) Gary R Whittaker et al.   Current Opinion in Virology

Mechanisms of Coronavirus Nsp1-Mediated Control of Host and Viral Gene Expression

(2021) Keisuke Nakagawa et al.   Cells

Molnupiravir promotes SARS-CoV-2 mutagenesis via the RNA template

(2021) Calvin J. Gordon et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Remdesivir is a delayed translocation inhibitor of SARS-CoV-2 replication

(2021) Jack P.K. Bravo et al.   MOLECULAR CELL

Structural basis for backtracking by the SARS-CoV-2 replication–transcription complex

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

Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome

(2021) Pramod R. Bhatt et al.   SCIENCE

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

(2021) Irwin Jungreis et al.   Nature Communications

Indels in SARS-CoV-2 occur at template-switching hotspots

(2021) Brianna Sierra Chrisman et al.   BioData Mining

Mass spectrometric based detection of protein nucleotidylation in the RNA polymerase of SARS-CoV-2

(2021) Brian J. Conti et al.   Communications Chemistry

Coupling of N7-methyltransferase and 3′-5′ exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading

(2021) Liming Yan et al.   CELL

Report of the National Institutes of Health SARS-CoV-2 Antiviral Therapeutics Summit

(2021) Matthew D Hall et al.   JOURNAL OF INFECTIOUS DISEASES

Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis

(2021) Florian Kabinger et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme

(2021) Chang Liu et al.   SCIENCE

Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

(2021) Irwin Jungreis et al.   VIROLOGY

The SARS-CoV-2 Nucleocapsid Protein and Its Role in Viral Structure, Biological Functions, and a Potential Target for Drug or Vaccine Mitigation

(2021) Zhihua Bai et al.   Viruses-Basel

The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from Middle East respiratory syndrome coronavirus

(2020) Calvin J Gordon et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

A Novel Coronavirus from Patients with Pneumonia in China, 2019

(2020) Na Zhu et al.   NEW ENGLAND JOURNAL OF MEDICINE

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

(2020)   Nature Microbiology

Structural basis for RNA replication by the SARS-CoV-2 polymerase

(2020) Quan Wang et al.   CELL

The Architecture of SARS-CoV-2 Transcriptome

(2020) Dongwan Kim et al.   CELL

Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency

(2020) Calvin J. Gordon et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets

(2020) Denisa Bojkova et al.   NATURE

Structure of replicating SARS-CoV-2 polymerase

(2020) Hauke S. Hillen et al.   NATURE

Remdesivir for the Treatment of Covid-19 — Preliminary Report

(2020) John H. Beigel et al.   NEW ENGLAND JOURNAL OF MEDICINE

Coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors

(2020) Matthew Hackbart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell entry mechanisms of SARS-CoV-2

(2020) Jian Shang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the RNA-dependent RNA polymerase from COVID-19 virus

(2020) Yan Gao et al.   SCIENCE

Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir

(2020) Wanchao Yin et al.   SCIENCE

An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice

(2020) Timothy P. Sheahan et al.   Science Translational Medicine

Structural Basis for Helicase-Polymerase Coupling in the SARS-CoV-2 Replication-Transcription Complex

(2020) James Chen et al.   CELL

The molecular virology of Coronaviruses

(2020) Ella Hartenian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A putative new SARS-CoV protein, 3c, encoded in an ORF overlapping ORF3a

(2020) Andrew E. Firth   JOURNAL OF GENERAL VIROLOGY

SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology

(2020) Natacha S. Ogando et al.   JOURNAL OF GENERAL VIROLOGY

Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2

(2020) Matthias Thoms et al.   SCIENCE

A molecular pore spans the double membrane of the coronavirus replication organelle

(2020) Georg Wolff et al.   SCIENCE

Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein

(2020) Andrew D. Davidson et al.   Genome Medicine

A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis

(2020) Eric J. Snijder et al.   PLOS BIOLOGY

SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses

(2020) Abhik K. Banerjee et al.   CELL

Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action

(2020) Egor P Tchesnokov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The enzymatic activity of the nsp14 exoribonuclease is critical for replication of MERS-CoV and SARS-CoV-2

(2020) Natacha S. Ogando et al.   JOURNAL OF VIROLOGY

The coding capacity of SARS-CoV-2

(2020) Yaara Finkel et al.   NATURE

SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation

(2020) Katharina Schubert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

β-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic Secretory Pathway

(2020) Sourish Ghosh et al.   CELL

Cryo-EM Structure of an Extended SARS-CoV-2 Replication and Transcription Complex Reveals an Intermediate State in Cap Synthesis

(2020) Liming Yan et al.   CELL

Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies

(2020) Mirko Cortese et al.   Cell Host & Microbe

The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2

(2020) Omer Ziv et al.   MOLECULAR CELL

Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

(2020) Adriana Savastano et al.   Nature Communications

SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

(2020) Steffen Klein et al.   Nature Communications

Remdesivir Is Effective in Combating COVID-19 because It Is a Better Substrate than ATP for the Viral RNA-Dependent RNA Polymerase

(2020) Tyler L. Dangerfield et al.   iScience

Identification and characterization of a human coronavirus 229E nonstructural protein 8-associated RNA 3′-terminal adenylyltransferase activity

(2019) Jana Tvarogová et al.   JOURNAL OF VIROLOGY

The hepatitis C virus RNA-dependent RNA polymerase directs incoming nucleotides to its active site through magnesium-dependent dynamics within its F motif

(2019) Kaouther Ben Ouirane et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nucleoside analogues for the treatment of coronavirus infections

(2019) Andrea J Pruijssers et al.   Current Opinion in Virology

Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors

(2019) Robert N. Kirchdoerfer et al.   Nature Communications

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

(2019) Adrian Viehweger et al.   GENOME RESEARCH

A Structure-Function Diversity Survey of the RNA-Dependent RNA Polymerases From the Positive-Strand RNA Viruses

(2019) Hengxia Jia et al.   Frontiers in Microbiology

Small-Molecule Antiviral β-D-N4-Hydroxycytidine Inhibits a Proofreading-Intact Coronavirus with a High Genetic Barrier to Resistance

(2019) Maria L. Agostini et al.   JOURNAL OF VIROLOGY

Nucleocapsid protein recruitment to replication-transcription complexes plays a crucial role in coronaviral life cycle

(2019) Yingying Cong et al.   JOURNAL OF VIROLOGY

Coronavirus Susceptibility to the Antiviral Remdesivir (GS-5734) Is Mediated by the Viral Polymerase and the Proofreading Exoribonuclease

(2018) Maria L. Agostini et al.   mBio

A planarian nidovirus expands the limits of RNA genome size

(2018) Amir Saberi et al.   PLoS Pathogens

β-D- N 4 -Hydroxycytidine Is a Potent Anti-alphavirus Compound That Induces a High Level of Mutations in the Viral Genome

(2017) Nadya Urakova et al.   JOURNAL OF VIROLOGY

Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA

(2017) François Ferron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Picornaviral polymerase structure, function, and fidelity modulation

(2017) Olve B. Peersen   VIRUS RESEARCH

Expression and Cleavage of Middle East Respiratory Syndrome Coronavirus nsp3-4 Polyprotein Induce the Formation of Double-Membrane Vesicles That Mimic Those Associated with Coronaviral RNA Replication

(2017) Diede Oudshoorn et al.   mBio

Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers

(2017) David Dulin et al.   Cell Reports

Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication

(2017) Eveline Kindler et al.   PLoS Pathogens

Coronaviruses — drug discovery and therapeutic options

(2016) Alimuddin Zumla et al.   NATURE REVIEWS DRUG DISCOVERY

mRNA capping: biological functions and applications

(2016) Anand Ramanathan et al.   NUCLEIC ACIDS RESEARCH

Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation

(2016) Bo Shu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling

(2016) Nerea Irigoyen et al.   PLoS Pathogens

Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses

(2015) Kathleen C. Lehmann et al.   NUCLEIC ACIDS RESEARCH

Structural basis and functional analysis of the SARS coronavirus nsp14–nsp10 complex

(2015) Yuanyuan Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for RNA replication by the hepatitis C virus polymerase

(2015) T. C. Appleby et al.   SCIENCE

Initiation of protein-primed picornavirus RNA synthesis

(2015) Aniko V. Paul et al.   VIRUS RESEARCH

Elongation-Competent Pauses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase

(2015) David Dulin et al.   Cell Reports

Continuous and Discontinuous RNA Synthesis in Coronaviruses

(2015) Isabel Sola et al.   Annual Review of Virology

The SARS coronavirus nucleocapsid protein – Forms and functions

(2014) Chung-ke Chang et al.   ANTIVIRAL RESEARCH

Nucleocapsid Phosphorylation and RNA Helicase DDX1 Recruitment Enables Coronavirus Transition from Discontinuous to Continuous Transcription

(2014) Chia-Hsin Wu et al.   Cell Host & Microbe

CoronavirusNsp10, a Critical Co-factor for Activation of Multiple Replicative Enzymes

(2014) Mickaël Bouvet et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities

(2014) Lorenzo Subissi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correction: In Vitro Reconstitution of SARS-Coronavirus mRNA Cap Methylation

(2014) Mickaël Bouvet et al.   PLoS Pathogens

Thinking Outside the Triangle: Replication Fidelity of the Largest RNA Viruses

(2014) Everett Clinton Smith et al.   Annual Review of Virology

From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses

(2013) Rolf Hilgenfeld et al.   ANTIVIRAL RESEARCH

SARS-CoV ORF1b-encoded nonstructural proteins 12–16: Replicative enzymes as antiviral targets

(2013) Lorenzo Subissi et al.   ANTIVIRAL RESEARCH

Arterivirus molecular biology and pathogenesis

(2013) E. J. Snijder et al.   JOURNAL OF GENERAL VIROLOGY

Infectious Bronchitis Virus Generates Spherules from Zippered Endoplasmic Reticulum Membranes

(2013) H. J. Maier et al.   mBio

Severe Acute Respiratory Syndrome Coronavirus Nonstructural Proteins 3, 4, and 6 Induce Double-Membrane Vesicles

(2013) M. M. Angelini et al.   mBio

The viral RNA capping machinery as a target for antiviral drugs

(2012) François Ferron et al.   ANTIVIRAL RESEARCH

RNA Polymerase Backtracking in Gene Regulation and Genome Instability

(2012) Evgeny Nudler   CELL

Non-canonical translation in RNA viruses

(2012) A. E. Firth et al.   JOURNAL OF GENERAL VIROLOGY

Severe Acute Respiratory Syndrome Coronavirus Protein nsp1 Is a Novel Eukaryotic Translation Inhibitor That Represses Multiple Steps of Translation Initiation

(2012) K. G. Lokugamage et al.   JOURNAL OF VIROLOGY

Viral Quasispecies Evolution

(2012) E. Domingo et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Mechanism of Nucleic Acid Unwinding by SARS-CoV Helicase

(2012) Adeyemi O. Adedeji et al.   PLoS One

RNA 3'-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex

(2012) M. Bouvet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribose 2′-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5

(2011) Roland Züst et al.   NATURE IMMUNOLOGY

Coronaviruses

(2011) Mark R. Denison et al.   RNA Biology

Crystal Structure and Functional Analysis of the SARS-Coronavirus RNA Cap 2′-O-Methyltransferase nsp10/nsp16 Complex

(2011) Etienne Decroly et al.   PLoS Pathogens

Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins

(2010) E. P. Plant et al.   JOURNAL OF VIROLOGY

Cooperative translocation enhances the unwinding of duplex DNA by SARS coronavirus helicase nsP13

(2010) Na-Ra Lee et al.   NUCLEIC ACIDS RESEARCH

Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase

(2010) P. Gong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arterivirus Nsp1 Modulates the Accumulation of Minus-Strand Templates to Control the Relative Abundance of Viral mRNAs

(2010) Danny D. Nedialkova et al.   PLoS Pathogens

Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication Is Revealed by Complete Genome Sequencing

(2010) Lance D. Eckerle et al.   PLoS Pathogens

Coronavirus Nucleocapsid Protein Facilitates Template Switching and Is Required for Efficient Transcription

(2009) S. Zuniga et al.   JOURNAL OF VIROLOGY

Functional screen reveals SARS coronavirus nonstructural protein nsp14 as a novel cap N7 methyltransferase

(2009) Y. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein

(2009) Ke Xu et al.   VIROLOGY

Coronavirus Nonstructural Protein 16 Is a Cap-0 Binding Enzyme Possessing (Nucleoside-2'O)-Methyltransferase Activity

(2008) E. Decroly et al.   JOURNAL OF VIROLOGY

The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein

(2008) Isabelle Imbert et al.   VIRUS RESEARCH

SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum

(2008) Kèvin Knoops et al.   PLOS BIOLOGY