Basic Virology
Find the latest information on the basic research on SARS-CoV-2 and other coronaviruses. Information is organized intosubcategories:
RNA Replication
April 2020
- Structure of replicating SARS-CoV-2 polymerase.
- Nidovirales: evolving the largest RNA virus genome.
- SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum.
- Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling.
- Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity.
- Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with 2019 Novel Coronavirus Disease, United States.
- Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors.
- Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication Is Revealed by Complete Genome Sequencing.
- Ribose 2'-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5.
- One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities.
- Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission.
May 2020
- Articles will be updated shortly.
Proteins & Translation
April 2020
- RNA 3'-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex.
- High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling.
- Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot.
May 2020
- A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein.
- Codon Usage and Phenotypic Divergences of SARS-CoV-2 Genes.
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Virus Assembly, Protein Processing and Structure
April 2020
- Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically-Sensitive Activation Loop.
- Self-Collected Oral Fluid and Nasal Swabs Demonstrate Comparable Sensitivity to Clinician Collected Nasopharyngeal Swabs for Covid-19 Detection.
- High-surety isothermal amplification and detection of SARS-CoV-2, including with crude enzymes.
- An Infectious cDNA Clone of SARS-CoV-2
- Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS-CoV-2.
- Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer.
- Unique and Conserved Features of Genome and Proteome of SARS-coronavirus, an Early Split-off From the Coronavirus Group 2 Lineage.
- Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA.
- Severe Acute Respiratory Syndrome Coronavirus ORF6 Antagonizes STAT1 Function by Sequestering Nuclear Import Factors on the Rough Endoplasmic Reticulum/Golgi Membrane.
- Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.
- Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.
May 2020
- Ligand-centered assessment of SARS-CoV-2 drug target models in the Protein Data Bank.
- Afucosylated immunoglobulin G responses are a hallmark of enveloped virus infections and show an exacerbated phenotype in COVID-19.
- The SARS-CoV-2 conserved macrodomain is a highly efficient ADP-ribosylhydrolase enzyme.
- Deducing the N- and O- glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2.
- Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites.
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Evolution & Phylogenetics
April 2020
- Genotyping coronavirus SARS-CoV-2: Methods and implications.
- Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2.
- Identification of super-transmitters of SARS-CoV-2.
- Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins.
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2.
- A new coronavirus associated with human respiratory disease in China.
- A planarian nidovirus expands the limits of RNA genome size.
- Equine arteritis virus is not a togavirus but belongs to the coronaviruslike superfamily.
- A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence.
May 2020
- RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look.
- Pathological findings of COVID-19 associated with acute respiratory distress syndrome.
- Infection and Rapid Transmission of SARS-CoV-2 in Ferrets.
- Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure.
- Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2.
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Host Immune Response
April 2020
- Gut microbiota may underlie the predisposition of healthy individuals to COVID-19.
- Will we see protection or reinfection in COVID-19?
- Down-regulated gene expression spectrum and immune responses changed during the disease progression in COVID-19 patients.
- Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection.
- Homologous 2′,5′-phosphodiesterases from disparate RNA viruses antagonize antiviral innate immunity.
May 2020
- Cross-reactive antibody response between SARS-CoV-2 and SARS-CoV infections.
- Viral and host factors related to the clinical outcome of COVID-19.
- Study on the expression levels of antibodies against SARS-CoV-2 at different period of disease and its related factors in 192 cases of COVID-19 patients.
- Immunogenic profile of SARS-CoV-2 spike in individuals recovered from COVID-19.
- The Dynamic Changes of Antibodies against SARS-CoV-2 during the Infection and Recovery of COVID-19.
- CD8+ T cell cross-reactivity against SARS-CoV-2 conferred by other coronavirus strains and influenza virus.
- Symptomatic SARS-CoV-2 infections display specific IgG Fc structures.
- Anti-Spike, anti-Nucleocapsid and neutralizing antibodies in SARS-CoV-2 hospitalized patients and asymptomatic carriers.
- Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19.
- Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals.
- The SARS-CoV-2 T-cell immunity is directed against the spike, membrane, and nucleocapsid protein and associated with COVID 19 severity.
- SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.
- Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19.
- Cross-talk between the airway epithelium and activated immune cells defines severity in COVID-19.
- Humoral immune response and prolonged PCR positivity in a cohort of 1343 SARS-CoV 2 patients in the New York City region.
- Serum protein profiling reveals a landscape of inflammation and immune signaling in early-stage COVID-19 infection.
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Animal Models & Epizootic Infections
April 2020
- Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model.
- Infection and Rapid Transmission of SARS-CoV-2 in Ferrets
- Simulation of the clinical and pathological manifestations of Coronavirus Disease 2019 (COVID-19) in golden Syrian hamster model: implications for disease pathogenesis and transmissibility.
- Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS–coronavirus 2.
May 2020
- Infection of bat and human intestinal organoids by SARS-CoV-2.
- Infection of dogs with SARS-CoV-2.
- Pathogenesis and transmission of SARS-CoV-2 in golden hamsters.
- Proteomics of SARS-CoV-2-infected host cells reveals therapy targets.
- Comparison of SARS-CoV-2 spike protein binding to ACE2 receptors from human, pets, farm animals, and putative intermediate hosts.
Viral Entry & Receptors
April 2020
- Neutralization of SARS-CoV-2 spike pseudotyped virus by recombinant ACE2-Ig.
- SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes.
- Structural and functional basis of SARS-CoV-2 entry by using human ACE2.
- Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion.
- Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.
- Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses.
- Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.
- SARS‐CoV‐2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells.
May 2020
- Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?
- A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2.
- Robust ACE2 protein expression localizes to the motile cilia of the respiratory tract epithelia and is not increased by ACE inhibitors or angiotensin receptor blockers.
- TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes.
- Key residues of the receptor binding motif in the spike protein of SARS-CoV-2 that interact with ACE2 and neutralizing antibodies.
- Site-specific glycan analysis of the SARS-CoV-2 spike.
- SARS-CoV-2 productively infects human gut enterocytes.
- A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells.
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