Basic Virology

Find the latest information on the basic research on SARS-CoV-2 and other coronaviruses.  Information is organized intosubcategories:

1. RNA Replication
2. Proteins & Translation
3. Virus Assembly, Protein Processing and Structure
4. Evolution & Phylogenetics
5. Host Immune Response
6. Animal Models & Epizootic Infections
7. Viral Entry & Receptors
8. Viral Replicate/Non-Structural Proteins/Enzymes

October 2020

• Articles to be updated shortly.

August 2020

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

July 2020

• RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus.
• Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex.
• Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms.

June 2020

• Replication of Severe Acute Respiratory Syndrome Coronavirus 2 in Human Respiratory Epithelium.
• A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis.
• Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform.

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.

October 2020

• Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 NSP1 protein.
• SARS-CoV-2 Nsp1 suppresses host but not viral translation through a bipartite mechanism.

September 2020

• The coding capacity of SARS-CoV-2.

August 2020

• Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome.

July 2020

• Integrative Vectors for Regulated Expression of SARS-CoV-2 Proteins Implicated in RNA Metabolism.
• Cytologic and molecular correlates of SARS-CoV-2 infection of the nasopharynx.
• Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2.
• The SARS-CoV-2 spike protein alters barrier function in 2D static and 3D microfluidic in vitro models of the human blood-brain barrier.
• Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing.

June 2020

• Critical Differences Between the Binding Features of the Spike Proteins of SARS-CoV-2 and SARS-CoV.
• Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses.
• Proteomic and Metabolomic Characterization of COVID-19 Patient Sera.

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.

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.

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October 2020

• *NEW *Research Tool Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
• Structural impact on SARS-CoV-2 spike protein by D614G substitution.
• Global analysis of more than 50,000 SARS-Cov-2 genomes reveals epistasis between 8 viral genes.
• Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein.

September 2020

• Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets for drug repurposing.
• Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes.
• Topography, spike dynamics and nanomechanics of individual native SARS-CoV-2 virions.
• SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.
• Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition.
• SARS CoV-2 nucleocapsid protein forms condensates with viral genomic RNA.
• Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion.
• Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection.
• The immunodominant and neutralization linear epitopes for SARS-CoV-2.

August 2020

• Structures and distributions of SARS-CoV-2 spike proteins on intact virions.
• Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography.
• Structure of Furin Protease Binding to SARS-CoV-2 Spike Glycoprotein and Implications for Potential Targets and Virulence.
• The SARS-CoV-2 Nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein.
• Structural basis of RNA cap modification by SARS-CoV-2.
• Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin.
• Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity.

July 2020

• Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein.
• A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells.
• Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate.

June 2020

• An in silico map of the SARS-CoV-2 RNA Structurome.
• A proposed role for the SARS-CoV-2 nucleocapsid protein in the formation and regulation of biomolecular condensates.
• Companion vaccine Bioinformatic design tool reveals limited functional genomic variability of SARS-Cov-2 Spike Receptor Binding Domain.
• Persistence of Severe Acute Respiratory Syndrome Coronavirus 2 in Aerosol Suspensions.
• Identification of common deletions in the spike protein of SARS-CoV-2.
• Structural analysis of the putative SARS-CoV-2 primase complex.
• The D614G mutation in SARS-CoV-2 Spike increases transduction of multiple human cell types.
• Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane.
• The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine.
• Discovery of G-quadruplex-forming sequences in SARS-CoV-2.

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.

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.

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October 2020

• *NEW An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic.
• *NEW Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic.
• Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic.
• Emergence of SARS-CoV-2 through recombination and strong purifying selection.

September 2020

• SARS-CoV-2 spike D614G variant exhibits highly efficient replication and transmission in hamsters.
• Origin and cross-species transmission of bat coronaviruses in China.
• Quantitative phylogenomic evidence reveals a spatially structured SARS-CoV-2 diversity.

August 2020

• Epidemiologically most successful SARS-CoV-2 variant: concurrent mutations in RNA-dependent RNA polymerase and spike protein.
• Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution.
• Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic.
• Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients.
• Discovery and Genomic Characterization of a 382-Nucleotide Deletion in ORF7b and ORF8 during the Early Evolution of SARS-CoV-2.

July 2020

• Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands.
• Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.
• A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.
• Conserved Genomic Terminals of SARS-CoV-2 as Co-evolving Functional Elements and Potential Therapeutic Targets.
• SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects.
• Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation.
• Snapshot of the evolution and mutation patterns of SARS-CoV-2.
• Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico.
• Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates.
• The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus.
• Sarbecovirus comparative genomics elucidates gene content of SARS-CoV-2 and functional impact of COVID-19 pandemic mutations.
• Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome.
• Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories.
• Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans.
• SARS-CoV-2 (COVID-19) structural and evolutionary dynamicome: Insights into functional evolution and human genomics.

June 2020

• The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera.
• ACE2 diversity in placental mammals reveals the evolutionary strategy of SARS-CoV-2.
• Assembly of an integrated human lung cell atlas reveals that SARS-CoV-2 receptor is co-expressed with key elements of the kinin-kallikrein, renin-angiotensin and coagulation systems in alveolar cells.
• High‐Coverage SARS‐CoV‐2 Genome Sequences Acquired by Target Capture Sequencing.

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.

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.

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October 2020

• *NEW SARS-CoV-2 triggers inflammatory responses and cell death through caspase-8 activation.
• *NEW Inborn errors of type I IFN immunity in patients with life-threatening COVID-19.
• *NEW Evasion of Type I Interferon by SARS-CoV-2.
• *Research Tool SARS-CoV-2 Infection of Pluripotent Stem Cell-Derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response.

September 2020

• Longitudinal immune profiling of mild and severe COVID-19 reveals innate and adaptive immune dysfunction and provides an early prediction tool for clinical progression.
• Longitudinal immune profiling reveals key myeloid signatures associated with COVID-19.
• Robust T cell response towards spike, membrane, and nucleocapsid SARS-CoV-2 proteins is not associated with recovery in critical COVID-19 patients.
• In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.
• IFITM proteins promote SARS-CoV-2 infection of human lung cells.
• Estimating the Binding of Sars-CoV-2 Peptides to HLA Class I in Human Subpopulations Using Artificial Neural Networks.
• SARS-CoV-2 Neutralizing Antibody Responses Are More Robust in Patients with Severe Disease.
• In severe COVID-19, SARS-CoV-2 induces a chronic, TGF-β-dominated adaptive immune response.
• Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19.
• Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms.
• Phenotypical and functional alteration of unconventional T cells in severe COVID-19 patients.
• Kinetics of viral clearance and antibody production across age groups in SARS-CoV-2 infected children.
• Quantifying antibody kinetics and RNA detection during early-phase SARS-CoV-2 infection by time since symptom onset.
• SARS-CoV-2 IgG and IgA antibody response is gender dependent; and IgG antibodies rapidly decline early on.
• SARS-CoV-2 Spike 1 Protein Controls Natural Killer Cell Activation via the HLA-E/NKG2A Pathway.
• Immune pathogenesis of COVID-19-related Multisystem Inflammatory Syndrome in Children (MIS-C).
• Direct activation of the alternative complement pathway by SARS-CoV-2 spike proteins is blocked by factor D inhibition.
• MHC class II transactivator CIITA induces cell resistance to Ebola virus and SARS-like coronaviruses.
• Sex differences in immune responses that underlie COVID-19 disease outcomes.
• Peripheral immunophenotypes in children with multisystem inflammatory syndrome associated with SARS-CoV-2 infection.
• SARS-CoV-2 specific T-cell responses and correlations with COVID-19 patient predisposition.

August 2020

• Acute SARS-CoV-2 Infection Impairs Dendritic Cell and T Cell Responses.
• Distinct Early Serological Signatures Track with SARS-CoV-2 Survival.
• Single-cell landscape of immunological responses in patients with COVID-19.
• Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans.
• IL-6 trans-signaling induces plasminogen activator inhibitor-1 from vascular endothelial cells in cytokine release syndrome.
• An inflammatory cytokine signature predicts COVID-19 severity and survival.
• Natural killer cell immunotypes related to COVID-19 disease severity.
• SARS-CoV2 vertical transmission with adverse effects on the newborn revealed through integrated immunohistochemical, electron microscopy and molecular analyses of Placenta.
• Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels.
• SARS-CoV-2 infection induces sustained humoral immune responses in convalescent patients following symptomatic COVID-19.
• Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19.
• A dynamic COVID-19 immune signature includes associations with poor prognosis.
• Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
• Single-cell analysis of two severe COVID-19 patients reveals a monocyte-associated and tocilizumab-responding cytokine storm.
• Type I and Type III IFN Restrict SARS-CoV-2 Infection of Human Airway Epithelial Cultures.
• COVID-19 Patients Form Memory CD8+ T Cells that Recognize a Small Set of Shared Immunodominant Epitopes in SARS-CoV-2.
• Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection.
• Next-Generation Sequencing of T and B Cell Receptor Repertoires from COVID-19 Patients Showed Signatures Associated with Severity of Disease.
• Activation and evasion of type I interferon responses by SARS-CoV-2.
• Longitudinal analyses reveal immunological misfiring in severe COVID-19.
• SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19.

July 2020

• Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19.
• Platelet activation and platelet-monocyte aggregates formation trigger tissue factor expression in severe COVID-19 patients.
• Severe SARS-CoV-2 infection in humans is defined by a shift in the serum lipidome resulting in dysregulation of eicosanoid immune mediators.
• SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls.
• SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses.
• Potently neutralizing and protective human antibodies against SARS-CoV-2.
• Elevated Glucose Levels Favor SARS-CoV-2 Infection and Monocyte Response through a HIF-1α/Glycolysis-Dependent Axis.
• Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications.
• Comprehensive mapping of immune perturbations associated with severe COVID-19.
• Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2.
• Dynamic changes of D-dimer and neutrophil-lymphocyte count ratio as prognostic biomarkers in COVID-19.
• Evidence for structural protein damage and membrane lipid remodeling in red blood cells from COVID-19 patients.
• Mutations from bat ACE2 orthologs markedly enhance ACE2-Fc neutralization of SARS-CoV-2.
• High levels of SARS-CoV-2 specific T-cells with restricted functionality in patients with severe course of COVID-19.
• SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response.
• Critical Role of Type III Interferon in Controlling SARS-CoV-2 Infection in Human Intestinal Epithelial Cells.
• SARS-CoV-2-specific T cells exhibit unique features characterized by robust helper function, lack of terminal differentiation, and high proliferative potential.
• Cross-sectional evaluation of humoral responses against SARS-CoV-2 Spike.
• Phenotype and kinetics of SARS-CoV-2-specific T cells in COVID-19 patients with acute respiratory distress syndrome.
• Single-cell transcriptomic analysis of SARS-CoV-2 reactive CD4 + T cells.
• COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis.

June 2020

• Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent COVID-19 patients.
• Autoinflammatory and autoimmune conditions at the crossroad of COVID-19.
• Analysis of a SARS-CoV-2-Infected Individual Reveals Development of Potent Neutralizing Antibodies with Limited Somatic Mutation.
• Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections.
• Convergent antibody responses to SARS-CoV-2 in convalescent individuals.
• Modulation of Extracellular ISG15 Signaling by Pathogens and Viral Effector Proteins.
• Proteomics Uncovers Immunosuppression in COVID-19 Patients with Long Disease Course.
• SARS-CoV-2 viral loads and serum IgA/IgG immune responses in critically ill COVID-19 patients.
• The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients.
• Type I and III interferons disrupt lung epithelial repair during recovery from viral infection.
• Type III interferons disrupt the lung epithelial barrier upon viral recognition.
• Longitudinal immune profiling reveals distinct features of COVID-19 pathogenesis.
• IgA dominates the early neutralizing antibody response to SARS-CoV-2.
• A SARS-CoV-2 serological assay to determine the presence of blocking antibodies that compete for human ACE2 binding.
• Longitudinal COVID-19 profiling associates IL-1Ra and IL-10 with disease severity and RANTES with mild disease.
• Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions.
• Beyond the Spike: identification of viral targets of the antibody response to SARS-CoV-2 in COVID-19 patients.
• A possible role of immunopathogenesis in COVID-19 progression.
• Impaired immune cell cytotoxicity in severe COVID-19 is IL-6 dependent.
• An inflammatory cytokine signature helps predict COVID-19 severity and death.
• Targeted Immunosuppression Distinguishes COVID-19 from Influenza in Moderate and Severe Disease.
• SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors.
• Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures.
• Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals.
• Profiling serum cytokines in COVID-19 patients reveals IL-6 and IL-10 are disease severity predictors.
• Cytokine biomarkers of COVID-19.

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.

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.

 

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October 2020

• Experimental infection of domestic dogs and cats with SARS-CoV-2: Pathogenesis, transmission, and response to reexposure in cats.

September 2020

• Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2 Infected Syrian Hamsters.
• A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures.
• Jumping back and forth: anthropozoonotic and zoonotic transmission of SARS-CoV-2 on mink farms.
• Ocular conjunctival inoculation of SARS-CoV-2 can cause mild COVID-19 in rhesus macaques.
• K18-hACE2 Mice for Studies of COVID-19 Treatments and Pathogenesis Including Anosmia.

August 2020

• SARS-CoV-2 infection of human ACE2-transgenic mice causes severe lung inflammation and impaired function.
• Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease.
• North American deer mice are susceptible to SARS-CoV-2.
• Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters.
• Evaluation of K18-hACE2 Mice as a Model of SARS-CoV-2 Infection.
• Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy.
• Transient lymphopenia and interstitial pneumonia with endotheliitis in SARS-CoV-2-infected macaques.
• Mouse Model of SARS-CoV-2 Reveals Inflammatory Role of Type I Interferon Signaling.
• Lethality of SARS-CoV-2 infection in K18 human angiotensin converting enzyme 2 transgenic mice.

July 2020

• SARS-CoV-2 infection induces germinal center responses with robust stimulation of CD4 T follicular helper cells in rhesus macaques.
• Comparison of Transgenic and Adenovirus hACE2 Mouse Models for SARS-CoV-2 Infection.
• Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters.
• SARS-CoV-2 infects and damages the mature and immature olfactory sensory neurons of hamsters.
• Primary exposure to SARS-CoV-2 protects against reinfection in rhesus macaques.

June 2020

• A SARS-CoV-2 Infection Model in Mice Demonstrates Protection by Neutralizing Antibodies.
• ARDS and Cytokine Storm in SARS-CoV-2 Infected Caribbean Vervets.
• A versatile mouse model of COVID-19.
• Establishment of an African green monkey model for COVID-19.
• The Role of Host Genetic Factors in Coronavirus Susceptibility: Review of Animal and Systematic Review of Human Literature.
• A Mouse Model of SARS-CoV-2 Infection and Pathogenesis.
• Antiviral Efficacies of FDA-Approved Drugs against SARS-CoV-2 Infection in Ferrets.

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.

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.

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October 2020

• *NEW SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo.
• *NEW Type 2 and interferon inflammation regulate SARS-CoV-2 entry factor expression in the airway epithelium.
• *NEW Sequences in the cytoplasmic tail of SARS-CoV-2 spike facilitate syncytia formation.
• *NEW Inhibition of SARS-CoV-2 viral entry in vitro upon blocking N- and O-glycan elaboration.
• *NEW Co-infection of influenza A virus enhances SARS-CoV-2 infectivity.
• *NEW Ultrastructural analysis of SARS-CoV-2 interactions with the host cell via high resolution scanning electron microscopy.
• *NEW Interaction of Human ACE2 to Membrane-Bound SARS-CoV-1 and SARS-CoV-2 S Glycoproteins.
• *NEW SARS-CoV-2 induces a more robust innate immune response and replicates less efficiently than SARS-CoV in the human intestines: an ex vivo study with implications on pathogenesis of COVID-19.
• *NEW Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium.
• *NEW Structural and functional modelling of SARS-CoV-2 entry in animal models.
• Common genetic variation in humans impacts in vitro susceptibility to SARS-CoV-2 infection.
• SARS-CoV-2 and three related coronaviruses utilize multiple ACE2 orthologs and are potently blocked by an improved ACE2-Ig.
• *Research Tool Heterogeneous expression of the SARS-Coronavirus-2 receptor ACE2 in the human respiratory tract.
• SARS-CoV-2 Uses CD4 to Infect T Helper Lymphocytes.
• Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.
• *Research Tool A Single-Cell RNA Expression Map of Human Coronavirus Entry Factors.
• Human Mesenchymal Stromal Cells Are Resistant to SARS-CoV-2 Infection under Steady-State, Inflammatory Conditions and in the Presence of SARS-CoV-2-Infected Cells.

September 2020

• Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.
• *Research Tool Structural models of human ACE2 variants with SARS-CoV-2 Spike protein for structure-based drug design.
• Activation of the SARS-CoV-2 Receptor Ace2 through JAK/STAT-Dependent Enhancers during Pregnancy.
• SARS-CoV-2 infects and induces cytotoxic effects in human cardiomyocytes.
• SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2.
• Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 disease severity.
• Neuroinvasion of SARS-CoV-2 in human and mouse brain.
• Structural characterization of the N-linked glycans in the receptor binding domain of the SARS-CoV-2 spike protein and their interactions with human lectins using NMR spectroscopy.
• Determinants of SARS-CoV-2 receptor gene expression in upper and lower airways.
• Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor.
• Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility.
• SARS-CoV-2 targets neurons of 3D human brain organoids.
• Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility.
• The SARS-CoV-2 multibasic cleavage site facilitates early serine protease-mediated entry into organoid-derived human airway cells.
• SARS-CoV-2 infects brain choroid plexus and disrupts the blood-CSF-barrier.
• In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.
• Dynamics of the ACE2-SARS-CoV-2/SARS-CoV spike protein interface reveal unique mechanisms.

August 2020

• Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding.
• Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity.
• Advances in research on ACE2 as a receptor for 2019-nCoV.
• Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans.
• SARS-CoV-2 infects human neural progenitor cells and brain organoids.
• Structure-guided covalent stabilization of coronavirus spike glycoprotein trimers in the closed conformation.
• SARS-CoV-2 Spike Protein Interacts with Multiple Innate Immune Receptors.
• Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor.
• Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry.
• A thermostable, closed SARS-CoV-2 spike protein trimer.
• The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity.
• A Replication-Competent Vesicular Stomatitis Virus for Studies of SARS-CoV-2 Spike-Mediated Cell Entry and Its Inhibition.
• The protein expression profile of ACE2 in human tissues.
• No evidence for basigin/CD147 as a direct SARS-CoV-2 spike binding receptor.

July 2020

• Interferons and viruses induce a novel primate-specific isoform dACE2 and not the SARS-CoV-2 receptor ACE2.
• Controlling the SARS-CoV-2 spike glycoprotein conformation.
• Structure-based design of prefusion-stabilized SARS-CoV-2 spikes.
• LY6E impairs coronavirus fusion and confers immune control of viral disease.
• The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State.
• Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus.
• Distinct conformational states of SARS-CoV-2 spike protein.
• Cryo-EM analysis of the post-fusion structure of the SARS-CoV spike glycoprotein.
• SARS-CoV-2 Spike protein hijacks VEGF-A/Neuropilin-1 receptor signaling to induce analgesia.
• Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors and suggest subtype specificity.
• A glycan cluster on the SARS-CoV-2 spike ectodomain is recognized by Fab-dimerized glycan-reactive antibodies.
• Glycans on the SARS-CoV-2 Spike Control the Receptor Binding Domain Conformation.
• LY6E Restricts Entry of Human Coronaviruses, Including Currently Pandemic SARS-CoV-2.
• SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain.
• High affinity binding of SARS-CoV-2 spike protein enhances ACE2 carboxypeptidase activity.
• A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike.
• Shielding and Beyond: The Roles of Glycans in SARS-CoV-2 Spike Protein.

June 2020

• COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles' heel conserved region to minimize probability of escape mutations and drug resistance.
• SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract.
• ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19.
• Neuropilin-1 facilitates SARS-CoV-2 cell entry and provides a possible pathway into the central nervous system.
• Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells.
• Neuropilin-1 is a host factor for SARS-CoV-2 infection.
• Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? Insights from All-Atoms Simulations.
• SARS-CoV-2 infection induces EMT-like molecular changes, including ZEB1-mediated repression of the viral receptor ACE2, in lung cancer models.
• Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors.

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.

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.

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October 2020

• Articles to be updated shortly

September 2020

• SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant.

August 2020

• Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation.
• Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15.
• Morphogenesis and cytopathic effect of SARS-CoV-2 infection in human airway epithelial cells.

July 2020

• Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2.
• Intracellular autoactivation of TMPRSS11A, an airway epithelial transmembrane serine protease.
• Genetic architecture of host proteins interacting with SARS-CoV-2.
• A molecular pore spans the double membrane of the coronavirus replication organelle.
• Molecular Basis for ADP-ribose Binding to the Mac1 Domain of SARS-CoV-2 Nsp3.
• Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs.
• Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography.
• Crystal Structure of the SARS-CoV-2 Non-structural Protein 9, Nsp9.

June 2020

• The ORF3a protein of SARS-CoV-2 induces apoptosis in cells.
• SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology.
• Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2.
• SARS-CoV-2 nsp13, nsp14, nsp15 and orf6 function as potent interferon antagonists.

May 2020

• Crystal structures of SARS-CoV-2 ADP-ribose phosphatase (ADRP): from the apo form to ligand complexes.

 

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