The coding capacity of SARS-CoV-2

  title={The coding capacity of SARS-CoV-2},
  author={Yaara Finkel and Orel Mizrahi and Aharon Nachshon and Shira Weingarten-Gabbay and David Morgenstern and Yfat Yahalom-Ronen and Hadas Tamir and Hagit Achdout and Dana Stein and Ofir Israeli and Adi Beth-Din and Sharon Melamed and Shay Weiss and Tomer Israely and Nir Paran and Michal Schwartz and Noam Stern-Ginossar},
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic 1 . To understand the pathogenicity and antigenic potential of SARS-CoV-2 and to develop therapeutic tools, it is essential to profile the full repertoire of its expressed proteins. The current map of SARS-CoV-2 coding capacity is based on computational predictions and relies on homology with other coronaviruses. As the protein complement varies among… 

Structural and molecular perspectives of SARS-CoV-2

Understanding the Role of SARS-CoV-2 ORF3a in Viral Pathogenesis and COVID-19

This review provides an in-depth analysis of ORF3a protein’s structure, origin, evolution, and mutant variants, and how these characteristics affect its functional role in viral pathogenesis and COVID-19.

SARS-CoV-2 utilizes a multipronged strategy to suppress host protein synthesis

It is revealed that infection leads to accelerated degradation of cytosolic cellular mRNAs which facilitates viral takeover of the mRNA pool in infected cells, and the translation of transcripts whose expression is induced in response to infection, including innate immune genes, is impaired.

Molecular Biology of SARS-CoV-2

The novel aspects of the SARS-CoV-2 coronavirus life cycle are highlighted, and how this and other viruses interact with the biochemistry of the host organism is described.

Parsing the role of NSP1 in SARS-CoV-2 infection

The results reveal the multifaceted approach nsp1 uses to shut off cellular protein synthesis and uncover the central role it plays in SARS-CoV-2 pathogenesis, explicitly through blockage of the IFN response.

Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2

An integrative analysis of eight independent SARS-CoV-2 transcriptomes generated using three sequencing strategies, five host systems, and seven viral isolates shows nc-sgRNAs make up as much as 33% of total sgRNAs in cell culture models of infection, are largely consistent in abundance across independent transcriptomes, and increase in abundance over time during infection.

Translational Control of COVID-19 and Its Therapeutic Implication

This review provides a comprehensive picture of recent advancements in the understanding of the molecular basis and complexity of SARS-CoV-2 protein translation and describes the potential of translational components as targets for therapeutic interventions.

Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs

Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19

This review focuses on genomic organization, structural and non-structural protein components, and potential prospective molecular targets for development of therapeutic drugs, convalescent plasm therapy, and a myriad of potential vaccines to tackle SARS-CoV-2 infection.

Restriction of SARS-CoV-2 replication by targeting programmed −1 ribosomal frameshifting

Merafloxacin impedes SARS-CoV-2 replication in Vero E6 cells, thereby providing proof-of-principle for targeting −1 PRF as a plausible and effective antiviral strategy for SARS and other coronaviruses.



A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing

A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.

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

The cellular infection profile of SARS-CoV-2 is revealed and the identification of drugs that inhibit viral replication is enabled, enabling the development of therapies for the treatment of COVID-19.

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

  • A. Firth
  • Biology
    The Journal of general virology
  • 2020
A recently published ribosome profiling study confirmed that ORF3c is indeed translated during infection, and is conserved across the subgenus Sarbecovirus, and encodes a 40–41 amino acid predicted transmembrane protein.

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

The sensitivity of the two viruses to three established inhibitors of coronavirus replication is very similar, but that SARS-CoV-2 infection was substantially more sensitive to pre-treatment of cells with pegylated interferon alpha.

SARS-CoV-2 infected host cell proteomics reveal potential therapy targets

The results reveal the cellular infection profile of SARS-CoV-2 and led to the identification of drugs inhibiting viral replication in human cells, and are expected to guide efforts to develop therapy options for COVID-19.

Beyond the Spike: identification of viral targets of the antibody response to SARS-CoV-2 in COVID-19 patients

This technique shows that antigens ORF3b and ORF8 allow detection of antibody early in infection in a specific manner and reveals the immuno-dominance of the N antigen in COVID-19 patients.

Identification of a common deletion in the spike protein of SARS-CoV-2

Data indicate the deletion of QTQTN, at the flank of polybasic cleavage site, is likely benefit the SARS-CoV-2 replication or infection in vitro but under strong purification selection in vivo since it is rarely identified in clinical samples; and there could be a very efficient mechanism for deleting this region from viral genome as the variants losing 23585-23599 is commonly detected after two rounds of cell passage.

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

A putative new gene, ORF3a*, overlapping ORF 3a in an alternative reading frame is identified, which is conserved across the subgenus Sarbecovirus, and encodes a 40–41 amino acid predicted transmembrane protein.