Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A novel cell culture system modeling the SARS-CoV-2 life cycle.

ABSTRACT: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the global pandemic of COVID-19. SARS-CoV-2 is classified as a biosafety level-3 (BSL-3) agent, impeding the basic research into its biology and the development of effective antivirals. Here, we developed a biosafety level-2 (BSL-2) cell culture system for production of transcription and replication-competent SARS-CoV-2 virus-like-particles (trVLP). This trVLP expresses a reporter gene (GFP) replacing viral nucleocapsid gene (N), which is required for viral genome packaging and virion assembly (SARS-CoV-2 GFP/ΔN trVLP). The complete viral life cycle can be achieved and exclusively confined in the cells ectopically expressing SARS-CoV or SARS-CoV-2 N proteins, but not MERS-CoV N. Genetic recombination of N supplied in trans into viral genome was not detected, as evidenced by sequence analysis after one-month serial passages in the N-expressing cells. Moreover, intein-mediated protein trans-splicing approach was utilized to split the viral N gene into two independent vectors, and the ligated viral N protein could function in trans to recapitulate entire viral life cycle, further securing the biosafety of this cell culture model. Based on this BSL-2 SARS-CoV-2 cell culture model, we developed a 96-well format high throughput screening for antivirals discovery. We identified salinomycin, tubeimoside I, monensin sodium, lycorine chloride and nigericin sodium as potent antivirals against SARS-CoV-2 infection. Collectively, we developed a convenient and efficient SARS-CoV-2 reverse genetics tool to dissect the virus life cycle under a BSL-2 condition. This powerful tool should accelerate our understanding of SARS-CoV-2 biology and its antiviral development.

SUBMITTER: Ju X

PROVIDER: S-EPMC7990224 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

A novel cell culture system modeling the SARS-CoV-2 life cycle

Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the global pandemic of COVID-19, and no effective antiviral agents and vaccines are available. SARS-CoV-2 is classified as a biosafety level-3 (BLS-3) agent, impeding the basic research into its biology and the development of effective antivirals. Here, we described a safe cell culture system for production of transcription and replication-competent, biologically contained SARS-CoV-2 virus like particles (trVLP) that express a reporter gene (GFP) replacing viral nucleocapsid gene, which is required for viral genome packaging and virion assembly (SARS-CoV-2-GFP/N trVLP). The complete viral life cycle can be exclusively achieved and confined in the cells expressing SARS-CoV or SARS-CoV-2 N proteins in trans, but not MERS-CoV N. Additionally, genetic recombination of N supplied in trans into viral genome was not detected, as evidenced by sequence analysis after one-month serial passages in N-expressing Caco-2 cells. Moreover, Intein-mediated protein trans-splicing approach was utilized to split the viral N gene into two independent vectors, and the ligated viral N protein could function in trans to recapitulate entire viral life cycle, further securing the biosafety of this cell culture model. To prove the suitability of this system in antivirals discovery, we developed a 96-well format high throughput screening to identify salinomycin, monensin sodium and lycorine chloride exhibiting potent antiviral activities against SARS-CoV-2 infection. Collectively, we propose that this cell culture system based on Intein-N genetic complementation to produce SARS-CoV-2 trVLP provides a safe means to dissect the virus life cycle, and thus accelerate our understanding of virus biology, as well as for more applied uses such as the screening and development of novel antivirals, and thus represent powerful tools for SARS-CoV-2 study.

2020-12-03 | GSE162629 | GEO

A novel cell culture system modeling the SARS-CoV-2 life cycle

Project description:A novel cell culture system modeling the SARS-CoV-2 life cycle

| PRJNA682433 | ENA

A role for HIFs in the SARS-CoV-2 life cycle

Project description:Calu-3 cells were infected with SARS-CoV2, before being treated with 50uM FG-4592 for 24 hours. The impact of cuture conditions on both the host and viral transcriptome were determined by RNA-sequencing.

2022-08-17 | GSE195870 | GEO

A robust cell culture system supporting the complete life cycle of hepatitis B virus.

Project description:The discovery of sodium taurocholate cotransporting polypeptide (NTCP) as the hepatitis B virus (HBV) receptor enabled researchers to create hepatoma cell lines susceptible to HBV infection. Infection in current systems, however, is inefficient and virus fails to spread. Infection efficiency is enhanced by treating cells with polyethylene glycol 8000 (PEG) during infection. However, this alone does not promote virus spread. Here we show that maintaining PEG in culture medium increases the rate of infection by at least one order of magnitude, and, most importantly, promotes virus spread. To demonstrate the utility of this system, we show that two interferon-stimulated genes (ISGs), ISG20 and tetherin, restrict HBV spread in NTCP-expressing hepatoma cells. Thus, this protocol can be easily applied to existing cell culture systems to study the complete HBV life cycle, including virus spread.

| S-EPMC5709435 | biostudies-literature

A bipotential organoid culture of respiratory epithelium for modeling SARS-CoV-2 infection

Project description:The airways and the alveoli of the human respiratory tract are lined by two distinct types of epithelium. We previously established long-term expanding human lung epithelial organoids from lung tissues and developed a ‘proximal’ differentiation protocol to generate mucociliary airway organoids, yet the derivation of alveolar organoids from adult lung has remained a challenge. Here we defined a ‘distal’ differentiation approach to generate alveolar organoids from the same source that allows the establishment of airway organoids. Alveolar organoids are enriched for AT1 and AT2 cells and functionally simulate the alveolar epithelium. AT2 cells in lung organoids act as the progenitor cells from which alveolar organoids emerge. Moreover, we demonstrate productive SARS-CoV-2 infection of alveolar organoids. We further optimize 2-dimensional (2D) airway organoids. When differentiated under a slightly acidic pH, these 2D airway organoids sustain enhanced viral replication and better recapitulate the high infectivity of SARS-CoV-2. Moreover, the optimized 2D airway organoids can model IgG transcytosis across the airway epithelium. Collectively, we establish a bipotential organoid culture system that can reproducibly expand the entire human respiratory epithelium in vitro for modeling respiratory diseases, including COVID-19.

2022-06-22 | GSE189514 | GEO

A novel 3D human glioblastoma cell culture system for modeling drug and radiation responses.

Project description:BackgroundGlioblastoma (GBM) is the most common primary brain tumor, with dismal prognosis. The failure of drug-radiation combinations with promising preclinical data to translate into effective clinical treatments may relate to the use of simplified 2-dimensional in vitro GBM cultures.MethodsWe developed a customized 3D GBM culture system based on a polystyrene scaffold (Alvetex) that recapitulates key histological features of GBM and compared it with conventional 2D cultures with respect to their response to radiation and to molecular targeted agents for which clinical data are available.ResultsIn 3 patient-derived GBM lines, no difference in radiation sensitivity was observed between 2D and 3D cultures, as measured by clonogenic survival. Three different molecular targeted agents, for which robust clinical data are available were evaluated in 2D and 3D conditions: (i) temozolomide, which improves overall survival and is standard of care for GBM, exhibited statistically significant effects on clonogenic survival in both patient-derived cell lines when evaluated in the 3D model compared with only one cell line in 2D cells; (ii) bevacizumab, which has been shown to increase progression-free survival when added to standard chemoradiation in phase III clinical trials, exhibited marked radiosensitizing activity in our 3D model but had no effect on 2D cells; and (iii) erlotinib, which had no efficacy in clinical trials, displayed no activity in our 3D GBM model, but radiosensitized 2D cells.ConclusionsOur 3D model reliably predicted clinical efficacy, strongly supporting its clinical relevance and potential value in preclinical evaluation of drug-radiation combinations for GBM.

| S-EPMC5463789 | biostudies-literature

A Novel Human Gastric Primary Cell Culture System for Modeling Helicobacter Pylori Infection In Vitro

Project description:We identified specific long-term culture conditions that allow the formation of 3-dimensional human gastric spheroids, which can be differentiated by withdrawal of Wnt3A and R-spondin1 to human gastric organoids. These cultures can expand indefinitely and exhibit important characteristics of human stomach tissue. Furthermore, these 3-dimensional cultures can be transferred into 2-dimensional primary epithelial cell layers, which can be successfully infected with H. pylori and thereby provide ideal conditions to study infections in vitro. Microarray experiments were performed as dual-color hybridizations on Agilent human whole genome catalog 44K arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

2014-12-10 | E-GEOD-58473 | biostudies-arrayexpress

Suramin Inhibits SARS-CoV-2 Infection in Cell Culture by Interfering with Early Steps of the Replication Cycle.

Project description:The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic that originated in Wuhan, China, in December 2019 has impacted public health, society, the global economy, and the daily lives of billions of people in an unprecedented manner. There are currently no specific registered antiviral drugs to treat or prevent SARS-CoV-2 infections. Therefore, drug repurposing would be the fastest route to provide at least a temporary solution while better, more specific drugs are being developed. Here, we demonstrate that the antiparasitic drug suramin inhibits SARS-CoV-2 replication, protecting Vero E6 cells with a 50% effective concentration (EC50) of ∼20 μM, which is well below the maximum attainable level in human serum. Suramin also decreased the viral load by 2 to 3 logs when Vero E6 cells or cells of a human lung epithelial cell line (Calu-3 2B4 [referred to here as "Calu-3"]) were treated. Time-of-addition and plaque reduction assays performed on Vero E6 cells showed that suramin acts on early steps of the replication cycle, possibly preventing binding or entry of the virus. In a primary human airway epithelial cell culture model, suramin also inhibited the progression of infection. The results of our preclinical study warrant further investigation and suggest that it is worth evaluating whether suramin provides any benefit for COVID-19 patients, which obviously requires safety studies and well-designed, properly controlled randomized clinical trials.

| S-EPMC7526844 | biostudies-literature

Drug discovery and development targeting the life cycle of SARS-CoV-2

Project description:A newly emerged coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belongs to the β-coronavirus family and shows high similarities with SARS-CoV. On March 11, 2020, the World Health Organization (WHO) declared SARS-CoV-2 a global pandemic, and the disease was named the coronavirus disease 2019 (COVID-19). The ongoing COVID-19 pandemic has caused over 46 million infections and over one million deaths worldwide, and the numbers are still increasing. Efficacious antiviral agents are urgently needed to combat this virus. The life cycle of SARS-CoV-2 mainly includes the viral attachment, membrane fusion, genomic replication, assembly and budding of virions. Accordingly, drug development against SARS-CoV-2 currently focuses on blocking spike protein binding to ACE2, inhibiting viral membrane fusion with host cells, and preventing the viral replication by targeting 3C-like protease, papain-like protease, RNA-dependent RNA polymerase as well as some host-cell proteins. In this review, the advances of drug development in these three major areas are elaborated.

| S-EPMC7848481 | biostudies-literature

Intracellular Life Cycle Kinetics of SARS-CoV-2 Predicted Using Mathematical Modelling.

Project description:SARS-CoV-2 infection represents a global threat to human health. Various approaches were employed to reveal the pathogenetic mechanisms of COVID-19. Mathematical and computational modelling is a powerful tool to describe and analyze the infection dynamics in relation to a plethora of processes contributing to the observed disease phenotypes. In our study here, we formulate and calibrate a deterministic model of the SARS-CoV-2 life cycle. It provides a kinetic description of the major replication stages of SARS-CoV-2. Sensitivity analysis of the net viral progeny with respect to model parameters enables the identification of the life cycle stages that have the strongest impact on viral replication. These three most influential parameters are (i) degradation rate of positive sense vRNAs in cytoplasm (negative effect), (ii) threshold number of non-structural proteins enhancing vRNA transcription (negative effect), and (iii) translation rate of non-structural proteins (positive effect). The results of our analysis could be used for guiding the search for antiviral drug targets to combat SARS-CoV-2 infection.

| S-EPMC8473439 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data