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Proteotyping of SARS-CoV-2 viral peptides in nasal swab simili

ABSTRACT: Detection by tandem mass spectrometry of a specific subset of SARS-CoV-2 viral peptides to illustrate the potential of shotgun proteomics for clinical diagnostic.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Betacoronavirus Sp.

DISEASE(S): Covid-19

SUBMITTER: Jean ARMENGAUD

LAB HEAD: Jean Armengaud

PROVIDER: PXD019686 | Pride | 2020-07-23

REPOSITORIES: Pride

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			Action	DRS
	F217723.dat	Other
	F217723_p0.01.mzid.gz	Mzid
	F217726.dat	Other
	F217726_p0.01.mzid.gz	Mzid
	F217728.dat	Other

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Publications

Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window.

Gouveia Duarte D Miotello Guylaine G Gallais Fabrice F Gaillard Jean-Charles JC Debroas Stéphanie S Bellanger Laurent L Lavigne Jean-Philippe JP Sotto Albert A Grenga Lucia L Pible Olivier O Armengaud Jean J

Journal of proteome research 20200805 11

Rapid but yet sensitive, specific, and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostics that would not require specific reagents are worthy to investigate not only for fighting the COVID-19 pandemic but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spect ...[more]

PMID: 32697082

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Proteotyping of SARS-CoV-2 viral peptides in nasal swab simili

Project description:Detection by tandem mass spectrometry of a specific subset of SARS-CoV-2 viral peptides to illustrate the potential of shotgun proteomics for clinical diagnostic.

2020-10-02 | MSV000086229 | MassIVE

The PDZ-binding motif of SARS-CoV envelope protein is a determinant of viral pathogenesis

Project description:A recombinant SARS-CoV lacking the envelope (E) protein is attenuated in vivo. Here we report that E protein PDZ-binding motif (PBM), a domain involved in protein-protein interactions, is a major virulence determinant in vivo. Elimination of SARS-CoV E protein PBM by using reverse genetics led to attenuated viruses (SARS-CoV-mutPBM) and to a reduction in the deleterious exacerbate immune response triggered during infection with the parental virus (SARS-CoV-wt). Cellular protein syntenin bound E protein PBM during SARS-CoV infection. Syntenin activates p38 MAPK leading to overexpression of inflammatory cytokines, and we have shown that active p38 MAPK was reduced in lungs of mice infected with SARS-CoVs lacking E protein PBM (SARS-CoV-mutPBM) as compared with the parental virus (SARS-CoV-wt), leading to a decreased expression of inflammatory cytokines and to viral attenuation. Therefore, E protein PBM is a virulence factor that activates pathogenic immune response most likely by using syntenin as a mediator of p38 MAPK induced inflammation. Three biological replicates were independently hybridized (one channel per slide) for each sample type (SARS-CoV-wt, SARS-CoV-mutPBM, Mock). Slides were Sure Print G3 Agilent 8x60K Mouse (G4852A-028005)

2014-10-31 | E-GEOD-52920 | biostudies-arrayexpress

Proteomics characterization of purified SARS-CoV-2 viral particles.

Project description:Shotgun proteomics characterization of purified SARS-CoV-2 viral particles.

2021-05-31 | PXD025131 | Pride

Extensive proteomic dataset of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus at Day 4 post-infection

Project description:Next-generation proteomics of Vero E6 cells infected by Italy-INMI1 SARS-CoV-2 virus for defining relevant viral peptides for detection. Cells from Day4 post-infection at 0.01 multiplicity of infection.

2020-05-29 | PXD018804 | Pride

Ab Initio Design of Amphipathic-Symmetric Peptides against SARS-CoV-2

Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe health crisis and huge socioeconomic upheaval internationally. This study proposes an ab initio design strategy to obtain antiviral peptides to against SARS-CoV-2 infection. The study employed database filtering technology to generate 7 amphipathic-symmetric peptides named DFTavPs with low cytotoxicity and random coil structure. Three DFTavPs promoted SARS-CoV-2 pseudoviruses infection and three DFTavPs inhibited virus infection, which are accompanied by up-regulation or down-regulation of SARS-CoV receptor angiotensin-converting enzyme 2 mRNA levels. Particularly, microRNA profiling showed that some differentially expressed microRNAs had potential to target key factors for cell entry of SARS-CoV-2. Furthermore, we explored the relationship of parameters and antiviral efficacy index (AEI). The results suggested that higher AEI of coronavirus was most likely to occur at mean amphipathic moment between 0.3 and 0.4. Automated machine learning was used to construct parameters-AEI regression models for various viruses. The Extra-Trees and CatBoost had a good predicting performance for AEI of coronavirus (R2=0.794 and Rpearson=0.897) and human immunodeficiency virus (R2=0.735 and Rpearson=0.859), respectively. Overall, this strategy is expected to efficiently obtain huge amounts of potential peptide drugs with anti-SARS-CoV-2 activity, and machine learning models could contribute to discovery of high antivirus-activity peptides.

2021-08-26 | GSE182562 | GEO

Proteomics characterization of purified SARS-CoV-2 viral particles for search of mutations.

Project description:Shotgun proteomics characterization of purified SARS-CoV-2 viral particles and interpretation in error-tolerant mode.

2021-05-31 | PXD025130 | Pride

A Retrospective Cohort Study for Main Postoperative Complications After SARS-CoV-2 Infection

Project description:To explore the relationship between SARS-CoV-2 infection in different time before operation and postoperative main complications (mortality, main pulmonary and cardiovascular complications) 30 days after operation; To determine the best timing of surgery after SARS-CoV-2 infection.

| 12454 | ecrin-mdr-crc

Nanomolar inhibition of SARS-CoV-2 infection by N-terminally extended HR2 peptides

Project description:Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies through changes of epitopes on the receptor binding domain of the viral spike glycoprotein (S). Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide inhibitors which block formation of the HR1HR2 six-helix bundle of the SARS-CoV-2 spike protein and thus interfere with viral membrane fusion; HR2 derived peptides are validated inhibitors of this process. Here, we identify a short N-terminal region that, when appended to the helical region of an HR2 peptide from previous studies, leads to potent inhibition of fusion. The extended peptide shows an ~100-fold increase in efficacy compared with the previously used 36-amino-acid version of HR2, effectively achieving single-digit nanomolar inhibition of SARS-CoV-2 in cell-based fusion, VSV-SARS-CoV-2 chimera, and authentic SARS-CoV-2 infection assays. The peptide also strongly inhibits all major SARS-CoV-2 variants to date. Structural studies of the HR1HR2 bundle reveal the formation of an extended, stabilized N-terminus that interacts with the HR2 triple helix, further stabilizing the HR1HR2 bundle. Together, these results suggest that regions outside the previously studied HR2 helical region may offer new opportunities for potent peptide-derived therapeutics for SARS-CoV-2 and its variants.

2022-09-21 | GSE203229 | GEO

SHAE002: SARS-CoV, SARS-dORF6 and SARS-BatSRBD infection of HAE cultures.

Project description:HAE cultures were infected with SARS-CoV, SARS-dORF6 or SARS-BatSRBD and were directly compared to A/CA/04/2009 H1N1 influenza-infected cultures. Cell samples were collected at various hours post-infection for analysis. Time Points = 0, 12, 24, 36, 48, 60, 72, 84 and 96 hrs post-infection for SARS-CoV, SARS-dORF6 and SARS-BatSRBD. Time Points = 0, 6, 12, 18, 24, 36 and 48 hrs post-infection for H1N1. Done in triplicate or quadruplicate for RNA Triplicates/quadruplicates are defined as 3/4 different wells, plated at the same time and using the same cell stock for all replicates. Time matched mocks done in triplicate from same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) will be used for the mock infections. Infection was done at an MOI of 2.

2013-07-31 | E-GEOD-47960 | biostudies-arrayexpress

SHAE004: SARS-CoV, SARS-dORF6 and SARS-BatSRBD infection of HAE cultures.

Project description:HAE cultures were infected with SARS-CoV, SARS-dORF6 or SARS-BatSRBD and were directly compared to A/CA/04/2009 H1N1 influenza-infected cultures. Cell samples were collected at various hours post-infection for analysis. Time Points = 0, 12, 24, 36, 48, 60, 72, 84 and 96 hrs post-infection for SARS-CoV, SARS-dORF6 and SARS-BatSRBD. Time Points = 0, 6, 12, 18, 24, 36 and 48 hrs post-infection for H1N1. Done in triplicate for RNA Triplicates are defined as 3 different wells, plated at the same time and using the same cell stock for all replicates. Time matched mocks done in triplicate from same cell stock as rest of samples. Culture medium (the same as what the virus stock is in) will be used for the mock infections. Infection was done at an MOI of 2 for SARS viruses and an MOI of 1 for H1N1.

2013-07-31 | E-GEOD-47962 | biostudies-arrayexpress

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