Rise of the SARS-CoV-2 Variants: can proteomics be the silver bullet?

Acharjee, Arup; Kingsly, Joshua Stephen; Kamat, Madhura; Kurlawala, Vishakha; Chakraborty, Aruna; Vyas, Priyanka; Vaishnav, Radhika A.; Srivastava, Sanjeeva

doi:10.1080/14789450.2022.2085564

Cited by 2 publications

(2 citation statements)

References 159 publications

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“…Dedicated to understanding the biology and pathogenesis of infection with microbes, including human viruses and bacteria, members of the infectious disease (ID) team have advanced MS-based methods for the detection of pathogenic proteins, virus-host protein interactions, and infection-induced alterations in protein abundance or posttranslational modifications. − A targeted mass spectrometry assay, TRUSTED, was developed by the Cristea group for the specific detection of viral proteins from the three Herpesviridae subfamilies, demonstrating its use for monitoring the effects of clinical therapeutic agents and anti- or pro-viral factors . Targeted mass spectrometry also defined the impact of diverse human viruses on membrane contact site proteins that link organelles in dynamic functional networks, leading to the discovery of a previously unrecognized mitochondria-ER encapsulation structure that aids virus production .…”

Section: Highlights From the B/d-hppmentioning

confidence: 99%

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

et al. 2022

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The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".

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Section: Highlights From the B/d-hppmentioning

confidence: 99%

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

et al. 2022

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“…Serological techniques are more robust in this regard as they are less susceptible to false-positives [ 4 , 5 ]. Omics technologies and big data analytics often have led to a panel of biomarkers for the prediction of disease severity [ 6 , 7 , 8 , 9 , 10 , 11 ] from the early days of the pandemic. However, they are of little or no translational value, especially in the event of a colossal hospitalization burden, as is often the case in outbreaks.…”

Section: Introductionmentioning

confidence: 99%

Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray

Acharjee

Ray

Salkar

et al. 2023

Viruses

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The amaranthine scale of the COVID-19 pandemic and unpredictable disease severity is of grave concern. Serological diagnostic aids are an excellent choice for clinicians for rapid and easy prognosis of the disease. To this end, we studied the humoral immune response to SARS-CoV-2 infection to map immunogenic regions in the SARS-CoV-2 proteome at amino acid resolution using a high-density SARS-CoV-2 proteome peptide microarray. The microarray has 4932 overlapping peptides printed in duplicates spanning the entire SARS-CoV-2 proteome. We found 204 and 676 immunogenic peptides against IgA and IgG, corresponding to 137 and 412 IgA and IgG epitopes, respectively. Of these, 6 and 307 epitopes could discriminate between disease severity. The emergence of variants has added to the complexity of the disease. Using the mutation panel available, we could detect 5 and 10 immunogenic peptides against IgA and IgG with mutations belonging to SAR-CoV-2 variants. The study revealed severity-based epitopes that could be presented as potential prognostic serological markers. Further, the mutant epitope immunogenicity could indicate the putative use of these markers for diagnosing variants responsible for the infection.

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Rise of the SARS-CoV-2 Variants: can proteomics be the silver bullet?

Cited by 2 publications

References 159 publications

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

Humoral Immune Response Profile of COVID-19 Reveals Severity and Variant-Specific Epitopes: Lessons from SARS-CoV-2 Peptide Microarray

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