A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples

SARS-CoV-2, a novel human coronavirus, has created a global disease burden infecting > 100 million humans in just over a year. RT-PCR is currently the predominant method of diagnosing this viral infection although a variety of tests to detect viral antigens have also been developed. In this study...

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Bibliographic Details
Published in:Clinical proteomics 2021-10, Vol.18 (1), p.25-25, Article 25
Main Authors: Mangalaparthi, Kiran K, Chavan, Sandip, Madugundu, Anil K, Renuse, Santosh, Vanderboom, Patrick M, Maus, Anthony D, Kemp, Jennifer, Kipp, Benjamin R, Grebe, Stefan K, Singh, Ravinder J, Pandey, Akhilesh
Format: Article
Language:English
Subjects:
Antibodies
Antigen-antibody reactions
Antigens
Automation
Chromatography
Coronaviruses
COVID-19
Data analysis
Disease transmission
Enrichment
Health aspects
Letter to the Editor
Machine learning
Mass spectrometry
Methods
Nucleocapsids
Peptides
Polymerase chain reaction
Proteins
Scientific equipment and supplies industry
Scientific imaging
Severe acute respiratory syndrome
Severe acute respiratory syndrome coronavirus 2
Viral antibodies
Viral antigens
Viruses
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Summary:SARS-CoV-2, a novel human coronavirus, has created a global disease burden infecting > 100 million humans in just over a year. RT-PCR is currently the predominant method of diagnosing this viral infection although a variety of tests to detect viral antigens have also been developed. In this study, we adopted a SISCAPA-based enrichment approach using anti-peptide antibodies generated against peptides from the nucleocapsid protein of SARS-CoV-2. We developed a targeted workflow in which nasopharyngeal swab samples were digested followed by enrichment of viral peptides using the anti-peptide antibodies and targeted parallel reaction monitoring (PRM) analysis using a high-resolution mass spectrometer. This workflow was applied to 41 RT-PCR-confirmed clinical SARS-CoV-2 positive nasopharyngeal swab samples and 30 negative samples. The workflow employed was highly specific as none of the target peptides were detected in negative samples. Further, the detected peptides showed a positive correlation with the viral loads as measured by RT-PCR Ct values. The SISCAPA-based platform described in the current study can serve as an alternative method for SARS-CoV-2 viral detection and can also be applied for detecting other microbial pathogens directly from clinical samples.
ISSN:1542-6416
1559-0275
DOI:10.1186/s12014-021-09331-z