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

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

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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12014-021-09331-z.