tetano
Editor, Senior Moderator
Clin Proteomics
. 2021 Oct 22;18(1):25.
doi: 10.1186/s12014-021-09331-z.
A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples
Kiran K Mangalaparthi[SUP] #[/SUP][SUP] 1 [/SUP], Sandip Chavan[SUP] #[/SUP][SUP] 1 [/SUP], Anil K Madugundu[SUP] 1 2 3 4 [/SUP], Santosh Renuse[SUP] 1 5 [/SUP], Patrick M Vanderboom[SUP] 1 [/SUP], Anthony D Maus[SUP] 1 [/SUP], Jennifer Kemp[SUP] 1 [/SUP], Benjamin R Kipp[SUP] 6 [/SUP], Stefan K Grebe[SUP] 1 7 [/SUP], Ravinder J Singh[SUP] 1 [/SUP], Akhilesh Pandey[SUP] 8 9 10 [/SUP]
Affiliations
Abstract
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.
Keywords: COVID-19; Mass spectrometry; Parallel reaction monitoring (PRM); SARS-CoV-2; SISCAPA.
. 2021 Oct 22;18(1):25.
doi: 10.1186/s12014-021-09331-z.
A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples
Kiran K Mangalaparthi[SUP] #[/SUP][SUP] 1 [/SUP], Sandip Chavan[SUP] #[/SUP][SUP] 1 [/SUP], Anil K Madugundu[SUP] 1 2 3 4 [/SUP], Santosh Renuse[SUP] 1 5 [/SUP], Patrick M Vanderboom[SUP] 1 [/SUP], Anthony D Maus[SUP] 1 [/SUP], Jennifer Kemp[SUP] 1 [/SUP], Benjamin R Kipp[SUP] 6 [/SUP], Stefan K Grebe[SUP] 1 7 [/SUP], Ravinder J Singh[SUP] 1 [/SUP], Akhilesh Pandey[SUP] 8 9 10 [/SUP]
Affiliations
- PMID: 34686148
- PMCID: PMC8532087
- DOI: 10.1186/s12014-021-09331-z
Abstract
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.
Keywords: COVID-19; Mass spectrometry; Parallel reaction monitoring (PRM); SARS-CoV-2; SISCAPA.