Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern

Abstract

The SARS-CoV-2 omicron variant presented significant challenges to the global effort to counter the pandemic. SARS-CoV-2 is predicted to remain prevalent for the foreseeable future, making the ability to identify SARS-CoV-2 variants imperative in understanding and controlling the pandemic. The predominant variant discovery method, genome sequencing, is time-consuming, insensitive, and expensive. Ultra­performance liquid chromatography–mass spectrometry (UPLC–MS) offers an exciting alternative detection modality provided that variant-containing peptide markers are sufficiently detectable from their tandem mass spectra (MS/MS). We have synthesized model tryptic peptides of SARS-CoV-2 variants alpha, beta, gamma, delta, and omicron and evaluated their signal intensity, HCD spectra, and reverse phase retention time. Detection limits of 781, 781, 65, and 65 amol are obtained for the molecular ions of the proteotypic peptides, beta (QIAPGQTGNIADYNYK), gamma (TQLPSAYTNSFTR), delta (VGGNYNYR), and omicron (TLVKQLSSK), from neat solutions. These detection limits are on par with the detection limits of a previously reported proteotypic peptide from the SARS-CoV-2 spike protein, HTPINLVR. This study demonstrates the potential to differentiate SARS-CoV-2 variants through their proteotypic peptides with an approach that is broadly applicable across a wide range of pathogens.

High-Sensitivity Detection toward SARS-CoV-2 S1 Glycoprotein by Parallel Reaction Monitoring Mass Spectrometry

“…The combination of multiple peptides could improve specificity and have the potential to detect SARS-CoV-2 variants. The main advantage of MS-based SARS-CoV-2 detection is flexibility. , Just slightly modifying the precursor m / z of five mutated targeted peptides from new variants to the target list of MS data acquisition, and extending the S1 subunit amino acid sequences of new variants to the constructed protein database, the detection of SARS-CoV-2 variants could be achieved.…”

Discriminative Identification of SARS-CoV-2 Variants Based on Mass-Spectrometry Analysis

“…This study evaluates the analytical method’s sensitivity for synthetic theoretical variant peptides, however this approach was not examined using cell-cultured SARS-CoV-2 variants. Variant detection is not only dependent on the prototypic peptides’ properties but also on the efficiency of variant tryptic digestion process and the highly complex background noise from the matrix of the cell-cultured virus [ 22 ]. Considering the current and probable future state of the growing repertoire of SARS-CoV-2 protein mutations, a method combining the universal detection of SARS-CoV-2 with the specific identification of SARS-CoV-2 variants would be valuable.…”