Detection of SARS CoV-2 coronavirus omicron variant with mass spectrometry

Abstract

Mass mapping using high resolution mass spectrometry can rapidly distinguish the omicron variant of the SARS-CoV2 coronavirus strains from other major variants of concern based on insertions, deletions and mutations within the surface spike protein.

Distinguishing common SARS-CoV2 omicron and recombinant variants with high resolution mass spectrometry

“…Mass spectrometry represents a useful and complementary approach for the molecular detection of infectious disease causing viruses. In particular, the role of high resolution mass spectrometry in the differentiation of SARS-CoV2 variants and sub-variants with high confidence 21,22 provide a broad framework for the implementation of a clinical analytic approach that offers benefits over lower resolution, low mass accuracy conventional MALDI-TOF or QTOF, and time and higher sample consuming LC-ESI-MS strategies 26 where liquid chromatographic separation and tandem MS/MS sequencing steps are necessary. 29 Even when so-called selective reaction monitoring (SRM) or multiple reaction monitoring (MRM) is employed, establishing precursor and fragment ion pairs that are efficiently produced and detected must be determined a priori, and the fragmentation (reaction) time and efficiency of peptide fragmentation remains a limitation.…”

“…20 Given the SARS-CoV2 virus contains a single genome segment, rather than a segmented one in the case of influenza, evidence for reassortment can be uncovered using this simpler viral protein strategy that identifies unique peptide biomarkers. These derive from the accumulation of multiple spike protein mutations that originate from different variants 21,22 and combine into a single recombinant form. Those that are ionised and detected in expressed spike protein forms can be used to detect and distinguish recombinant viruses in proteolytically digested whole virus clinical specimens.…”

Detection of Mutant Peptides of SARS-CoV-2 Variants by LC/MS in the DDA Approach Using an In-House Database

“…The major challenge to all types of detection methods arises with the emergence of variants that results in the escape of the virus from testing and raises the need for the re-assessment of testing methods. Predominantly, the MS-based studies have shown the identification of viral peptides belonging to the protein sequence of the SARS-CoV-2 Wuhan strain available on UniProt, very few studies have considered the SARS-CoV-2 variants. − In those studies, either the targeted assay was designed using the genome sequencing information or the mass mapping method was used for variant peptide detection employing MALDI. The unavailability of protein sequences of the variants in popular peptide search tools like UniProt limits the scope of the mutational studies and variant detection of SARS-CoV-2 using mass spectrometry.…”

Charting and tracking the evolution of the SARS CoV-2 coronavirus variants of concern with protein mass spectrometry

“…15 Here we investigate its ability to chart and study the evolution of SARS-CoV2 for over 3000 strains of the virus and distinguish major variants of concern on the tree by means of identifying the presence of variant-specific peptide markers. 16…”