Molecular Fingerprinting of the Omicron Variant Genome of SARS-CoV-2 by SERS Spectroscopy

Abstract

The continuing accumulation of mutations in the RNA genome of the SARS-CoV-2 virus generates an endless succession of highly contagious variants that cause concern around the world due to their antibody resistance and the failure of current diagnostic techniques to detect them in a timely manner. Raman spectroscopy represents a promising alternative to variants detection and recognition techniques, thanks to its ability to provide a characteristic spectral fingerprint of the biological samples examined under all circumstances. In this work we exploit the surface-enhanced Raman scattering (SERS) properties of a silver dendrite layer to explore, for the first time to our knowledge, the distinctive features of the Omicron variant genome. We obtain a complex spectral signal of the Omicron variant genome where the fingerprints of nucleobases in nucleosides are clearly unveiled and assigned in detail. Furthermore, the fractal SERS layer offers the presence of confined spatial regions in which the analyte remains trapped under hydration conditions. This opens up the prospects for a prompt spectral identification of the genome in its physiological habitat and for a study on its activity and variability.

Raman Fingerprints of SARS-CoV-2 Omicron Subvariants: Molecular Roots of Virological Characteristics and Evolutionary Directions

“…As previously shown for other SARS-CoV-2 variants, , the RNA Raman fractions do not generally match those obtained by genome analyses because of the combined effects of base-pairing, signal cross sections, and differences in viral nucleoproteins associated with preferential RNA sites . Such amplified differences in RNA-bases-related Raman signals is indeed a very fortunate circumstance since they enable viral speciation down to the subvariant level without the need of RNA sequencing and within a very short time of a Raman measurement (i.e., in the order of minutes). ,, …”

“…127 Such amplified differences in RNA-bases-related Raman signals is indeed a very fortunate circumstance since they enable viral speciation down to the subvariant level without the need of RNA sequencing and within a very short time of a Raman measurement (i.e., in the order of minutes). 33,34,128 The interaction between RNA viruses and host innate and adaptive responses represents a quite complex issue whose underlying mechanisms are generally multifactorial and conspicuously hidden in the details of enzymatic chemistry. Based on bioinformatics studies, 129,130 it has been suggested that RNA viruses are capable of adapting their genome to inhibit and divert the innate cell defenses beyond the process of merely coding it for developing structural and nonstructural proteins for virion assembly and genome replication.…”

Ion-Mediated Protein Stabilization on Nanoscopic Surfaces

“…The data processing such as background subtraction and smoothening was performed using the second derivative and adjacent averaging method, respectively, present in the Origin 2020b software . The amide I region was deconvoluted by fitting Voigt profiles corresponding to the expected amide I vibrations of individual secondary structures, as reported elsewhere. , …”

“…39 The amide I region was deconvoluted by fitting Voigt profiles corresponding to the expected amide I vibrations of individual secondary structures, as reported elsewhere. 40,41 Computational Methods. The crystallographic structure of Lyz was taken from the RCSB protein data bank (PDB ID 1AKI).…”

Fast, low-cost and highly specific colorimetric RT-LAMP assays for inference of SARS-CoV-2 Omicron BA.1 and BA.2 lineages

“…Although sensitive, the process of conjugating gold nanoparticles and antibodies takes more than three hours, and the total analysis requires at least 40 minutes. Leonardi et al (2022), 27 explored surface-enhanced Raman scattering (SERS) to reveal, for the first time, the vibrational fingerprints of the genome of the SARS-CoV-2 Omicron variant. Silver dendrites allowed quick and univocal discrimination of this variant through vibrational evaluations.…”