To assess whether Raman spectroscopy with spectral barcoding can distinguish RNA from SARS-CoV-2 variants and subvariants.
Approach:
Samples: Researchers analyzed extracted RNA from the original Japanese isolate and 19 variants or subvariants, including 12 Omicron subvariants.
Measurement: A confocal Raman spectrometer with a 532-nm laser collected spectra across 400–1,800 cm⁻¹; 10 measurements from different locations were averaged for each sample.
Analysis: The team computationally deconvolved overlapping spectral bands and converted selected features into barcodes, then compared results with predicted RNA secondary structures.
Key Findings:
Raman barcodes differed across all 20 samples, while principal component analysis distinguished only some strains.
Spectral differences were associated with RNA backbone conformation, phosphate bonds, base pairing, and secondary structure.
Signals near 432 and 1,460 cm⁻¹ were associated with structural features including hairpin-loop number and stem length.
The method detects structural effects of sequence variation; it does not sequence RNA or identify individual nucleotide substitutions.
Interpretation:
The authors presented Raman analysis as a potential complement to next-generation sequencing for studying viral RNA structure, not as a replacement.
Limitations:
The proof-of-concept study used a finite set of purified RNA samples from cell-culture supernatants.
Recognition of previously unseen variants or strains differing by only a few mutations remains unknown.
Performance with clinical specimens containing host material and variable viral RNA concentrations has not been tested.
