This study analyzed biochemical modifications in cells due to SARS-CoV-2 infection using confocal Raman microscopy, comparing them to measles virus infection. A virus-specific Raman molecular signature was identified, enabling distinction between infected and non-infected cells with high accuracy (98.9% for SARS-CoV-2, 97.2% for measles). Increased tryptophan levels were observed in SARS-CoV-2-infected cells, suggesting a potential new biomarker for COVID-19. This research demonstrates the application of Raman spectroscopy for studying virus-host interactions and identifying therapeutic targets.