In recent decades, biomedical sensors based on surface-enhanced Raman spectroscopy (SERS), which reveals unique spectral features corresponding to individual molecular vibrational states, have attracted intensive attention. However, the lack of a system for precisely guiding biomolecules to active hotspot regions has impeded the broad application of SERS techniques. Herein, we demonstrate the irreversible active engineering of three-dimensional (3D) interior organo-hotspots via electrochemical (EC) deposition onto metal nanodimple (ECOMD) platforms with viral lysates. This approach enables organic seed-programmable Au growth and the spontaneous bottom-up formation of 3D interior organo-hotspots simultaneously. Because of the net charge effect on the participation rate of viral lysates, the number of interior organo-hotspots in the ECOMDs increases with increasingly positive polarity. The viral lysates embedded in the ECOMDs function as both a dielectric medium for field confinement and an analyte, enabling the highly specific and sensitive detection of SARS-CoV-2 lysates (SLs) at concentrations as low as 10-2 plaque forming unit/mL. The ECOMD platform was used to trace and detect the SLs in human saliva and diagnose of the delta-type SARS-CoV-2 in clinical environments;the results indicate that the proposed platform can provide point-of-care diagnoses of infectious diseases.