In this article, a novel approach is proposed to detect the concentration of virus with different refractive indices in saliva using 2-D photonic crystal (PC) structures. The proposed $18\times17$ hexagonal PC structure consists of air holes in a silicon slab with silicon-on-insulator (SOI) techniques. The plane wave expansion (PWE) method is used to find the photonic band gap (PBG). The mid-gap wavelength of PBG increases linearly with a refractive index (RI) of infiltrated samples in air holes. The change in PBG size increases linearly by an average slope of 4.45 with respect to the change in RI concentration. The proposed sensor exhibits a maximum sensitivity of 1206.4 nm/RIU for 100% concentration of virus and minimum sensitivity of 950.4 nm/RIU for 0% concentration of virus with an ultra-fast average response time of 10.6 fs to test the samples. The present work can be useful for sensing variation in bio-molecular RI and other infection’s presence in various biological targets at an early stage.