Human cytomegalovirus (HCMV) is a well known hallmark of increasing morbidity and mortality in humans with acquired impairment in innate and adaptive immunity indicating high seroprevalence rate of 83%. This study aims to identify novel drug targets as disease biomarkers in HCMV-infected hosts. Thereby datasets were collected from NCBI SRA Database and were further analyzed through RNA-seq pipeline to identify differentially expressed genes between HCMV-infected hosts and healthy individuals. Subsequently functional enrichment analysis of highly significant genes was performed through enrichR. RNA-seq analysis identified 1974 differentially expressed genes in HCMV-infected hosts including 678 over-modulated and 1028 down-modulated genes. Nevertheless, present DGE analysis study has reported novel drug targets including 5 protein-coding genes (RRAGD, SPINK1, NAP1L2, PKIG and LXN) and 2 pseudogenes (EEF1A1P38, WFDC21P). Additionally dysregulated genes have been found to be highly enriched in immune system related biological processes mainly Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, PI3K-Akt signaling pathway, TNF signaling pathway and IL-17 signaling pathway indicating positive correlation between dysregulated immune-system mechanisms and HCMV replication. Hence this study has proposed novel therapeutic targets for early detection and treatment of HCMV infection that would positively influence public health. However wet laboratory explorations are required to ensure safety and efficacy of proposed drug targets.