molecular diagnosis of viral infections

context: detection of causative pathogen is crucial for treatment strategies in most infections. molecular diagnosis as a more sensitive and specific method, has become the best option to investigate certain pathogens, mainly viruses. recent scientific and technological approaches resulted in changing the area of diagnostic microbiology. evidence acquisition: a comprehensive online search of data bases was done and all appropriate articles and documents retrieved were reviewed thoroughly and systematically. results: many new user-friendly commercial assays have been developed for this purpose. during recent decades, remarkable efforts have been made for genomes sequencing of micro organisms. investigation of nucleic acids in detection of variety of organisms related to infectious diseases such as nosocomial infections, sexually transmitted diseases, and immunocompromised host infections. conclusions: the most application of molecular techniques is in epidemiological and clinical investigations in viral infections such as hpv, genotyping for hcv and hiv resistance to viral polymerase inhibitors due to structural origin. recent approaches such as microarrays and next-generation sequencing are expected to have a huge impact in the next revolution of pathogen identification. in this review, we focused on the most recently molecular approaches in diagnosis of viral infection and their characteristics.