Among standard and molecular approaches currently used for diagnosis of sexually transmitted infection (STI), sensitive high throughput techniques (HTS) based on the random amplification of genomes including microarrays and high throughput sequencing have enabled significant contributions to multiple areas in virology, including virus discovery, molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. By overcoming conventional methods of viral identification, metagenomics, which gives access to all nucleic acids present in a given sample, allows the description and characterization of biological sample viral communities including unknown or variant of viruses associated with several human diseases. Although the application of viral metagenomics to clinical samples is made difficult by the fact that viral sequences represent a very low proportion compared to host DNA sequences. Leading to the requirement of high depth of sequencing and intensive bioinformatics analyses to increase the probability of virus detection, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here we focused on the use of new approaches to viral STI diagnosis including the current deep sequencing platforms, based on the recent available data.
