Next-Generation Sequencing (NGS) Based Detection of Viral Pathogens

Viral diseases are some of the most widespread causes of human death worldwide. Diagnosis of the pathogenic viruses using next-generation sequencing (NGS) technologies can play a vital task in dealing with the global viral epidemics. NGS based diagnostic approaches are more sensitive and efficient compared to traditional methods. NGS technology has the capability to screen multiple pathogens simultaneously as well as identify quasispecies and new or previously unknown viruses. Bioinformatics analysis and interpretation of high throughput sequencing datasets can help in screening different samples or products for viral contamination. Besides, it also allows an in-depth phylogenetic analysis which can predict the pathogenicity and potential host range of the virus. Dedicated bioinformatics analysis pipelines are now available for automated identification of viruses and their integration sites in the host genome from clinical samples using NGS data. This review will focus on the different applications of NGS to viral diagnosis.