Complex association of human host and pathogenic viruses makes a necessity to understand the overall host and virus interaction network. Identification of virus population and its systematic classification will help in understanding the viral association with the disease outcome. Metagenomics is a recently developing approach for the detection of pathogens in the samples with precise interpretation in a short period of time. Metagenomic approaches have been employed for studying the predominance or spread of the virus within a particular locality and nature of virus during infection. Metagenomics is basically a collective approach of lab-based techniques and in-silico methods for identification of pathogenic viruses without culturing them in specific aseptic conditions. Lack of unique conserved genes in viruses has made metagenomics study difficult in this juncture. Other challenges in the field of metagenomics are like cellular DNA contamination, free environmental DNA contamination and continuous evolution of viruses. Recent studies have shed light on the advancement of this field in virus identification and characterization however still needs further investigations to overcome the challenges. Current chapter focuses on the application and challenges faced in metagenomic analysis of human viral infections.
Part of the book: Metagenomics for Gut Microbes