Recent advancement in next-generation sequencing (NGS) technologies hasrevolutionized the sequencing technology for research and diagnostic applications by virtue of its high throughput and accuracy of data generation. In animal virology, NGS has been successfully used formetagenomicsbased discovery of previously unknown viruses. Moreover, NGS technologies are alsoemployed for study of viral dynamics and genetic characterization of viral genomes.The absenceof proof reading during genome replication inseveral viruses along with high replication rate, results in formation of several genetically related viral variants known as quasi-species which in turn, got selected and established itself as new virus variant by antiviral drugs or immune system itself. The identification ofviral quasi species havingbiological significance is difficult using conventional sequencing approach. However, NGS may provide exact sequence information about these virus clones. NGS is a powerful tool to investigate deeper insights ofvirus activities such as viral genetic diversity, vaccine candidate selection, identification of viral reservoirs in nature, re-emergence of viral disease after treatment interruptions, development of drug resistance etc. Keywords: Virus, NGS, Ion Torrent, Illumina sequencing