**Analysis of Next-generation Sequencing Data in Virology - Opportunities and Challenges**

Sunitha M. Kasibhatla, Vaishali P. Waman, Mohan M. Kale and Urmila Kulkarni-Kale

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/61610

#### **Abstract**

Viruses are the most abundant and the smallest organisms, which are relatively simple to sequence. Genome sequence data of viruses for individual species to populations out‐ number that of other species. Although this offers an opportunity to study viral diversity at varying levels of taxonomic hierarchy, it also poses challenges for systematic and struc‐ tured organization of data and its downstream processing. Extensive computational anal‐ yses using a number of algorithms and programs have opened exciting opportunities for virus discovery and diagnostics, apart from augmenting our understanding of the intri‐ guing world of viruses. Unravelling evolutionary dynamics of viruses permits improved understanding of phenomena such as quasispecies diversity, role of mutations in host switching and drug resistance, which enables the tangible measurements of genotype and phenotype of viruses. Improved understanding of geno-/serotype diversity in corre‐ lation with antigenic diversity will facilitate rational design and development of effica‐ cious vaccines against emerging and re-emerging viruses. Mathematical models developed using the genomic data could be used to predict the spread of viruses due to vector switching and the (re)emergence due to host switching and, thereby, contribute to‐ wards designing public health policies for disease management and control.

**Keywords:** Virus/viral evolution, population diversity, recombination, selection pressure, phylogeny and typing
