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

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 outnumber 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 structured organization of data and its downstream processing. Extensive computational analyses using a number of algorithms and programs have opened exciting opportunities for virus discovery and diagnostics, apart from augmenting our understanding of the intriguing 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 correlation with antigenic diversity will facilitate rational design and development of efficacious 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 towards designing public health policies for disease management and control.

Sequencing of animal viruses: quality data assurance for NGS bioinformatics

“…deep sequencing) that we were unable to accomplish in our work. As reviewed in Quiñones-Mateu et al (2014) [42], this approach is being increasingly used in diagnostic laboratories, given the significance of VAF in human clinical virology [43]. It would be of great interest to implement this practice on a routine basis also for animal viruses, where the selection at viral population level of signatures implicated in immune evasion and host jump are particularly relevant [44–48].…”

Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology

“…Unfolding evolutionary dynamics of viruses enhances the understanding of quasispecies diversity and the involvement of mutations in drug resistance and host switching, enabling the genotypic and phenotypic characterization of viruses (Kasibhatla et al, 2016). Zhang et al (2011), with the aid of deep and whole-genome sequencing, reported Grapevine vein clearing virus (DNA virus) in six grapevine cultivars linked with the vein-clearing symptom for the first time in Indiana, Missouri, and Illinois, indicating its widespread distribution in the Midwest of the United States.…”

Are We Ready for NGS HIV Drug Resistance Testing? The Second “Winnipeg Consensus” Symposium

“…While HIV pol gene sequencing largely serves the needs for HIVDR genotyping, such sequencing data is often also applied in molecular epidemiology, such as cluster analysis. Thus far, NGS-based cluster analyses are largely based upon (1) NGS consensus sequences that simply mimic SS sequences; (2) reconstructed viral variants using quasispecies reconstruction tools that often perform poorly on HIV NGS data [ 56 , 57 ].…”