Introduction

Viral genome information can be used to investigate viral pathogenesis and evolution as well as assisting in vaccine development and the study of vaccine resistance. Viral mutations can now be explored in detail by characterizing viral genomes from different hosts or even within a single individual. For example, thousands of SARS-CoV-2 variants have been discovered in the past two years, including several “variants of concern” that have been identified by the World Health Organization at the time of this ebook’s publication.

The identification and characterization of viral genome strains is now a routine task thanks to advancements in read sequencing technology and sequence assembly and analysis software. Thousands of viral genomes have been published, with more being added daily.

But while the task of viral genome analysis may be routine, many researchers find it frustrating and time-consuming. DNASTAR recently surveyed over 100 virologists and genomics researchers about the challenges they face in identifying and characterizing viral samples. They pointed out several shortcomings in most assembly and analysis software as a significant barrier to easily performing this workflow.

This ebook will guide you through the process of viral genome sequencing and characterization: from choosing a sequencing strategy for templated or de novo assembly, through downstream analysis. It will also show the results from our survey, including a discussion of the top challenges faced by virologists performing this important work.