Abstract

Pox viruses (Poxviridae) are a large family of viruses, and members of it have various vertebrate and arthropod species as their natural hosts. The most widely known species in the family are the now extinct variola virus from the genus orthopoxvirus as the cause of smallpox, and vaccinia virus, a related, likely horsepox virus, which served as the source for the smallpox vaccine that allowed eradication of that disease.

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• Which special challenges does one encounter during sequence data analysis of pox viruses?
• How can standard workflows for viral mutation calling and consensus generation be adapted to the particularities of pox viruses?
• How can viral consensus sequences, multiple-sequence alignments and mutation calls be generated from each other and used to answer questions about the data?

Learning Objectives

• Learn how to deal with pox virus genomes inverted terminal repeats through a combination of wet lab protocol and tailored bioinformatics
• Construct a sample consensus genome from mapped reads
• Explore a recombinant pox virus genome via a multiple-sequence alignment of consensus genome and references and through lists of mutations derived from it