Fundamentals of Viral Genomics

Description

In this four part short course, Steph Lunn introduces the molecular microbiology and genomics of viral pathogens, including:

  • Why molecule biology concepts are relevant to understanding viral genomics
  • What do viral genomes look like, what are viral replication strategies, and what information is encoded in a viral genome?
  • Viral genome evolution: assumptions of viral genomes, reassortment, recombination, mutation, selection, and evolution
  • Viral genome diversity: the diversity of viral genomes, sense of viral genomes, and the reproductive life cycle of a virus and how it can impact the genomic epidemiology, surveillance, and sequencing
Learning Objectives

Part I: Molecular Biology of Viral Genomics

  • Briefly explain why molecule biology concepts are relevant to understanding viral genomics
  • Define the dogma of molecular biology as it relates to the flow of genetic information
  • Connect the concepts of replication, transcription, and translation as it relates to virus biology and the changes that we could see in the genome
  • Describe features of DNA
  • Discuss directionality and explain its importance and relevance to viral genomics
  • Briefly summarize the processes of replication, transcription, and translation

Part II: Viral Genome Overview

  • Discuss the type of genetic material viruses can be made of
  • Give some examples of viral genome structures
  • Explain how classifying viruses by replication strategies can be beneficial to understanding viral genomes
  • Discuss what makes viral genomes compact and efficient
  • Discuss how viral genomes are a biological parts list
  • Provide some examples of information that is encoded in a viral genome and what information is not encoded in a viral genome

Part III: Viral Genome Evolution

  • Discuss how genetic variation can occur in viruses
  • Discuss the impact of reassortment on analyses
  • Define mutation rate and why it’s difficult to quantify
  • Discuss how genome sequences can allow us to infer an estimate of the substitution rate
  • Briefly explain how evolution can change viral populations, and how viral genomes evolve in response to selective pressure
  • Give examples of how viral genomes can adapt to host interactions

Part IV: Viral Genome Diversity

  • ­Explain how viruses can be diverse, and why understanding the biology of the viral pathogen you’re working with impacts how you think about and use the data
  • Explain how “sense” relates to viral genomes
  • Distinguish between positive-sense RNA and negative-sense RNA
  • Discuss some genomic elements of viral genomes
  • Discuss how families of viral groups can be similar and different in genome organization
  • Describe how the reproductive life cycle of a virus impact the changes we see in the genome
  • Discuss how whole genome sequencing only manages to capture a fraction of viral diversity