99480 - Viral Genetics and Genomics

Learning outcomes

At the end of the course, the Student knows the characteristics of viruses and sub-viral agents and their peculiarity in the biological world. The Student knows the basics of the biology of viruses and their interaction with host cells; the organization of viral genomes and replicative strategies of different classes of viruses; the theories of the origin of viruses; viral genome evolution; the technologies for viral genome engineering; the applications of genetically engineered viruses; the applications of viral genomic information in epidemiology and outbreak tracing and prediction.

Course contents

PART 1
INTRODUCTION
Viruses defined, the criteria of virus classification, virus structure and composition.
The phases of the viral replication cycle.
Viral growth curve. Methods of virus culture and identification.
Different outcomes of virus infection: productive, abortive, persistent and latent infections. Mechanisms of virus entry into the host cell and transport of subviral components to different cellular compartments.

VIRAL GENETICS
The viral replicative groups I-VII (Baltimore system).
Replication and gene expression strategies in relation with the organization of the viral genome (RNA viruses with positive or negative polarity, monopartite or segmented genomes; retroviruses, hepadnaviruses; DNA viruses with double-stranded or single-stranded genome).
Genetic economy strategies.
Subviral agents, definitions and properties: viroids and satellites.


PART 2
VIRUS GENOME EVOLUTION
Origin of viruses.
Origin of diversity in virus genomes.
Mutations rate versus genome stability and/or size.
Viral quasispecies.
Paleovirology.
Endogenous retroviruses and non-retroviral integrated genomes.
Emerging viruses.
Pandemic viruses.
VIRUS GENOMICS
The macro-evolution perspective: understanding the virosphere (virus origin, genome evolution, evolution time scales, and virus-host interactions)
Applied perspective: epidemiologic transmission and pathogenesis of viral infections; patient management and public health; prediction of virus emergence.
Resources and applications for viral genomics.
VIRUS GENOME ENGINEERING
Recombineering technologies, infectious cDNA clones, replicon systems.
Applications of genetically engineered viruses (phages, animal viruses, plant viruses).
Viruses and nanotechnologies: virus-based nanoparticles.


PART 3
Group activities and seminars on updated literature.
Invited seminar lectures.

Readings/Bibliography

Principles of Virology, 4th Edition (2015), S.Flint et al, ASM Press.

"FIELDS Virology", Sixth Edition, Lippincott Williams & Wilkins, 2013.

Online resources (NCBI, ViralZone, etc.).

Teaching methods

Classroom lectures with Powerpoint presentations
Interactive lectures, polls
Self-evaluation tests
Group activities
Student Journal Clubs

Assessment methods

The exam consists in written tests and the evaluation of the Student Journal Club presentation. The dates of the written tests will be published on AlmaEsami.

Teaching tools

Power-point presentations
Multimedia (movies)
Online polls

Office hours

See the website of Laura Menotti