1. Obligate parasites of cells: Discovery
The virosphere and its metagenome
Complexity and "dark matter"
Selfish information and the essence of being viral
The emergence of egotistical replicators
The viral empire
2. Viruses, genes, and ecosystems: Lifestyles and life cycles
Lysogeny: exercising temperance
Kill the winner
Gene brokers
Selfishness driving adaptive evolution
Phages and the microbiome
Unfriendly competition
Chemical warfare
3. Potentiation of bacterial diseases by phages: For a charm of powerful trouble
Toxic enablers
Choose your poison
Treasure islands
Prophage induction and antibiotic drug resistance
4. Viruses and higher organisms: Viruses, cells, organisms, and populations
"Just a virus"
Human rhinoviruses
Uncommon diversity
Accidents of pathogenesis
Mutation, diversity, and quasipecies
5. The flu: no common cold: Antigenic escape artists
Human influenza a virus
Epidemic influenza: dress for the season
Quasispecies, sequence clusters, and codon bias
Correlating genetic and antigenic evolution
Seeding of seasonal epidemics
Pandemic influenza: the emperor with no clothes
6. Alternative virus lifestyles: Latency: 'til death do us part
All in the family Herpesviridae
7. Evolutionary mechanisms of DNA viruses: Gene duplication and gene capture
Poxvirus evolution
Poxvirus party tricks
Small DNA virus evolution
8. Viroids and megaviruses: extremes: Viroids: the smallest
Evolutionary reliquary
Megaviruses: the biggest
Big and bigger
Virophages: fleas upon fleas
Chimerism
Megavirus origins: mavericks at heart
10. HIV-1: a very modern pandemic: A new disease and a new virus
Anatomy of HIV-1
HIV in the making
Socioepidemiology of AIDS: a man-made epidemic
Within-host evolution: a very personal arms race
Short-sighted evolution
Adaptive evolution: an evolving relationship
Outrunning the red queen
Medicine at the virus-host interface
Resistance is futile
10. Cross-species infections: means and opportunity: A rogue's gallery of emerging viruses
Adaptive evolution in zoonosis
Fitness landscape
A shifting fitness landscape
The paradox in RNA virus evolution
RNA viruses and molecular clocks
Arboviruses: vector-borne viruses
Evolutionary compromise
Host restriction
11. Future pandemic influenza: enemy at the gates: Real and present danger
Pandemic threat level
The pandemic phenotype
Outbreak
12. Ebolavirus: EBOV Makona
What we were afraid to say about Ebola
Evolution or adaptive change
EBOV persistence
13. Viral zoonoses and animal reservoirs: The usual suspects
Filovirus origins
Bats and viral zoonoses
A special relationship
Tolerance and resistance
14. Endogenous retroviruses: our viral heritage: Genome invasion by retroviruses
Endogenization in progress
Change agents
Domestication of ERV genes
Endogenous viral elements
15. Viruses as human tools: Myxoma virus: biological control
Genomics of an attenuated poxvirus
Orthopoxviruses: past solutions and future problems
Live-attenuated viruses
Attenuation by design
Virus therapeutics
Doctor's little helpers
Oncolytic viruses
16. Humanity and viruses: The human future and viruses
Beauty in design.