The HIV Infection model -- The CTL Model -- Simulating an HIV Infection In Vivo -- The Escape Formula -- Early and Late Escapes -- Understanding Escape -- More Topics about Escape from Immune Control -- HIV's Cloaking Device: The Fascinating Story of Nef -- Retroviral Sex and Escape -- The Ne Business Again and a Proposed Experiment -- Can a T-cell Vaccine Block Escape? -- The STEP Trial and the Future of T-cell Vaccines -- Short Tutorial on Dynamical Models -- Deterministic Modeling: A Cautionary Example -- The Infection Model Defined -- The CTL Model Defined -- On Simulation Techniques -- Derivation of the Escape Formula -- Statistics of the Mutant Lineage in Classical Genetics -- Extinction Probabilities with Extra Poisson Variation -- Computing the Boundaries -- Co-existence or Replacement? -- The Nef-Deletion Threshold Formulas -- Modeling Retroviral Sex.

In the relatively few decades since the introduction of HIV into the human population, variants of the virus have diverged to such an extent that, were the discussion about something other than viruses, said variants could easily be classified as different species. This book will consider these evolutionary variations, as well as the different and, at times, opposing theories attempting to explain them. It will compare and contrast the ways in which the immune system and drugs affect the virus's evolution, and the implications of these for vaccine development. The issue will be explored and explained through "ecological genetics," which postulates that all living organisms have, besides rivals, enemies. This is divergent from the more traditional school of "population genetics," which emphasizes that evolution occurs among rival species (or variants thereof) that compete for niches or resources in a fixed, unreactive environment. Both models will be formulated using mathematical models, which will be included in the book. Finally, it will consider the possibilities for designing a vaccine that blocks HIV from escaping the immune system.