ABSTRACT
In this chapter, we provide a basic introduction to human immunodeficiency virus (HIV) biology and evolution and highlight many applications of comparative genomics. The wealth of available HIV sequence data has been used to investigate the epidemic history, HIV transmission dynamics, and within-host evolution of the virus. Because of the clinical impact, the main focus of within-host evolutionary studies has been the development of resistance to antiviral drug treatment. Therefore, our discussion
12.1 Introduction .................................................................................................220 12.2 HIV Primer ................................................................................................. 221
12.2.1 HIV Biology .................................................................................. 221 12.2.2 HIV Genetic Variability ................................................................224 12.2.3 Drug Targets and Viral Drug Resistance ......................................224
