HIV-1 Sequence Variation: Drift, Shift, and Attenuation

The introduction and global dissemination of the retrovirus human immunodeficiency virus type-1 (HIV-1) in humans represents a dramatic and deadly example of recent genome emergence and expansion; since the beginning of the pandemic, over 50 million people have been infected and over 16 million of those have died of AIDS. As with all RNA viruses, HIV-1 replication is characterized by very high mutation rates. Technical advances made in DNA sequencing and the recovery of rare nucleic acids from diverse sources have facilitated the sequencing of HIV-1 on a massive scale. These studies have revealed the remarkable genome plasticity and continuing diversification of HIV-1 strains; the significance of this diversity for viral pathogenesis remains a major question in the field.