Introduction: Human and Simian Immunodeficiency Viruses

HIVs, the causes of acquired immune deficiency syndrome (AIDS), are closely related to simian (monkey and ape) immunodeficiency viruses (SIVs). These and other similar viruses are retroviruses. Retroviruses are characterised by their RNA genomes, which once inside a host cell, are reverse transcribed into DNA and then integrated into the host cell's genome. The integrated viral genome is known as a provirus. You will be working with proviral DNA sequences.

The origins of HIVs were mysterious when these viruses were first discovered in the early 1980s. There are two types of HIVs. HIV type 1 (HIV-1) is more widespread and causes more severe disease than HIV type 2 (HIV-2). HIV-1 is also far more diverse than HIV-2. HIV-1 is classified into three major groups: M, N, and O. The viruses causing the AIDS pandemic (widespread epidemic) belong to Group M. Group M is subdivided into several subtypes. You will be analysing sequences from HIV-1 Group M Subtypes A, B, C, D, F, G, H, J, K. The HIV-1 viruses infecting people in North America, Europe and Australia are mostly from Group M Subtype B. All groups and subtypes of HIV-1 and HIV-2 are found in Africa.

Both HIV-1 and HIV-2 are closely related to SIVs found in a variety of African primate species. This lead early on to researchers hypothesising that HIVs had jumped to humans from one or more African primate species. It was suggested that close contact between humans and monkeys that were kept as pets or hunted for food had allowed the SIVs to jump hosts. In this tutorial you will use molecular phylogenetics to determine the evolutionary relationships of HIVs and SIVs, and so determine from which African primates HIVs originated.


Next Page: The Sequences

Phylogenetics: Build a Phylogeny of HIVs and SIVs
Exercise 2: Molecular Phylogenetics of HIVs and SIVs
Exercise 3: The Origin of the HIV-1 Pandemic