HIV Evolution: Fast or Slow?

Abstract

It is known that in the human immunodeficiency virus (HIV) genome regions responsible for interactions with the host's immune system, namely, cytotoxic T-lymphocyte (CTL) epitopes, tend to be clustered together, sometimes found in more conserved parts of genome. On the other hand, more variable regions tend to have lower density of CTL epitopes. Furthermore, high recombination rate, coupled with high mutation rate, results in overall high diversity of HIV sequences, which is expected to result in little if any association between different regions of a genome. Or is it not? Employing data mining technique, we show that indeed some rather strong associations between different regions of HIV genome can be detected, even when circulating recombinant forms are considered. This can partly be attributed to strong functional constraints acting on protein sequences and certain CTL epitopes regions in particular.