Homologous recombination, where the fragment of transferred genetic information replaces a homologous fragment within its destination DNA/RNA molecule, is important from an evolutionary perspective because within individual genomes it can both remove harmful mutations and facilitate the accumulation of beneficial mutations. By creating novel BAY-678 combinations of nucleotide polymorphisms homologous recombination can also enable far wider exploration of a sequence space than is achievable by mutation alone. Homologous recombination, hereafter referred to simply as recombination, features prominently in the evolution of many viruses. In these organisms recombination does not necessarily involve the breakage and re-ligation of DNA/RNA molecules. In retroviruses such as HIV, for example, it predominantly occurs when RNA copies of the viral genome are being reverse transcribed into DNA by the viral enzyme, reverse transcriptase. Every HIV virion contains two complete genomes and the reverse transcriptase will generally switch between these an average of approximately two to four times per replication cycle. If the two co-packaged HIV genomes are genetically different then such DMH2 template switching could yield a detectably recombinant genome. Although the capacity to recombine can provide viral species with a number of evolutionary benefits, many of the individual recombination events that occur between any particular pair of viruses will be deleterious; especially if they occur between distantly related genomes. By bringing together divergent genome fragments that have largely independent evolutionary histories, recombination can potentially cause disruptions in coevolved intra-genome interaction networks. Examples of intra-genome interactions include base-pairing interactions in RNA structures, sequence specific protein-DNA interactions, interactions between proteins and interactions between amino acids within three-dimensional protein folds. Natural selection should disfavour the survival of recombinant genomes in which such interactions are disrupted and it is therefore expected that patterns of recombination evident within circulating viruses might display evidence of such selection.