Before revision: The human immuno-deficiency virus sub-type 1 (HIV-1) is evolving to keep up with a changing fitness landscape, due to the various drugs introduced to stop the virus's replication. As the virus adapts, the information the virus encodes about its environment must change, and this change is reflected in the amino-acid composition of proteins, as well as changes in viral RNAs, binding sites, and splice sites. Information can also be encoded in the interaction between residues in a single protein as well as across proteins, leading to a change in the epistatic patterns that can affect how the virus can change in the future.
After revision: Epistatic interactions between residues in a single protein as well as across proteins, leading to a change in the epistatic patterns that can affect how the virus can change in the future.