Types of analyzed amino acid substitutions in the pool of viral quasispecies over time.

A: Viral mutations by their relationship to HIV-1 wild type. Number at the top of each graph indicates amino acid position in Gag, and is followed by frequencies of observed amino acids in the extended HIV-1 subtype C consensus. Dynamics of Asn at amino acid position 242 represents escape mutation from the wild type virus, and is delineated by circled E with arrow. Kinetics of Lys at position 302 demonstrates reverse mutation to the wild type virus. Viral mutation at position 28, Arg-to-Lys substitution, occurs without involvement of the wild type virus, and therefore, is interpreted as escape from non-wild type. B: Viral mutations by their fraction in the pool of viral quasispecies are classified as minor (position 186), dominant (position 114), complete (position 370), or transient (position 419). Number at the top of each graph stays for the amino acid position in Gag followed by the most common amino acids in the HIV-1 subtype C consensus, which is used to identify escape from and reversions to wild type virus. Circled letters with arrows indicate reverse mutations to and escape mutations from HIV-1 subtype C wild type. C: Viral mutations by their presence in the earliest pool of viral quasispecies are classified as de novo mutation (position 146), or pre-existing mutation (position 278). Circled letters with arrows indicate escape or reverse mutations.