Heterosexual Transmission of Subtype C HIV-1 Selects Consensus-Like Variants without Increased Replicative Capacity or Interferon-α Resistance
(A) Nucleotide sequences for all 115 single genomes amplified from six linked transmission pairs were aligned to the curated LANL consensus/ancestral alignment and a maximum likelihood tree was generated. (B) Single genome nucleotide sequences for each viral gene (gag, pol, vif, vpr, vpu, tat, rev, env, & nef) were translated to their amino acids and then concatenated. These were aligned with LANL consensus/ancestral concatenated protein sequences and a maximum likelihood tree was generated. Transmitted/founder sequences from linked recipients are in blue, donor non-transmitted variants are in red, LANL database curated consensus/ancestral sequences are shown in black, where the LANL subtype C consensus is indicated by a green circle. Black arrows indicate virus variants from the donor quasispecies that were selected for generation of non-transmitted (NT) infectious molecular clones.