Early Nef/Env mutations may determine elite control in ΔGY infection. (A) Average viral loads of ΔGY-controllers and ΔGY-non-controllers. Curves diverge at day 21 after infection (double arrows). (B) Location of mutations. Nonsynonymous mutations (black lines) were observed in plasma virus in ΔGY-controllers and ΔGY-non-controllers. 5–50 sequences were examined per time point. Only mutations reaching a frequency (fn) of >20% at ≥1 time point(s) are shown. (C–K) Time course for appearance of mutations in plasma virus in ΔGY-non-controllers (C–E) and ΔGY-controllers (F–K). The shaded area indicates the 21 days before divergence of the plasma SIV RNA values (double arrows). Double lines indicate mutations affecting 2 ORFs. Only mutations reaching a frequency of >20% are shown. aa, amino acid.