The R5 AIDS HIV-1 clone ACH142-*E11 Nef has a higher progression score than the Nefs from two patient ACH142 derived pre-AIDS R5 HIV-1 clones, 32D2 and 8G9. A Clustal W alignment of predicted Nef amino acid sequences is shown. Gaps in the alignment are represented by a dash. Bold amino acid residues represent changes of interest between isolates. Numbers above the alignment represent the amino acid position in this alignment. Bold, italicized residues were used to calculate the Nef progression score according to the method of Kirchhoff et al . Upper case bold italicized letters indicate residues that are more common in progressors. Lower case bold italicized letters indicate residues that are more common in non-progressors.