Proviral nef sequence analysis of the cases. (A) nef sequences obtained from C1 to C3 are aligned with the clade B consensus sequence. Dots indicate identity with the consensus sequence; dashes, gaps; and asterisks, stop codons. Sequence variations in C1 and C2 occurred in regions of common length polymorphisms. Premature stop codons occurred in all 5 sequences obtained from C3 and were not due largely to G to A hypermutation. (B) A phylogenetic tree of nef sequences from 3 cases (C1, ×; C2, †; C3, ★) and other chronically infected patients from another study (M.S., personal communication), including conventional LTNPs/ECs (black circles), viremic progressors (solid black upward turning arrow heads), and Rx<50 (solid black downward turning arrow heads) was constructed for each patient by classic, maximum-likelihood and Bayesian methods. Other clade subtype nef sequences are included for comparison.