Monitoring the evolution of human immunodeficiency virus type 1 (HIV-1) drug resistance requires measuring the frequency of closely related genetic variants making up the complex viral quasispecies found in vivo. In order to resolve both major and minor (>2%) protease gene variants differing by one or more nucleotide substitutions, we analyzed PCR products derived from plasma viral quasispecies by using a combination of denaturing gradient gel electrophoresis and DNA heteroduplex tracking assays. Correct population sampling of the high level of genetic diversity present within viral quasispecies could be documented by parallel analysis of duplicate, independently generated PCR products. The composition of genetically complex protease gene quasispecies remained constant over short periods of time in the absence of treatment and while plasma viremia fell >100-fold following the initiation of protease inhibitor ritonavir monotherapy. Within a month of initiating therapy, a strong reduction in the genetic diversity of plasma viral populations at the selected protease locus was associated with rising plasma viremia and the emergence of drug resistance. The high levels of protease genetic diversity seen before treatment reemerged only months later. In one patient, reduction in genetic diversity at the protease gene was observed concomitantly with an increase in diversity at the envelope gene (E. L. Delwart, P. Heng, A. Neumann, and M. Markowitz, J. Virol. 72:2416-2421, 1998), indicating that opposite population genetic changes can take place in different HIV-1 loci. The rapid emergence of drugresistant HIV-1 was therefore associated with a strong, although only transient, reduction in genetic diversity at the selected locus. The denaturing gradient-heteroduplex tracking assay is a simple method for the separation and quantitation of very closely related, low-frequency, genetic variants within complex viral populations.The short generation time, high mutation rate, and large population size of human immunodeficiency virus type 1 (HIV-1) make it one of the fastest evolving viruses known (2, 3). Genetically complex HIV-1 quasispecies rapidly evolve following generally clonal primary infection in men (7,25,46,49,50). In women, heterosexually acquired HIV-1 appears more genetically diverse than in men (23). In the absence of selection, drug-resistant mutants are expected to be of lower replicative fitness than wild-type viruses and therefore are only expected and actually detected as minority variants (2, 3, 19, 31). Antiviral drug selection can then rapidly drive such mutants into the majority. The analysis of HIV-1 quasispecies in vivo is needed to improve our understanding of the complex viral population changes associated with such rapid evolution. Detailed analysis of differentiated viral populations is complicated by several factors. Low-frequency variants are difficult to detect by direct population sequencing of PCR products (45), while a subcloning and sequencing approach will focus sequencing on the most frequent...