Denaturing gradient gel electrophoresis (DGGE) was used to study the diversity of hepatitis C virus (HCV) quasispecies. Optimized DGGE running conditions were applied to screen for variations in sequences cloned from amplicons originating from the nonstructural 5b (NS5b) gene of HCV in blood of hemophilia patients, intravenous drug users, and blood donors (five specimens from each study group, ca. 40 clones studied per specimen). Clones identified by DGGE as unique were sequenced. NS5b sequence entropy and mean genetic distance in hemophiliacs did not differ significantly from those in the other groups, pointing to a lack of correlation between HCV diversity and the multiplicity of past HCV exposures. DGGE was also applied to investigate variation in the HCV envelope 2/hypervariable region 1 (E2/HVR-1) in serum samples serially taken from two patients during the seroconversion phase of HCV infection. E2/HVR-1 sequence entropy changes were small and not correlated with rising anti-HCV antibody levels, reflecting mutational changes not mediated by antibody selection.Most studies assessing the diversity of hepatitis C virus (HCV) quasispecies are conducted by amplifying selected portions of the genome by PCR, isolating individual subgenomic fragments by a cloning procedure, and then characterizing the nucleotide sequence of each clone (15,17,20). Evaluating the diversity of HCV quasispecies in clinical specimens often requires the sequencing of a large number of clones. Less onerous procedures, e.g., those that analyze single-strand conformation polymorphism and heteroduplex mobility of PCR amplicons, have been described (11,18,26). We have developed an alternative procedure based on denaturing gradient gel electrophoresis (DGGE) (10) that permits intrahost HCV genetic diversity to be screened more comprehensively.In the DGGE procedure, double-stranded (ds) DNA is electrophoresed through an acrylamide gel containing a gradient of denaturant that increases in the direction of electrophoresis. The DNA molecules melt when they reach a part of the gel that is sufficiently denaturing. At this position, denaturation starts to occur at melting domains of the molecule. As electrophoresis proceeds, conditions become more denaturing and more domains melt. Single-stranded domains, as they are formed, retard the movement of the DNA through the gel matrix. Sequence differences of as little as 1 base can dramatically alter the stability of the melting domains. However, at positions of the gel where the concentration of denaturants is high, DNA can become completely single stranded and the migration is no longer dependent on sequence. To prevent complete denaturation of ds DNA, a "GC-clamp" is attached to one of the PCR primers, facilitating the detection of mutations along the whole length of a DNA molecule (23). The sensitivity of DGGE in distinguishing between mutations is highly dependent on the quality of the gradient gels and the differences in migratory positions of DNA molecules and is not necessarily related to the numbe...