A total of 240 stored serum specimens from 30 transfusion recipients and 120 blood donors from the TransfusionTransmitted Viruses Study (TTVS) were evaluated with the objective of establishing transmission of hepatitis C virus (HCV) by specific blood donors. Phylogenetic analysis of hypervariable region 1 (HVR1) and HCV genotyping were performed on the genomic region encoding amino acids 329 to 410. Amino acid distances between HVR1 sequences were calculated by the Kimura formula. Bootstrap analysis of HVR1 sequences provided support for linking recipients to specific donors. Linear regression analysis showed no differences between donor and recipient HVR1 sequences 7.9 weeks posttransfusion, but donor and recipient sequences diverged thereafter (r ؍ 0.690). The initial lag phase in the evolution of HVR1 in the infected recipient was attributed to the time required to mount host immunologic defenses against the virus. Within-recipient divergence in HVR1 was determined from analyses of serial specimens collected within 2 weeks after the alanine transaminase peak, at the end of the original study (1974)(1975)(1976)(1977)(1978)(1979), and in the follow-up study (1987-present). HVR1 remained invariant over a period of 6.7 to 9.5 days (95% CI) during acute infection. Within-patient divergence in HVR1 increased over a period of 11 to 15 years (r ؍ 0.771), reaching the degree of divergence observed between unlinked subjects. In cases in which transfusion involved more than one HCV subtype, only one of the HCV subtypes established infection in the recipient. Subtype-specific differences in HVR1 were shown. (HEPATOLOGY 2001;34:424-429.)Transmission of RNA viruses from one individual to another may result in selection of one viral quasispecies over another possibly as the result of a different set of host immune pressures. In reports of single source outbreaks, analyses of the envelope genes of human immunodeficiency virus type 1 (HIV-1) or hepatitis C virus (HCV) showed that the viral quasispecies in the recipients usually differed from each other and from that of the source. [1][2][3][4] The inference that the virus established in a given recipient differed from the source virus is not as simple as it appears, for several reasons. The genomic region of the virus that is used to detect differences in viral quasispecies may be critical. Hypervariable region 1 (HVR1) has been used in the study of HCV transmission on the supposition that a very high degree of diversity affords a better chance of distinguishing one viral species from another. 4 In fact, studies on HIV-1 transmission showed that the viral genomic region displaying the highest degree of diversity was less informative for showing transmission than a region that showed a lesser degree of diversity. 5,6 Moreover, the time elapsed between the transmission event and the collection of sample from the recipient may be critical in the application of sequence analysis to the study of virus transmission. HVR1 can encode peptides that generate neutralizing antibodies...