Longitudinal evaluation of the structure of replicating and circulating hepatitis C virus quasispecies in nonprogressive chronic hepatitis C patients

In previous cross-sectional studies, we demonstrated that, in most patients with chronic hepatitis C, the composition and complexity of the circulatin g hepatitis C virus (HCV) population do not coincide with those of the viru s replicating in the liver. In the subgroup of patients with similar comple xities in both compartments, the ratio of quasispecies complexity in the li ver to that in serum (liver/serum complexity ratio) of paired samples corre lated with disease stage. In the present study we investigated the dynamic behavior of viral population parameters in consecutive paired liver and ser um samples, obtained 3 to 6 years apart, from four chronic hepatitis C pati ents with persistently normal transaminases and stable liver histology. We sequenced 359 clones of a genomic fragment encompassing the E2(p7)-NS2 junc tion, in two consecutive liver-serum sample pairs from the four patients an d in four intermediate serum samples from one of the patients. The results show that the liver/serum complexity ratio is not stable but rather fluctua tes widely over time. Hence, the liver/serum complexity ratio does not iden tify a particular group of patients but a particular state of the infecting quasispecies. Phylogenetic analysis and signature mutation patterns showed that virtually all circulating sequences originated from sequences present in the liver specimens. The overall behavior of the circulating viral quas ispecies appears to originate from changes in the relative replication kine tics of the large mutant spectrum present in the infected liver.