Abstract

The role of the HCV NS3/4A protease in ablating the signaling pathway involved in the production of interferon (IFN)-α/β suggests a relationship between NS3/4A proteolytic activity and a patient's response to IFN-based therapy. To identify viral factors associated with the HCV treatment response, we analyzed the pre-treatment NS3/4A protease gene quasispecies composition of 56 HCV genotype 1/HIV-1 co-infected patients treated in our clinic with pegIFN plus ribavirin (RBV). The catalytic efficiency of the dominant quasispecies (i.e. the most abundant) from each quasispecies was also assayed for Cardif cleavage and correlated with treatment outcome. A total of 1745 clones were isolated and sequenced. Significantly less nucleotide quasispecies heterogeneity and lower Shannon's entropy values were detected within the responder group (p < 0.05). A correlation was also found between the efficiency of NS3/4A protease Cardif cleavage and therapy outcome. Proteases from sustained responder patients were more efficient at processing Cardif (mean ± SEM, 0.8960 ± 0.05568; n=19) than proteases from non-responders (mean ± SEM, 0.7269 ± 0.05306; n=37; p < 0.05). Finally, the amino acid p-distance was significantly less in patients with an IL28B risk allele (p < 0.01), suggesting that IL28B risk allele carriers exert a lower positive selection pressure on the NS3/4A protease. NS3/4A protease efficiency in cleaving Cardif may be associated with the pegIFN-RBV treatment response, as shown in our cohort of HIV/HCV-co-infected patients. Greater NS3/4A nucleotide heterogeneity and higher Shannon's entropy values in non-responders suggest that less HCV quasispecies complexity may favor a better response to pegIFN-RBV.