NS3 protease resistance-associated substitutions in liver tissue and plasma samples from patients infected by hepatitis C virus genotype 1A or 1B

Abstract

The presence of naturally occurring resistance-associated substitutions (RASs) in the HCV-protease domain has been poorly investigated in the liver, the main site of HCV replication. We evaluated the natural resistance of the virus to NS3 protease inhibitors in liver tissue and plasma samples taken from HCV-infected patients. RASs were investigated by means of viral population sequencing in liver tissue samples from 18 HCV-infected patients harbouring genotype 1a or genotype 1b; plasma samples from 12 of these patients were also available for virological investigation. A discordant genotype was found in two of the 12 patients (16.6%) who provided samples from both compartments. Sequence analysis of the NS3 protease domain showed the presence of RASs in four of the 18 liver tissue samples (22.2%), two of which showed cross-resistance to protease inhibitors in clinical use or phase 2-3 trials. The analysis of the 12 paired tissues and plasma samples excluded the presence of RASs in the plasma compartment. The dominance of discordant genotypes in the paired liver and plasma samples of some HCV-infected patients suggests mixed infection possibly leading to the selective advantage of different genotype in the two compartments. The presence of RASs at intra-hepatic level is not uncommon and may lead to the early emergence of cross-resistant strains.

HCV resistance compartmentalization within tumoral and non‐tumoral liver in transplanted patients with hepatocellular carcinoma

“…Some studies have already supported HCV compartmentalization in the liver, although limited to single genes and to GT-1b infection, and rarely discriminating between the liver specimen typology. [30][31][32] Conflicting results in recent studies, however, have both supported and contradicted this phenomenon. Evidence of HCV liver compartmentalization has been observed in the envelope and core genes by Sanger-sequencing 33,34 . Conversely, a similar distribution of HCV-quasispecies by UDPS from two subjects disputed HCV compartmentalization, 35 although limited to the envelope-genes and without discriminating between liver tissue typology.…”

The Investigation of Drug Resistance Substitutions in NS3 Protease Sequence of Hepatitis C Virus from Non-Responder Patients

“…The Substitutions and Their Frequency in Sample Sequences. The more prevalent substitutions were indicated by underline marker and PIs resistance mutations were bolded and genotypes (Vallet et al, 2005;Lopez-Labrador et al, 2008;Paolucci et al, 2012;Martinez et al, 2017;Morsica et al, 2017). Although there are a couple of reports regarding this issue around the world, in Iran limited publications have considered it.…”

“…Three classes of DAAs are candidates of marketing nowadays that among them telaprevir, boceprevir and glecaprevir are NS3 protease inhibitors (PIs) (Lamb, 2017;Morsica et al, 2017). PIs drugs inhibit NS3 protease activity by occupying the activation site or surrounding motifs, consequently inhibiting HCV viral replication (Lamb, 2017).…”

NS3 Variability in Hepatitis C Virus Genotype 1A Isolates from Liver Tissue and Serum Samples of Treatment-Naïve Patients with Chronic Hepatitis C

“…This discrepancy might be due to differences in the assays (based on population or deep sequencing) utilized in the different studies, as well as to the choice to investigate only specific RASs while excluding others, and the increasing number of RASs over time recognized to be involved in resistance to PIs [4]. Furthermore, it has to be taken into account that the present study included the analysis of viral isolates from the liver that is the site where virus replication takes place and HCV quasispecies show the highest complexity at both nucleotide and aa levels [11,12,[14][15][16]. It is known that the composition of viral population in the serum does not necessarily reflect those of the viral population in the liver.…”

“…NS3 polymorphisms of HCV G1a potentially conferring resistance to PIs have been investigated in HCV isolates from the serum of patients, whereas -apart from anecdotic cases [11][12][13] -no extensive evaluation of isolates from the liver that is the site of virus replication and where HCV quasispecies diversity reaches the highest level of complexity [11,12,[14][15][16] has been performed so far. In addition, almost all the studies have evaluated the presence of RASs by performing population sequencing, which is known to have a quite low sensitivity (15-20% frequency within the HCV quasispecies) to detect viral variants [4,17].…”