Polymorphisms associated with resistance to protease inhibitors in naïve patients infected with hepatitis C virus genotype 1 in Argentina: Low prevalence of Q80K

Highlights

• A high prevalence of resistance-associated substitutions (RASs) was detected in HCV-1 from Argentinean naïve patients.

• The prevalence of RASs was higher in HCV-1b than in HCV-1a.

• A great prevalence of double mutants (17.2%) was detected in HCV-1b but not in HCV-1a.

• Q80K polymorphism was not detected in patients carrying HCV-1a, even in patients belonging to clade 1.

• The phylogenetic analysis showed that Argentinean samples were distributed randomly among sequences around the world.

Abstract

Incorporation of direct acting antivirals (DAA) in the treatment of Hepatitis C Virus (HCV) significantly increases sustained virologic response rates. However, despite the greater potency offered by these antivirals, drug resistance plays a key role in patients with failure to DAA. Nevertheless, there is no information about the prevalence of resistance-associated substitutions (RASs) in Argentina.

The aim of this study was to analyze HCV variants resistant to protease inhibitors (PI) in naïve patients infected with HCV genotype 1 from Argentina.

In this retrospective cross-sectional study, 103 patients infected with HCV-1 were included. Eighteen positions related with RASs were analyzed by Sanger at baseline and phylogenetic analysis was performed to determine the diversification of this samples.

The analyzed RASs were present in 38 out of 103 patients (36.9%) infected with HCV-1. Patients infected with subtype HCV-1b had higher prevalence of baseline RASs than patients infected with HCV-1a [51.6% vs. 12.8%, respectively (p < 0.001)]. The Q80K polymorphism was not found in HCV-1a samples, even when 51% of them belonged to cluster 1, which is associated with a high frequency of Q80K. Phylogenetic analysis showed that Argentinean samples were intermingled with sequences from other geographic regions.

RASs to PI were highly prevalent and subtype dependent in treatment-naïve Argentinean patients. Surprisingly, Q80K polymorphism was not detected in our study population. The phylogenetic analysis showed no relationship between our samples and other samples from Brazil which also present a low prevalence of Q80K. This study supports the need for surveillance of resistance in patients who will be treated with DAA in each particular country since the observed RASs have very different prevalence worldwide.

Introduction

The development of direct-acting antivirals (DAA) significantly increased sustained virologic response (SVR) rates in the treatment of chronic hepatitis C virus (HCV), while lowering the rates of adverse events (Bacon et al., 2011, Zeuzem et al., 2011, Forns et al., 2014, Jacobson et al., 2014, Lawitz et al., 2014, Forns et al., 2015, Krishnan et al., 2015). However, despite the significantly greater efficacy and tolerability offered by these antivirals, patients are still failing to reach virologic curation. In this context, drug resistance plays a key role in patients with failure to DAA-containing therapies (Zeuzem et al., 2011, Forns et al., 2014, Jacobson et al., 2014, Lawitz et al., 2014, Poveda et al., 2014, Forns et al., 2015, Krishnan et al., 2015, Sarrazin, 2016). Since selection of resistant variants did not represent an important issue in the era of therapy based on pegylated interferon plus ribavirin alone, the use of DAA is leading to a paradigm shift in the management of HCV treatment.

HCV NS3 protease was the first target used for therapeutic intervention, however it shows a high degree of genetic variability (Poveda et al., 2014, Sarrazin, 2016). Several resistance-associated substitutions (RASs) to NS3 protease inhibitors (PIs) have been described with generally low frequency in HCV genotype 1-infected patients (Poveda et al., 2014). Still, some polymorphisms, such as Q80K, which is highly prevalent and confers no substantial loss of replicative fitness in many patients, seem to be an exception for the treatment with simeprevir (SMV) and asunaprevir (ASV) (Bae et al., 2010, Sarrazin et al., 2015).

In particular, SMV was recently approved for its use in Argentina in patients with chronic HCV infection. It has been widely reported that the antiviral efficacy of SMV is adversely affected by the RASs, especially by Q80K polymorphism in patients infected with HCV genotype 1a (HCV-1a) (Bae et al., 2010, Jacobson et al., 2014, Poveda et al., 2014, Sarrazin et al., 2015, Sarrazin, 2016). Nevertheless, the prevalence of Q80K is diverse and varies by geographic region. In this sense, Q80K variant is a pre-existing RAS frequently found in HCV-1a-infected patients from North America (48.1%) and Europe (19.4%) but it was rarely detected in Brazil and Uruguay (1.8%) (Bae et al., 2010, Peres-da-Silva et al., 2012, de Carvalho et al., 2014, Lisboa-Neto et al., 2015, Sarrazin et al., 2015, Echeverría et al., 2016). However, there is no information on the prevalence of Q80K and other RASs in Argentina. For this reason, there is a big controversy about the necessity of testing the RASs in patients infected with HCV-1a in our country before the initiation of therapy including PIs.

On the other hand, Pickett et al. demonstrated that HCV-1a could be separated into two distinct clades, named 1 and 2 (Pickett et al., 2011). Additionally, several works associated the presence of Q80K polymorphism to clade 1 (Peres-da-Silva et al., 2012, Ehret et al., 2014, Nguyen et al., 2015). For this reason, the phylogenetic analysis of the Argentinean samples could provide important information about the clade prevalence and its relationship with sequences from other countries.

Therefore, the aim of this study was to determine the prevalence of PI resistances, in particular the Q80K polymorphism, in an Argentinean cohort of treatment-naïve patients with chronic HCV-1 infection.