There are seven confirmed hepatitis C virus (HCV) genotypes, with whole-genome nucleotide sequences differing by Ͼ30%, and each can be further subdivided into related subtypes (67 confirmed), with nucleotide sequence divergence of between 15% and 30% (1).Genotype identification has long been used in clinical practice, because major genotypes have different response rates and require different doses and durations of pegylated interferon and ribavirin (PR) treatment. In contrast, until recently, subtype identification was mainly used in epidemiological studies. However, both in vitro studies and clinical trials with different classes of direct-acting antiviral (DAA) agents (NS3 protease, NS5A-, and nucleos[t]ide and nonnucleos[t]ide NS5B-polymerase inhibitors), given with PR or in interferon-free combinations, have shown lower response rates for HCV genotype 1a than for HCV genotype 1b (2-8). Moreover, at least for HCV genotype 1, both the frequency and the pattern of resistance to different DAA classes are subtype specific (9). A striking example is the NS3-Q80K polymorphism, naturally found in Ͼ30% of naive subtype 1a patients but in Ͻ1% of subtype 1b patients (10), which conveys 30%-to-40%-lower sustained-virologic-response (SVR) rates to the macrocyclic protease inhibitor simeprevir (2). Similarly, all subtype 1g sequences identified naturally carry a mutation conferring resistance to linear NS3 protease inhibitors (11).Subtype-specific differences in the genetic barrier to resistance appear to correlate to the RNA-dependent RNA polymerase mu-
f Sofosbuvir displays a high phenotypic barrier to resistance, and it is a component of several combination therapies for hepatitis C virus (HCV) infections. HCV fitness can be a determinant of decreased sensitivity to direct-acting antiviral agents such as telaprevir or daclatasvir, but fitness-dependent decreased drug sensitivity has not been established for drugs with a high phenotypic barrier to resistance. Low-and high-fitness HCV populations and biological clones derived from them were used to infect Huh-7.5 hepatoma cells. Sofosbuvir efficacy was analyzed by measuring virus progeny production during several passages and by selection of possible sofosbuvir resistance mutations determined by sequencing the NS5B-coding region of the resulting populations. Sofosbuvir exhibited reduced efficacy against high-fitness HCV populations, without the acquisition of sofosbuvirspecific resistance mutations. A reduced sofosbuvir efficacy, similar to that observed with the parental populations, was seen for high-fitness individual biological clones. In independently derived high-fitness HCV populations or clones passaged in the presence of sofosbuvir, M289L was selected as the only substitution in the viral polymerase NS5B. In no case was the sofosbuvir-specific resistance substitution S282T observed. High HCV fitness can lead to decreased sensitivity to sofosbuvir, without the acquisition of specific sofosbuvir resistance mutations. Thus, fitness-dependent drug sensitivity can operate with HCV inhibitors that display a high barrier to resistance. This mechanism may underlie treatment failures not associated with selection of sofosbuvirspecific resistance mutations, linked to in vivo fitness of pretreatment viral populations. Hepatitis C virus (HCV) infection affects about 2.3% of the world population, with treatment and patient management costs being an important burden for health systems (1). Treatment efficacy, quantified as the rate of sustained viral response, has improved markedly with the introduction of direct-acting antiviral agents (DAAs) (2). DAAs include inhibitors of the viral protease NS3-4A (telaprevir [TPV], boceprevir, simeprevir, paritaprevir/ritonavir, asunaprevir, etc.), of nonstructural protein NS5A (daclatasvir [DCV], ledipasvir, ombitasvir, etc.), and the polymerase NS5B (nonnucleoside analogues, such as dasabuvir, and one nucleoside analogue, such as sofosbuvir [SOF]). Many DAAs have been licensed for human use, and others are still in preclinical and clinical assessment.A major issue in antiviral treatments is the selection of inhibitor-resistant mutants leading to treatment failure. Selection is influenced by genetic and phenotypic barriers to resistance. The genetic barrier depends on the number and type of mutations needed for the RNA to encode amino acid substitutions needed to confer resistance. The phenotypic barrier is determined by the fitness cost inflicted upon the virus by the mutations associated with resistance. Barriers vary depending on the nature of the antiviral agent, the viral ...
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