Comparison of the Mechanisms of Drug Resistance among HIV, Hepatitis B, and Hepatitis C

Human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) are the most prevalent deadly chronic viral diseases. HIV is treated by small molecule inhibitors. HBV is treated by immunomodulation and small molecule inhibitors. HCV is currently treated primarily by immunomodulation but many small molecules are in clinical development. Although HIV is a retrovirus, HBV is a double-stranded DNA virus, and HCV is a single-stranded RNA virus, antiviral drug resistance complicates the development of drugs and the successful treatment of each of these viruses. Although their replication cycles, therapeutic targets, and evolutionary mechanisms are different, the fundamental approaches to identifying and characterizing HIV, HBV, and HCV drug resistance are similar. This review describes the evolution of HIV, HBV, and HCV within individuals and populations and the genetic mechanisms associated with drug resistance to each of the antiviral drug classes used for their treatment

Comparison of the Mechanisms of Drug Resistance among HIV, Hepatitis B, and Hepatitis C

Human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) are the most prevalent deadly chronic viral diseases. HIV is treated by small molecule inhibitors. HBV is treated by immunomodulation and small molecule inhibitors. HCV is currently treated primarily by immunomodulation but many small molecules are in clinical development. Although HIV is a retrovirus, HBV is a double-stranded DNA virus, and HCV is a single-stranded RNA virus, antiviral drug resistance complicates the development of drugs and the successful treatment of each of these viruses. Although their replication cycles, therapeutic targets, and evolutionary mechanisms are different, the fundamental approaches to identifying and characterizing HIV, HBV, and HCV drug resistance are similar. This review describes the evolution of HIV, HBV, and HCV within individuals and populations and the genetic mechanisms associated with drug resistance to each of the antiviral drug classes used for their treatment

A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads

ABSTRACT Motivation: G→A hypermutation is an innate antiviral defense mechanism, mediated by host enzymes, which leads to the mutational impairment of viruses. Sensitive and specific identification of hostmediated G→A hypermutation is a novel sequence analysis challenge, particularly for viral deep sequencing studies. For example, two of the most common hepatitis B virus (HBV) reverse transcriptase (RT) drug-resistance mutations, A181T and M204I, arise from G→A changes and are routinely detected as low-abundance variants in nearly all HBV deep sequencing samples. Results: We developed a classification model using measures of G→A excess and predicted indicators of lethal mutation and applied this model to 325,920 unique deep sequencing reads from plasma virus samples from 45 drug-treatment-naïve HBV-infected individuals. The 2.9% of sequence reads that were classified as hypermutated by our model included most of the reads with A181T and/or M204I, indicating the usefulness of this model for distinguishing viral adaptive changes from host-mediated viral editing. Availability: Source code and sequence data are available a

A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads

Motivation: G → A hypermutation is an innate antiviral defense mechanism, mediated by host enzymes, which leads to the mutational impairment of viruses. Sensitive and specific identification of host-mediated G → A hypermutation is a novel sequence analysis challenge, particularly for viral deep sequencing studies. For example, two of the most common hepatitis B virus (HBV) reverse transcriptase (RT) drug-resistance mutations, A181T and M204I, arise from G → A changes and are routinely detected as low-abundance variants in nearly all HBV deep sequencing samples

List of known <i>in</i><i>vitro</i> and <i>in</i><i>vivo</i> amino acid substitutions resistant to NS5B polymerase inhibitors used in this study (NS5B residues 244–496).

<p>*<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Lam1" target="_blank">[6]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Tong1" target="_blank">[9]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Thompson1" target="_blank">[11]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Troke1" target="_blank">[15]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Lawitz1" target="_blank">[18]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Lam2" target="_blank">[54]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Shih1" target="_blank">[55]</a>.</p><p>**L320F when in combination with L159F confers low level resistance to MCB <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Tong1" target="_blank">[9]</a>, L320I or V321I when in combination with C223H confers low level resistance to GS-938 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Lam2" target="_blank">[54]</a>.</p

Low-abundance NS5B drug-resistant variants found in 30/77 G1a and in 12/39 G1b treatment-naïve HCV samples.

1<p>In parenthesis, abundance of the variant is indicated (in % and number of reads in which the mutation is detected over the number of total reads).</p

Similar Prevalence of Low-Abundance Drug-Resistant Variants in Treatment-Naive Patients with Genotype 1a and 1b Hepatitis C Virus Infections as Determined by Ultradeep Pyrosequencing

<div><p>Background and Objectives</p><p>Hepatitis C virus (HCV) variants that confer resistance to direct-acting-antiviral agents (DAA) have been detected by standard sequencing technology in genotype (G) 1 viruses from DAA-naive patients. It has recently been shown that virological response rates are higher and breakthrough rates are lower in G1b infected patients than in G1a infected patients treated with certain classes of HCV DAAs. It is not known whether this corresponds to a difference in the composition of G1a and G1b HCV quasispecies in regards to the proportion of naturally occurring DAA-resistant variants before treatment.</p><p>Methods</p><p>We used ultradeep pyrosequencing to determine the prevalence of low-abundance (<25% of the sequence reads) DAA-resistant variants in 191 NS3 and 116 NS5B isolates from 208 DAA-naive G1-infected patients.</p><p>Results</p><p>A total of 3.5 million high-quality reads of ≥200 nucleotides were generated. The median coverage depth was 4150x and 4470x per NS3 and NS5B amplicon, respectively. Both G1a and G1b populations showed Shannon entropy distributions, with no difference between G1a and G1b in NS3 or NS5B region at the nucleotide level. A higher number of substitutions that confer resistance to protease inhibitors were observed in G1a isolates (mainly at amino acid 80 of the NS3 region). The prevalence of amino acid substitutions that confer resistance to NS5B non-nucleoside inhibitors was similar in G1a and G1b isolates. The NS5B S282T variant, which confers resistance to the polymerase inhibitors mericitabine and sofosbuvir, was not detected in any sample.</p><p>Conclusion</p><p>The quasispecies genetic diversity and prevalence of DAA-resistant variants was similar in G1a and G1b isolates and in both NS3 and NS5B regions, suggesting that this is not a determinant for the higher level of DAA resistance observed across G1a HCV infected patients upon treatment.</p></div

Contribution of each mutational category (transition and transversion) to the development of drug-resistant substitutions (variants) in the NS3 and NS5B proteins reported in this study.

<p>The genetic barrier score (GBS) was calculated according to the model described by Van de Vijver et al.(50) A score of 1 is assigned to transitions (A↔G and C↔T) and 2.5 to transversions (A↔C, A↔T, G↔C and G↔T). Natural polymorphisms are indicated in italic. Numbers of isolates are indicated in parenthesis.</p

List of known <i>in</i><i>vitro</i> and <i>in</i><i>vivo</i> amino acid substitutions resistant to NS3 protease inhibitors used in this study (NS3 residues 31 to 175).

<p>*For conciseness, 2 representatives from each PI class were chosen <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-DeMeyer1" target="_blank">[1]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Jacobson1" target="_blank">[3]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Lenz1" target="_blank">[35]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Lenz2" target="_blank">[37]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-Lin1" target="_blank">[50]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0105569#pone.0105569-LePogam4" target="_blank">[53]</a>.</p