Naturally occurring dominant drug resistance mutations occur infrequently in the setting of recently acquired hepatitis C

Abstract

Background: Direct-acting antivirals (DAAs) are predicted to transform hepatitis C therapy, yet little is known about the prevalence of naturally occurring resistance mutations in recently acquired HCV. This study aimed to determine the prevalence and frequency of drug resistance mutations in the viral quasispecies among HIV-positive and -negative individuals with recent HCV.

Methods: The NS3 protease, NS5A and NS5B polymerase genes were amplified from 50 genotype 1a participants of the Australian Trial in Acute Hepatitis C. Amino acid variations at sites known to be associated with possible drug resistance were analysed by ultra-deep pyrosequencing.

Results: A total of 12% of individuals harboured dominant resistance mutations, while 36% demonstrated non-dominant resistant variants below that detectable by bulk sequencing (that is, <20%) but above a threshold of 1%. Resistance variants (<1%) were observed at most sites associated with DAA resistance from all classes, with the exception of sofosbuvir.

Conclusions: Dominant resistant mutations were uncommonly observed in the setting of recent HCV. However, low-level mutations to all DAA classes were observed by deep sequencing at the majority of sites and in most individuals. The significance of these variants and impact on future treatment options remains to be determined. Clinicaltrials.gov NCT00192569.

Conflict of interest statement

Conflict of interest statement

Dr. Applegate reports grants from National Health and Medical Research Council and from National Health and Medical Research Council during the conduct of the study; Dr. Gaudieri reports grants from National Health and Medical Research Council of Australia during the conduct of the study; Ms. Plauzolles has nothing to disclose; Dr. Chopra has nothing to disclose. Dr. Grebely reports grants and personal fees from Merck, grants from Gilead, grants from Janssen, grants from Abbvie outside the submitted work; Associate Professor Lucas has nothing to disclose; Dr. Hellard reports grants from null outside the submitted work; Dr. Luciani has nothing to disclose; Professor Dore reports grants, personal fees and non-financial support from Roche, grants, personal fees and non-financial support from Merck, grants and personal fees from Janssen, grants, personal fees and non-financial support from Gilead, grants, personal fees and non-financial support from Bristol-Myers Squibb, grants and personal fees from Abbvie, grants from Vertex, grants from Boeringher Ingelheim outside the submitted work. Dr. Matthews reports grants from NHMRC during the conduct of the study; grants and other from Gilead Inc, grants and other from Janssen, other from Roche, other from BMS, grants and other from MSD outside the submitted work.

Figures

Figure 1

Flow chart describing the selection of ATAHC participants for inclusion in this analysis.

Figure 2. Percentage of individuals with resistance mutations present in the (A) NS3 protease gene (n=49), NS5B polymerase gene (n=49) and (C) NS5A gene (n=13)

Resistance mutations are represented as occuring at >50% (“Dominant”, solid bars), >1–50% (grey hatched bars), >0.1–1% (light grey hatched bars). All mutations known to confer resistance at each position were catergorised together, irrespective of the amino acid change. For particpants who had evidence of multiple mutations at one site (eg. Both M423T andM423V), the mutation seen at higher % was reported. No mutations were found to occur in the range between 3 and 88%. Dominant resistant mutations generally occurred at > 98%.

Figure 3. Number of resistance mutations in the NS3 protease gene, within each participant, exhibited at > 0.1% frequency

The occurrence of at least one acid change known to confer resistance was included as varation at that site. Individuals demonstrated a range of the number of resistance mutations found >0.1% (0 – 9 sites).