Single nucleotide polymorphisms in the bepirovirsen binding site have limited impact on treatment response in chronic hepatitis B

BACKGROUND & AIMS: Single nucleotide polymorphisms (SNPs) in the HBV genome may impact the efficacy of novel drugs for chronic HBV infection. This analysis of the B-Clear study (NCT04449029) evaluated the frequency of baseline and treatment-emergent SNPs in the bepirovirsen binding site and their association with virological response. METHODS: HBV sequencing was attempted for all baseline samples collected from B-Clear participants and for selected post-baseline samples from participants meeting predefined resistance-monitoring criteria. Participants were categorized according to nucleos(t)ide analogue (NA) treatment status and hepatitis B surface antigen (HBsAg) response. SNPs were identified using next-generation sequencing and reported if the allelic frequency was ≥5%. The effects of binding site SNPs on viral fitness and susceptibility to bepirovirsen were assessed in vitro. RESULTS: Baseline sequences were obtained for 40% (90/226) and 96% (219/229) of On-NA and Not-on-NA participants, respectively. Baseline SNPs were identified in 7% (22/309) of participants. These participants showed numerically smaller HBsAg reductions than those without SNPs, but 18% (4/22) achieved transient HBsAg loss. Post-baseline sequences were obtained for 22% (49/226) and 62% (143/229) of On-NA and Not-on-NA participants, respectively. Of 16 post-baseline SNPs, eight were treatment-emergent. SNPs were detected at 12 of the 20 binding site positions; however, only two SNPs had an allelic frequency >50% (C1589A [max 99%] and C1600T [max 99%]). Six SNPs showed sufficient viral fitness to be evaluated for susceptibility to bepirovirsen in vitro. C1589A demonstrated the largest reduction in susceptibility (4.1-fold) to bepirovirsen. CONCLUSIONS: Most participants achieved >1 log reductions in HBsAg, including transient HBsAg loss in some. Although participants with baseline SNPs showed numerically smaller HBsAg reductions, further investigation is required to better understand potential mechanisms of resistance to bepirovirsen. IMPACT AND IMPLICATIONS: HBV sequence polymorphisms can contribute to antiviral resistance in the treatment of chronic HBV infection. Therefore, it is important for healthcare professionals to understand the prevalence and emergence of single nucleotide polymorphisms (SNPs) within the bepirovirsen binding site and their potential impact on virological response. Findings from this phase IIb clinical study demonstrate that the vast majority (92%) of non-responders, partial responders, or relapsers did not harbor bepirovirsen binding site SNPs. Moreover, participants with binding site SNPs (7% of participants) still achieved reductions in hepatitis B surface antigen. These results suggest that routine testing for specific HBV variants prior to bepirovirsen administration is not currently warranted, and that resistance due to altered sequence complementarity is likely minimal and multifactorial. Ongoing phase III studies of bepirovirsen will provide additional context to further evaluate the need for variant testing and to better elucidate potential resistance mechanisms.