| description |
Background Chronic hepatitis B (CHB) is prevalent worldwide. The infectious agent, hepatitis B virus (HBV) replicates rapidly and is error-prone, leading to rapid evolution of closely related but not identical viral variants, including those that can escape host immune responses and antiviral treatments. The complexity of CHB is further characterised by the presence of HBV viral variants with large deletions in the genome generated via splicing (spHBV). Although spHBV variants are incapable of autonomous replication, their replication is rescued by wild-type HBV. SpHBV variants have been shown to enhance wild-type virus replication, and their prevalence increases with liver disease progression. Results We employed single-molecule deep sequencing on whole HBV genomes extracted from longitudinal samples of a post-liver transplant CHB subject, collected over a 15-year period that include a liver explant. By employing novel bioinformatics methods, we found complex evolution of the viral variants across a period of changing treatment regimens. The spHBV detected in the liver explant remained present post-transplantation, along with emergence of a highly diverse novel spHBV population as well as viral variants with multiple deletions in the preS genes. Our analysis also showed rapid adaptation of HBV viral populations to treatment regimens with evolving drug resistance phenotypes and evidence of purifying selection across the whole genome. Conclusion Single-molecule sequencing allows characterising, in unprecedented detail, the evolution of HBV viral populations and offers unique insights into the evolution of defective and spliced HBV variants following liver transplantation and complex treatment regimes, impacting clinical outcome. |