Profiles of HBV DNA integration in humans with hepatitis B virus infection: Insights for antiviral treatment

Abstract

<p>Background & Aims: HBV integration profiles in the natural history of chronic HBV infection (CHB) have not been well-defined. Hence, we aimed to determine HBV integration profiles across different CHB phases. Methods: We delineated integration profiles from liver biopsies of 55 patients in different CHB phases (3 HBsAg-positive/HBeAg-positive infection; 13 HBsAg-positive/HBeAg-positive hepatitis; 7 HBsAg-positive/HBeAg-negative infection; 12 HBsAg-positive/HBeAg-negative hepatitis; 10 HBsAg seroclearance; 10 occult HBV). Target-capture next-generation sequencing (NovaSeq-6000) was performed, and integrations were characterized on AVID (integrations defined as chimeric fusions in ≥1 soft-clipped reads and ≥2 total reads). Results: HBV integrations were detected in 35 HBsAg-positive (100%), 8 (80%) HBsAg seroclearance, and 7 (70%) occult HBV patients, respectively. There was a stepwise decrease in integration events from HBsAg-positive/HBeAg-positive (median 9.6 [IQR 9.3-10.1] log integrations per liver), HBsAg-positive/HBeAg-negative (8.7 [8.4-9.0] log integrations) and HBsAg-negative patient groups (7.3 [6.8-7.7] log integrations) (p <0.001 for trend). There were no differences in integration frequencies in chronic infection (ALT < the upper limit of normal) and chronic hepatitis (ALT ≥ the upper limit of normal) for either HBeAg-positive or -negative patients (all p >0.05). No significant differences in integration frequencies were noted between HBsAg seroclearance and occult HBV groups (p >0.05). HBV genome integration breakpoints clustered around nucleotide 1800 in all disease phases. Human genome breakpoints were also delineated, and LINC00486 was the most frequently involved human gene in all disease phases. Conclusion: We characterized the HBV DNA integration patterns and genome breakpoints of patients in different CHB disease phases. These findings enhance our understanding of the natural history of CHB. Impact and implications: HBV integration profiles in the natural history of chronic HBV infection have not been well-defined. We utilized next-generation sequencing in a well-characterized cohort of patients with HBV at different disease phases, demonstrating a stepwise decrease in integration events as HBV progressed from HBeAg-positive to HBeAg-negative, and then to HBsAg-negative phases. Human and viral genome breakpoints were also identified. These findings enhance our understanding of the natural history of CHB, and provide insights for antiviral treatment.</p>