Large-scale viral genome analysis identifies novel clinical associations between hepatitis B virus and chronically infected patients

Ondřej Podlaha ,S Shalimar ,Young‐Suk Lim ,Yang Liu,Calvin Q Pan,Mani Subramanian,Anuj Gaggar,M.r Brunetto ,Scott Fung,Prasenjit Mukherjee,Edward Gane,Zhaoshi Jiang,Wan‐Long Chuang ,John F Flaherty ,Neeru Bhardwaj,María Buti ,Patrick Marcellin,Namiki Izumi,Henry Lik‐Yuen Chan ,Kosh Agarwal

doi:10.1038/s41598-019-46609-7

Abstract

Despite the high global prevalence of chronic hepatitis B (CHB) infection, datasets covering the whole hepatitis B viral genome from large patient cohorts are lacking, greatly limiting our understanding of the viral genetic factors involved in this deadly disease. We performed deep sequencing of viral samples from patients chronically infected with HBV to investigate the association between viral genome variation and patients’ clinical characteristics. We discovered novel viral variants strongly associated with viral load and HBeAg status. Patients with viral variants C1817T and A1838G had viral loads nearly three orders of magnitude lower than patients without those variants. These patients consequently experienced earlier viral suppression while on treatment. Furthermore, we identified novel variants that either independently or in combination with precore mutation G1896A were associated with the transition from HBeAg positive to the negative phase of infection. These observations are consistent with the hypothesis that mutation of the HBeAg open reading frame is an important factor driving CHB patient’s HBeAg status. This analysis provides a detailed picture of HBV genetic variation in the largest patient cohort to date and highlights the diversity of plausible molecular mechanisms through which viral variation affects clinical phenotype.

Highlights

Despite the high global prevalence of chronic hepatitis B (CHB) infection, datasets covering the whole hepatitis B viral genome from large patient cohorts are lacking, greatly limiting our understanding of the viral genetic factors involved in this deadly disease
The most significant associations were observed between the viral load and two non-synonymous variants C1817T (HBc gene Q > STOP; HBx gene C > C; likelihood ratio test [LRT] p = 1.7 × 10−33, Fig. 1a) and A1838G (HBc gene I > V; HBx gene: STOP > STOP; LRT p = 1.3 × 10−81, Fig. 1a)
It is well known that the transition from hepatitis B e antigen (HBeAg) positive to negative phase of hepatitis B virus (HBV) infection is generally marked by a reduction in viral replication and viral load[10,11,12,13,14,15]

Summary

Introduction

Despite the high global prevalence of chronic hepatitis B (CHB) infection, datasets covering the whole hepatitis B viral genome from large patient cohorts are lacking, greatly limiting our understanding of the viral genetic factors involved in this deadly disease. We identified novel variants that either independently or in combination with precore mutation G1896A were associated with the transition from HBeAg positive to the negative phase of infection These observations are consistent with the hypothesis that mutation of the HBeAg open reading frame is an important factor driving CHB patient’s HBeAg status. Current clinical practice guidelines of the European Association for the Study of the Liver (EASL) recognize five phases of HBV infection determined by a combination of clinical factors such as the viral load (serum levels of HBV DNA), the presence of viral hepatitis B e antigen (HBeAg), hepatitis B s antigen (HBsAg) levels, alanine aminotransferase (ALT) levels, and the stage of liver fibrosis[3]. We undertook a more comprehensive analysis of associations between HBV single nucleotide variants and patient clinical characteristics by looking at the whole viral genome across a large patient cohort

Methods

Results

Conclusion