1
Gilead Sciences Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA. [email protected].
2
Auckland Clinical Studies, Auckland, New Zealand.
3
Internal Medicine, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.
4
Liver Unit, University Hospital of Pisa Hepatology Unit, University Hospital of Pisa, Pisa, Italy.
5
Toronto General Hospital, Toronto, ON, Canada.
6
Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
7
Division of Gastroenterology and Hepatology, Department of Medicine, NYU Langone Health, NYU School of Medicine, New York, NY, USA.
8
Gilead Sciences Inc., 333 Lakeside Drive, Foster City, CA, 94404, USA.
9
Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo, Japan.
10
All India Institute of Medical Sciences, Department of Gastroenterology, New Delhi, India.
11
Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea.
12
Service d'Hépatologie, Hôpital Beaujon, Clichy, France.
13
Liver Unit, Department of Medicine, Hospital General Universitari Vall d'Hebron and Ciberehd del Instituto Carlos III, Barcelona, Spain.
14
The Chinese University of Hong Kong, Hong Kong, China.
15
Kings College Hospital, London, UK.
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.