Whole genome deep sequencing analysis of viral quasispecies diversity and evolution in HBeAg seroconverters
Su-Ru Lin,
Ta-Yu Yang,
Cheng-Yuan Peng,
You-Yu Lin,
Chia-Yen Dai,
Hurng-Yi Wang,
Tung-Hung Su,
Tai-Chung Tseng,
I-Jung Liu,
Huei-Ru Cheng,
Yueh-Chi Shen,
Fang-Yi Wu,
Chun-Jen Liu,
Ding-Shinn Chen,
Pei-Jer Chen,
Hung-Chih Yang,
Jia-Horng Kao
Affiliations
Su-Ru Lin
Department of Microbiology, National Taiwan University, Taipei, Taiwan
Ta-Yu Yang
Department of Microbiology, National Taiwan University, Taipei, Taiwan
Cheng-Yuan Peng
School of Medicine, China Medical University, Taichung, Taiwan; Department of Internal Medicine, Center for Digestive Medicine, China Medical University Hospital, Taichung, Taiwan
You-Yu Lin
Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
Chia-Yen Dai
Department of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Hepato-Biliary Division, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
Hurng-Yi Wang
Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
Tung-Hung Su
Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
Tai-Chung Tseng
Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
I-Jung Liu
Cardinal Tien Junior College of Healthcare and Management, New Taipei City, Taiwan
Huei-Ru Cheng
Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
Yueh-Chi Shen
Department of Microbiology, National Taiwan University, Taipei, Taiwan
Fang-Yi Wu
Department of Microbiology, National Taiwan University, Taipei, Taiwan
Chun-Jen Liu
Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
Ding-Shinn Chen
Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University, Taipei, Taiwan; Genomics Research Center, Academia Sinica, Taipei, Taiwan
Pei-Jer Chen
Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
Hung-Chih Yang
Department of Microbiology, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; National Taiwan University No. 1, Sec. 1, Ren-Ai Road, Taipei 10051, Taiwan; Tel.: +886 2 312 3456 #88299; fax:+886 2 2391 5293.
Jia-Horng Kao
Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan; Corresponding authors. Addresses: National Taiwan University, No. 7 Chung San South Road, Taipei 10002, Taiwan; Tel.: +886 2 312 3456 #67307; fax:+886 2 2382 5962.
Summary: Background & Aims: We aimed to investigate how viral quasispecies of the HBV whole genome evolves and diversifies in response to HBeAg seroconversion and viral control utilising next-generation sequencing (NGS). Methods: Fifty HBeAg-positive chronic hepatitis B patients, including 18 treatment-naïve and 32 interferon (IFN)-treated individuals, were recruited. Serial HBV whole genomes in serum were analysed by NGS to determine sequence characteristics and viral quasispecies. Results: HBV quasispecies diversity, measured by nucleotide diversity, was negatively correlated with viral load and hepatitis activity. Spontaneous HBeAg seroconverters exhibited significantly greater viral quasispecies diversity than treatment-naïve non-seroconverters from >1 year before seroconversion (0.0112 vs. 0.0060, p 1 year after seroconversion (0.0103 vs. 0.0068, p <0.01). IFN-induced HBeAg seroconverters tended to have higher viral genetic diversity than non-seroconverters along with treatment. Particularly, the IFN responders, defined as IFN-induced HBeAg seroconversion with low viraemia, exhibited significantly greater genetic diversity of whole HBV genome at 6 months post-IFN treatment than IFN non-responders (0.0148 vs. 0.0106, p = 0.048). Moreover, spontaneous HBeAg seroconverters and IFN responders exhibited significantly higher evolutionary rates and more intra-host single-nucleotide variants. Interestingly, in spontaneous HBeAg seroconverters and IFN responders, there were distinct evolutionary patterns in the HBV genome. Conclusions: Higher HBV quasispecies diversity is associated with spontaneous HBeAg seroconversion and IFN-induced HBeAg seroconversion with low viraemia, conferring a favourable clinical outcome. Lay summary: HBeAg seroconversion is a landmark in the natural history of chronic HBV infection. Using next-generation sequencing, we found that the nucleotide diversity of HBV was negatively correlated with viral load and hepatitis activity. Patients undergoing HBeAg seroconversion had more diverse HBV genomes and a faster viral evolution rate. Our findings suggest HBeAg seroconversion is driven by host selection pressure, likely immune selection pressure.
