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Deep sequencing shows that HBV basal core promoter and precore variants reduce the likelihood of HBsAg loss following tenofovir disoproxil fumarate therapy in HBeAg-positive chronic hepatitis B
  1. Julianne Bayliss1,
  2. Lilly Yuen1,
  3. Gillian Rosenberg1,
  4. Darren Wong1,7,
  5. Margaret Littlejohn1,
  6. Kathleen Jackson1,
  7. Anuj Gaggar3,
  8. Kathryn M Kitrinos3,
  9. G Mani Subramanian3,
  10. Patrick Marcellin4,
  11. Maria Buti5,
  12. Harry L A Janssen6,
  13. Ed Gane2,
  14. Vitina Sozzi1,
  15. Danni Colledge1,
  16. Rachel Hammond1,
  17. Rosalind Edwards1,
  18. Stephen Locarnini1,
  19. Alexander Thompson7,
  20. Peter A Revill1
  1. 1Division of Molecular Research and Development, Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
  2. 2New Zealand Liver Transplant Unit, Auckland City Hospital, Auckland, New Zealand
  3. 3Gilead Sciences, Foster City, California, USA
  4. 4Hôpital Beaujon, University of Paris, Clichy, France
  5. 5Liver Unit, Valle d'Hebron (Ciberehd) University Hospital, Barcelona, Spain
  6. 6Toronto Center for Liver Diseases, Toronto Western and General Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
  7. 7Department of Gastroenterology, St. Vincent's Hospital, Melbourne, Victoria, Australia
  1. Correspondence to Dr Peter A Revill, Division of Molecular Research and Development, Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, The Peter Doherty Institute, 792 Elizabeth St, Melbourne, VIC 3000, Australia; peter.revill{at}


Objective Hepatitis B e antigen (HBeAg) seroconversion and hepatitis B surface antigen (HBsAg) loss are important clinical outcomes for patients with chronic hepatitis B (CHB) treated with antiviral therapy. To date, there have been few studies that have evaluated viral sequence markers predicting serological response to nucleos(t)ide analogue (NA) treatment.

Design We used next-generation sequencing (NGS) and quantitative HBV serology (HBeAg and HBsAg) to identify viral sequence markers associated with serological response to long-term tenofovir disoproxil fumarate therapy among HBeAg-positive patients. In the GS-US-174-0103 study, approximately half the patients seroconverted to anti-HBe by week 192 and 11% of patients exhibited HBsAg loss, the closest outcome to functional cure. The frequency of HBV variants that have previously been associated with HBV clinical outcomes was evaluated. HBV viral diversity in baseline sequences generated by NGS was calculated using Shannon entropy.

Results NGS analysis of HBV sequences from 157 patients infected with genotypes A to D showed the frequency of variants in the basal core promoter (BCP) and precore (PC) regions varied by genotype and that these mutations were associated with the absence of HBsAg loss. This was the case even when mutations were present at frequencies below the threshold of detection by population sequencing. Increased viral diversity across the HBV genome as determined by NGS was also associated with reduced likelihood of HBsAg loss.

Conclusion Patients with detectable BCP and/or PC variants and higher viral diversity have a lower probability of HBsAg loss during long-term NA therapy. Strategies to achieve functional cure of HBV infection through combination therapy should consider using NGS to stratify patients according to BCP/PC sequence. Consideration should also be given to earlier initiation of therapy prior to the emergence of BCP/PC variants.

Trial registration number NCT00116805; Post result.


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