Clinical application of estimating hepatitis B virus quasispecies complexity by massive sequencing: correlation between natural evolution and on-treatment evolution

PLoS One. 2014 Nov 13;9(11):e112306. doi: 10.1371/journal.pone.0112306. eCollection 2014.

Abstract

Aim: To evaluate HBV quasispecies (QA) complexity in the preCore/Core regions in relation to HBeAg status, and explore QA changes under natural evolution and nucleoside analogue (NUC) treatment.

Methods: Ultra-deep pyrosequencing of HBV preCore/Core regions in 30 sequential samples (baseline [diagnosis], treatment-free, and treatment-nonresponse) from 10 retrospectively selected patients grouped according to HBeAg status over time: HBeAg+ (N = 4), HBeAg- (N = 2), and fluctuating HBeAg (transient seroreversion/seroconversion pattern) (N = 4). QA complexity was defined by Shannon entropy, mutation frequency, nucleotide diversity, and mutation frequency of amino acids (MfAA) in preCore and Core.

Results: The QA was less complex in HBeAg+ than in HBeAg- or fluctuating HBeAg. High complexity in preCore was associated with decreased viral replication (preCore MfAA negatively correlated with HBV-DNA, p = 0.005). QA complexity in the treatment-free period negatively correlated with values seen during treatment. Specific variants were mainly selected in the Core region in HBeAg- and fluctuating HBeAg patients, suggesting higher immune pressure than in HBeAg+.

Conclusions: The negative correlation between QA natural evolution and on-treatment evolution indicates the importance of pre-treatment QA study to predict QA changes in NUC nonresponders. Study of QA complexity could be useful for managing HBV infection.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • DNA, Viral*
  • Evolution, Molecular*
  • Female
  • Hepatitis B / drug therapy
  • Hepatitis B / virology*
  • Hepatitis B e Antigens / chemistry
  • Hepatitis B virus / classification
  • Hepatitis B virus / genetics*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Longitudinal Studies
  • Male
  • Middle Aged
  • Mutation
  • Nucleotides / chemistry
  • Reproducibility of Results
  • Retrospective Studies
  • Treatment Outcome

Substances

  • DNA, Viral
  • Hepatitis B e Antigens
  • Nucleotides

Grants and funding

This study was funded by Instituto de Salud Carlos III (grant PI12/01893), cofinanced by the European Regional Development Fund (ERDF). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.