Ultra-deep pyrosequencing analysis of the hepatitis B virus preCore region and main catalytic motif of the viral polymerase in the same viral genome

Maria Homs, Maria Buti, Josep Quer, Rosendo Jardí, Melanie Schaper, David Tabernero, Israel Ortega, Alex Sanchez, Rafael Esteban, Francisco Rodriguez-Frias

Research output: Contribution to journalArticleResearchpeer-review

37 Citations (Scopus)

Abstract

Hepatitis B virus (HBV) pregenomic RNA contains a hairpin structure (ε) located in the preCore region, essential for viral replication. ε stability is enhanced by the presence of preCore variants and ε is recognized by the HBV polymerase (Pol). Mutations in the retrotranscriptase domain (YMDD) of Pol are associated with treatment resistance. The aim of this study was to analyze the preCore region and YMDD motif by ultra-deep pyrosequencing (UDPS). To evaluate the UDPS error rate, an internal control sequence was inserted in the amplicon. A newly developed technique enabled simultaneous analysis of the preCore region and Pol in the same viral genome, as well as the conserved sequence of the internal control. Nucleotide errors in HindIII yielded a UDPS error rate <0.05. UDPS study confirmed the possibility of simultaneous detection of preCore and YMDD mutations, and demonstrated the complexity of the HBV quasispecies and cooperation between viruses. Thermodynamic stability of the ε signal was found to be the main constraint for selecting main preCore mutations. Analysis of ε-signal variability suggested the essential nature of the ε structural motif and that certain nucleotides may be involved in ε signal functions. © The Author(s) 2011. Published by Oxford University Press.
Original languageEnglish
Pages (from-to)8457-8471
JournalNucleic Acids Research
Volume39
Issue number19
DOIs
Publication statusPublished - 1 Oct 2011

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