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Journal of Virology, February 2009, p. 1718-1726, Vol. 83, No. 4
0022-538X/09/$08.00+0     doi:10.1128/JVI.02011-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Use of Massively Parallel Ultradeep Pyrosequencing To Characterize the Genetic Diversity of Hepatitis B Virus in Drug-Resistant and Drug-Naive Patients and To Detect Minor Variants in Reverse Transcriptase and Hepatitis B S Antigen ^,

Mariacarmela Solmone, Donatella Vincenti, Mattia Carlo Felice Prosperi, Alessandro Bruselles, Giuseppe Ippolito, and Maria Rosaria Capobianchi^*

National Institute for Infectious Diseases Lazzaro Spallanzani, Rome, Italy

Received 24 September 2008/ Accepted 27 November 2008

Direct population sequencing and reverse hybridization (line probe assay [LiPA])-based methods are the most common methods for detecting hepatitis B virus (HBV) drug resistance mutations, although only mutations present in viral quasispecies with a prevalence of 20% can be detected by sequencing, and only known mutations are detected by LiPA. Massively parallel ultradeep pyrosequencing (UDPS; GS FLX platform) was used to analyze HBV quasispecies in reverse transcriptase (RT) and hepatitis B S antigen (HBsAg) from five drug-naive patients and eight drug-resistant patients. Eight primer pairs were used to obtain partially overlapping amplicons, covering the RT gene from codons 1 to 288 and the complete overlapping HBsAg sequence. A 1% mutation frequency was selected as the cutoff based on an error rate estimated on plasmid DNA. This technology enabled simultaneous analysis of between 2,852 and 18,016 clonally amplified fragments from each patient. The results indicate that UDPS has a relative sensitivity much higher than both direct sequencing and LiPA. In addition, the UDPS results are quantitative, allowing establishment of the relative frequency of both known mutations and novel substitutions. Some of the detected RT substitutions led to changes also in HBsAg. On the whole, genotype D presented a higher heterogeneity than genotype A. Considering the high quantity of information that can be provided by a single test from one patient, the short turnaround time, the information on substitution frequency, and the detection of rare variants, there are strong advantages conferred by UDPS, and the new method could play a relevant role in the clinical management of HBV infection and therapy.

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* Corresponding author. Mailing address: Laboratory of Virology, National Institute for Infectious Diseases (INMI) L. Spallanzani, Via Portuense 292, 00149 Rome, Italy. Phone: 390655170434. Fax: 39065594555. E-mail: capobianchi{at}inmi.it

Published ahead of print on 10 December 2008.

Supplemental material for this article may be found at http://jvi.asm.org/.

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Journal of Virology, February 2009, p. 1718-1726, Vol. 83, No. 4
0022-538X/09/$08.00+0     doi:10.1128/JVI.02011-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

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