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Updated: Aug 7, 2026
Detection of Low Copy Number Integrated Viral DNA Formed by In Vitro Hepatitis B Infection
Published on: November 7, 2018
Deep sequencing of hepatitis B virus using Ion Torrent fusion primer method
Johan Ringlander1, Maria E Andersson1, Kasthuri Prakash2
1Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden; Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.
Background:
Hepatitis B virus (HBV) infection is worldwide a major cause of liver cirrhosis and hepatocellular carcinoma. Thousands of years ago, several HBV genotypes (A-I) evolved and have, as a result of human migration, become globally disseminated. Sequencing of HBV is used for genotyping, and investigation of outbreaks or of antiviral resistance. The present study describes a simplified deep sequencing of the whole HBV genome.
Methods:
Sequencing by Ion Torrent was evaluated and its performance compared with Sanger sequencing on clinical samples.
Results:
Amplification of overlapping segments spanning the entire HBV genome was successful at HBV DNA levels in serum as low as 100 IU/mL. The use of primers carrying adapter tags generated libraries without the need for fragmentation and ligation steps, and inclusion of barcode sequences allowed parallel analysis of multiple samples. A streamlined bioinformatic platform generated consensus sequences and superior mutation assessment as compared with Sanger sequencing, with which there was a 99.8 % average agreement.
Conclusion:
Deep sequencing of the whole HBV genome by using PCR primers tagged with adapters that prepare overlapping amplicons for Ion Torrent analysis was efficient and accurate.
