Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)

Anna L McNaughton, Hannah E Roberts, David Bonsall, Mariateresa de Cesare, Jolynne Mokaya, Sheila F Lumley, Tanya Golubchik, Paolo Piazza, Jacqueline B Martin, Catherine de Lara, Anthony Brown, M Azim Ansari, Rory Bowden, Eleanor Barnes, Philippa C Matthews

Research output: Contribution to journalArticle (Academic Journal)peer-review

Abstract

Advancing interventions to tackle the huge global burden of hepatitis B virus (HBV) infection depends on improved insights into virus epidemiology, transmission, within-host diversity, drug resistance and pathogenesis, all of which can be advanced through the large-scale generation of full-length virus genome data. Here we describe advances to a protocol that exploits the circular HBV genome structure, using isothermal rolling-circle amplification to enrich HBV DNA, generating concatemeric amplicons containing multiple successive copies of the same genome. We show that this product is suitable for Nanopore sequencing as single reads, as well as for generating short-read Illumina sequences. Nanopore reads can be used to implement a straightforward method for error correction that reduces the per-read error rate, by comparing multiple genome copies combined into a single concatemer and by analysing reads generated from plus and minus strands. With this approach, we can achieve an improved consensus sequencing accuracy of 99.7% and resolve intra-sample sequence variants to form whole-genome haplotypes. Thus while Illumina sequencing may still be the most accurate way to capture within-sample diversity, Nanopore data can contribute to an understanding of linkage between polymorphisms within individual virions. The combination of isothermal amplification and Nanopore sequencing also offers appealing potential to develop point-of-care tests for HBV, and for other viruses.

Original languageEnglish
Pages (from-to)7081
JournalScientific Reports
Volume9
Issue number1
DOIs
Publication statusPublished - 8 May 2019

Keywords

  • Adolescent
  • Adult
  • Cohort Studies
  • Data Accuracy
  • Female
  • Genome, Viral/genetics
  • Haplotypes
  • Hepatitis B/genetics
  • Hepatitis B virus/genetics
  • High-Throughput Nucleotide Sequencing/methods
  • Humans
  • Male
  • Nanopore Sequencing/methods
  • Plasmids/genetics
  • Polymorphism, Genetic
  • Viral Load/genetics
  • Whole Genome Sequencing/methods
  • Young Adult

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