DOI: 10.1101/470633Nov 14, 2018Paper

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

BioRxiv : the Preprint Server for Biology
Anna L McNaughtonPhilippa C Matthews


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 facilitated by the large-scale generation of full-length virus genome data. Here we describe advances to a protocol to exploit the circular HBV genome structure, using isothermal rolling-circle amplification to enrich for HBV DNA and to generate 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 comparing reads generated from plus and minus strands. Thus we can achieve improved consensus sequencing accuracy of 99.7% and resolve intra-sample sequence variants to form whole-genome haplotypes. The combination of isothermal amplification and Nanopore sequencing offers the longer-term potential to develop point-of-care tests for HBV, whic...Continue Reading

Related Concepts

Drug Resistance
Hepatitis B Virus
Disease Transmission
DNA Amplification
DNA Amplification Techniques

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