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

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-...

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Autores principales:	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
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/23ce459625d44afd94bf0f71124bebc7
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spelling	oai:doaj.org-article:23ce459625d44afd94bf0f71124bebc72021-12-02T16:08:27ZIllumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)10.1038/s41598-019-43524-92045-2322https://doaj.org/article/23ce459625d44afd94bf0f71124bebc72019-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-43524-9https://doaj.org/toc/2045-2322Abstract 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.Anna L. McNaughtonHannah E. RobertsDavid BonsallMariateresa de CesareJolynne MokayaSheila F. LumleyTanya GolubchikPaolo PiazzaJacqueline B. MartinCatherine de LaraAnthony BrownM. Azim AnsariRory BowdenEleanor BarnesPhilippa C. MatthewsNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-14 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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 Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)
description	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.
format	article
author	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
author_facet	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
author_sort	Anna L. McNaughton
title	Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)
title_short	Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)
title_full	Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)
title_fullStr	Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)
title_full_unstemmed	Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)
title_sort	illumina and nanopore methods for whole genome sequencing of hepatitis b virus (hbv)
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/23ce459625d44afd94bf0f71124bebc7
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Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)

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