Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides

Abstract DNA viruses can exploit host cellular epigenetic processes to their advantage; however, the epigenome status of most DNA viruses remains undetermined. Third generation sequencing technologies allow for the identification of modified nucleotides from sequencing experiments without specialize...

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Autores principales:	Zack Saud, Matthew D. Hitchings, Tariq M. Butt
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/910265d96d3141afb85f3f7de68fb1c2
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spelling	oai:doaj.org-article:910265d96d3141afb85f3f7de68fb1c22021-12-02T17:19:15ZNanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides10.1038/s41598-021-97158-x2045-2322https://doaj.org/article/910265d96d3141afb85f3f7de68fb1c22021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97158-xhttps://doaj.org/toc/2045-2322Abstract DNA viruses can exploit host cellular epigenetic processes to their advantage; however, the epigenome status of most DNA viruses remains undetermined. Third generation sequencing technologies allow for the identification of modified nucleotides from sequencing experiments without specialized sample preparation, permitting the detection of non-canonical epigenetic modifications that may distinguish viral nucleic acid from that of their host, thus identifying attractive targets for advanced therapeutics and diagnostics. We present a novel nanopore de novo assembly pipeline used to assemble a misidentified Camelpox vaccine. Two confirmed deletions of this vaccine strain in comparison to the closely related Vaccinia virus strain modified vaccinia Ankara make it one of the smallest non-vector derived orthopoxvirus genomes to be reported. Annotation of the assembly revealed a previously unreported signal peptide at the start of protein A38 and several predicted signal peptides that were found to differ from those previously described. Putative epigenetic modifications around various motifs have been identified and the assembly confirmed previous work showing the vaccine genome to most closely resemble that of Vaccinia virus strain Modified Vaccinia Ankara. The pipeline may be used for other DNA viruses, increasing the understanding of DNA virus evolution, virulence, host preference, and epigenomics.Zack SaudMatthew D. HitchingsTariq M. ButtNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zack Saud Matthew D. Hitchings Tariq M. Butt Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
description	Abstract DNA viruses can exploit host cellular epigenetic processes to their advantage; however, the epigenome status of most DNA viruses remains undetermined. Third generation sequencing technologies allow for the identification of modified nucleotides from sequencing experiments without specialized sample preparation, permitting the detection of non-canonical epigenetic modifications that may distinguish viral nucleic acid from that of their host, thus identifying attractive targets for advanced therapeutics and diagnostics. We present a novel nanopore de novo assembly pipeline used to assemble a misidentified Camelpox vaccine. Two confirmed deletions of this vaccine strain in comparison to the closely related Vaccinia virus strain modified vaccinia Ankara make it one of the smallest non-vector derived orthopoxvirus genomes to be reported. Annotation of the assembly revealed a previously unreported signal peptide at the start of protein A38 and several predicted signal peptides that were found to differ from those previously described. Putative epigenetic modifications around various motifs have been identified and the assembly confirmed previous work showing the vaccine genome to most closely resemble that of Vaccinia virus strain Modified Vaccinia Ankara. The pipeline may be used for other DNA viruses, increasing the understanding of DNA virus evolution, virulence, host preference, and epigenomics.
format	article
author	Zack Saud Matthew D. Hitchings Tariq M. Butt
author_facet	Zack Saud Matthew D. Hitchings Tariq M. Butt
author_sort	Zack Saud
title	Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
title_short	Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
title_full	Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
title_fullStr	Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
title_full_unstemmed	Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
title_sort	nanopore sequencing and de novo assembly of a misidentified camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/910265d96d3141afb85f3f7de68fb1c2
work_keys_str_mv	AT zacksaud nanoporesequencinganddenovoassemblyofamisidentifiedcamelpoxvaccinerevealsputativeepigeneticmodificationsandalternateproteinsignalpeptides AT matthewdhitchings nanoporesequencinganddenovoassemblyofamisidentifiedcamelpoxvaccinerevealsputativeepigeneticmodificationsandalternateproteinsignalpeptides AT tariqmbutt nanoporesequencinganddenovoassemblyofamisidentifiedcamelpoxvaccinerevealsputativeepigeneticmodificationsandalternateproteinsignalpeptides
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Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides

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