No Cover Image

Journal article 715 views 82 downloads

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

Zack Saud, Matthew Hitchings Orcid Logo, Tariq Butt Orcid Logo

Scientific Reports, Volume: 11, Issue: 1

Swansea University Authors: Zack Saud, Matthew Hitchings Orcid Logo, Tariq Butt Orcid Logo

  • 58104.pdf

    PDF | Version of Record

    © The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License

    Download (2.16MB)

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...

Full description

Published in: Scientific Reports
ISSN: 2045-2322
Published: Springer Science and Business Media LLC 2021
Online Access: Check full text

URI: https://cronfa.swan.ac.uk/Record/cronfa58104
Tags: Add Tag
No Tags, Be the first to tag this record!
first_indexed 2021-09-27T09:41:42Z
last_indexed 2021-10-23T03:25:19Z
id cronfa58104
recordtype SURis
fullrecord <?xml version="1.0"?><rfc1807><datestamp>2021-10-22T17:08:38.7374998</datestamp><bib-version>v2</bib-version><id>58104</id><entry>2021-09-27</entry><title>Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides</title><swanseaauthors><author><sid>b4bba3ec2ff9600c4cead048e1969984</sid><firstname>Zack</firstname><surname>Saud</surname><name>Zack Saud</name><active>true</active><ethesisStudent>false</ethesisStudent></author><author><sid>be98847c72c14a731c4a6b7bc02b3bcf</sid><ORCID>0000-0002-5527-4709</ORCID><firstname>Matthew</firstname><surname>Hitchings</surname><name>Matthew Hitchings</name><active>true</active><ethesisStudent>false</ethesisStudent></author><author><sid>85d1c2ddde272a1176e74978e25ebece</sid><ORCID>0000-0002-8789-9543</ORCID><firstname>Tariq</firstname><surname>Butt</surname><name>Tariq Butt</name><active>true</active><ethesisStudent>false</ethesisStudent></author></swanseaauthors><date>2021-09-27</date><deptcode>FGSEN</deptcode><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.</abstract><type>Journal Article</type><journal>Scientific Reports</journal><volume>11</volume><journalNumber>1</journalNumber><paginationStart/><paginationEnd/><publisher>Springer Science and Business Media LLC</publisher><placeOfPublication/><isbnPrint/><isbnElectronic/><issnPrint/><issnElectronic>2045-2322</issnElectronic><keywords/><publishedDay>7</publishedDay><publishedMonth>9</publishedMonth><publishedYear>2021</publishedYear><publishedDate>2021-09-07</publishedDate><doi>10.1038/s41598-021-97158-x</doi><url/><notes>Preprint version of the article is available at 10.21203/rs.3.rs-89149/v1</notes><college>COLLEGE NANME</college><department>Science and Engineering - Faculty</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>FGSEN</DepartmentCode><institution>Swansea University</institution><apcterm/><lastEdited>2021-10-22T17:08:38.7374998</lastEdited><Created>2021-09-27T10:40:12.9150689</Created><path><level id="1">Faculty of Science and Engineering</level><level id="2">School of Biosciences, Geography and Physics - Biosciences</level></path><authors><author><firstname>Zack</firstname><surname>Saud</surname><order>1</order></author><author><firstname>Matthew</firstname><surname>Hitchings</surname><orcid>0000-0002-5527-4709</orcid><order>2</order></author><author><firstname>Tariq</firstname><surname>Butt</surname><orcid>0000-0002-8789-9543</orcid><order>3</order></author></authors><documents><document><filename>58104__21009__1a7fea3c47764c3eb5eb96e7cb5951eb.pdf</filename><originalFilename>58104.pdf</originalFilename><uploaded>2021-09-27T10:41:23.2946277</uploaded><type>Output</type><contentLength>2264866</contentLength><contentType>application/pdf</contentType><version>Version of Record</version><cronfaStatus>true</cronfaStatus><documentNotes>&#xA9; The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License</documentNotes><copyrightCorrect>true</copyrightCorrect><language>eng</language><licence>https://creativecommons.org/licenses/by/4.0/</licence></document></documents><OutputDurs/></rfc1807>
spelling 2021-10-22T17:08:38.7374998 v2 58104 2021-09-27 Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides b4bba3ec2ff9600c4cead048e1969984 Zack Saud Zack Saud true false be98847c72c14a731c4a6b7bc02b3bcf 0000-0002-5527-4709 Matthew Hitchings Matthew Hitchings true false 85d1c2ddde272a1176e74978e25ebece 0000-0002-8789-9543 Tariq Butt Tariq Butt true false 2021-09-27 FGSEN 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. Journal Article Scientific Reports 11 1 Springer Science and Business Media LLC 2045-2322 7 9 2021 2021-09-07 10.1038/s41598-021-97158-x Preprint version of the article is available at 10.21203/rs.3.rs-89149/v1 COLLEGE NANME Science and Engineering - Faculty COLLEGE CODE FGSEN Swansea University 2021-10-22T17:08:38.7374998 2021-09-27T10:40:12.9150689 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Zack Saud 1 Matthew Hitchings 0000-0002-5527-4709 2 Tariq Butt 0000-0002-8789-9543 3 58104__21009__1a7fea3c47764c3eb5eb96e7cb5951eb.pdf 58104.pdf 2021-09-27T10:41:23.2946277 Output 2264866 application/pdf Version of Record true © The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License true eng https://creativecommons.org/licenses/by/4.0/
title Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
spellingShingle Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
Zack Saud
Matthew Hitchings
Tariq Butt
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
author_id_str_mv b4bba3ec2ff9600c4cead048e1969984
be98847c72c14a731c4a6b7bc02b3bcf
85d1c2ddde272a1176e74978e25ebece
author_id_fullname_str_mv b4bba3ec2ff9600c4cead048e1969984_***_Zack Saud
be98847c72c14a731c4a6b7bc02b3bcf_***_Matthew Hitchings
85d1c2ddde272a1176e74978e25ebece_***_Tariq Butt
author Zack Saud
Matthew Hitchings
Tariq Butt
author2 Zack Saud
Matthew Hitchings
Tariq Butt
format Journal article
container_title Scientific Reports
container_volume 11
container_issue 1
publishDate 2021
institution Swansea University
issn 2045-2322
doi_str_mv 10.1038/s41598-021-97158-x
publisher Springer Science and Business Media LLC
college_str Faculty of Science and Engineering
hierarchytype
hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Biosciences, Geography and Physics - Biosciences{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Biosciences, Geography and Physics - Biosciences
document_store_str 1
active_str 0
description 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.
published_date 2021-09-07T04:14:21Z
_version_ 1763753970301403136
score 11.016683