Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides.
Amino Acid Motifs
Amino Acid Sequence
DNA Viruses
/ genetics
Defective Viruses
/ genetics
Epigenome
Genome, Viral
Molecular Sequence Annotation
Nanopore Sequencing
Orthopoxvirus
/ genetics
Protein Sorting Signals
/ genetics
Sequence Analysis, DNA
/ methods
Sequence Deletion
Software
Species Specificity
United Arab Emirates
Vaccines, Attenuated
Vaccinia virus
/ genetics
Viral Proteins
/ genetics
Viral Vaccines
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
07 09 2021
07 09 2021
Historique:
received:
20
09
2020
accepted:
19
08
2021
entrez:
8
9
2021
pubmed:
9
9
2021
medline:
17
11
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34493784
doi: 10.1038/s41598-021-97158-x
pii: 10.1038/s41598-021-97158-x
pmc: PMC8423768
doi:
Substances chimiques
Protein Sorting Signals
0
Vaccines, Attenuated
0
Viral Proteins
0
Viral Vaccines
0
Types de publication
Comparative Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
17758Informations de copyright
© 2021. The Author(s).
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