Utility of a Sequence-Independent, Single-Primer-Amplification (SISPA) and Nanopore Sequencing Approach for Detection and Characterization of Tick-Borne Viral Pathogens

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dc.authorid0000-0001-5008-9443
dc.authorid0000-0002-5493-0807
dc.authorid0000-0001-5422-1982
dc.authorid0000-0002-3301-6215
dc.authorid0000-0001-8185-3176
dc.authorscopusid55258915300
dc.authorscopusid57222107690
dc.authorscopusid57221541784
dc.authorscopusid37032155300
dc.authorscopusid26326680200
dc.authorscopusid15769247000
dc.authorscopusid52263886700
dc.authorwosidhacioglu, sabri/ABG-9827-2021
dc.authorwosidOzkul, Aykut/A-1973-2016
dc.authorwosidERGUNAY, KORAY/I-8368-2013
dc.contributor.authorBrinkmann, Annika
dc.contributor.authorUddin, Steven
dc.contributor.authorKrause, Eva
dc.contributor.authorSurtees, Rebecca
dc.contributor.authorDinçer, Ender
dc.contributor.authorKar, Sırrı
dc.contributor.authorNitsche, Andreas
dc.date.accessioned2022-05-11T14:28:43Z
dc.date.available2022-05-11T14:28:43Z
dc.date.issued2021
dc.departmentFakülteler, Fen Edebiyat Fakültesi, Biyoloji Bölümü
dc.description.abstractCurrently, next generation sequencing (NGS) is the mainly used approach for identification and monitorization of viruses with a potential public health threat in clinical and environmental samples. To facilitate detection in NGS, the sequence-independent, single-primer-amplification (SISPA) is an effective tool for enriching virus sequences. We performed a preliminary assessment of SISPA-nanopore sequencing as a potential approach for screening tick-borne viruses in six specimens with detectable Crimean-Congo hemorrhagic fever virus (CCHFV) and Jingmen tick virus (JMTV) sequences. A comparison of unbiased NGS and SISPA followed by nanopore sequencing was carried out in 4 specimens with single and pooled ticks. The approach was further used for genome sequencing in culture-grown viruses. Overall, total/virus-specific read counts were significantly elevated in cell culture supernatants in comparison to single or pooled ticks. Virus genomes could be successfully characterized by SISPA with identities over 99%. Genome coverage varied according to the segment and total read count. Base calling errors were mainly observed in tick specimens and more frequent in lower viral loads. Culture-grown viruses were phylogenetically-related to previously-reported local viruses. In conclusion, the SISPA + nanopore sequencing was successful in generating data comparable to NGS and will provide an effective tool for broad-range virus detection in ticks.
dc.identifier.doi10.3390/v13020203
dc.identifier.issn1999-4915
dc.identifier.issue2en_US
dc.identifier.pmid33572847
dc.identifier.scopus2-s2.0-85101468296
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://doi.org/10.3390/v13020203
dc.identifier.urihttps://hdl.handle.net/20.500.11776/6918
dc.identifier.volume13
dc.identifier.wosWOS:000623315000001
dc.identifier.wosqualityQ2
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.institutionauthorKar, Sırrı
dc.language.isoen
dc.publisherMdpi
dc.relation.ispartofViruses-Basel
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectNGS
dc.subjectSISPA
dc.subjectcrimean-congo hemorrhagic fever
dc.subjectjingmen tick virus
dc.subjecttick
dc.titleUtility of a Sequence-Independent, Single-Primer-Amplification (SISPA) and Nanopore Sequencing Approach for Detection and Characterization of Tick-Borne Viral Pathogens
dc.typeArticle

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