dc.contributor.author | Brinkmann, Annika | |
dc.contributor.author | Uddin, Steven | |
dc.contributor.author | Krause, Eva | |
dc.contributor.author | Surtees, Rebecca | |
dc.contributor.author | Dinçer, Ender | |
dc.contributor.author | Kar, Sırrı | |
dc.contributor.author | Nitsche, Andreas | |
dc.date.accessioned | 2022-05-11T14:28:43Z | |
dc.date.available | 2022-05-11T14:28:43Z | |
dc.date.issued | 2021 | |
dc.identifier.issn | 1999-4915 | |
dc.identifier.uri | https://doi.org/10.3390/v13020203 | |
dc.identifier.uri | https://hdl.handle.net/20.500.11776/6918 | |
dc.description.abstract | Currently, 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. | en_US |
dc.language.iso | eng | en_US |
dc.publisher | Mdpi | en_US |
dc.identifier.doi | 10.3390/v13020203 | |
dc.rights | info:eu-repo/semantics/openAccess | en_US |
dc.subject | NGS | en_US |
dc.subject | SISPA | en_US |
dc.subject | crimean-congo hemorrhagic fever | en_US |
dc.subject | jingmen tick virus | en_US |
dc.subject | tick | en_US |
dc.title | Utility of a Sequence-Independent, Single-Primer-Amplification (SISPA) and Nanopore Sequencing Approach for Detection and Characterization of Tick-Borne Viral Pathogens | en_US |
dc.type | article | en_US |
dc.relation.ispartof | Viruses-Basel | en_US |
dc.department | Fakülteler, Fen Edebiyat Fakültesi, Biyoloji Bölümü | en_US |
dc.authorid | 0000-0001-5008-9443 | |
dc.authorid | 0000-0002-5493-0807 | |
dc.authorid | 0000-0001-5422-1982 | |
dc.authorid | 0000-0002-3301-6215 | |
dc.authorid | 0000-0001-8185-3176 | |
dc.identifier.volume | 13 | en_US |
dc.identifier.issue | 2 | en_US |
dc.institutionauthor | Kar, Sırrı | |
dc.relation.publicationcategory | Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı | en_US |
dc.authorscopusid | 55258915300 | |
dc.authorscopusid | 57222107690 | |
dc.authorscopusid | 57221541784 | |
dc.authorscopusid | 37032155300 | |
dc.authorscopusid | 26326680200 | |
dc.authorscopusid | 15769247000 | |
dc.authorscopusid | 52263886700 | |
dc.authorwosid | hacioglu, sabri/ABG-9827-2021 | |
dc.authorwosid | Ozkul, Aykut/A-1973-2016 | |
dc.authorwosid | ERGUNAY, KORAY/I-8368-2013 | |
dc.identifier.wos | WOS:000623315000001 | en_US |
dc.identifier.scopus | 2-s2.0-85101468296 | en_US |
dc.identifier.pmid | 33572847 | en_US |