Utility of a Sequence-Independent, Single-Primer-Amplification (SISPA) and Nanopore Sequencing Approach for Detection and Characterization of Tick-Borne Viral Pathogens
| Autor: | Aykut Ozkul, Koray Ergünay, Steven Uddin, Andreas Nitsche, Rebecca Surtees, Sirri Kar, Sabri Hacıoğlu, Annika Brinkmann, Ender Dinçer, Eva Krause |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Crimean–Congo hemorrhagic fever crimean-congo hemorrhagic fever viruses 030106 microbiology lcsh:QR1-502 jingmen tick virus Genome Viral Tick Genome DNA sequencing Virus lcsh:Microbiology 03 medical and health sciences Ticks Virology medicine Animals ddc:610 Phylogeny DNA Primers biology Communication Flaviviridae SISPA High-Throughput Nucleotide Sequencing biology.organism_classification medicine.disease tick Nanopore Sequencing 030104 developmental biology Infectious Diseases NGS Hemorrhagic Fever Virus Crimean-Congo Base calling Nanopore sequencing 610 Medizin und Gesundheit Viral load Arboviruses |
| Zdroj: | Viruses Viruses, Vol 13, Iss 203, p 203 (2021) |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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