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

• Published in: Viruses Vol. 13; no. 2; p. 203
• Main Authors: Brinkmann, Annika, Uddin, Steven, Krause, Eva, Surtees, Rebecca, Dinçer, Ender, Kar, Sırrı, Hacıoğlu, Sabri, Özkul, Aykut, Ergünay, Koray, Nitsche, Andreas
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 29.01.2021; MDPI
• Subjects: Animals; Arachnids; Arboviruses - genetics; Arboviruses - isolation & purification; Cell culture; Communication; Crimean hemorrhagic fever; crimean-congo hemorrhagic fever; DNA Primers - genetics; Flaviviridae - genetics; Flaviviridae - isolation & purification; Genome, Viral - genetics; Genomes; Hemorrhage; Hemorrhagic Fever Virus, Crimean-Congo - genetics; Hemorrhagic Fever Virus, Crimean-Congo - isolation & purification; High-Throughput Nucleotide Sequencing; jingmen tick virus; Nanopore Sequencing - methods; Next-generation sequencing; NGS; Pathogens; Phylogeny; Public health; SISPA; tick; Ticks - virology; Vectors (Biology); Viruses; United States > US; Germany; SISPA; crimean-congo hemorrhagic fever; NGS; jingmen tick virus; tick
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v13020203

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.