Utility of a Sequence-Independent, Single-Primer-Amplification (SISPA) and Nanopore Sequencing Approach for Detection and Characterization of Tick-Borne Viral Pathogens
Abstract
:1. Introduction
2. Materials and Methods
2.1. Specimens, NGS and SISPA
2.2. Sequence Handling and Phylogenetic Analysis
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Kumar, A.; Murthy, S.; Kapoor, A. Evolution of selective-sequencing approaches for virus discovery and virome analysis. Virus Res. 2017, 239, 172–179. [Google Scholar] [CrossRef] [PubMed]
- Quick, J.; Loman, N.J.; Duraffour, S.; Simpson, J.T.; Severi, E.; Cowley, L.; Bore, J.A.; Koundouno, R.; Dudas, G.; Mikhail, A.; et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 2016, 530, 228–232. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Fernandez-Cassi, X.; Rusiñol, M.; Martínez-Puchol, S. Viral concentration and amplification from human serum samples prior to application of next-generation sequencing analysis. Methods Mol. Biol. 2018, 1838, 173–188. [Google Scholar] [PubMed]
- Chrzastek, K.; Lee, D.H.; Smith, D.; Sharma, P.; Suarez, D.L.; Pantin-Jackwood, M.; Kapczynski, D.R. Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses. Virology 2017, 509, 159–166. [Google Scholar] [CrossRef] [PubMed]
- Rosseel, T.; Scheuch, M.; Höper, D.; De Regge, N.; Caij, A.B.; Vandenbussche, F.; Van Borm, S. DNase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe. PLoS ONE 2012, 7, e41967. [Google Scholar] [CrossRef] [PubMed]
- Lewandowski, K.; Xu, Y.; Pullan, S.T.; Lumley, S.F.; Foster, D.; Sanderson, N.; Vaughan, A.; Morgan, M.; Bright, N.; Kavanagh, J.; et al. Metagenomic nanopore sequencing of influenza virus direct from clinical respiratory samples. J. Clin. Microbiol. 2019, 58, e00963-19. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Mansfield, K.L.; Jizhou, L.; Phipps, L.P.; Johnson, N. Emerging tick-borne viruses in the twenty-first century. Front. Cell. Infect. Microbiol. 2017, 7, 298. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- World Health Organization. Prioritizing Diseases for Research and Development in Emergency Contexts. Available online: www.who.int/blueprint/priority-diseases/en/ (accessed on 28 December 2020).
- Kuhn, J.H.; Wiley, M.R.; Rodriguez, S.E.; Bào, Y.; Prieto, K.; Travassos da Rosa, A.P.; Guzman, H.; Savji, N.; Ladner, J.T.; Tesh, R.B.; et al. Genomic characterization of the genus Nairovirus (family Bunyaviridae). Viruses 2016, 8, 164. [Google Scholar] [CrossRef] [PubMed]
- Jia, N.; Liu, H.B.; Ni, X.B.; Bell-Sakyi, L.; Zheng, Y.C.; Song, J.L.; Li, J.; Jiang, B.G.; Wang, Q.; Sun, Y.; et al. Emergence of human infection with Jingmen tick virus in China: A retrospective study. EBioMedicine 2019, 43, 317–324. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Qin, X.C.; Shi, M.; Tian, J.H.; Lin, X.D.; Gao, D.Y.; He, J.R.; Wang, J.B.; Li, C.X.; Kang, Y.J.; Yu, B.; et al. A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proc. Natl. Acad. Sci. USA 2014, 111, 6744–6749. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zhang, X.; Wang, N.; Wang, Z.; Liu, Q. The discovery of segmented flaviviruses: Implications for viral emergence. Curr. Opin. Virol. 2020, 40, 11–18. [Google Scholar] [CrossRef] [PubMed]
- Dinçer, E.; Hacıoğlu, S.; Kar, S.; Emanet, N.; Brinkmann, A.; Nitsche, A.; Özkul, A.; Linton, Y.M.; Ergünay, K. Survey and characterization of Jingmen tick virus variants. Viruses 2019, 11, 1071. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ergünay, K.; Dinçer, E.; Kar, S.; Emanet, N.; Yalçınkaya, D.; Polat Dinçer, P.F.; Brinkmann, A.; Hacıoğlu, S.; Nitsche, A.; Özkul, A.; et al. Multiple orthonairoviruses including Crimean-Congo hemorrhagic fever virus, Tamdy virus and the novel Meram virus in Anatolia. Ticks Tick Borne Dis. 2020, 11, 101448. [Google Scholar] [CrossRef] [PubMed]
- Moreno, G.; O’connor, D. Sequence-Independent, Single-Primer Amplification of RNA viruses V.4. Protocols 2020. [Google Scholar] [CrossRef]
- Available online: https://www.protocols.io/view/sequence-independent-single-primer-amplification-o-bhk4j4yw (accessed on 19 December 2020).
- Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215, 403–410. [Google Scholar] [CrossRef]
- Thompson, J.D.; Higgins, D.G.; Gibson, T.J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22, 4673–4680. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Kumar, S.; Stecher, G.; Li, M.; Knyaz, C.; Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 2018, 35, 1547–1549. [Google Scholar] [CrossRef] [PubMed]
- Parras-Moltó, M.; Rodríguez-Galet, A.; Suárez-Rodríguez, P.; López-Bueno, A. Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses. Microbiome 2018, 6, 119. [Google Scholar] [CrossRef] [PubMed]
- Brinkmann, A.; Ergünay, K.; Radonić, A.; Kocak Tufan, Z.; Domingo, C.; Nitsche, A. Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics. PLoS Negl. Trop. Dis. 2017, 11, e0006075. [Google Scholar] [CrossRef] [PubMed]
Specimen | Content | Target | Read Count | Ratio | ||||
---|---|---|---|---|---|---|---|---|
NGS | SISPA | |||||||
Total | Specific | Total | Specific | Total | Specific | |||
1 | Single tick (Rhipicephalus turanicus) | CCHFV | 885,295 | 35,471 | 84,421 | 61 | 10.5 | 581.5 |
2 | Single tick (Rhipicephalus sanguineus s. l.) | CCHFV | 1,319,498 | 14,073 | 136,582 | 404 | 9.7 | 34.8 |
3 | Pooled ticks (Rhipicephalus bursa) 9 individuals | CCHFV | 1,009,534 | 331,006 | 82,513 | 2054 | 12.2 | 161.2 |
4 | Pooled ticks (Rhipicephalus bursa) 15 individuals | JMTV | 1,852,008 | 467,009 | 33,024 | 294 | 56.1 | 1588.5 |
5 | Cell culture supernatant | CCHFV | n.a. | n.a. | 433,112 | 1630 | n.a. | n.a. |
6 | Cell culture supernatant | JMTV | n.a. | n.a. | 111,482 | 14,407 | n.a. | n.a. |
Virus | Origin | Genome Segment/Gene | Sequence Length | Coverage | Identity | Indels | Substitutions | Ambiguities | Homopolymers Corrected | |
---|---|---|---|---|---|---|---|---|---|---|
NGS | SISPA | |||||||||
CCHFV | Specimen 1 | L | 12,122 | 7347 | 60.6% | 99.8% | 4 | 2 | 3 | 22 |
M | 5352 | − | − | − | − | − | − | |||
S | 1573 | 1372 | 87.2% | 99.5% | 1 | 1 | 5 | 2 | ||
Specimen 2 | L | 12,122 | 11,725 | 96.7% | 99.9% | 1 | 3 | 7 | 20 | |
M | 5404 | 1878 | 34.7% | 99.6% | 5 | − | 3 | 5 | ||
S | 1573 | 989 | 62.8% | 99.8% | 1 | − | − | 1 | ||
Specimen 3 | L | 12,122 | 12,099 | 99.8% | 99.9% | − | 2 | 11 | ||
M | 5352 | 5338 | 99.7% | 99.8% | 1 | 2 | 1 | 14 | ||
S | 1573 | 1568 | 99.6% | 100% | − | − | − | 1 | ||
Specimen 5 a | L | 12,121 | 12,116 | 99.9% | n.a. | − | n.a. | − | 11 | |
M | 5332 | 5314 | 99.6% | n.a. | − | n.a. | 1 | 11 | ||
S | 1621 | 1597 | 98.5% | n.a. | − | n.a. | 1 | 4 | ||
JMTV | Specimen 4 | 1 (NSP1) | 2894 | 2732 | 94% | 99.9% | 1 | 1 | 1 | 6 |
2 (VP1) | 2549 | 2087 | 81.8% | 99.8% | − | 1 | 2 | 8 | ||
3 (NSP2) | 2643 | 2538 | 96.0% | 99.9% | − | 2 | − | 3 | ||
4 (VP2/3) | 2635 | 1547 | 58.7% | 99.2% | 4 | 5 | 2 | 4 | ||
Specimen 6 b | 1 (NSP1) | 2894 | 2879 | 99.4% | 99.9% | 1 | 0.1 | − | 11 | |
2 (VP1) | 2549 | 2514 | 98.6% | 99.8% | − | 0.3 | − | 10 | ||
3 (NSP2) | 2643 | 2610 | 98.7% | 100% | − | − | − | 2 | ||
4 (VP2/3) | 2635 | 2592 | 98.3% | 99.8% | − | 0.4 | − | 5 |
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Brinkmann, A.; Uddin, S.; Krause, E.; Surtees, R.; Dinçer, E.; Kar, S.; Hacıoğlu, S.; Özkul, A.; Ergünay, K.; Nitsche, A. Utility of a Sequence-Independent, Single-Primer-Amplification (SISPA) and Nanopore Sequencing Approach for Detection and Characterization of Tick-Borne Viral Pathogens. Viruses 2021, 13, 203. https://doi.org/10.3390/v13020203
Brinkmann A, Uddin S, Krause E, Surtees R, Dinçer E, Kar S, Hacıoğlu S, Özkul A, Ergünay K, Nitsche A. Utility of a Sequence-Independent, Single-Primer-Amplification (SISPA) and Nanopore Sequencing Approach for Detection and Characterization of Tick-Borne Viral Pathogens. Viruses. 2021; 13(2):203. https://doi.org/10.3390/v13020203
Chicago/Turabian StyleBrinkmann, Annika, Steven Uddin, Eva Krause, Rebecca Surtees, Ender Dinçer, Sırrı Kar, Sabri Hacıoğlu, Aykut Özkul, Koray Ergünay, and Andreas Nitsche. 2021. "Utility of a Sequence-Independent, Single-Primer-Amplification (SISPA) and Nanopore Sequencing Approach for Detection and Characterization of Tick-Borne Viral Pathogens" Viruses 13, no. 2: 203. https://doi.org/10.3390/v13020203