Innovation – Open view page
General information
| Innovation ID | 301 |
| Version ID | 37 |
| Innovation Title | VirusDetect: high-throughput sequencing of small RNAs for virus detection |
| Innovation description | VirusDetect is a bioinformatics pipeline that efficiently analyzes large scale small RNA (sRNA) datasets for both known and novel virus identification. The technology has proven to be highly efficient, sensible and reliable in plant and animal virus detection. |
| Reporting Staff | Jan Kreuze (CIP) |
| Year (Reporting) | 2019 |
| Reporting status | Approved |
| Innovation Type | Research and Communication Methodologies and Tools |
Stage reached
| Stage of Innovation | Stage 4: uptake by next user |
| Year (Stage) | 2019 |
| Stage Description | 3 NARS have been applying the technology to identify viruses affecting important food crops: Mikocheni Agricultural Research Institute (Tanzania) for bean viruses; Gulu University (Uganda) and Crop Research Institute (Ghana) for sweetpotato viruses. Kenya Plant Health Inspectorate Service (Kenya) is planning to use the technology for sweetpotato viruses. |
| Next User Organization | NARES/NARS |
| Has a lead organization | yes |
| Lead Organization | International Potato Center |
| Top 5 contributors | No contributors |
Contributions and mapping
| All partners | Boyce Thompson Institute-Advanced Research Institutions; French National Research Institute for Agriculture, Food and Environment-Advanced Research Institutions; Hasselt University-Academic Institutions (universities, colleges, etc.); International Potato Center-CGIAR Center/Program (Center); United States Department of Agriculture-Government; University of Liège, Faculty of Gembloux Agro‐Bio Tech-Academic Institutions (universities, colleges, etc.) |
| Main CRP | CGIAR Research Program on Roots, Tubers and Bananas |
| Flagship project | FP3-Resilient RTB crops |
| Cluster | CC3.1-Management of RTB-critical pests and diseases under changing climates, through risk assessment, surveillance, enhanced modeling, and advanced IPM |
| Other CRPs-Flagships-Clusters |
Scope
| Geographic scope | Global |
| Regions | |
| Countries |
Targeted outcomes
| Main Sub-IDO | Enhanced individual capacity in partner research organizations through training and exchange |
| Other Sub-IDO | Increased resilience of agro-ecosystems and communities, especially those including smallholders |
| Other Sub-IDO |
Evidences
| Evidences | "S. Massart, Michela Chiumenti, Kris De Jonghe, Rachel Glover, Annelies Haegeman, Igor Koloniuk, Petr Kominek, Jan Kreuze, Denis Kutnjak, Leonidas Lotos, Francois Maclot, Varvara Maliogka, Hans Maree, Thibaut Olivier, Antonio Olmos, Mikhail Pooggin, Jean-Sebastien Reynard, Ana Ruiz-Garcia, Dana Safarova, Pierre Schneeberger, Noa Sela, Silvia Turco, Eeva Vainio, Eva Varallyay, Eric Verdin, Marcel Westenberg, Yves Brostaux Brostaux, Thierry Candresse. (7/2/2019). Virus Detection by High-Throughput Sequencing of Small RNAs: Large-Scale Performance Testing of Sequence Analysis Strategies. Phytopathology, 109 (3)."Kreuze, J.F., Perez, A., Untiveros, M., Quispe, D., Fuentes, S., Barker, I., Simon, R., 2009. Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology 388, 1–7. [https://doi.org/10.1016/j.virol.2009.03.024] Pooggin MM (2018) Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization. Front. Microbiol. 9:2779. [https://doi.org/10.3389/fmicb.2018.02779] Small RNA sequencing and assembly for virus detection (Training sessions) [https://sites.google.com/cgxchange.org/srsa-workshop-lima2018/home] Godfrey Wokorach, Geoffrey Otim, Joyce Njuguna, Hilary Edema, Vincent Njung'e, Eunice M. Machuka, Nasser Yao, Francesca Stomeo, Richard Echodu, Genomic analysis of Sweet potato feathery mottle virus from East Africa, Physiological and Molecular Plant Pathology, Volume 110, 2020, 101473, ISSN 0885-5765 [https://doi.org/10.1016/j.pmpp.2020.101473] Nordenstedt N, Marcenaro D, Chilagane D, Mwaipopo B, Rajama¨ki M-L, Nchimbi-Msolla S, et al. (2017) Pathogenic seedborne viruses are rare but Phaseolus vulgaris endornaviruses are common in bean varieties grown in Nicaragua and Tanzania. PLoS ONE 12(5): e0178242 [https://doi.org/10.1371/journal.pone.0178242] Comprehensive Surveys of Bean common mosaic virus and Bean common mosaic necrosis virus and Molecular Evidence for Occurrence of Other Phaseolus vulgaris Viruses in Tanzania Beatrice Mwaipopo, Susan Nchimbi-Msolla, Paul J. R. Njau, Deogratius Mark, and Deusdedith R. Mbanzibwa Plant Disease 2018 102:11, 2361-2370 [https://doi.org/10.1094/PDIS-01-18-0198-RE] "Yi Zheng, Shan Gao, Chellappan Padmanabhan, Rugang Li, Marco Galvez, Dina Gutierrez, Segundo Fuentes Delgado, Kai-Shu Ling, Jan Kreuze, Zhangjun Fei. (30/1/2017). VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs. Virology, 500, pp. 130-138."VirusDetect Home - Website [https://research.cip.cgiar.org/confluence/display/VIR/VirusDetect+Home] |
Linked Elements
| Milestones |
| Outcome Impact Case | Small RNA sequencing and VirusDetect a bioinformatics pipeline that assist in the detection of known and new and novel viruses is being used beyond RTB https://hdl.handle.net/20.500.11766.1/52f13f |
| Policy |