Using Nanopore sequencing technology to reduce/eliminate costly and time-consuming laboratory-based enrichment
Funding period: 2022–2025
Leads: Oliver Lung and Peter Kruczkiewicz
Total GRDI funding: $112,500
The CFIA National Centre for Foreign Animal Disease (NCFAD) conducts essential diagnostic and surveillance testing for high-risk animal diseases. Since NCFAD deals with diverse known and unknown pathogens and host species, sequencing has become crucial for identifying and analyzing pathogens. However, laboratory-based protocols required to enrich for virus DNA and RNA may add several days to sequencing turnaround times. This project will assess and implement new adaptive sampling technology for Oxford Nanopore sequencers to enrich for viruses on the sequencer itself while reducing costs and labour and minimizing hands-on laboratory work.
Research tool/process
- Scripts for automation of Oxford Nanopore LSK-114 library preparation on the Hamilton NGS STAR liquid-handling system. Contributors: O. Lung, D. Sullivan, O. Vernygora
Publications
- Domshy, K.A., Lung, O., Nebroski, M., Kruczkiewicz, P., Ayilara, I., Woods, L.W., Lowe, E., Davies, J.L. (2023). Adenoviral hemorrhagic disease in a farmed elk (Cervus canadensis) in Alberta, Canada. The Canadian Veterinary Journal 64(6): 524-528. (No DOI available)
- Ambagala, A., Goonewardene, K., Kanoa, I.E., Than, T.T., Nguyen, V.T., Lai, T.N.H., Nguyen, T.L., Erdelyan, C.N.G., Robert, E., Tailor, N., Onyilagha, C., Lamboo, L., Handel, K., Nebroski, M., Vernygora, O., Lung, O., Le, V.P. 2024. Characterization of an African Swine Fever Virus Field Isolate from Vietnam with Deletions in the Left Variable Multigene Family Region. Viruses. 16(4) DOI: https://doi.org/10.3390/v16040571
- Oksana V., Sullivan D., Nielsen O., Huntington, K.B., Rouse, N., Popov, V., Lung, O. 2024. Senecavirus cetus a novel picornavirus isolated from cetaceans represents a major host switching to the marine environment. PREPRINT https://doi.org/10.21203/rs.3.rs-3900733/v1
Contact us
For additional information, please contact:
Genomics R&D Initiative
Email: info@grdi-irdg.collaboration.gc.ca