Funding period: 2023-2026
Leads: Oliver Lung
Total GRDI funding: $202,000
The CFIA National Centre for Foreign Animal Disease (NCFAD) conducts essential surveillance and diagnostic testing for high-consequence animal diseases. The Genomics Unit operates a unique sequencing lab in containment level 3 to accurately identify and characterize high-risk pathogens. However, the unit has seen a significant increase in sample sequencing requests. This project will improve the unit's efficiency by implementing new methods for Oxford Nanopore Technologies and Illumina sequencers to replace expensive and outdated methods, thereby streamlining operations, reducing costs, and enhancing the lab's response capabilities to animal health threats.
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
Scripts for automation of Nextera XT library preparation on Hamilton NGS STAR liquid-handling system. Contributors: O. Lung, D. Sullivan, O. Vernygora, M. Fisher, K. Handel
SOP Rapid Sequencing of Avian Influenza Virus (AIV) Amplicons on the Oxford Nanopore GridION. Contributors: O. Lung
Custom Agilent NGS SureSelect Fish virus panel. Contributors: O. Lung, O. Vernygora
Custom MyBaits fish virus enrichment capture probe panel. Contributors: O. Lung, O. Vernygora
Custom Agilent SureSelect non-mosquito virus enrichment capture probe panel. Contributors: O. Lung, D. Sullivan
Custom Agilent SureSelect mosquito virus enrichment capture probe panel design. Contributors: O. Lung, D. Sullivan
Custom MyBaits pan-coronavirus enrichment capture probe panel. Contributors: O. Lung, M. Nebroski
Custom AmpliSeq for Illumina pan-coronavirus primer panel. Contributors: O. Lung, M. Nebroski
Custom Illumina DNA Prep with Enrichment pan-arbovirus capture probe panel design. Contributors: O. Lung, D. Sullivan
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
Lung, O., Fisher, M., Nebroski, M., McGregor, G., Schwantje, H., Joseph, T. (2022). Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada. Microbiology Resource Announcements, [online] 11(10), https://doi.org/10.1128/mra.00662-22
Pickering, B., Lung, O., Maguire, F., Kruczkiewicz, P., Kotwa, J.D., Buchanan, T., Gagnier, M., Guthrie, J.L., Jardine, C.M., Marchand-Austin, A., Massé, A., McClinchey, H., Nirmalarajah, K., Aftanas, P., Blais-Savoie, J., Chee, H.Y., Chien, E., Yim, W., Banete, A., Griffin, B.D., Yip, L., Goolia, M., Suderman, M., Pinette, M., Smith, G., Sullivan, D., Rudar, J., Vernygora, O., Adey, E., Nebroski, M., Goyette, G., Finzi, A., Laroche, G., Ariana, A., Vahkal, B., Côté, M., McGeer, A.J., Nituch, L., Mubareka, S., Bowman, J. (2022). Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission. Nature Microbiology, [online] 7(12), 2011-2024. https://doi.org/10.1038/s41564-022-01268-9
Sultana, A., Bienzle, D., Weese, S., Pickering, B., Kruczkiewicz, P., Smith, G., Pinette, M., Lung, O. (2024). Whole-genome sequencing of SARS-CoV-2 from the initial cases of domestic cat infections in Canada. Microbiology Resource Announcements, [online] 13(4) https://doi.org/10.1128/mra.01295-23
Contact us
Genomics R&D Initiative
Email: info@grdi-irdg.collaboration.gc.ca