Funding period: 2020-2023
Leads: Peter Kruczkiewicz and Oliver Lung
Total GRDI funding: $139,000
High-throughput sequencing (HTS) has been widely adopted as the primary diagnostic method for high-resolution pathogen characterization through international initiatives such as PulseNet. It allows unambiguous high-resolution whole-genome identification of microbial pathogens. However due to the large volume and high complexity of the data, significant challenges exist in storing, managing, processing, analyzing, and reporting HTS data in a performant, secure, and accessible way compliant with international QA standards. These challenges are amplified when sequencing viruses with different genome structures requiring extensive documentation of wet-lab processes to guide downstream HTS data analysis. Across CFIA and the scientific community, a variety of free, open-source software systems are used to handle data management, analysis, and reporting. This project aims to develop and expand bioinformatics pipelines and tools for the analysis of animal virus sequence data and animal health diagnostics.
Publications
- Caliendo, V, Lewis, NS, Pohlmann, A, Baillie, SR, Banyard, AC, Beer, M, Brown, IH, Fouchier, RAM, Hansen, RDE, Lameris, TK, Lang, AS, Laurendeau, S, Lung, O, Robertson, G, van der Jeugd, H, Alkie, TN, Thorup, K, van Toor, ML, Waldenström, J, Yason, C, Kuiken, T, Berhane, Y. 2022. Transatlantic spread of highly pathogenic avian influenza H5N1 by wild birds from Europe to North America in 2021. Scientific Reports, [online] 12(1), https://doi.org/10.1038/s41598-022-13447-z
- Harrison, TMR, Rudar, J, Ogden, N, Steeves, R, Lapen, DR, Baird, D, Gagné, N, Lung, O. 2022. In silico identification of multiple conserved motifs within the control region of Culicidae mitogenomes. Scientific Reports, [online] 12(1), https://doi.org/10.1038/s41598-022-26236-5
- Pickering, B, Lung, O, Maguire, F, Kruczkiewicz, P, Kotwa, JD, Buchanan, T, Gagnier, M, Guthrie, JL, Jardine, CM, Marchand-Austin, A, Massé, A, McClinchey, H, Nirmalarajah, K, Aftanas, P, Blais-Savoie, J, Chee, HY, Chien, E, Yim, W, Banete, A, Griffin, BD, 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, AJ, 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
- 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
Contact us
For additional information, please contact:
Genomics R&D Initiative
Email: info@grdi-irdg.collaboration.gc.ca