About Us

Medical Microbiology and Infectious Diseases - University of Manitoba

Grace’s  research involves obtaining whole genome sequence data of SARS-CoV-2 from clinical samples across Canada and analyzing genomic data to investigate the viral evolution in Canada over the next year of the current COVID-19 pandemic.

  • Samantha LeeJuly 14, 2021 at 2:23 pm

    Hi Grace,

    Can you comment on the sample processing ability of this timeline? As in, how quickly could this timeline be used to examine genomic differences in 100, 10000, etc. samples?

    Is this pipeline current being applied to examine the evolution of newer variants of interest (e.g. the delta variant) in Canada?

    • Grace SeoJuly 15, 2021 at 3:14 am

      Hi Samantha,

      We are currently using the data analysis pipeline discussed in my poster (Figure 2) for variant detection and updating the timeline phylogenetic tree for Canada (Figure 3).
      Ever since we optimized the sequencing and pipeline protocol last year, we’ve been using this pipeline to detect many Variants of Concern (for example B.1.1.7) when it got introduced in Canada and also many Variants of Interest.

      As for your question regarding sample processing ability, we can get the result within 24 hours of sequencing for multiple samples at once. We usually batch our samples (up to 96 samples per plate/run) and we perform multiple sequencing runs a day if samples were received for sequencing. (Please note that we provide sequencing for the samples that jurisdictions have requested and sent to us).

      Within 24 hours of sequencing, we can examine genomic differences in any samples to detect variants provided that clinical samples had sufficient viral load, sample quality was optimal (i.e. properly frozen during transportation etc.), and complete genome sequence of the virus was successfully obtained.

      Nanopore sequencing runs overnight. Once sequencing is complete, bioinformaticians perform data analysis using the established pipeline (Figure 2) then biologists or scientists carefully vet through the lineage and VOC/VOI results which is then reported to sample originating jurisdictions. We continue to add sequencing results to the existing database used for updating Canadian phylogenetic tree with timeline and to the public database for global genomic surveillance.

      I hope my response answered your questions. If not, please let me know. Thanks for your question!

Leave a Reply

Your email address will not be published. Required fields are marked *