Webinar recording:
Scaling Surveillance Sequencing for Illumina and Nanopore Technologies

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About this webinar recording

CVR Genomics, the sequencing facility at the University of Glasgow Centre for Virus Research (CVR), has a remit to provide the CVR community and its collaborators with expertise in high-throughput sequencing to contribute to the understanding of viruses. The team has developed extensive knowledge in viral genomics and expertise in a range of specialist techniques and technologies, including metagenomics, bulk transcriptomics, and targeted enrichment with sequencing on Illumina and Oxford Nanopore instruments. This broad knowledge forms a crucial foundation for tailoring protocols to the individual needs of each project.

In early 2020, CVR received the first Scottish case of COVID-19 for full-genome sequencing. The pandemic highlighted the importance of large-scale surveillance sequencing and the challenges of higher throughputs. CVR initially opted for the low-throughput ARTIC amplicon protocol, which the lab adapted for high-throughput sequencing using the SPT Labtech mosquito nano-dispensing robots and Illumina sequencing. Amplicon enrichment of viral genomes is well suited to large-scale sequencing workflows but carries a high risk of contamination. One way to reduce this is to streamline the workflows, which CVR accomplished first with high-throughput Oxford Nanopore libraries and finally with Nimagen amplicon and Illumina sequencing. This enabled not just an increase in the number of samples (to ~400 per batch) but also in reliability, with a reduction in the time taken, the number of people required, and, importantly, the cost per sample.

In this webinar, Katherine Smollett, research associate at CVR Genomics, will discuss:

  • The challenges of viral genomics.
  • Adapting sequencing workflows to academic questions.
  • Comparing probe and amplicon-based targeted enrichment methods.
  • Surveillance sequencing considerations.
  • Switching to automated protocols.
  • Managing contamination.

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