Viral genome sequencing and sequence-dependent detection methods have been applied to the diagnosis and management of viral infections for decades.  However, the introduction of next-generation sequencing (NGS) technologies is transforming how clinical microbiology laboratories diagnose and manage infectious diseases.  Whole genome sequencing (WGS) of hundreds of microbes can be undertaken in hours enabling real time genomics for diagnostics, transmission investigation and infection control.

This exciting new Genomics and Clinical Virology course combines practical hands-on laboratory and bioinformatics training with faculty lectures by, and discussions with, leaders in this crucial and expanding area.

The course is aimed at virology Clinical Scientists and Specialist Registrars who are planning to implement NGS in clinical diagnostic laboratories. Researchers (PhD, postdoc or more senior level) who have an interest in learning how to carry out NGS of viral genomes are also welcome to apply. The course will concentrate on the application of cutting edge genomic techniques that can be implemented now and explore new approaches that will enter practice in the near future.

The practical parts of the course will include laboratory sessions focusing on the preparation of sequencing libraries for metagenomics and PCR-based approaches. Particular emphasis will be placed on how to improve the efficiency of viral NGS by undertaking variations in library preparation techniques - such as target enrichment by probe hybridization. 

Participants will also gain hands-on experience in bioinformatics analysis of the output data, with focus on reference mapping and de novo assembly approaches as well as downstream analyses such as phylogenetic inference, epitope identification and drug resistance identification.

There will also be lectures and demonstrations of the potential applications of NGS in clinical laboratories, limitations and pitfalls of the techniques and clinical case studies e.g. in infection control.

Please Note: Limited bursaries are available for clinical and academic applicants from anywhere in the world to attend this course. In addition, CPD accreditation will be sought from the Royal College of Pathologists.

Learning Outcomes
After attending the course, participants should be able to:

  • Carry out NGS including wet lab preparation and bioinformatic analysis of real samples
  • Create sequencing libraries and analyse samples derived from patients with viral infections (e.g. HIV, HCV, EBOV, Zika)
  • Evaluate how to improve the efficiency of NGS by carrying out variations in library preparation technique (e.g. target enrichment)
  • Evaluate the pitfalls of NGS interpretation in clinical viral diagnostics
  • Evaluate potential future applications of NGS in clinical diagnostic laboratories and appreciate the limitations of the technique
Application Deadline:

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