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 of hundreds of microbes can be undertaken in hours enabling real time genomics for diagnostics, transmission investigation and infection control.

What will I learn?

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

The course is aimed at virology Clinical Scientists and Specialist Registrars who are planning to implement NGS in clinical diagnostic laboratories. Virology researchers at PhD, postdoc or more senior level who have an interest in learning how to carry out NGS of viral genomes are also encouraged 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 part of the course will provide laboratory sessions that will focus on the preparation of sequencing libraries for metagenomics and PCR-based approaches with particular emphasis 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 gain practical experience in bioinformatics analysis of the output data with focus on reference mapping and de novo assembly approaches, and downstream analyses such as phylogenetic inference, epitope identification and drug resistance identification.

There will 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.