Genomics and Clinical Virology

(The current plan is to run a face to face course but this will be reviewed prior to selection of participants taking into consideration any Covid pandemic restrictions. A virtual course could be offered as an alternative.)

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 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 researchers at PhD, postdoc or more senior level who have an interest in learning how to carry out NGS of viral genomes, and Clinical Scientists and Specialist Registrars who are planning to implement NGS in clinical diagnostic laboratories. 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 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.

What will I learn?

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 and the use of long-read technologies.

Participants will gain practical experience in Linux/Unix command line usage, bioinformatics analysis of the output data with focus on quality control of NGS data, reference mapping and de novo assembly approaches, and downstream analyses such as phylogenetic inference and variants associated with drug resistance. 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 ​​and outbreak investigations including the ongoing SARS-CoV-2 pandemic.

CPD Accreditation
The course is approved annually for CPD accreditation by the Royal College of Pathologists (43 credits in 2019).

PLEASE NOTE: Bursaries are available for clinical and academic applicants from anywhere in the world to attend this course. Please see the “Cost / Bursaries” tab below for more information.

Programme

The course will cover a wide range of cutting-edge viral WGS laboratory techniques and *bioinformatics analysis in practical classes, demonstrations or lectures. The areas and issues to be addressed will include:

• Background to viral WGS approaches
• Sample handling and preparation
• Library preparation techniques
• Target enrichment methods e.g. probe-based sequence capture or PCR-based
• Viral metagenomics
• Technique discrimination – the appropriate technique to use in different scenarios
• Next generation and third generation sequencing platforms
• Bioinformatics analysis including different viral genome assembly approaches, variant calling, viral metagenomics, multiple sequence alignment and phylogenetic inference. 
• Data interpretation
• Validation and accreditation of viral WGS diagnostic service
• Case studies in outbreak investigation and infection control

Laboratory 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. SARS-CoV-2, 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
• Demonstrate how viral WGS can be used to inform transmission patterns and evaluate the effectiveness of interventions
• Apply Linux/Unix command line to perform bioinformatics tasks
• Construct whole genomes by means of De novo assembly of NGS data and use standard tools to perform reference mapping
• Generate consensus sequences and call variants
• Use metagenomics tools such as KRAKEN and Centrifuge to detect and identify viral pathogens
• Compute multiple sequence alignments and build phylogenetic trees to understand viral evolution and transmission dynamics

*Please note: Bioinformatic training will include the use of Linux/Unix command-line. Though participants learn to use the command line during the course, familiarity with these resources is recommended. There are numerous online introductory tutorials to the Linux/Unix operating system and command line, including:

http://www.ee.surrey.ac.uk/Teaching/Unix
http://swcarpentry.github.io/shell-novice/

Organisers

Prerequisites
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.

Please note: Bioinformatic training will include the use of UNIX/Linux command-line analysis and familiarity with these resources is recommended. There are numerous online introductory tutorials to the UNIX/Linux operating system and commad line, including:

http://www.ee.surrey.ac.uk/Teaching/Unix
http://swcarpentry.github.io/shell-novice/

CPD Accreditation
The course is approved annually for CPD accreditation by the Royal College of Pathologists.

How to Apply
Please click the Apply button above to begin the online application process. Places are limited and will be awarded on merit. If you have any problems with the online application process, please contact us.

Please note: Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g. supervisor, line manager or head of department). A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline. Applications without a supporting statement cannot be considered.

Travel visas
Successful applicants will be provided with a support letter for their visa application, if required.

Please visit the following websites for further information on visiting the UK:

• UK Border Agency website
• Information for general visitors and business visitors

*The course fee is subsidised by Wellcome Genome Campus Advanced Courses and Scientific Conferences.

Bursaries
Advanced Courses are subsidised for non-commercial applicants from anywhere in the world. Additional, limited bursaries are available (up to a 50% reduction of the course fee) and are awarded on merit. If you would like to apply for a bursary, please complete the bursary section of the online application form.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.

Additional funding opportunities
Visit our support page for additional financial support currently available.