Genomics and Clinical Virology

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.

CPD Accreditation
The course has been approved for 43 CPD credits by the Royal College of Pathologists

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 for more information.

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
• Data interpretation
• Validation and accreditation of viral WGS diagnostic service
• Case studies in outbreak investigation and infection control

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

*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/

Lead instructors
Judith Breuer University College London, UK
Nick Loman University of Birmingham, UK
Tamyo Mbisa Public Health England, UK
Emma Thomson MRC-University of Glasgow Centre for Virus Research, UK

Guest instructor
Chris Wymant Big Data Institute, University of Oxford, UK

Module leads
Wet lab
Ana Da Silva Filipe MRC-University of Glasgow Centre for Virus Research, UK
Carmen Manso Public Health England, UK

Bioinformatics
Sreenu Vattipally MRC-University of Glasgow Centre for Virus Research, UK
Sunando Roy University College London, UK

Guest speakers
Andrew Leigh Brown University of Edinburgh, UK
Karin Metzner University Hospital Zurich, Switzerland
Oliver Pybus University of Oxford, UK

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 has been approved for 43 CPD credits by the Royal College of Pathologists

How to Apply
Please complete the online application form. 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 contact the event organiser if you require a letter to support a travel visa application to the UK.

Non-European Economic Area or Swiss nationals may be required to have a visa to enter the UK. Early application is strongly advised, as this process can take 6-8 weeks or longer.

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 and applies to non-commercial applicants. Please contact us for the commercial fee.

Bursaries
Limited bursaries are available (up to 50% reduction on 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.

Where there are many bursary applications, the selection committee may issue smaller amounts.

Bursaries can be applied for as part of the course application form. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. The decision of the selection committee is final.

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.

Accommodation services phishing scam – please be vigilant. More information.

Feedback from the 2017 course:

“EXCELLENT COURSE! Both inspiring and practical. Compliments for all organisors, teachers, technicians and everybody else involved. (Don’t change too much!)”
“The entire training program was very relevant to clinical virology and there was a good balance for all aspects of training (wet lab, bioinformatics, lectures).”
“Congratulations to organizers”
“Thanks so much for organising an inspiring and fascinating course!”
“Thank you for organizing the course! It’s one of the best I’ve attended.”
“Overall excellent course, I feel very lucky to have had the opportunity to attend.”
“Thank you for organising, thoroughly enjoyed the course and learnt a huge amount.”