Aug 5 5 – 9 August 2019 at the University of Hong Kong

Croucher Summer Courses

Every summer the Croucher Foundation funds short courses that aim to educate and inspire postgraduate students and early career researchers from Hong Kong an...

Computational Genomics of Viral Evolution and Epidemiology

Recent breakthrough in genome sequencing technology has largely expanded its application in infectious disease studies, and is considered as a game changer. The sequencing cost and procedures are substantially reduced, and the portability is greatly improved such that it is almost possible to sequence virus genomes anywhere. Genomic sequencing and analyses are found to be very useful in pathogen surveillance, clinical diagnosis, treatment, vaccination, risk assessment, disease prevention and etc. However, these genomic analyses are currently largely limited to bioinformatics specialists. It is realistic to anticipate that non-bioinformatics-specialists such as clinicians will have to work with viral genome sequences in the future, or at least to understand the analysis concepts, results and limitations for accurate interpretation. To fill this gap, our course will bring a number of world-leading experts in this field from various parts of the world into Hong Kong to share their unique knowledge and skills with the local postgraduate students and professionals in Hong Kong and Asia.

This Croucher summer course co-runs with VEME2019 workshop, and will provide 90 participants (30 for each of the three parallel modules) with both theoretical and practical training in bioinformatics techniques as applied in virology and molecular epidemiology, and particularly focus on the phylodynamics methods and large-scale next-generation sequencing (NGS) analytics which are the state-of-the-art methodology in the field. 


Graduate House, The University of Hong Kong.


In this five-day workshop, participants will be learning in 3 parallel modules on the first four full days:

  • Phylogenetic Inference Module
  • Evolutionary Hypothesis Testing Module
  • NGS Module

Then Friday will be running the three AM and three PM half-day modules on various advanced specialized topics related to the study of virus evolution and epidemiology. Students can choose one AM and one PM modules on the application form. The six half-day modules on Friday are:

  • (AM) Module 1: Large phylogenies
  • (AM) Module 2: Transmission cluster investigation
  • (AM) Module 3: Molecular adaption
  • (PM) Module 4:  Visualization of large phylogenies with metadata
  • (PM) Module 5:  Recombination and networks
  • (PM) Module 6:  Tools for viral NGS & phylogenetic analysis

The course will be taught by 30 world-renowned researchers from top international universities and research institutions. More information about the teacher profiles and daily schedules of the course can be found in both VEME2019 and HKU-CGVEE websites.


If you are interested, please go to VEME2019 application form to submit your basic information and preference of modules, plus:

  • Abstract of the poster presentation (mandatory)
  • Background experience
  • Letter of motivation

The application deadline is 31st March 2019. Selections will be made by the beginning of May. 

Although this course targets postgraduate students, post-docs and medical professionals in early career, there is no restriction on the education background. The participant selection is based on:

  • Quality of the abstract: abstracts will be reviewed and priority will be given to applicants who are first author on the abstract.
  • Letter of motivation: how urgent/important is your need for training?
  • Each module is preferably restricted to 1 participant from the same laboratory/research team.
  • We strive for participation from diverse countries


Instruction for registration and payment will be provided after the participant selection. The registration fee of 900 Euro covers attendance, lunches and coffee breaks. Among the 90 accepted participants, 30 participants (mainly from Hong-Kong, China and neighbouring countries) will be selected for Croucher grant support, which have reduced registration fee (HK$5,000) covering accommodation in addition. Among them, 5 will be further awarded with the scholarships that waive the registration fees and provide financial support for travel to Hong Kong. More information about the grant and financial support is in HKU-CGVEE website. If you are interested in getting grant support and scholarships, please remember to indicate that on the application form (the last question on the form).


Course director and co-director:

  • Dr. Tommy T.Y. Lam ( State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong
  • Prof. Anne-Mieke Vandamme ( Rega Institute, Katholieke Universiteit Leuven

Organising committee:

  • Prof. Joseph T.K. Wu ( School of Public Health, The University of Hong Kong
  • Prof. Philippe Lemey ( Rega Institute, Katholieke Universiteit Leuven

For inquiry related to VEME, please contact Cathy De Meyer (; for Croucher Summer Course support and local arrangement, please contact Miky Wong (


A Croucher Summer Course in partnership with the University of Hong Kong.