NEW Lecture/Discussion

Establishing Capacity for Pathogen Genomics

7–12 May 2023

Ethiopian Public Health Institute, Addis Ababa, Ethiopia

Develop skills to advance capacity for pathogen genomics in Africa


We are pleased to announce the Establishing Capacity for Pathogen Genomics workshop organised, funded and hosted by COG-Train (a collaboration between Wellcome Connecting Science and Cambridge University),  Africa Centres for Disease Control (Africa CDC) and the Ethiopian Public Health Institute (EHPI).

The COVID-19 pandemic has accentuated the urgent need to incorporate genomics in routine detection and surveillance of infectious diseases. Information about emerging pathogen variants was used to develop policies to effectively monitor spread of the virus. At a national level and for many public health organisations building capacity for pathogen genomics is now a priority. 

This workshop aims to empower African-based scientists and public health professionals to build capacity for pathogen genomics in research and service delivery in public health. The workshop will focus on practical approaches and challenges in establishing genomics capacity, including sequencing and data infrastructure set-up, maintenance and resource management.  An overview of genomics and data analysis pipelines will provide participants with a holistic picture from sample collection to interpretation. Participants will also benefit from the experience of other experts in the communication of data to enable decision-making in a public health context.  

The tools and strategies developed at this workshop will equip participants with skills to design and develop their own training in pathogen genomics, further strengthening regional capacity, workforce and sustainability. A series of round table and panel discussions will enable participants to share knowledge and strategies for workforce planning, building sustainable models for sequencing and data science, establishing consortia, networks and mentorship initiatives.

Target audience: Research and healthcare professionals based in Africa interested in implementing effective strategies for establishing and implementing pathogen genomics and surveillance capacity. Priority will be given to individuals in public health institutions who have started, or are planning to set up, infrastructure and data pipelines for pathogen genomics. Applicants must have some  knowledge in genomics, clinical management or public health, and interested in developing skills to train others.


The 5.5. Day workshop will start at approximately 12.00 on 07 May and close at approximately 17.00 on Friday 12 May 2023. The workshop will consist of live lectures, workshops, knowledge exchange and networking, case studies, world café, individual and group projects and action setting.

Topics will include:

  •         Practical approaches to establishing genomics and data infrastructure
  •         Data workflows, analysis and interpretation
  •         Pathogen genomics application in local and global contexts
  •         Data collection, linkage and integration
  •         Communication of data and public health decision-making
  •         Effective methods, tools, resources for training others in pathogen genomics

Round-table discussions:

  •         Building a sustainable model for sequencing capacity and data science
  •         Establishing workforce capacity for pathogen genomics
  •         Frameworks for genomic surveillance for research and public health practice skills training
  •         Consortium, network establishment and mentorship

All participants are requested to attend all of the sessions and participate in networking to benefit fully from discussions and interactions.

Instructors and speakers

Workshop Developers and Organisers

Abebe Aseffa
Ethiopian Public Health Institute

Alice Matimba
Wellcome Connecting Science

Harris Onywera
Africa CDC

Leigh Jackson
University of Exeter

Treasa Creavin
Wellcome Connecting Science

Melanie Sharpe
Wellcome Connecting Science

Instructors and Guest speakers

Sofonias K. Tessema
Africa CDC

How to apply

Applicants are expected to be scientists or healthcare professionals with some knowledge in genomics, clinical management or public health and interested in developing skills to train others.

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.



The course is subsidised by COG-Train and is free to attend for non-commercial applicants.

Please contact us for the commercial fee.

A limited number of bursaries are available for each course. These are awarded on merit to cover travel, accommodation and sustenance.

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.

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