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Regional molecular epidemiology training for eastern Africa animal health service providers

22 April 2015 - A regional training on molecular epidemiology was conducted in Kampala, Uganda from the 13-17 April 2015 facilitated by Makerere University in collaboration with FAO (ECTAD Eastern Africa & EMPRES Lab unit) and the Swedish National Veterinary Institute at the Sheraton Hotel, in Kampala, Uganda. The training was funded by Defense Threat Reduction Agency/Cooperative Biological Engagement Program (DTRA/CBEP) and facilitated by FAO in collaboration with both Makerere University and the Swedish National Veterinary Institute (SVA).

Advanced characterization of pathogens through genome sequencing can help in collection of important genetic information such as the origin of the pathogens, their biological properties (antiviral or antimicrobial resistance) as well identify re-assortment events or mutations. The use of molecular genetics methods to reconstruct relationships of sequences of pathogens is a vital part of biological research, diagnosis, characterisation of pathogens and ultimately disease control. Such methods underpin studies on the evolution and epidemiology of animal parasites and disease-causing organisms. The methods are needed to understand the contrasting roles of vertical and horizontal inheritance in genome evolution, and more generally they allow an objective understanding of the patterns and processes of disease spread and maintenance. To support better prevention and control of animal diseases, FAO has provided several bioinformatics training courses to laboratory technicians, veterinarians and molecular epidemiologists from both diagnostic and research laboratories of FAO Member States . They have also procured sequencing equipment and reagents and provided access to sequencing services1 to national veterinary laboratories. Furthermore they developed a collaboration with the Swiss Institute of Bioinformatics (SIB) for the development of an e-learning course on bioinformatics in animal viral pathogens.

Nineteen trainees drawn from Ethiopia (4), Kenya (4), Tanzania (3) and Uganda (8) participated in the training comprising of epidemiologists and laboratory experts. The workshop objectives were to (i) enhance participants’ knowledge concerning methods for molecular characterization of pathogens, types of data to be collected, generated and their use in epidemiological analysis; (ii) assist in developing Country Action Plans to enable use of the Genetic Sequencing Services available within the region and knowledge attained through the training; and (iii) update participants on activities being implemented with the support of Defense Threat Reduction Agency/Cooperative Biological Engagement Program (DTRA/CBEP). The course comprised both theory and practical hands-on that also included a visit and a practical session at the Makerere University molecular biology laboratory.

The training was a very good opportunity for the epidemiologist and laboratory groups to work together, a situation that is not very common as adduced from the training process. The five day training covered elements of general issues on Transboundary animal diseases i.e. contemporary challenges and risk analysis of their management, genomes as contemporary tools in epidemiology, molecular evolution of viruses, application of sequence information in epidemiology and methods in phylogenetic reconstructions. Other topics covered were on FAO’s initiative for the access to sequencing services, hands on computer practical exercises, linking isolate and outbreak data on the FAO animal health platform with examples on influenza and FMD, pathogen evolution and update on the activities of eastern Africa DTRA project. At the end of training, Country representatives worked to develop their action plans to enable better use of the Genetic Sequencing Services available.

After exhaustive and fruitful discussions during the training sessions, participants recommended the following:

  1. FAO to explore the possibility storing the sequences produced by the countries by using the sequencing service in FAO database as a back-up measure in case of unforeseen events that may interfere with the country database;
  2. Countries to be supported to purchase of a critical software (codon aligner) as well as pursue the possibility of free software;
  3. Countries to identify additional focal points on Molecular Epidemiology based on country participation and encourage sharing of information within the laboratory network at country level;
  4. FAO to make readily available the sequencing handbook for all users to fully utilize the sequencing service2;
  5. Countries to be supported to organize molecular epidemiology trainings and refresher training;
  6. Country representatives to the molecular epidemiology training workshop to share the knowledge from the Kampala’s workshop with colleagues from all divisions at the department of veterinary services headquarters;
  7. Countries to take necessary action to better coordinate activities from the public Veterinary Services and the academic and other research institutions in Molecular Epidemiology & diagnostics.

Country representatives agreed to establish a Molecular Epidemiology Working Group (ME-WG) to promote use of molecular data and for information sharing. The ME-WG will be facilitated by Makerere University in collaboration with FAO. The terms of reference (TORs) and modus operandi will be developed by end of May 2015.


1 FAO launched the sequencing service initiative in March 2014 to facilitate the access to DNA sequencing for laboratories that have no access to PCR sequencers in sub-Saharan Africa. FAO signed an agreement with a commercial partner to perform the sequencing. An online system was set up so that laboratories can order sequencing services and submit their samples directly to the company. FAO headquarters together with its joint FAO/IAEA division has already provided training to these laboratories to ensure the quality of their PCR products before sending them to a commercial partner for sequencing.

2 Given the importance of using the same protocols to reach standardized results, FAO shared with the countries benefiting from the sequencing service a sequencing handbook with 20 protocols to identify and sequence key pathogens.


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Facilitators and participants of the regional molecular epidemiology training. (© FAO)


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