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.

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Avian influenza FAO mission in Benin and Togo

09 April 2015 - Following the recent H5N1 outbreaks in Western Africa since late December 2014, FAO, through the Crisis Management Centre-Animal Health (CMC-AH), has recently deployed rapid assessment missions, in the Republic of Benin, from 22 to 28 February 2015, and in the Togolese Republic, from 1 to 7 March 2015. Both missions were requested to assess the level of preparedness and response capacities of both countries towards a potential H5N1 incursion. At the end of each mission, the team met with the countries’ officials and made the following recommendations:

The Republic of Benin

Representatives from public and private sectors were highly committed to awareness activities and to the control and seizure of illegally imported poultry and poultry products. However, a need for greater clarity involving responsibilities of the veterinary services (VS), the national agency for food safety (ABSSA), and the national agency for civil protection (ANPC) when dealing with animal disease emergencies, and the shortage of human resources, were noted by the mission. These were seen as constraints which could hamper disease surveillance and proper response capacities. Information collected during the mission allowed prioritization of areas of actions:

  • The current level of surveillance, particularly in areas at highest risk of introduction of avian influenza, could be improved through the organization of coordination meetings, the activation of the national, regional, and commune HPAI committees and the setting and the development of active surveillance in the regions at high risk. In this regard, the national epidemiosurveillance network (RESUREP) is expected to play a major role;
  • A strong emphasis could be put on communication efforts in the country. The strengthening of existing communication platforms and surveillance networks, where both the public and private sectors can share information, is foreseen. Dissemination of prevention and control information to target groups (poultry industry, private veterinarians, Customs) will be further developed;
  • A sustainable, adequate training and equipment is a prerequisite for efficient control of HPAI. A high priority should be given to the training of the epidemiological surveillance network and the field staff (ABSSA and VS) on good culling practices, disinfection, and carcasses disposal. Both of the veterinary laboratories at Bohicon and Parakou should be equipped with reagents and the VS, the Regional Agriculture Centre for Rural Development (CARDER), and ABSSA with personal protection equipment (PPE), gloves, and rubbish bags. At this level, very promising funding opportunities seemed possible to support immediate preventive action such as supporting surge teams, trainings, provision of lab reagents and equipment, active surveillance in at risk zones and regional coordination.

The Togolese Republic

During the various meetings, the mission team noticed that the veterinary services as well as the farmers’ community were mobilized against the illegal introduction of poultry and poultry products from infected countries. At the time of the mission in Togo, the veterinary services had launched an awareness campaign among the main partners as per the well-documented country contingency plan. Despite these swift measures, constraints to an effective response such as the need to strengthen the surveillance system, to insure biosecurity of poultry producers and to refresh field disease knowledge/skill of all the field veterinary agents were noted by the experts. The main recommendations of the mission are:

  • Implement actions to strengthen the country surveillance abilities: through sustained support to the surveillance network (REMATO), awareness of different field actors, such as farmers, private and public veterinarians, training of laboratory staff and procurement of sufficient test kits;
  • Insure optimal response capacities through adequate stock of consumables, practical training of field officers on response activities (poultry slaughtering, disinfections, burial, etc.) and implementing an emergency funding mechanism for the Animal Health Directorate;
  • Increase regional communication on suspicions and outbreaks, both for veterinary services and farmers ’associations in Western Africa.

These recommendations and other mission findings were presented to government officials, stakeholders and the local donor community at the conclusion of each mission.

FAO followup on these recommendations will ensure that early detection and early response will prevent jeopardizing livelihoods and food security of millions of households in the region.

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Grippe aviaire au Benin: Une mission de la FAO pour l’état des lieux

Cotonou. Une mission de l’Organisation des Nations Unies pour l’Alimentation et l’Agriculture  (FAO) a séjourné au Bénin du 22 au 28 février 2015. Ceci pour aider le gouvernement du béninois au regard de la situation épidémiologique qui prévaut au Nigéria concernant la prolifération du virus influenza hautement pathogène (IAHP) H5N1 dans les élevages de 17 Etats de ce pays frontalier à faire un point.

Sollicité par le Gouvernement du Bénin, l’Organisation des Nations Unies pour l’Alimentation et l’Agriculture (FAO), a pu évaluer le niveau de préparation du pays vis-à-vis du risque d’introduction du virus et appuyer le pays dans la prévention et aussi dans la riposte en cas d’apparition d’un foyer de grippe aviaire. Au terme de la mission d’une équipe de quatre experts venant du  Centre de Gestion de crise – santé animale (CMC-AH) à Rome, les experts ont dressé une liste de cinq (5) recommandations pour amener le pays à être prêt dans la prévention et la riposte au cas échéant.

Ainsi, le Bénin avec l’appui des partenaires techniques et financiers doit mettre à jour le Plan d’Intervention d’Urgence (PIU), notamment dans son volet coordination des différents acteurs; tenir compte des recommandations des missions d’évaluation des écarts par rapports aux standards internationaux (PVS) de l’organisation mondiale de la santé animale (OIE) dans l’organisation/restructuration des Services vétérinaires avec notamment la restauration d’une chaîne de commande directe sous l’autorité du délégué de l’OIE; renforcer les capacités de contrôle et de surveillance y compris les laboratoires; élaborer une stratégie de communication ciblée et adaptée à la situation épidémiologique notamment envers les professionnels de la filière avicole et renforcer la concertation sous régionale.

Les experts ont diagnostiqué bien de situations à risques avant de faire ces recommandations. Ils ont fait le constat d’un système de contrôle frontalier et intérieur défaillant se traduisant par une augmentation de l’introduction et des points de vente des poussins d’un jour au statut vaccinal inconnu, de volailles adultes et d’œufs de consommation en provenance du Nigéria par voie routière (bus de transport, motocyclettes); la multiplication de petits élevages familiaux de volailles à partir des poussins importés exacerbés par la chute des prix de ces animaux (de 200  CFA à 75 CFA pour les poussins coquelets et de 1000 CFA à 300 CFA pour les poussins pondeurs).

Leur déplacement sur le terrain avec des séances de travail avec le Directeur de la Production Animale, délégué national de l’OIE, les responsables de l’Agence Béninoise de Sécurité Sanitaire des Aliments (ABSSA), le personnel technique des laboratoires vétérinaires de Bohicon et Parakou, les représentants des organisations d’éleveurs de volailles, l’Union Nationale des Aviculteurs Professionnels (UNAP), l’Interprofession Avicole du Bénin(IAB), les vétérinaires privés a également permis d’observer un niveau de communication insuffisant avec la faiblesse du niveau de sensibilisation et d’information des éleveurs et des professionnels des Services du Ministère de l’Agriculture de l’Élevage et de la Pêche (MAEP) sur la situation qui prévaut au Nigéria sur les pratiques préventives telles que la biosécurité dans les élevages, les marchés, etc., la sous-utilisation du réseau de surveillance épidémiologique (RESUREP).

A tout ceci s’ajoute le Plan d’Intervention d’Urgence (PIU) qui est non opérationnel. La non activation des comités nationaux, régionaux et communaux de lutte contre la grippe aviaire pour susciter et maintenir un état de veille comme le prévoit le PIU; la saisie et la destruction des produits illégalement importés dans des conditions ne respectant pas les mesures de biosécurité et de bien-être animal. Ces activités ont été essentiellement réalisées à ce jour par les agents de l’Agence Béninoise de Sécurité Alimentaire (ABSSA), en marge des dispositions du Plan d’Intervention d’Urgence (PIU). A ce jour, plus de 35 000 poussins ont été saisis et détruits avec l’assistance des forces de l’ordre. Ce nombre est nettement en deçà des effectifs illégalement introduits du fait des capacités limitées de contrôle. 

Un manque de coordination des mesures de prévention entre les structures techniques du MAEP (ABSSA, DPA, Laboratoire, etc.) est perçu. Les Services vétérinaires sont désorganisés du fait d’un modèle d’organisation qui s’écarte des standards de l’OIE (notamment l’absence d’une chaîne de commande) et  de l’insuffisance des ressources humaines et logistiques en particulier en ce qui concerne le Réseau de Surveillance Epidémiologique (RESUREP) et la non opérationnalisation du mandat sanitaire ainsi que l’absence d’une concertation en termes de partage d’informations et de savoir avec le Nigéria dans les stratégies de prévention et de lutte contre la maladie.

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Call for proposals: EuroScience seeks scientific programme ideas for ESOF Manchester 2016

Representatives from the ESOF host city of Manchester and EuroScience, a grassroots association which acts on behalf of Europe’s scientific community, are calling for session proposals to populate the science programme at ESOF 2016, Europe’s largest general scientific conference.

ESOF 2016 (EuroScience Open Forum) takes place from 22-27 July in Manchester, the city where Marx met Engels and Rolls met Royce.

Similarly ESOF 2016 will be a meeting of minds, bringing together many of the world’s foremost scientific thinkers, innovators and scholars.

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