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ARCHIVE LATEST Sub-Saharan Africa HPAI situation update

15 February 2017, 17:00 hours; Rome


Information provided herein is current as of the date of issue. Information added or changed since the last Sub-Saharan Africa HPAI situation update appears in red. For poultry cases with unknown onset dates, reporting dates were used instead. FAO compiles information communicated by field officers on the ground in affected countries, from regional offices, and from World Organisation for Animal Health [OIE], as well as peer-reviewed scientific articles. FAO makes every effort to ensure, but does not guarantee, accuracy, completeness or authenticity of the information. The designation employed and the presentation of material in the map do not imply the expression of any opinion whatsoever on the part of FAO concerning the legal or constitutional status of any country, territory or sea area, or concerning the delimitation of frontiers.



Situation: Highly pathogenic avian influenza virus (H5N1 and H5N8 subtypes) with pandemic potential in countries of Sub-Saharan Africa.
Confirmed countries: Burkina Faso, Cameroon, Côte d’Ivoire, Ghana, Niger, Nigeria, Togo and Uganda.
Animal/environmental findings: Please see individual country reports below.
Number of human cases: None reported to date.

Map 1. Officially reported HPAI outbreaks (H5N1 and H5N8 subtypes) in Sub-Saharan Africa, by onset date (1 June 2016 - 15 February 2017)

Officially reported HPAI outbreaks (H5N1 and H5N8 subtypes) in Sub-Saharan Africa, by onset date (1 June 2016 - 15 February 2017)
Click to enlarge. Note: In addition to the countries shown on the map, Burkina Faso, Cameroon, Côte d'Ivoire and Togo were affected by H5N1 HPAI (in the period between 1 December 2014 and 1 October 2016).



 Situation update

Nigeria H5N1 HPAI

  • Number of outbreaks to date: 782
  • Regions affected: Abia, Abuja, Adamawa, Anambra, Bauchi, Bayelsa, Benue, Delta, Ebonyi, Edo, Enugu, Gombe, Imo, Jigawa, Kaduna, Kano, Katsina, Kebbi, Lagos, Nassarawa, Ogun, Oyo, Plateau, Rivers, Sokoto and Zamfara
  • Outbreaks reported since last update: Eight: 6 in Plateau, 1 in Abuja 1 in Bauchi
  • Most recent outbreak: observed on 09 February 2017 in Low cost in Jos South Municipality

Uganda H5N8 HPAI

  • Number of outbreaks to date: 22
  • Regions affected: Kalangala, Masaka and Wakiso
  • Outbreaks reported since last update: 18; in Kalangala, Masaka and Kalangala Districts
  • Most recent outbreak: reported on 6 February 2017 in Wakiso district


Table 1. Summary of countries with no new H5N1 HPAI events reported



1° Administrative regions affected

Date of last outbreak report

Date of last observed outbreak

# reported outbreaks to date

Burkina Faso Bazenga, Boulkiemde, Houet, Kadiogo, Poni, Sanguié, Comoe, Kourweogo, Boulgou, Ioba, Nayala, Yatenga 02/10/2015 21/07/2015 94
Ghana Greater Accra, Ashanti, Central, Eastern, Volta, Western 23/11/2016 26/10/2016 63
Cameron Adamaoua, Centre, South, West 14/09/2016 29/08/2016 18
Côte d’Ivoire Abidjan, Bassam, Belier, Bouaké, Comoe, Gontougo, Lagunes 03/10/2016 27/07/2016 67
Niger Maradi, Niamay 02/07/2016 21/02/2016 2
Togo Maritime 24/08/2016 19/08/2016 2

Figure 1. Case counts of reported H5N1 HPAI poultry outbreaks in Sub-Saharan African countries by MONTH based on onset date

Case counts of reported H5N1 HPAI poultry outbreaks in Sub-Saharan African countries by MONTH based on onset date
Click to enlarge - Note: Where onset date was not available, reporting date was used (source: EMPRES-i).


 FAO's support to countries

Global level

  • HQ (AGAH/EMPRES), ECTAD-Accra and RAF liaising with affected countries and those at risk;
  • USD 6.2 million mobilized from FAO internal resources (SFERA and TCP), AfDB, ROK and USAID (under GHSA funding and the EPT2 program) to support assessments and immediate response;
  • FAO issued a press release on H5N8 HPAI in Uganda on 1 February 2017, the first time that HPAI was confirmed in the East Africa region;
  • A webinar titled Intercontinental spread of H5N8 highly pathogenic avian influenza – Analysis of the current situation and recommendations for preventive action, targeting national veterinary services and FAO regional and country teams, was conducted by FAO on 24 November 2016 [link]
  • EMPRES Watch, September 2016: H5N8 highly pathogenic avian influenza (HPAI) of clade detected through surveillance of wild migratory birds in the Tyva Republic, the Russian Federation – potential for international spread [link]
  • FAO issued a press release on H5N1 HPAI in West and Central Africa on 13 July 2016, calling for increased vigilance in the region;
  • FAO issued a Qualitative Risk Assessment addressing H5N1 Highly Pathogenic Avian Influenza spread in the Central African region.

Regional level

  • The regional HPAI emergency prevention and control programme, developed on the basis of the recommendations of the first regional coordinating meeting held in Abuja in June 2015, considers a cluster approach, based on countries’ disease status: endemic (Nigeria only), infected/previously infected, at risk.
  • A regional meeting aimed at endorsing this programme was co-organized with ECOWAS on 28 and 29 November 2016 in Abuja, Nigeria. The meeting enriched and adopted the regional programme for HPAI prevention and control. ECOWAS member States urged FAO, ECOWAS Commission and other partners to mobilize funding for its implementation. Other recommendation include the principle of an annual regional meeting on HPAI to discuss disease situation and progress made.

Cameroon (H5N1)

  • More than four (4) tons of material and equipment were provided by FAO, including personal protective equipment (PPE), materials for cleaning and disinfecting, and posters for risk communication. Additional 15 000 boot covers, reagents, PCR kits and various lab consumables were provided to the Directorate of Veterinary Services (DVS) and LANAVET at the Ministry of Livestock, Fisheries and Animal Industries (MINEPIA).
  • An Emergency TCP (496,000 USD) aiming at fostering national response capacities towards HPAI eradication was approved by FAO and signed by FAOR and the Minister in charge of Livestock on 20 September 2016. Implementation of the TCP is ongoing. 
  • Movement control regarding live poultry and poultry products has been reinforced since the disease was confirmed in the country in May 2016.

Ghana (H5N1)

  • A TCP emergency, aiming at strengthening the country capacity to prevent reintroduction and control the spread of the disease is currently being implemented.
  • A National consultant has been engaged for the following activities:
    • Compile inventories for the Veterinary Laboratories in Accra and Kumasi with regards to laboratory reagents and consumables required for effective HPAI diagnostic services;
    • Perform needs assessment for the two laboratories;
    • Provide training for laboratory staff in good laboratory practices for sampling, storage and shipment of samples;
    • Assist the implementation of biosecurity and biosafety protocols in the laboratories;
    • Perform an evaluation of the necropsy rooms in the Accra and Kumasi laboratories and suggest ways to improve biosecurity levels;
    • Provide training for laboratory staff on rapid antigen testing for HPAI diagnosis.
  • A series of workshops on HPAI disease recognition and biosecurity measures are being conducted in areas near countries with recorded HPAI outbreaks. The most recent workshop was an Epidemiology Workshop in Kumasi-Ashanti region on 6 October 2016 for Veterinary Epidemiologists, Veterinarians and Technical support staff. The workshop was conducted by an International Veterinary Epidemiology Consultant and attended by 20 participants. Specifics of HPAI outbreak investigations and the use of GPS in disease mapping were covered.
  • HPAI diagnostic services continue to be provided by the Accra Veterinary Diagnostic Laboratory on a nationwide basis.

Côte d’Ivoire (H5N1)

  • Surveillance protocols have been implemented since 1 March 2016 in major live bird markets, including in Abidjan, Bouaké and Agnibilekrou.
  • A stakeholder meeting has been held from 24 to 25 October 2016 in Bassam to agree on priority activities and implementation modalities on HPAI control activities.
  • Nine trainings of two days each were provided for paraveterinarians between 20 September and 14 October 2016 on clinical sign recognition and reporting. Four trainings for field staff are planned to be held by the end of 2016. This includes a training on the national contingency plan for which a national consultant will be hired.

Togo (H5N1)

  • FAO provided preliminary assistance to the Veterinary Services for disease control. This included assistance in the establishment of response teams, drafting of a short term action plan, meeting with WHO, participation in a press conference with the Minister in charge of livestock, WHO, and MoH as well as preparation of daily sitreps.
  • An EMPRES mission was conducted from 12 to 16 September 2016 with the main objectives to assess the outbreak situation, identify risk factors for introduction and further spread as well as to assess local capacities and resources. Two veterinary epidemiologists were deployed together with a risk communication specialist. Since the first two outbreaks that were epidemiologically linked there were no further reports. An action plan was established together with the Veterinary Services, to lay out next steps for trainings, implementation of an active surveillance program and communication activities, among others.
  • Advanced genetic characterization of the virus identified in Togo confirmed that it belongs to clade, which is the same clade circulating also in other West and Central African countries.

Nigeria (H5N8)

  • A shipment of material provided by FAO including reagents for PCR (sampling and tests) to support the National Veterinary Research Institute Laboratory in VOM.

Uganda (H5N8)

  • 9 February 2017: The International Reference Laboratory for avian influenza IZSVe confirmed H5N8 HPAI clade virus of group B (Tyva-like) in 17 out of 18 samples received from Uganda. A joint surveillance team supported by FAO under GHSA funding received from USAID collected these samples in the week of 30 January 2017. From a total of 213 samples collected, 10% were positive, showing a higher susceptibility for ducks. Further testing of samples may happen through the Uganda Virus Research Institute (UVRI).
  • The FAO/ECTAD team participates at the Regional Consultative Meeting on Transboundary Pests and Diseases in Harare, 14-16 February 2017.
  • The FAO/ECTAD team contributed to drafting the National Response Plan together with the Ministry of Agriculture, Animal Industry and Fisheries (MAAIF). FAO/ECTAD is liaising closely with PREDICT 2, UVRI and CDC Uganda. The draft HPAI response plan is under review and will be submitted to MAAIF for clearance once feedback has been received.
  • FAO/ECTAD is part of the National Task Force (NTF). A joint mission by the National Animal Disease Diagnostics and Epidemiology Centre (NADDEC), Uganda Wildlife Authority (UWA), MoH and FAO was fielded. FAO/ECTAD is coordinating joint surveillance activities and sharing of findings with the NTF.
  • Budget plans were developed by the MoH and approved by the NTF. These will now be shared with partners (already sent to Ministry of Finances).
  • A PPE shipment arrived at Entebbe airport (waiting for customs clearance) from Dubai through FAO under USAID EPT-2 funding.
  • FAO/ECTAD team has joined the MAAIF team to develop an FAO Technical Coorporation Programme Emergency project (TCPE). A first draft is under development.


 Peer-reviewed Publications

  • Nagarajan S. et al. Novel Reassortant Highly Pathogenic Avian Influenza (H5N8) Virus in Zoos, India. Emerg Infect Dis., Apr (2017) [Reference]. In October 2016, HPAI H5N8 viruses were detected in waterfowls in two different zoos in India. Suggestion of virus spread through migratory birds during winter as viruses found were different from the H5N8 isolated in May 2016 in China and the Russian Federation.
  • Pearce M.B. et al. Enhanced virulence of clade highly pathogenic avian influenza A H5N1 viruses in ferrets. Virology, Feb (2017) [Reference]. Investigation of both human and avian A(H5N1) isolates collected from 2006 to 2013 to determine their ability to cause disease in a ferret model. All A(H5N1) viruses tested replicated with efficiency in the respiratory tract of the models. Clade and isolates were associated with lethality in ferrets.
  • Kang H.M. et al. Experimental infection of mandarin duck with highly pathogenic avian influenza A (H5N8 and H5N1) viruses. Vet Microbiol., Jan (2017) [Reference]. Study showing pathogenicity and transmissibility of H5N8 (clade and H5N1 (clades 2.2 and in experimentally infected mandarin ducks. Results suggested that H5N8 viruses spread efficiently in mandarin ducks.
  • Marchenko V.Y. et al. Reintroduction of highly pathogenic avian influenza A/H5N8 virus of clade in Russia. Arch Virol., Jan (2017) [Reference]. Analysis of H5N8 virus clade isolated in 2016 during spring and fall seasons in the Russian Federation. Strains showed different antigenic and genetic features from the H5N8 strain that circulated in the country in 2014. The investigated strains also showed high pathogenicity for mice.
  • Peeters B. et al. Genetic versus antigenic differences among highly pathogenic H5N1 avian influenza A viruses: Consequences for vaccine strain selection. Virology, Jan (2017) [Reference]. Study correlating genetic distances between several H5N1 viruses from different clades with antigenic differences and vaccine performance by generating H5-specific antisera and determining cross-reactivity and antigenic distances between 12 different viruses. Antigenic distances correlated better with genetic variation in 27 selected, antigenically-relevant H5 residues than in the complete HA1 domain.