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Sub-Saharan Africa HPAI situation update

15 September 2021, 17:00 hours; Rome

The next issue will be distributed on 13 October 2021. If interested in a previous issue please send an email to EMPRES-Animal Health specifying the intended use of the document.


Information provided herein is current as of the date of issue. Information added or changed since the last Sub-Saharan 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 Organization 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, H5N8 and H5N6 subtypes) with pandemic potential in countries of Sub-Saharan Africa since February 2017.
Confirmed countries (H5): Benin*, Lesotho* and Ghana*.
Confirmed countries (H5N1): Botswana*, Burkina Faso, Cameroon, Côte d’Ivoire*, Ghana, Mali*, Mauritania*, Niger*, Nigeria*, Senegal*, South Africa* and Togo*.
Confirmed countries (H5N6): Nigeria.
Confirmed countries (H5N8): Cameroon, Democratic Republic of the Congo, Namibia, Niger, Nigeria, South Africa*, Uganda and Zimbabwe.
Animal/environmental findings: 33 new events since last update (11 August 2021).
Number of human cases: 0 new events since last update (11 August 2021).
* Countries reporting cases in the current wave (since 01 October 2020)

Map. Officially reported HPAI outbreaks (H5N1, H5N6 and H5N8 subtypes) in Sub-Saharan Africa, by onset date (1 October 2020 – 15 September 2021)

Officially reported HPAI outbreaks (H5N1, H5N6 and H5N8 subtypes) in Sub-Saharan Africa, by onset date
Click to enlarge. Note:  Map A shows confirmed HPAI events observed since 01 October 2020. Precise geolocations of 20 H5N1 HPAI outbreaks in Nigeria are not yet publicly available; Map B shows confirmed HPAI events observed between 01 October 2019 and 30 September 2020.


 Situation update

Table. Highly pathogenic avian influenza events reported in animals since 1 October 2020


Country (administrative regions affected)

Last event observed

#Events since last update

Total #events since 1 October 2020

Species affected during last observed events


Benin (Oueme)




Unspecified domestic birds

Ghana (Greater Accra, Central)




Domestic unspecified birds

Lesotho (Leribe, Maseru) 28/05/2021 0 2 Domestic chickens







Domestic chickens

Côte d'Ivoire





Unspecified domestic birds

Mali (Bamako, Koulikoro, Sikasso)




Domestic chickens and other unspecified domestic birds

Mauritania (Trarza)





Niger (Niamey, Tillaberi)




Domestic chickens, and other unspecified domestic birds

Nigeria (Bayelsa, Delta, Kano, Lagos, Plateau, Bauchi, Gombe, Nasarawa, Kaduna, Edo and Niger States)




Ostriches, geese, turkeys, layer chickens, and Peacocks

Senegal (Thies, Saint Louis)

23/01/2021 0


Domestic chickens, and wild Rose Pelicans (Pelecanus onocrotalus)

South Africa (Eastern Cape, Free State, Gauteng, KwaZulu-Natal, Limpopo, Mpumalanga, North West, Western Cape) 16/08/2021 26 91 (including 25 in wild birds) Domestic chickens. Ostrich,  and other unspecified domestic birds, and wild bird species including African Sacred Ibis (Threskiornis aethiopicus), Rose Pelican (Pelecanus onocrotalus), Hartlaub's gull (Chroicocephalus hartlaubii), Kelp gull (Larus dominicanus), Yellow-billed Duck (Anas undulata), Black Swan (Cygnus atratus), Grey Headed Gull (Chroicocephalus cirrocephalus), African Fish Eagle (Haliaeetus vocifer), Egyptian Goose (Alopochen aegyptiacus), Spur-winged Goose (Plectropterus gambensis) Spotted Eagle-owl (Bubo africanus), Secretary bird (Sagittarius serpentarius), African penguin (Spheniscus demersus), and Unspecified (Laridae)

Togo (Maritime)




Domestic chickens


South Africa (Western Cape)




Unspecified domestic birds

* Veterinary Services in Ghana have confirmed H5N1 HPAI as a causative agent for these events, official notification is awaited.


For a summary of H5N1, H5N6, and H5N8 HPAI events reported in sub-Saharan African countries in previous waves (i.e. before 1 October 2020) please contact EMPRES-Animal Health


 FAO's support to countries

Global level

  • FAO published the third edition of the Good emergency management practice - The essentials: A guide to preparing for animal health emergencies, freely available at this link.
  • FAO in collaboration with OIE organized a webinar on H5 HPAI occurrence and prevention in North Africa on 20 May 2021.
  • As part of the OIE/FAO Network of Expertise on Animal Influenzas, FAO attended the Zoonotic Influenza Sessions of the WHO Vaccine Composition Meeting held from 2 to 4 March 2021. The report is now available online. [link]
  • On 26 February 2021, the OFFLU issued a statement on Highly Pathogenic Avian Influenza in the Russian Federation relating to its detection in poultry workers. [link]
  • The FAO/CMS-led Scientific Task Force on Avian Influenza and Wild Birds issued a statement on 12 February 2021: H5N8 (and other subtypes) Highly Pathogenic Avian Influenza in poultry and wild birds - Winter of 2020/2021 with focus on management of protected areas in the African Eurasian region. [link]
  • WHO developed an online training course entitled Strengthening collaboration between human and animal health sectors for improved health security, freely available at this link. The course covers the Tripartite Zoonosis Guide and associated tools in Module 2.
  • The Tripartite Joint Risk Assessment (JRA) Operational Tool to address zoonotic health threats at the animal-human-environment interface is now available online [link]
  • On 13 November 2020, FAO sent an alert message on the risk of H5Nx HPAI re-introduction to Chief Veterinary Officers and FAO offices of at-risk countries in Africa region.
  • Report of the WHO Vaccine Composition Meeting October 2020 [link]
  • The Tripartite Zoonoses Guide is now available in all UN languages [link]
  • Report of the WHO Vaccine Composition Meeting February 2019 [link]
  • Focus On  “2016–2018 Spread of H5N8 highly pathogenic avian influenza (HPAI) in sub-Saharan Africa: epidemiological and ecological observations” [link]
  • Focus On “Highly Pathogenic H5 Avian Influenza in 2016 and 2017 – Observations and future perspectives” [link]
  • Risk Assessment addressing H5N8 HPAI in Uganda and the risk of spread to neighbouring countries, April 2017. [link]
  • Qualitative Risk Assessment addressing H5N1 Highly Pathogenic Avian Influenza spread in the Central African region [link]
  • 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 to support assessments and immediate response

Regional level

  • FAO-ECTAD Regional Office for West and Central Africa:
    • Is supporting the recently established Regional Incident Coordination Group (ICG) for West Africa on HPAI under the leadership of Economic Community of West African States (ECOWAS) Regional Animal Health Centre (RAHC), which held their first virtual meeting on 15 September 2021.
    • Is supporting ECOWAS in the organization of the ECOWAS Seventh Annual Regional Animal Health Networks (RAHN) Meeting to be held on 21-24 September 2021.
    • Supported Mauritania, Senegal, Mali, Burkina Faso, Côte d’Ivoire, Togo, Niger, and Nigeria in managing the poultry mortality events due to H5 HPAI, as well as at-risk countries as regional level coordination in 2021.
    • Supported ECOWAS in the organization of a virtual emergency consultative meeting and refresher training on resurgence of HPAI in the ECOWAS region held on 17th – 19th February 2021.
    • Supported Liberia in April 2020 to conduct a risk assessment and risk mapping addressing HPAI introduction, spread, and occurrence in the country.
    • Supported Nigeria in May 2019 to conduct assessment mission for technical guidance on control, containment and eradication of HPAI in the country.

National level

  • Ethiopia:
    • FAO organized a face-to-face meeting on the operationalization of the Tripartite Joint Risk Assessment (JRA) operational tool, 2-6 March 2021, in Adama. The meeting was attended by 25 participants from MoA, MoH, Wildlife, sub-national animal health services, WHO, FAO, and other partners. The participants worked in groups to jointly identify and assess risks associated with HPAI and RVF for generating relevant data, information and recommendations to manage and reduce risks at the animal-human-environment interfaces.
    • NAHDIC received Proficiency Test results on avian influenza and Newcastle disease and scored 97.4% and 100%, respectively for the molecular and the serological tests of both diseases.
  • Côte d’Ivoire:
    • A joint leadership and Good emergency management practice (GEMP) multisectoral training including a table top simulation exercise on avian influenza was organized from 9 to 13 August 2021 involving  48 participants from different institutions and ministries of the National One Health Platform.
    • Investigation of poultry mortalities reported on 10 August 2021 in the locality of Mondoukou in the southeastern region of Grand Bassam was conducted and confirmed H5N1 HPAI virus as the causative agent.
    • FAO ECTAD Côte d’Ivoire facilitated support from emergency stockpile with EPI, Reagents, and consumable to support the country controlling the event. FAO ECTAD Côte d’Ivoire also supported and jointly participated in investigations in live poultry markets and wild bird resting areas (wetlands) for risk assessment.
    • A total of 1 186 samples including 296 cloacal swabs, 296 tracheal swabs and 594 environmental swabs were collected from healthy, sick, and dead birds. All these samples were sent to the national Central Veterinary Laboratory (CVL) of Bingerville for testing.
    • In the affected poultry farms more than 300 000 poultry were culled by veterinary services as part of ongoing sanitary measures to control the spread of the virus.
  • FAO SNE together with FAOR Mauritania and regional ECTAD in Accra supported Mauritania in managing the mortality event in pelicans due to H5N1 HPAI.
  • FAO ECTAD Niger and Mali supported the national governments to conduct further investigation, enhance the capacity of the national laboratory and provide direct support through provision of PPEs, disinfectant’s, reagents and consumables.
  • The Tripartite (FAO-OIE-WHO) co-organized with national ministries and One Health Platforms Joint Risk Assessment National Workshop in the Democratic Republic of the Congo (19-22 January 2021), addressing HPAI and Ebola, and in Senegal (15-18 December 2020), addressing HPAI and Rift Valley fever.
  • FAO ECTAD Senegal supported the development of the national emergency preparedness and response plan for HPAI and standard operating procedures (SOPs) for biosecurity, sample collection and shipment, and carcass disposal, and supported the national government in testing this plan through a simulation exercise.

Peer-reviewed Publications

  • El-Shall, N. A., Awad, A. M., & Sedeik, M. E. Examination of the protective efficacy of two avian influenza H5 vaccines against clade H5N8 highly pathogenic avian influenza virus in commercial broilers. Research in veterinary science, 140, 125–133. Advance online publication. [reference]
  • Tarek, M., Naguib, M. M., Arafa, A. S., Tantawy, L. A., Selim, K. M., Talaat, S., & Sultan, H. A. Epidemiology, Genetic Characterization, and Pathogenesis of Avian Influenza H5N8 Viruses Circulating in Northern and Southern Parts of Egypt, 2017-2019. Animals: an open access journal from MDPI, 11(8), 2208. [reference]