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Sub-Saharan Africa HPAI situation update

11 May 2022, 17:00 hours; Rome

The next issue will be distributed on 08 June 2022. 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 boundaries and names shown and the designations used on these map(s) do not imply the expression of any opinion whatsoever on the part of FAO concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers and boundaries. Dashed lines on maps represent approximate border lines for which there may not yet be full agreement.



Situation: Highly pathogenic avian influenza virus (H5N1, H5N2, H5N8 and H5N6 subtypes) with pandemic potential in countries of Sub-Saharan Africa since February 2017.
Confirmed countries (H5): Lesotho*.
Confirmed countries (H5N1): Benin*, Botswana, Burkina Faso*, Cameroon, Côte d’Ivoire*, Ghana*, Lesotho*, Mali*, Mauritania, Namibia*, Niger*, Nigeria*, Senegal*, South Africa*, and Togo*.
Confirmed countries (H5N6): Nigeria.
Confirmed countries (H5N2): Nigeria*
Confirmed countries (H5N8): Cameroon, Democratic Republic of the Congo, Namibia, Niger, Nigeria, South Africa, Uganda, and Zimbabwe.
Animal/environmental findings: 17 new events since last update (13 April 2022).
Number of human cases: 0 new events since last update (10 November 2021).
* Countries reporting cases in the current wave (since 01 October 2021)

Map. Officially reported HPAI outbreaks (H5N1, H5N2 and H5N8 subtypes) in Sub-Saharan Africa, by onset date (1 October 2021 – 11 May 2022)

Officially reported HPAI outbreaks (H5N1, H5N2 and H5N8 subtypes) in Sub-Saharan Africa, by onset date
Click to enlarge. Note:  Map A shows confirmed HPAI events observed since 01 October 2021. Map B shows confirmed HPAI events observed between 01 October 2020 and 30 September 2021.


 Situation update

Table 1. Highly pathogenic avian influenza events reported in animals since 1 October 2021
(i.e. current wave)


Country (administrative regions affected)

Last event observed

#Events since last update

Total #events since 1 October 2021

Species affected during last observed events


(Leribe, Maseru)

28/05/2021 (reported in December 2021)



Unspecified domestic birds


Benin (Oueme)




Unspecified domestic birds

Burkina Faso




Domestick chickens

Côte d'Ivoire
(District Autonome d’Abidjan, Comoe)




Domestic chickens and other unspecified domestic birds

Ghana (Ashanti, Brong Ahafo, Central, Greater Accra, Northern, Upper West, Volta, and Western)




Unspecified domestic birds





Domestic chickens

Namibia (Erongo)




Wild Cape Cormorant (Phalocrocorax capensis)

Niger (Dosso, Maradi, Niamey, Tillabéri, Zinder)

21/02/2022 0 14

Domestic chickens and other unspecified birds

(Abuja, Anambra, Bauchi, Borno, Edo, Gombe, Kaduna, Kano, Kogi, Nassarawa, Niger, Ogun, Plateau, Rivers, Zamfara)




Domestic chickens and other unspecified birds





Wild Rose Pelicans (Pelecanus onocrotalus)

South Africa (Eastern Cape, Free State, Gauteng, KwaZulu-Natal, Limpopo, Mpumalanga, North West, Western Cape)


6 (including 1 in wild birds)

98 (including 30 in wild birds)

Domestic chickens, ostriches, and other unspecified domestic birds, and various wild bird species1





Domestic chickens, Guinea Fowl


Nigeria (Bauchi)




Domestic chickens

1 To date, wild bird species affected in South Africa include: Arctic skua (Stercorarius parasiticus), Black Swan (Cygnus atratus), Cape Cormorant (Phalocrocorax capensis), Common Tern (Sterna hirundo), Egyptian goose (Alopochen aegyptiaca), Hartlaub's Gull (Chroicocephalus hartlaubii), Jackass Penguin (Spheniscus demersus), Kelp Gull (Larus dominicanus), Oystercatcher (Haematopus Ostralegus), Sandwich Tern (Thalasseus sandvicensis), Stork (Cicona sp.) and Swift Tern (Thalasseus bergii).


For a summary of H5N1, H5N6, and H5N8 HPAI events reported in sub-Saharan African countries in previous waves (i.e. before 1 October 2021) please contact EMPRES-Animal Health


 FAO's support to countries

Global level

  • Report of the WHO Vaccine Composition Meeting – February 2022. [link]
  • Avian influenza report of the OIE/FAO Network of expertise on animal influenzas (OFFLU) covering the period September 2021 – February 2022. [link]
  • The International Alliance for Biological Standardization (IABS) will hold a meeting on 25-26 October 2022 addressing High Pathogenicity Avian Influenza Vaccination Strategies to prevent and control HPAI: Removing unnecessary barriers for usage. Registration possible at this link.
  • On 18 February 2022, FAO issued an alert to Chief Veterinary Officers, FAO offices, and wild bird partner organizations on the increased risk of Highly Pathogenic Avian Influenza outbreaks in wild bird populations in Africa.
  • FAO held a webinar entitled Managing HPAI in wild birds on 10 February 2022. The recording of the webinar is available at these links: part 1 & part 2.
  • The Scientific Task Force on Avian Influenza and Wild Birds issued a statement on 24 January 2022 relative to recent mass mortality in some wild bird populations in the United Kingdom and Israel. [link]
  • The OFFLU Network issued a statement on 24 December 2021 addressing the recent introduction of H5N1 HPAI in Canada. [link]
  • WHO published an assessment on 19 November 2021 addressing the risk associated with highly pathogenic avian influenza A(H5N6) virus. [link]
  • The OFFLU network issued an avian influenza statement on 10 November 2021 addressing recent H5Nx highly pathogenic avian influenza virus reassortments. [link]
  • On 29 October 2021, FAO sent an alert message on the risk of H5Nx HPAI (re-)introduction along migratory flyways to Chief Veterinary Officers and FAO offices of at-risk countries in Eurasia and Africa regions.
  • FAO in collaboration with OIE organized a webinar on H5 HPAI occurrence and prevention in North Africa on 20 May 2021.
  • 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.
  • 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:
    • Samples recently submitted by NVRI-Vom, Nigeria for confirmatory analysis to the FAO/OIE AI Reference Laboratory in Padova, Italy confirmed H5N1 HPAI, with one sample characterized as H5N2 HPAI. This is the first time H5N2 has been detected in commercial poultry in Nigeria. Previous detections of H5N2 were in wild birds more than 10 years ago. The phylogenetic analysis confirmed that the H5N1 viruses belong to clade and are closely related to viruses that have been circulating in poultry in Senegal, Niger and Nigeria since early 2021. This may suggest persistent circulation of the virus in West Africa. Advanced genetic characterization of H5N2 HPAI indicated potential re-assortment between H5N1 HPAI and H9N2 LPAI viruses.
    • In collaboration with HQ (Lab Unit/Emergency stock pile), supported Benin, Burkina Faso, Côte d’Ivoire, Ghana, Togo, and Nigeria in sending their samples positive for H5N1 to the reference laboratory in Padova for further confirmation and sequencing. Results from Padova have been received for Senegal, Niger, Mali and Nigeria samples.
    • Results received for Senegal in wild birds-Pelicans identified all H5N1 viruses as belonging to clade In particular, they are highly related to the HPAI H5N1 viruses currently circulating in Europe (epidemic wave 2021-2022) and cluster separately from the H5N1 identified in Senegal in December 2020-January 2021, therefore indicating a novel virus incursion in the country.
    • Results for Niger in poultry from the recent outbreaks (in 2022) cluster with the H5N1 viruses previously identified in 2021 and Nigeria in 2021, and with H5N1 viruses which circulated in Europe from October 2020 to December 2021.
    • Results for Mali in poultry showed that the H5N1 subtype viruses belong to clade, the genetic group responsible for the ongoing epidemic incursion into Central Asia and Europe, which has been recently identified also in the African continent. Together, they cluster with H5N1 samples collected in the Netherlands, Italy, Nigeria, Scotland (H5N1) and Slovakia (H5N5) between October 2020 and March 2021.
    • Supported 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 second virtual meeting on 11 March 2022 with the participation of all 15 West Africa Countries. The first ICG meeting was held on 15 September 2021.
    • Supported ECOWAS in the organization of the ECOWAS Seventh Annual Regional Animal Health Networks (RAHN) Meeting held on 21-24 September 2021 in Abidjan, Cote d’Ivoire.
    • Supported Benin, Burkina Faso, Côte d’Ivoire, Ghana, Togo, Mali, Mauritania, Niger, Nigeria, and Senegal in managing the poultry and wild bird mortality events due to H5 HPAI, as well as at-risk countries as regional level coordination in 2022.
    • 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 and December 2021 to conduct assessment mission for technical guidance on control, containment and eradication of HPAI in the country.
    • In collaboration with EMC-AH, supported Togo in May 2019 and October 2021 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:
    • As part of government support, compensation of about 150 poultry owners whose flocks had to be depopulated during the 2021 HPAI emergency response started on 3 February 2022.
    • On 27 January 2022, veterinary services retrospectively notified to OIE two H5N1 HPAI outbreaks in domestic birds in Abidjan district – in Grand-Bassam and Bingerville localities). The events occurred on 10 and 21 November 2021.
    • FAO ECTAD Côte d’Ivoire supported the national government to conduct investigations and with enhancing the capacity of the national laboratory through the provision of personal protective equipment (PPE), disinfectant, reagents, and consumables using the FAO emergency stockpile and the online primers and probes ordering service set up by FAO HQ.
    • Following investigations conducted after high poultry mortalities were reported on 10 August 2021 in Mondoukou, the national Central Veterinary Laboratory (CVL) of Bingerville confirmed southeastern region of Grand Bassam, samples positive for H5N1 HPAI. This was confirmed by the reference laboratory in Padova, Italy. Additional samples were collected in live poultry markets in different locations and in migratory birds in water flyways in the initial outbreak areas. FAO ECTAD Cote d’Ivoire will support the shipment of these samples to the reference laboratory in Padova to identify phylogenetic links.
    • Thus far, preliminary analysis of the partial HA gene sequence of the H5N1 viruses indicates that the viruses are highly pathogenic and belong to the clade Further complete phylogenetic and molecular analysis of the HA gene confirmed a closed relationship between H5N1 HPAI viruses detected in Côte d’Ivoire and H5N1 viruses isolated in Nigeria and in Europe during 2020-2021.
    • In 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. A cleaning and disinfection operation of live poultry markets in Abidjan District was conducted by the veterinary services aiming at limiting the spread of the virus.
    • Countrywide sensitization of Poultry Sanitary Defense Groups and poultry breeders for strengthening biosecurity measures, disease surveillance, and real-time reporting in poultry farms and markets are ongoing by veterinary services from 29 November 2021 up to 18 December 2021 with the support of FAO, USAID, and active participation of IPRAVI (Ivorian poultry Interprofession).
  • The FAO country offices in Benin and Togo provided PPE, lab reagents, and consumables from the emergency stockpile and assisted in sending samples to the reference laboratory (Padova) to support the countries in controlling the disease. The FAO country office in Togo also assisted in the EMC-AH mission in Togo.
  • 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 Ghana, Niger, Nigeria 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.

Important links

  • Report of the WHO Vaccine Composition Meeting – September 2021. [link]
  • FAO published the third edition of the Good emergency management practice - The essentials: A guide to preparing for animal health emergencies. [link]
  • The Tripartite Joint Risk Assessment (JRA) Operational Tool to address zoonotic health threats at the animal-human-environment interface is now available online in all UN languages. [link]
  • The Tripartite Zoonoses Guide is now available in all UN languages. [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]


Peer-reviewed Publications

Kotey, E.N., Asante, I.A., Adusei-Poku, M., Arjarquah, A., Ampadu, R., Rodgers, D., Nyarko, E.O., Asiedu, W., Dafeamekpor, C., Wiley, M.R., Mawuli, G., Obeng, R.A., Nyarko, S.O., Magnusen, V., Kodua, E., Attram, N., Nimo-Paintsil, S.C., Pratt, C., Fox, A.T., Letizia, A., Ampofo, W.K. Phylogenetic and genetic characterization of influenza A H9N2 viruses isolated from backyard poultry in selected farms in Ghana. Vet Med Sci. 2022 Apr 21. [reference] This study presents poultry surveillance data from the years 2017 to 2019 from biannual surveillance for influenza viruses among poultry at military barracks throughout Ghana. Influenza A H9N2 virus was detected in 11 avian species and phylogenetic analysis of viral haemagglutinin (HA) protein confirms the possibility of importation of viruses from North Africa and Burkina Faso.