Animal Health

Sub-Saharan Africa HPAI situation update

12 January 2023, 17:00 hours; Rome


Situation: Highly pathogenic avian influenza virus (H5N1, H5N2, H5N6 and H5N8 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, Réunion (France)*, Gabon, Ghana, Guinea, Lesotho, Mali, Mauritania, Namibia, Niger*, Nigeria*, Senegal, South Africa*, and Togo.

Confirmed countries (H5N6): Nigeria.

Confirmed countries (H5N2): Nigeria, South Africa*.

Confirmed countries (H5N8): Cameroon, Democratic Republic of the Congo, Namibia, Niger, Nigeria, South Africa, Uganda, and Zimbabwe.

Animal/environmental findings: 13 new events since last update on 14 December 2022.

Number of human cases: 0 new events since last update (Last reported case:10 November 2021).

* Countries reporting cases in current wave (since 1 October 2022).

Map. Officially reported HPAI outbreaks (H5N1, H5N2 and H5N8 subtypes) in sub-Saharan Africa, by onset date (1 October 2021 – 12 January 2023)

Officially reported HPAI outbreaks (H5N1, H5N2 and H5N8 subtypes) in sub-Saharan Africa, by onset date (1 October– 12 January 2023)

Note: Map A shows confirmed HPAI events observed from 1 October 2022 to 12 January 2023 (current wave). Map B shows HPAI events observed from 01 October 2021 to 30 September 2022 (previous wave).

Situation update

Table 1. High pathogenicity avian influenza events reported in animals since 1 October 2022 (i.e. previous wave)

Virus Country
regions affected)
Last event observed #Events since last update Total #events since 1 October 2022 Species affected during last observed events


Réunion (France)




Unspecified domestic birds

South Africa
(Gauteng, KwaZulu-Natal, Letsemeng, Free State, Western Cape)




Unspecified domestic birdsDomestic chickens, ostriches, and other unspecified domestic birds, and various wild bird species1Domestic chickens

Niger (Tahoua, Tillaberi)




Domestic birds

Nigeria (Bayelsa, Delta, Niger, Oyo, Sokoto)




Domestic birds


South Africa




Unspecified domestic birds

For a summary of H5N1, H5N6, and H5N8 HPAI events reported in sub-Saharan African countries in previous waves (i.e. before 1 October 2022) please contact EMPRES-Animal Health

Peer-reviewed publications

Mosaad Z, Elhusseiny MH, Zanaty A, Fathy MM, Hagag NM, Mady WH, Said D, Elsayed MM, Erfan AM, Rabie N, Samir A, Samy M, Arafa A-S, Selim A, Abdelhakim AM, Lindahl JF, Eid S, Lundkvist Å, Shahein MA, Naguib MM. Emergence of Highly Pathogenic Avian Influenza A Virus (H5N1) of Clade in Egypt, 2021–2022. Pathogens. 2023; 12(1):90. [reference] It was confirmed detection of (H5N1) of Clade in Egypt through swab and tissue samples collected from migratory birds in the period of Oct-2021 and March-2022. The study concluded that detection of the HPAI H5N1 strain of clade in wild birds in Egypt underlines the risk of the introduction of this strain into the local poultry population. Which is the case in the 2nd half of 2022.

Levy, S., Abd Alhadi, M., Azulay, A., Kahana, A., Bujanover, N., Gazit, R., McGargill, M. A., Friedman, L. M., & Hertz, T. (2022). FLU-LISA: High throughput antibody profiling using antigen microarraysImmunology and cell biology, 10.1111/imcb.12618. Advance online publication. [reference] This study offers an alternative to the traditional ELISA which can be used for profiling IgG, IgA and IgM responses to multiple antigens simultaneously.

Letsholo, S. L., James, J., Meyer, S. M., Byrne, A. M. P., Reid, S. M., Settypalli, T. B. K., Datta, S., Oarabile, L., Kemolatlhe, O., Pebe, K. T., Mafonko, B. R., Kgotlele, T. J., Kumile, K., Modise, B., Thanda, C., Nyange, J. F. C., Marobela-Raborokgwe, C., Cattoli, G., Lamien, C. E., Brown, I. H., Banyard, A. C. (2022). Emergence of High Pathogenicity Avian Influenza Virus H5N1 Clade in Wild Birds and Poultry in BotswanaViruses14(12), 2601. [reference] Botswana reported its first outbreak of HPAI to the World Organisation for Animal Health (WOAH) in 2021. An H5N1 virus was detected in a fish eagle, doves, and chickens which showed high similarity to those clade viruses which have been identified across a broad range of locations. The detection of H5N1 in Botswana has important implications for disease management, wild bird conservation, tourism, public health, economic empowerment of vulnerable communities and food security in the region.

Nemeth, N. M., Ruder, M. G., Poulson, R. L., Sargent, R., Breeding, S., Evans, M. N., Zimmerman, J., Hardman, R., Cunningham, M., Gibbs, S., & Stallknecht, D. E. (2023). Bald eagle mortality and nest failure due to clade highly pathogenic H5N1 influenza a virusScientific reports13(1), 191. [reference] This study shows an alarming rate of bald eagle nest failure and mortality attributed to HP IAV along the southeastern U.S. coast. It is likely that bald eagles become infected through consumption of infected waterfowl. These results and similar reports of raptor mortality in Europe, Asia, and Africa, indicate a clear threat to raptor health and warrants continued efforts to understand these potential impacts.

Cousins, T., Pentecost, M., & VAN Helden, L. (2022). Containment and conversion: Urban livelihoods and the circulation of value amid South Africa's avian influenza outbreakAmerican ethnologist49(3), 413–426. [reference] This study discusses the anthropological considerations around avian influenza outbreaks and response in South Africa.

Elfeil, W. K., Youssef, H., Sedeek, A., El-Shemy, A., Abd-Allah, E. M., Elkady, M. F., El Sayed, E. K., Bazid, A. I., & Abdallah, M. S. (2022). Protective Efficacy of Inactivated H9N2 Vaccine in Turkey Poults under Both Experimental and Field ConditionsVaccines10(12), 2178. [reference] This study evaluates the efficacy of a whole inactivated H9N2 vaccine in turkey poults kept under laboratory and commercial farm conditions.

FAO's support to countries

Global level
  • FAO-SNE has scheduled a webinar to present an overview of the health situation of the HPAI disease globally and in the countries of North Africa and to strengthen the capacities of the countries to detect the disease and household management. [link]
  • The WHO published a rapid assessment of risk associated with recent influenza A(H5N1) clade viruses Rapid risk assessment. [link]
  • OFFLU held an online discussion on 5 December 2022 to discuss the avian influenza situation in poultry and wild birds for experts to share experiences on the most recent wave of outbreaks in different countries. A summary can be found here.
  • FAO participated in the 7th World One Health Congress held in Singapore from 8 to 11 November 2022 and presented preliminary results of the Qualitative Risk Assessment addressing H5 HPAI risk of introduction in Central America, South America and the Caribbean.
  • The 7th World One Health Congress is being held in Singapore from 7 to 11 November 2022.
  • International Alliance for Biological Standardization (IABS) held a meeting on 25-26 October 2022 addressing High Pathogenicity Avian Influenza Vaccination Strategies to prevent and control HPAI: Removing unnecessary barriers for usage.Conclusions and recommendations are now available.
  • The Quadripartite has published the One Health Joint Plan of Action (OH-JPA). It provides a framework for action and proposes a set of activities that the four organizations can offer together to enable countries to advance and scale up One Health in managing human, animal, plant and environment health threats.
  • FAO through its Virtual Learning Center developed an Avian Influenza Preparedness Course. A regional course for East Africa was launched on 3 November 2022. More information available at this link.
  • The OFFLU published the Vaccine Composition Meeting covering the period February – September 2022 for avian influenza and  swine influenza.
  • The Zoonotic Session of the WHO Vaccine Composition Meeting was held on 20 September 2022. The report of the meeting is available on the WHO website. [link]
  • On 19 September 2022, FAO published the guidelines entitled Guiding principles for the design of avian influenza active surveillance in Asia: Designing active, comprehensive, risk-based avian influenza surveillance. [link]
  • The Tripartite (FAO-WOAH-WHO) together with the WOAH/FAO Network of Expertise on Animal Influenza (OFFLU) has conducted a joint rapid risk assessment addressing the recent influenza A(H3N8) human infection in China. [link]
  • Avian influenza report of the WOAH/FAO Network of expertise on animal influenzas (OFFLU) covering the period September 2021 – February 2022. [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 High pathogenicity 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 high pathogenicity avian influenza A(H5N6) virus. [link]
  • The OFFLU network issued an avian influenza statement on 10 November 2021 addressing recent H5Nx high pathogenicity avian influenza virus reassortments. [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 (NSAH/EMPRES), ECTAD-Accra and RAF liaising with affected countries and those at risk for HPAI introduction and spread.
  • USD 6.2 million mobilized from FAO internal resources (SFERA and TCP), AfDB, ROK and USAID to support assessments and immediate response for HPAI introduction and spread.
Regional level
  • FAO-ECTAD Regional Office for West and Central Africa:
    • In collaboration with HQ (Lab Unit/Emergency stockpile), supported Benin, Côte d’Ivoire, Ghana, Guinea, Mali, Niger, Togo, and Nigeria in sending their H5N1-positive samples to the reference laboratory in Padova, Italy for further confirmation and sequencing. So far during 2022, the results received for these countries are follows:
      • Results for Nigeria confirmed H5N1 HPAI in poultry, 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.
      • Results received for Senegal identified all H5N1 viruses from wild birds (Pelicans) as belonging to clade In particular, they are closely related to the H5N1 HPAI 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 from the recent outbreaks in poultry (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 showed that the H5N1 subtype viruses in poultry 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 Netherland, Italy, Nigeria, Scotland (H5N1) and Slovakia (H5N5) collected between October 2020 and March 2021.
      • Results for Guinea confirmed that H5N1 viruses isolated from poultry fall within clade and are closely related to H5N1 HPAI viruses identified in West Africa since early 2021. In addition, these viruses appear closely related to H5N1 HPAI viruses from Nigeria, Niger, and Senegal from 2020-2022, except for the PA gene which clusters with H9N2 viruses of the G1 lineage collected in West Africa between 2017 and 2020; thus, this may suggest that the H5N1 viruses circulating in Guinea are H5N1/H9N2 reassortant viruses.
  • 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 Benin, Burkina Faso, Côte d’Ivoire, Ghana, Guinea, Togo, Mali, Mauritania, Niger, Nigeria, Gabon 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.
National level
  • Gabon:
    • An FAO-EMC emergency field mission was conducted in Gabon from 4 to 8 July 2022 in response to the recent H5N1 HPAI outbreaks reported in Estuaire Province. The FAO-EMC team collaborated with the General Directorate of Livestock to investigate affected farms, assess the emergency response capacity, identify the current gaps in the animal health surveillance system, including the capacity of the Central Veterinary Laboratory of Libreville for the diagnosis of priority diseases, and develop tailored recommendations. The current outbreak has been managed and no additional outbreaks were reported since mid-May 2022.
  • 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 WOAH 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.
    • FAO ECTAD Guinea, in collaboration with EMC-AH, supported the Government of Guinea to undertake a HPAI risk assessment mission to identify risk factors for introduction and spread as well as assessing the capacity of the Veterinary Services in terms of readiness for HPAI emergency response.
  • FAO ECTAD Guinea, in collaboration with EMC-AH, supported the Government of Guinea to undertake a HPAI risk assessment mission to identify risk factors for introduction and spread as well as assessing the capacity of the Veterinary Services in terms of readiness for HPAI emergency response.
  • Senegal:
    • FAO ECTAD Senegal supported veterinary services to respond to the HPAI outbreak in Saint-Louis Region through a follow-up mission. During the mission conducted from 7 to 12 March 2022, FAO ECTAD provided equipment (PPEs, disinfectants, consumables, fuel, etc.), and livestock feed for impacted communities around the park in order to respond to and control the HPAI outbreak in the National park of Djoudj, Saint-Louis Region.
    • In addition, FAO ECTAD supported the LNERV laboratory by procuring and providing reagents and consumables for the detection of HPAI outbreaks.
    • FAO supported LNERV laboratory for samples transportation and sequencing of HPAI viruses to Padova international reference laboratory.
  • FAO ECTAD Ghana, Niger, Nigeria and Mali supported the national governments to conduct further investigation, enhance the capacity of national laboratories, and provide direct support through provision of PPEs, disinfectant’s, reagents and consumables.
Next issue: 9 February 2023
The disease situation updates are produced by the FAO Emergency Prevention System for Animal Health (EMPRES-AH) as part of its mission to increase global disease intelligence.

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 orange. 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 the World Organisation for Animal Health [WOAH], 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.


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