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ARCHIVE Sub-Saharan Africa HPAI situation update

13 February 2019, 17:00 hours; Rome

The next update will be issued on 13 March 2019


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 (H5N1): Burkina Faso, Cameroon, Côte d’Ivoire, Ghana, Niger, Nigeria and Togo.
Confirmed countries (H5N8): Cameroon, Democratic Republic of the Congo, Namibia, Niger, Nigeria, South Africa, Uganda and Zimbabwe.
Animal/environmental findings: Please see reports from individual countries 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 October 2017 – 13 February 2019)

Officially reported HPAI outbreaks (H5N1 and H5N8 subtypes) in Sub-Saharan Africa, by onset date
Click to enlarge. Note:  Map A shows confirmed H5N8 HPAI events observed since 01 October 2018; Map B shows confirmed H5N1 and H5N8 HPAI events observed between 01 October 2017 and 30 September 2018.


 Situation update

Namibia H5N8 HPAI

  • Number of outbreaks* to date: 2 (in Jackass penguins)
  • Regions affected: Karas
  • Outbreaks reported since last update: 2
  • Most recent outbreaks: Observed on 27 January 2019 on Halifax Island, Karas

Nigeria H5N8 HPAI

  • Number of outbreaks* to date: 6
  • Regions affected: Bauchi, Kano, Nasarawa, Ogun
  • Outbreaks reported since last update: 2 (in poultry)
  • Most recent outbreaks: Observed on 19 January 2019 in Bauchi

South Africa H5N8 HPAI

  • Number of outbreaks* to date: 201
  • Regions affected: Eastern Cape, Free State, Gauteng, Limpopo, Kwazulu-Natal, Mpumalanga, North West, Northern Cape, Western Cape.
  • Outbreaks reported since last update: 1 (in ostriches)
  • Most recent outbreaks: Observed on 20 November 2018 in Western Cape


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


1° Administrative regions affected

Date of last observed outbreak

Date of last outbreak report

# reported outbreaks to date

Burkina Faso Bazéga, Boulkiemde, Houet, Kadiogo, Poni, Sanguié, Comoe, Kourweogo, Boulgou, Ioba, Nayala, Nahouri*, Yatenga 21/07/2015 02/10/2015 68*
Cameroon Adamaoua, Centre, South and West 31/03/2017 31/03/2017 22
Côte d’Ivoire Abidjan, Bassam, Belier, Bouaké, Comoe, Gontougo, Lagunes 27/08/2016 03/10/2016 67
Ghana Greater Accra, Ashanti, Central, Eastern, Volta, Western 26/10/2016 23/11/2016 63
Niger Maradi, Niamay 21/02/2016 02/07/2016 2
Nigeria Abia, 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 29/05/2017 02/06/2017 800
Togo Maritime 27/03/2018 18/04/2018 4

*Please note that the administrative regions affected and the total number of confirmed H5N1 HPAI outbreaks in Burkina Faso has been revised based on information received from the country.


Table 2. Summary of countries with no new H5N8 HPAI events reported



1° Administrative regions affected

Date of last observed outbreak

Date of last outbreak report

# reported outbreaks to date

Cameroon Extreme North 02/01/2017 14/02/2017 1
Dem. Rep. Of the Congo Ituri 01/12/2017 03/03/2018 35
Niger Tillaberi 23/01/2017 13/04/2017 1
Uganda Budaka, Kalangala, Masaka and Wakiso Districts 16/01/2017 06/02/2017 24
Zimbabwe Mashonaland 17/05/2017 01/06/2017 1


 FAO's support to countries

Global level

  • Report of the WHO Vaccine Composition Meeting September [link] and February 2018 [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. [link]
  • Press release on H5N8 HPAI in Uganda on 1 February 2017, the first time that HPAI was confirmed in the East Africa region [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 (under GHSA funding and the EPT2 program) to support assessments and immediate response

National level

  • FAO ECTAD Kenya supported the Government of Kenya to review and update their HPAI preparedness and response plan, which was developed in 2008 as HPAI contingency plan for the animal health sector. The review was conducted on 1-2 November 2018 employing a multi-sectoral approach in order to ensure inclusion of human health aspects and resulting in a multi-sectoral national HPAI preparedness and response plan.
  • Under the FAO EPT2/Stockpile project funded by USAID FAO provided the national veterinary services and laboratories of GHSA-1 project countries in Africa with PPEs and materials for avian influenza sample collection, transport, storage and analysis.
  • ECTAD Ethiopia, in collaboration with a Human Resources for Health (HRH-2030) USAID project, supported the Emerging Pandemic Threats-Technical Working Group to review and enrich the multi-sectoral HPAI preparedness and response plan based on the comments and suggestion received during a validation workshop held in July 2018.
  • FAO ECTAD Tanzania supported the Government of the United Republic of Tanzania to review their 2012 National Avian and Pandemic Influenza Emergency Preparedness and Response Plan (NAPIP). The revised document will be merged with the Pandemic Influenza Preparedness and Response Plan drafted for the Public Health sector. The WHO Checklist for Pandemic Influenza Risk and Impact Management will be used to identify gaps.
  • FAO ECTAD Nigeria supported the Government of the Federal Republic of Nigeria as follows:
    • thirty five (35) staff of the Federal Department of Veterinary and Pest Control Services of the Federal Ministry of Agriculture and Rural Development (FMARD) were trained from 12 to 14 November 2018 on Good Emergency Management Practices (GEMP) in Abuja;
    • forty (40) field veterinary officers and human health doctors were trained on disease outbreak investigation, mainly management of Avian Influenza outbreaks using a One Health Approach from 15 to 17 November 2018 in Abuja;
    • disease surveillance agents were trained on epidemiological field investigation;
    • poultry farmers and live bird market (LBM) operators received training on biosecurity measures;
    • a consultative meeting on vaccination against HPAI as an alternative control measure was organized in December 2018.
  • HQ (AGAH/EMPRES), ECTAD-Accra and RAF provided PPEs, disinfection materials, boots, protective eyewear and sample shipping boxes to the Government of the Federal Republic of Nigeria. ECTAD-Accra further provided technical expertise to conduct risk assessment and risk mapping for HPAI in five states.


Peer-reviewed Publications

  • Vergne T, Meyer A, Long PT, Elkholly DA, Inui K, Padungtod P, Newman SH, Fournié G, Pfeiffer DU. Optimising the detectability of H5N1 and H5N6 highly pathogenic avian influenza viruses in Vietnamese live-bird markets. Sci Rep. 2019 Jan 31;9(1):1031. doi: 10.1038/s41598-018-37616-1. [references] In this study, the authors estimate the sensitivity and specificity of five different sample types for detecting AIVs subtypes H5N1 and H5N6 in Vietnamese LBMs: oropharyngeal duck samples, solid and liquid wastes, poultry drinking water and faeces. Study results suggest that the sensitivity of environmental samples for detecting H5N1 viruses is equivalent to that of oropharyngeal duck samples; however, taking oropharyngeal duck samples was estimated to be more effective in detecting H5N6 viruses than taking any of the four environmental samples. This study also stressed that the specificity of the current surveillance strategy in LBMs was not optimal leading to some false positive LBMs. Using simulations, the authors identified 42 sampling strategies, all involving the collection of both environmental and oropharyngeal duck samples, more parsimonious than the current strategy and expected to be highly sensitive for both viruses at the LBM level.
  • Kayed AS, Kandeil A, Gomaa MR, El-Shesheny R, Mahmoud S, Hegazi N, Fayez M, Sheta B, McKenzie PP, Webby RJ, Kayali G, Ali MA. Surveillance for avian influenza viruses in wild birds at live bird markets, Egypt, 2014-2016. Influenza Other Respir Viruses. 2019 Feb 3. doi: 10.1111/irv.12634. [references] In this study, surveillance for AIV among hunted and captured wild birds in Egypt was conducted in order to understand the characteristics of circulating viruses. Sampling of wild bird species occurred in two locations along the Mediterranean Coast of Egypt in the period from 2014 to 2016. A total of 1316 samples (cloacal and oropharyngeal swabs) were collected from 20 different species of hunted or captured resident and migratory birds sold at live bird markets. Eighteen AIVs (1.37%) were isolated from migratory Anseriformes at live bird markets. Further characterization of the viral isolates identified five hemagglutinin (H3, H5, H7, H9, and H10) and five neuraminidase (N1, N2, N3, N6, and N9) subtypes, which were related to isolates reported in the Eurasian region. Two of the 18 isolates were highly pathogenic H5N1 viruses related to clade 2.2.1, while three isolates were G1-like H9N2 viruses. The results revealed significant diversity of AIVs in Anserifromes sold at live bird markets in Egypt. This allows for genetic exchanges between imported and enzootic viruses and put the exposed humans at a higher risk of infection with zoonotic viruses.
  • Huynh HTT, Truong LT, Meeyam T, Le HT, Punyapornwithaya V. Individual and flock immunity responses of naïve ducks on smallholder farms after vaccination with H5N1 Avian Influenza vaccine: a study in a province of the Mekong Delta, Vietnam. Peer. 2019 Jan 16;7:e6268. doi: 10.7717/peerj.6268. [references] This study aimed to evaluate antibody responses of immunologically naïve domestic ducks to H5N1 avian influenza vaccine currently used in the national mass vaccination program of Vietnam. Blood samples of 166 ducks were tested for antibody titres before vaccination, 21 days after primary vaccination, and 21 days after booster vaccination. No sampled ducks showed anti-H5 seropositivity pre-vaccination. The geometric mean titer (GMT) of the vaccinated ducks was 5.30 after primary vaccination, with 80% of the vaccinated ducks showing seropositivity. This result indicates that the immunity of duck flocks met the targets of the national poultry H5N1 HPAI mass vaccination program. GMT and seropositive rates of the ducks were 6.48 and 96.3%, respectively, after booster vaccination, which were significantly higher than those after primary vaccination. Flock-level seroprotection rate significantly increased from 68% to 84.7%
  • Shehata AA, Sedeik ME, Elbestawy AR, Zain El-Abideen MA, Ibrahim HH, Kilany WH, Ali A. Co-infections, genetic, and antigenic relatedness of avian influenza H5N8 and H5N1 viruses in domestic and wild birds in Egypt. Poult Sci. 2019 Jan 22. doi: 10.3382/ps/pez011. [references] In this study, 50 Egyptian poultry farms of commercial broilers (N = 39) and commercial layers (N = 11) suffering from respiratory problems and mortality were investigated between January 2016 to December 2017. Samples were also collected from quail (N = 4), Bluebird (Sialis, N = 1), and Greenfinch (Chloris chloris, N = 1) for analysis. Respiratory viral pathogens were screened by PCR and positive samples were subjected to virus isolation and genetic identification. Antigenic relatedness of isolated avian influenza (AI) H5 subtype was evaluated using cross-hemagglutination inhibition. Results revealed that the incidence of single virus infections in commercial broilers was 64.1% (25/39), with the highest incidence for ND (33.3%) and H9N2 (20.5%), followed by H5N1 (7.7%) and H5N8 (2.7). Meanwhile, mixed infections were observed in 7.7-2.6% of broiler farms but up to 27.3% in layer farms. Partial HA gene sequence analysis showed the clustering of the selected AI H5N8 within the clade, while H5N1 clustered with the clade The low genetic and antigenic relatedness between AI H5N1 and H5N8 viruses suggest the need for modification of poultry vaccination strategies for avian influenza in Egypt along with strict biosecurity measures.
  • Badolo A, Burt F, Daniel S, Fearns R, Gudo ES, Kielian M, Lescar J, Shi Y, von Brunn A, Weiss SR, Hilgenfeld R. Third Tofo Advanced Study Week on Emerging and Re-emerging Viruses, 2018. Antiviral Res. 2019 Feb;162:142-150. doi:10.1016/j.antiviral.2018.12.015. [reference] The Third Tofo Advanced Study Week on Emerging and Re-Emerging Viruses (3rd TASW) was held in Praia do Tofo, Mozambique, from September 02 to 06, 2018. It brought together 55 participants from 10 African countries as well as from Belgium, China, Germany, Singapore, and the USA. Meeting sessions covered aspects of the epidemiology, diagnosis, molecular and structural biology, vaccine development, and antiviral drug discovery for emerging RNA viruses that are current threats in Africa and included flaviviruses (dengue and Zika), alphaviruses (chikungunya), coronaviruses, filoviruses (Ebola), influenza viruses, Crimean Congo hemorrhagic fever virus, Rift Valley fever Virus, Lassa virus, and others. This report summarizes the lectures held at the meeting and highlights advances in the field.