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ARCHIVE Sub-Saharan Africa HPAI situation update

12 February 2020, 17:00 hours; Rome

The next update will be issued on 11 March 2020


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, H5N8 and H5N6 subtypes) with pandemic potential in countries of Sub-Saharan Africa since February 2017.
Confirmed countries (H5N1): Burkina Faso, Cameroon, Côte d’Ivoire, Ghana, Niger, Nigeria 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: Please see reports from individual countries below.
Number of human cases: None reported to date
* Countries reporting cases in the current wave (since 01 October 2019)

Map 1. Officially reported HPAI outbreaks (H5N1, H5N6 and H5N8 subtypes) in Sub-Saharan Africa, by onset date (1 October 2018 – 12 February 2020)

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 2019; Map B shows confirmed H5N1 and H5N8 HPAI events observed between 01 October 2018 and 30 September 2019. * The event of H5N6 HPAI in Map A, while reported on 23/12/2019, was observed on 25/06/2019.


 Situation update

South Africa H5N8 HPAI

  • Number of outbreaks observed since 1 October 2019: 4
  • Region affected: Western Cape
  • Outbreaks reported since last update: 2
  • Most recent outbreak: Observed on 30 October 2019 in Western Cape


Table 1. Summary of countries with no new H5N6 HPAI events reported since last update (15 January 2020)


1° Administrative regions affected

Date of last observed outbreak

# reported outbreaks for the current wave

Date of last outbreak observed in previous waves

# reported outbreaks in previous waves








For a summary of H5N1 and H5N8 HPAI events reported in sub-Saharan African countries before the current wave (i.e. before 01 October 2019) see Update 09/10/2019.


 FAO's support to countries

Global level

  • 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. [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 to support assessments and immediate response

National level

  • FAO ECTAD Ethiopia organized joint risk assessment (JRA) in collaboration with WHO on 16-19 July 2019 in Bishoftu. About 23 participants attended from Ministry of Agriculture and Natural Resource (MoA), Ministry of Health (MoH)/Ethiopian Public Health Institute (EPHI), Ethiopian Wildlife Conservation Authority (EWCA), Environment, Forest and Climate Chage Commission (EFCCC) and partners. The trainees applied the JRA tool on Rift Valley fever (RVF) and highly pathogenic avian influenza (HPAI) using a One Health approach.
  • FAO ECTAD Ethiopia co-facilitated the OH Zoonotic Disease re-prioritization workshop with various partners on 26 September 2019 in Addis Ababa, using the CDC tool. Out of 41 zoonotic diseases listed, Anthrax, Rabies, Brucellosis, RVF and zoonotic avian influenza were prioritized and agreed by MoA, MoH and environment under participation of all sub-national states.
  • 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.
  • 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.
  • ECTAD-RAF and ECTAD Nigeria trained 30 state veterinary officers of Adamawa, Borno and Ypbe states in the northeast Nigeria affected by the insurgency on HPAI recognition, disease outbreak investigation, control and containment from 3 to 6 July 2019.
  • In 2018-19, FAO ECTAD Tanzania facilitated the review of the National Pandemic Influenza Emergency Preparedness and Response Plan that was originally developed in 2012. The review process is on-going in 2020 to align the plan to WHO Pandemic frameworks.
  • FAO ECTAD Tanzania in collaboration with One Health Coordination supported the pilot of the Joint Risk Assessment (JRA) on 26-28 March 2019 in Dar es Salaam. The workshop brought together experts from veterinary services, public health, environment, wildlife authorities and academia, and was funded by the United States Defense Threat Reduction Agency (DTRA) and conducted with technical support from FAO and WHO. Zoonotic avian influenza, a threat that is circulating in other African countries and may be introduced via trade, cross-border movement or through wild bird migration was among the risks assessed [link].

Peer-reviewed Publications

  • Almayahi ZK, Al Kindi H, Davies CT, Al-Rawahi B, Al-Jardani A, Al-Yaqoubi F, Jang Y, Jones J, Barnes JR, Davis W, Bo S, Lynch B, Wentworth DE, Al-Maskari Z, Maani AA, Al-Abri S. First report of human infection with avian influenza A(H9N2)virus in Oman: The need for a One Health approach. Int J Infect Dis. 2020 Feb;91:169-173. doi: 10.1016/j.ijid.2019.11.020. Epub 2019 Nov 22. [reference]This paper focusses on the case of a 14-month-old female in Oman with an A(H9N2) virus infection, and discusses the urgency that a multisector One Health approach be established to combat the threat of avian influenza at the animal-human interface. In addition to enhancements of surveillance and control in poultry, there is a need to develop screening and preventive programs for high-risk occupations.
  • Kariithi HM, Welch CN, Ferreira HL, Pusch EA, Ateya LO, Binepal YS, Apopo AA, Dulu TD, Afonso CL, Suarez DL. Genetic characterization and pathogenesis of the first H9N2 low pathogenic avian influenza viruses isolated from chickens in Kenyan live bird markets. Infect Genet Evol. 2020 Mar;78:104074. doi: 10.1016/j.meegid.2019.104074. Epub 2019 Oct 18.[reference] In this paper, avian influenza virus (AIV)-specific real-time RT-PCR (RRT-PCR) was used to screen 282 oropharyngeal swabs collected from chickens at six live bird markets (LBMs) and 33 backyard poultry farms in Kenya through planned surveillance. 8 positive samples were detected, and virus was then isolated in five eggs from RRT-PCR positive samples, before being sequenced, and identified as H9N2 low pathogenic AIV (LPAIV) G1 lineage. Virus pathogenesis and transmissibility was assessed by inoculating low and medium virus doses of a representative Kenyan H9N2 LPAIV isolate into experimental chickens and exposing them to naïve uninfected chickens at 2 -days post inoculation (dpi). This is the first reported detection of H9N2 LPAIV from Kenya and it was shown to be infectious and transmissible in chickens by direct contact and represents a new disease threat to poultry and potentially to people.