Genetic characterization of highly pathogenic avian Influenza H5Nx clade 2.3.4.4b reveals independent introductions in nigeria.

Among recurrent sanitary emergencies able to spread rapidly worldwide, avian influenza is one of the main constraints for animal health and food security. In West Africa, Nigeria has been experiencing repeated outbreaks of different strains of avian influenza virus (AIV) since 2006 and is also recognized as a hot spot in the region for the introduction of emerging strains by migratory wild birds. Here, we generated complete genomes of 20 highly pathogenic avian influenza (HPAI) H5N8 viruses collected during active surveillance in Nigerian live bird markets (LBM) and from outbreaks reported in the country between 2016 and 2019. Phylogenetic analysis reveals that the Nigerian viruses cluster into four separate genetic groups within HPAI H5 clade 2.3.4.4b. The first group includes 2016-2017 Nigerian viruses with high genetic similarity to H5N8 viruses detected in Central African countries, while the second includes Nigerian viruses collected both in LBM and poultry farms (2018-2019), as well as in Cameroon, Egypt and Siberia. A natural reassortant strain identified in 2019 represents the third group: H5N8 viruses with the same gene constellation were identified in 2018 in South Africa. Finally, the fourth introduction represents the first detection in the African continent of the H5N6 subtype, which is related to European viruses. Bayesian phylogeographic analyses confirmed that the four introductions originated from different sources and provide evidence of the virus spread within Nigeria, as well as diffusion beyond its borders. The multiple epidemiological links between Nigeria, Central and Southern African countries highlight the need for harmonized and coordinated surveillance system to control AIV impact. Improved surveillance at the Wetlands, LBMs and early warning of outbreaks are crucial for prevention and control of AIV, which can be potentially zoonotic and be a threat to human health.

Live Bird Markets in Nigeria: A Potential Reservoir for H9N2 Avian Influenza Viruses.

Since 2006, multiple outbreaks of avian influenza (AI) have been reported in Nigeria involving different subtypes. Surveillance and molecular epidemiology have revealed the vital role of live bird markets (LBMs) in the dissemination of AI virus to commercial poultry farms. To better understand the ecology and epidemiology of AI in Nigeria, we performed whole-genome sequencing of nineteen H9N2 viruses recovered, from apparently healthy poultry species, during active surveillance conducted in nine LBMs across Nigeria in 2019. Analyses of the HA gene segment of these viruses showed that the H9N2 strains belong to the G1 lineage, which has zoonotic potential, and are clustered with contemporary H9N2 identified in Africa between 2016 and 2020. We observed two distinct clusters of H9N2 viruses in Nigeria, suggesting different introductions into the country. In view of the zoonotic potential of H9N2 and the co-circulation of multiple subtypes of AI virus in Nigeria, continuous monitoring of the LBMs across the country and molecular characterization of AIVs identified is advocated to mitigate economic losses and public health threats.

Prioritization of zoonotic diseases of public health significance in Nigeria using the one-health approach.

Nigeria, with a population of over 190 million people, is rated among the 10 countries with the highest burden of infectious and zoonotic diseases globally. In Nigeria, there exist a sub-optimal surveillance system to monitor and track priority zoonoses. We therefore conducted a prioritization of zoonotic diseases for the first time in Nigeria to guide prevention and control efforts. Towards this, a two-day in-country consultative meeting involving experts from the human, animal, and environmental health backgrounds prioritized zoonotic diseases using a modified semi-quantitative One Health Zoonotic Disease Prioritization tool in July 2017. Overall, 36 of 52 previously selected zoonoses were identified for prioritization. Five selection criteria were used to arrive at the relative importance of prioritized diseases based on their weighted score. Overall, this zoonotic disease prioritization process marks the first major step of bringing together experts from the human-animal-environment health spectrum in Nigeria. Importantly, the country ranked rabies, avian influenza, Ebola Virus Disease, swine influenza and anthrax as the first five priority zoonoses in Nigeria. Finally, this One Health approach to prioritizing important zoonoses is a step that will help to guide future tracking and monitoring of diseases of grave public health importance in Nigeria.

First detection of highly pathogenic H5N6 avian influenza virus on the African continent.

Since 2013, highly pathogenic avian influenza (HPAI) subtype H5N6 (clade 2.3.4.4) has been reported in wild birds and poultry in Asia as well as in other parts of the globe. In Africa, information on the presence of this virus subtype is lacking. This study reports the first detection of a HPAI (H5N6) virus (clade 2.3.4.4b) in a duck from a live bird market in Nigeria, whose genome is closely related to the European 2017-2018 H5N6 viruses, indricating a recent virus introduction into the African continent.