Alice Fusaro, Bianca Zecchin, Bram Vrancken, Celia Abolnik, Rose Ademun, Yao P. Akpeli, Abdou Alassane, Joseph Adongo Awuni, Emmanuel Couacy-Hymann, M’Bétiégué Coulibaly, Emilie Go-Maro, Tony Joannis, Simon Dikmu JUMBO, Germaine Minoungou, Clement Meseko, SOULEY Maman Moutari , Deo Birungi Ndumu, Augustin Twabela, Abel WADE, Lidewij Wiersma, Gianpiero Zamperin, Adelaide Milani, Philippe Lemey, Isabella Monne
In the last two decades, four intercontinental epidemic waves of the highly pathogenic avian influenza virus (HPAIV) of the A/goose/Guangdong/1/1996 lineage have been reported. The worldwide spread of this strain has caused important damages to the poultry industry, but it also represents a serious concern for public health since the virus can be occasionally transmitted to humans. The African continent has been reached by three of these four waves, which resulted in the introduction of three distinct genetic clades, namely clade 2.2 in 2006, clade 184.108.40.206c in 2014 and clade 220.127.116.11 in 2016. The virus has become endemic in poultry in some African regions, such as Egypt and West Africa, where multiple clades are currently co-circulating, creating the opportunity of genetic reassortment and of emergence of viruses with unknown biological properties. To shed light on the potential risk of virus spread from Africa to the other continents, we compared the global HPAIV H5 transmission patterns of these clades and explored the contributions of different avian host populations to virus dissemination.
For each of the three clades, we generated a dataset which included representative sequences from several affected regions throughout the world and from different host species. Based on the spatial distribution and host origin of the available sequences, we identified 9 discrete regions - West Europe, East Europe, Middle East, East Asia, North-Central Asia, South Asia, West Africa, Central-east Africa and South Africa - and 4 host traits - domestic Galliformes, domestic Anseriformes, wild Anseriformes and other wild bird species. We reconstructed the history of epidemic spreads in space and time simultaneously with the host switching patterns through Bayesian phylogeographic analyses in both discrete and continuous space for each dataset using the BEAST v1.8.4 program.
We identified multiple introductions of clade 2.2 from Europe and of clade 18.104.22.168-B from South and North-Central Asia into the African continent, while a single virus spread from South Asia to Africa seems to have been responsible of the 22.214.171.124c incursion. A joint analysis of host dynamics and continuous spatial diffusion indicates that the incursion of the H5 clades into Africa has been driven by wild Anseriformes and domestic Galliformes hosts, thus suggesting that both migratory birds and live poultry trade may have played an important role in the spread of the virus into Africa. Our results identify only few virus migrations from Africa to the Middle East, likely through poultry trade, while no virus movement from Africa to other continents has been observed.
Overall, this study suggests that Africa mainly serves as a sink of the virus. However, the routes of virus introduction into Africa by means of both wild and domestic birds may change at each epidemic wave, making it difficult to predict the source for the next incursion.
Poster at the 2nd National Congress of the Italian Society for Virology in Rome, Italy (28-30 November 2018)