The emergence and diversification of panzootic H5N1 influenza viruses

Abstract

The Asian highly pathogenic avian influenza H5N1 virus was first detected in the goose population of Guangdong, China in 1996. The viruses in this lineage are unique in their ecological success, demonstrating an extremely broad host range and becoming established in poultry over much of Asia and in Africa. H5N1 viruses have also diverged into multiple clades and subclades that generally do not cross neutralize, which has greatly confounded control measures in poultry and pre-pandemic vaccine strain selection. Although H5N1 viruses currently cannot transmit efficiently between mammals they exhibit high mortality in humans and recent experimental studies have shown that it is possible to generate an H5N1 virus that is transmissible in mammals. In addition to causing unprecedented economic losses, the long-term presence of the H5N1 virus in poultry and its frequent introductions to humans continue to pose a significant pandemic threat. Here we provide a summary of the genesis, molecular epidemiology and evolution of this H5N1 lineage, particularly the factors that have contributed to the continued diversification and ecological success of H5N1 viruses, with particular reference to the poultry production systems they have emerged from.

Keywords: Ecology; Highly pathogenic avian influenza; Pandemic; Poultry markets.

Figure 1

Changes in world domestic duck population from 1959 to 2010. Green and red solid lines indicate millions of ducks in China and world total, while dashed blue line shows percentage of world duck population in China (from FAO, 2012d).

Figure 2

A stylized phylogenetic tree of H5N1 virus haemagglutinin genes showing the evolutionary relationships among virus clades. Colored triangles indicate virus lineages that have been isolated predominantly from poultry only (orange) or poultry and wild birds (blue) since January 2010. Country names indicate areas that the virus lineages have been detected. Grey triangles indicate virus lineages that have not been detected since January 2010. Compiled from references FAO (2012a–c) and WHO (2012b and 2013). The phylogenetic tree was generated in PAUP* (Swofford, 2003) using the alignment provided as supplementary information in WHO/OIE/FAO (2012).