Geographical and Historical Patterns in the Emergences of Novel Highly Pathogenic Avian Influenza (HPAI) H5 and H7 Viruses in Poultry

Abstract

Over the years, the emergence of novel H5 and H7 highly pathogenic avian influenza viruses (HPAI) has been taking place through two main mechanisms: first, the conversion of a low pathogenic into a highly pathogenic virus, and second, the reassortment between different genetic segments of low and highly pathogenic viruses already in circulation. We investigated and summarized the literature on emerging HPAI H5 and H7 viruses with the aim of building a spatio-temporal database of all these recorded conversions and reassortments events. We subsequently mapped the spatio-temporal distribution of known emergence events, as well as the species and production systems that they were associated with, the aim being to establish their main characteristics. From 1959 onwards, we identified a total of 39 independent H7 and H5 LPAI to HPAI conversion events. All but two of these events were reported in commercial poultry production systems, and a majority of these events took place in high-income countries. In contrast, a total of 127 reassortments have been reported from 1983 to 2015, which predominantly took place in countries with poultry production systems transitioning from backyard to intensive production systems. Those systems are characterized by several co-circulating viruses, multiple host species, regular contact points in live bird markets, limited biosecurity within value chains, and frequent vaccination campaigns that impose selection pressures for emergence of novel reassortants. We conclude that novel HPAI emergences by these two mechanisms occur in different ecological niches, with different viral, environmental and host associated factors, which has implications in early detection and management and mitigation of the risk of emergence of novel HPAI viruses.

Keywords: low pathogenic to highly pathogenic conversion; novel HPAI emergences; phylogeography; reassortment; spatial and temporal pattern.

Figure 1

Map of highly pathogenic avian influenza (HPAI) subtype H5 and H7 conversions during three time periods; yellow (before 1996), red (1996–2005) and green (2006–2015). The shapefile data used to produce these maps were made with Natural Earth (http://www.naturalearthdata.com/). The graticule is composed of a 20-degree increments and the coordinate system is Eckert IV (EPSG: 54012).

Figure 2

Map of Highly pathogenic avian influenza (HPAI) subtype H5 and H7 reassortments during two time periods; red (1996–2005) and green (2006–2015). The shapefile data used to produce these maps were made with Natural Earth (http://www.naturalearthdata.com/). The graticule is composed of a 20-degree increments and the coordinate system is Eckert IV (EPSG: 54012).

Figure 3

Time-scaled phylogeographic history of H5 and H7 sequences associated with HPAI conversions and reassortments. Branch colors represent the most probable location of the parental node of each branch. Tip labels indicate the subtype and are colored according to the associated event, i.e., conversion (in red) or reassortment (in green). When they are lower than 0.95, posterior probabilities of the most probable ancestral state (i.e. geographic location) are reported next to internal nodes.