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.
Highlights
Pathogenic Avian Influenza (HPAI) viruses of the H5 and H7 subtypes represent a global human health concern [1] in addition to causing severe economic losses in the poultry industry [2]
A total of 127 highly pathogenic avian influenza viruses (HPAI) reassortments were documented since 1959 (Figure 2; Table S1 in Supplementary Information (SI)) and only two of the reassortments were reported from H7 subtype, while the remainder was all reported in H5 subtype
The spatial and phylogenetic descriptive studies indicate that conversion and reassortment events, which are the two main evolutionary mechanisms by which a novel HPAI could emerge in the poultry systems, appear to show distinct geographical patterns
Summary
Pathogenic Avian Influenza (HPAI) viruses of the H5 and H7 subtypes represent a global human health concern [1] in addition to causing severe economic losses in the poultry industry [2] These viruses have an eight-segmented genome, and undergo frequent genetic reassortment and mutations leading to creation of genetic diversity and emergence of novel viruses. Contact rates can increase during migration periods, such as in stopover sites, where the host diversity is significant with several species, age groups, of different immune status congregating together This considerable diversity in host range selects sets of virus subtypes in the low pathogenic form that are capable of maintaining transmission cycles through different hosts [4]. Epizootics caused by HPAI in wild bird populations are seldom, and were mostly documented for virus strains that had previously been associated with poultry farming [6]
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