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.

Surveillance for avian influenza viruses in wild birds at live bird markets, Egypt, 2014‐2016

“…Reassortment was observed considerably in all non‐enzootic viruses detected in this study. This is highly evident in the case of H7N3 viruses as was seen in other regions . The genes of these viruses were related to genes from other Eurasian viruses of various subtypes.…”

“…This is highly evident in the case of H7N3 viruses as was seen in other regions. 26 The genes of these Figure S2). Previous studies showed that the allele A AIVs are more common than allele B.…”

Parallel Evolution in the Emergence of Highly Pathogenic Avian Influenza A Viruses

“…replicates (Stamatakis 2014). All HP clusters were flagged within the large-scale topologies according to the presence of more than one basic residue within the consensus cleavage site in the HA protein sequence, and by confirming their HP status with case reports in the literature (Dhingra, et al 2018).…”

“…As a recent example, the outbreak of H7N9 viruses in early 2018 caused over 1567 infections and 615 deaths among people in China (Lam and Pybus 2018). Low virulence lineages of avian influenza viruses can mutate to highly virulent strains, resulting geographically and temporally independent HP outbreaks that have generated huge economic losses in the poultry industry, and pose an increased risk for avian-to-human spread (Dhingra, et al 2018) (Short, et al 2015). Thus, understanding the mechanisms driving the evolution of virulence in avian influenza viruses is critical.…”

Reverse‐transcription recombinase‐aided amplification assay for H7 subtype avian influenza virus

“…The H7 subtype AIV has spread worldwide and has been detected in China (Wu et al, ), the United States (Olsen et al, ), Korea (Lee et al, ), Bangladesh (El‐Shesheny et al, ), Australia (Scott et al, ), Cambodia (Horwood et al, ) and Belgium (Van Borm et al, ). The pathogenic H7 subtype AIV changed from low pathogenicity in birds to high pathogenicity in both humans and birds (Dhingra et al, ). H7 subtype AIV can lead to severe economic losses in the poultry industry, and its rapid detection in the field can limit its spread in poultry and decrease the risk of human infection.…”