Respiratory disease due to mixed viral infections in poultry flocks in Egypt between 2017 and 2018: Upsurge of highly pathogenic avian influenza virus subtype H5N8 since 2018

Abstract

For several years, poultry production in Egypt has been suffering from co-circulation of multiple respiratory viruses including highly pathogenic avian influenza virus (HPAIV) H5N1 (clade 2.2.1.2) and low pathogenic H9N2 (clade G1-B). Incursion of HPAIV H5N8 (clade 2.3.4.4b) to Egypt in November 2016 via wild birds followed by spread into commercial poultry flocks further complicated the situation. Current analyses focussed on 39 poultry farms suffering from respiratory manifestation and high mortality in six Egyptian governorates during 2017-2018. Real-time RT-PCR (RT-qPCR) substantiated the co-presence of at least two respiratory virus species in more than 80% of the investigated flocks. The percentage of HPAIV H5N1-positive holdings was fairly stable in 2017 (12.8%) and 2018 (10.2%), while the percentage of HPAIV H5N8-positive holdings increased from 23% in 2017 to 66.6% during 2018. The proportion of H9N2-positive samples was constantly high (2017:100% and 2018:63%), and H9N2 co-circulated with HPAIV H5N8 in 22 out of 39 (56.8%) flocks. Analyses of 26 H5, 18 H9 and 4 N2 new sequences confirmed continuous genetic diversification. In silico analysis revealed numerous amino acid substitutions in the HA and NA proteins suggestive of increased adaptation to mammalian hosts and putative antigenic variation. For sensitive detection of H9N2 viruses by RT-qPCR, an update of primers and probe sequences was crucial. Reasons for the relative increase of HPAIV H5N8 infections versus H5N1 remained unclear, but lack of suitable vaccines against clade 2.3.4.4b cannot be excluded. A reconsideration of surveillance and control measures should include updating of diagnostic tools and vaccination strategies.

Wild Birds in Live Birds Markets: Potential Reservoirs of Enzootic Avian Influenza Viruses and Antimicrobial Resistant Enterobacteriaceae in Northern Egypt

“…H5N8: Phylogenetic analysis of the full HA gene of the four H5N8 viruses indicated that they clustered together within clade 2.3.4.4 group B (Figure 1) with recently isolated Egyptian H5N8 strains from domestic birds. Sample 2 clustered with 2018 strains with the characteristic amino acid substitution 175L previously reported in recent Egyptian samples [21]. All four samples possessed multibasic cleavage sites in the motif PLREKRRKR/GLF and six potential glycosylation sites at positions 10, 23, 165, 286, 483, and 542 (H5 numbering).…”

H5 Influenza Viruses in Egypt

“…Cocirculation of HPAI (H5N1, H5N8) and LPAI (H9N2) viruses in poultry provides an opportunity for reassortment. Co-infection of birds with A(H5) and A(H9N2) viruses in Egypt is not uncommon, yet few reassortments have been detected to date (Abdelwhab el et al 2010;Kayali et al 2016;Hassan et al 2019). A(H5N1)/ A(H9N2) reassortants have been detected in other countries where these viruses cocirculate, suggesting that there is not complete incompatibility between their gene segments (Monne et al 2013;Marinova-Petkova et al 2016).…”

Comparison of pathogenicity of subtype H9 avian influenza wild-type viruses from a wide geographic origin expressing mono-, di-, or tri-basic hemagglutinin cleavage sites

“…Despite their classification as LPAIV, they are associated with severe disease in poultry leading to significant economic losses [15,16]. It has been suggested that the strikingly distinct clinical signs induced in experimental and natural H9N2 infections are due to opportunistic viral and bacterial co-infections with H9N2 acting in synergy as an immunosuppressive agent [16][17][18][19].…”