Active surveillance and genetic evolution of avian influenza viruses in Egypt, 2016–2018

Ahmed Kandeil,Joseph T Hicks,Sean G Young,Ahmed N El Taweel,Ahmed S Kayed,Yassmin Moatasim,Omnia Kutkat,Ola Bagato,Pamela P Mckenzie,Zhipeng Cai,Rebecca Badra,Mohamed Kutkat,Justin Bahl,Richard J Webby,Ghazi Kayali,Mohamed A Ali

doi:10.1080/22221751.2019.1663712

Abstract

ABSTRACT Egypt is a hotspot for avian influenza virus (AIV) due to the endemicity of H5N1 and H9N2 viruses. AIVs were isolated from 329 samples collected in 2016–2018; 48% were H9N2, 37.1% were H5N8, 7.6% were H5N1, and 7.3% were co-infections with 2 of the 3 subtypes. The 32 hemagglutinin (HA) sequences of the H5N1 viruses formed a well-defined lineage within clade 2.2.1.2. The 10 HA sequences of the H5N8 viruses belonged to a subclade within 2.3.4.4. The 11 HA of H9N2 isolates showed high sequence homology with other Egyptian G1-like H9N2 viruses. The prevalence of H5N8 viruses in ducks (2.4%) was higher than in chickens (0.94%). Genetic reassortment was detected in H9N2 viruses. Antigenic analysis showed that H9N2 viruses are homogenous, antigenic drift was detected among H5N1 viruses. AI H5N8 showed higher replication rate followed by H9N2 and H5N1, respectively. H5N8 was more common in Southern Egypt, H9N2 in the Nile Delta, and H5N1 in both areas. Ducks and chickens played a significant role in transmission of H5N1 viruses. The endemicity and co-circulation of H5N1, H5N8, and H9N2 AIV coupled with the lack of a clear control strategy continues to provide avenues for further virus evolution in Egypt.

Highlights

Avian influenza virus (AIV) is a diverse viral pathogen maintained in wild birds and exists in high pathogenic (HPAI) and low pathogenic (LPAI) forms
The cartography of the Egyptian H9N2 viruses showed that, except for drifted H9N2 viruses initially isolated from quails in 2014 [10], all viruses fell into one cluster (Figure 4(B))
During our previous active surveillance in domestic poultry in Egypt, both H5N1 and H9N2 subtypes were commonly detected in birds, with a 5% infection rate during August 2009 to July 2010 that increased to 10% (H5N1, H9N2 and H5N1/H9N2 co-infection) from August 2010 to January 2013 [11]

Summary

Introduction

Avian influenza virus (AIV) is a diverse viral pathogen maintained in wild birds and exists in high pathogenic (HPAI) and low pathogenic (LPAI) forms. Since the first detection of HPAI H5N1 subtype in 1996, the virus has evolved into 10 genetically-defined clades (0–9) and has spread throughout the world. It has been hypothesized that clade 2.2.1.1 viruses emerged as vaccine escape mutants due to vaccine application [5]. Further evolution of these viruses led to a new phylogenetic cluster, clade 2.2.1.2 [4]. Several H5N8 outbreaks have been detected in domestic poultry in several governorates in Egypt [8]. Despite this wide dissemination of H5N8 viruses, there have been no reports of associated human infections

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