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

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.

鉴于H5N1与H9N2亚型禽流感病毒（avian influenza virus, AIV）在埃及呈地方性流行，该国成为禽流感病毒的高发疫区。研究团队从2016至2018年采集的329份样本中分离得到禽流感病毒：其中48%为H9N2亚型，37.1%为H5N8亚型，7.6%为H5N1亚型，另有7.3%为三种亚型中两种的混合感染。H5N1毒株的32条血凝素（hemagglutinin, HA）序列在2.2.1.2进化分支内形成了特征明确的进化谱系。H5N8毒株的10条HA序列隶属于2.3.4.4进化分支下的一个亚分支。11株H9N2分离株的HA序列与其他埃及地区G1样H9N2毒株呈现高度序列同源性。H5N8毒株在鸭群中的检出率（2.4%）高于鸡群（0.94%）。H9N2毒株中检测到基因重配现象。抗原性分析结果显示，H9N2毒株抗原性均一；而H5N1毒株中则检测到抗原漂移现象。各亚型的复制速率以H5N8最高，其次依次为H9N2与H5N1。H5N8毒株在埃及南部更为常见，H9N2毒株主要分布于尼罗河三角洲地区，而H5N1毒株在上述两个区域均有分布。鸭与鸡在H5N1毒株的传播过程中发挥了重要作用。H5N1、H5N8及H9N2亚型禽流感病毒在埃及的地方性流行与共同循环，加之缺乏明确的防控策略，持续为该地区病毒的进一步进化提供了条件。