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.

中文翻译：

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埃及2016-2018年禽流感病毒的主动监测和遗传进化。

由于H5N1和H9N2病毒的流行，埃及是禽流感病毒（AIV）的热点地区。从2016-2018年收集的329个样本中分离出AIV; H9N2占48％，H5N8占37.1％，H5N1占7.6％，三种亚型中的2种共感染7.3％。H5N1病毒的32个血凝素（HA）序列在进化枝2.2.1.2中形成了明确定义的血统。H5N8病毒的10个HA序列属于2.3.4.4中的子小节。H9N2分离株的11 HA具有与其他埃及G1样H9N2病毒的高序列同源性。鸭中H5N8病毒的患病率（2.4％）高于鸡（0.94％）。在H9N2病毒中检测到遗传重配。抗原分析表明，H9N2病毒是同质的，在H5N1病毒中检测到抗原性漂移。AI H5N8显示出更高的复制率，其次是H9N2和H5N1，分别。H5N8在埃及南部，尼罗河三角洲的H9N2和两个地区的H5N1中更为常见。鸭子和鸡在H5N1病毒的传播中起着重要作用。H5N1，H5N8和H9N2禽流感的流行性和共同流通，加上缺乏明确的控制策略，继续为埃及进一步的病毒进化提供了途径。