A High Diversity of Eurasian Lineage Low Pathogenicity Avian Influenza A Viruses Circulate among Wild Birds Sampled in Egypt

Surveillance for influenza A viruses in wild birds has increased substantially as part of efforts to control the global movement of highly pathogenic avian influenza A (H5N1) virus. Studies conducted in Egypt from 2003 to 2007 to monitor birds for H5N1 identified multiple subtypes of low pathogenicity avian influenza A viruses isolated primarily from migratory waterfowl collected in the Nile Delta. Phylogenetic analysis of 28 viral genomes was performed to estimate their nearest ancestors and identify possible reassortants. Migratory flyway patterns were included in the analysis to assess gene flow between overlapping flyways. Overall, the viruses were most closely related to Eurasian, African and/or Central Asian lineage low pathogenicity viruses and belonged to 15 different subtypes. A subset of the internal genes seemed to originate from specific flyways (Black Sea-Mediterranean, East African-West Asian). The remaining genes were derived from a mixture of viruses broadly distributed across as many as 4 different flyways suggesting the importance of the Nile Delta for virus dispersal. Molecular clock date estimates suggested that the time to the nearest common ancestor of all viruses analyzed ranged from 5 to 10 years, indicating frequent genetic exchange with viruses sampled elsewhere. The intersection of multiple migratory bird flyways and the resulting diversity of influenza virus gene lineages in the Nile Delta create conditions favoring reassortment, as evident from the gene constellations identified by this study. In conclusion, we present for the first time a comprehensive phylogenetic analysis of full genome sequences from low pathogenic avian influenza viruses circulating in Egypt, underscoring the significance of the region for viral reassortment and the potential emergence of novel avian influenza A viruses, as well as representing a highly diverse influenza A virus gene pool that merits continued monitoring.

作为防控高致病性甲型禽流感（H5N1）病毒全球扩散工作的一部分，野生鸟类甲型流感病毒（influenza A viruses）监测工作已大幅加强。2003年至2007年在埃及开展的H5N1鸟类监测研究中，研究人员从尼罗河三角洲采集的迁徙水禽体内分离出多亚型低致病性甲型禽流感病毒（low pathogenicity avian influenza A viruses）。研究对28株病毒的全基因组开展了系统发育分析（phylogenetic analysis），以推断其最近共同祖先，并识别潜在的重配病毒（reassortants）。分析纳入了候鸟迁飞路线（migratory flyway）模式，以评估重叠迁飞路线间的基因流（gene flow）。总体而言，这些病毒与欧亚、非洲及/或中亚支系的低致病性病毒亲缘关系最近，且隶属于15个不同亚型。部分内部基因似乎源自特定迁飞路线：黑海-地中海迁飞路线（Black Sea-Mediterranean flyway）、东非-西亚迁飞路线（East African-West Asian flyway）。剩余基因则源自广泛分布于多达4条不同迁飞路线的病毒混合种群，这凸显了尼罗河三角洲在病毒扩散中的重要性。分子钟年代估算（molecular clock dating）结果显示，本次分析的所有病毒的最近共同祖先出现时间距今约5至10年，表明这些病毒与其他地区分离的毒株存在频繁的基因交流。多条候鸟迁飞路线在此交汇，加之尼罗河三角洲地区流感病毒基因支系多样性极高，这为病毒重配创造了有利条件，本研究鉴定的基因构型（gene constellation）也证实了这一点。综上，本研究首次对埃及流行的低致病性甲型禽流感病毒的全基因组序列开展了全面系统发育分析，凸显了该地区在病毒重配及新型甲型禽流感病毒潜在出现中的重要意义，同时该区域也拥有高度多样的甲型流感病毒基因库，值得持续开展监测。