Genetic evolution of influenza H9N2 viruses isolated from various hosts in China from 1994 to 2013.

Influenza H9N2 subtype viruses and their reassortants (such as H7N9) are posing increasing threats to birds and humans in China. During 2009–2013, multiple novel subtype viruses with H9N2 original genes emerged in China. Yet, the genetic evolution of H9N2 viruses in various host organisms in China has not been systematically investigated since 2009. In the present study, we performed large-scale sequence analysis of H9N2 viral genomes from public databases, representing the spectrum of viruses isolated from birds, mammals and humans in China from 1994 to 2013, and updated the clade classification for each segment. We identified 117 distinct genotypes in 730 H9N2 viruses. We analyzed the sequences of all eight segments in each virus and found three important time points: the years 2000, 2006 and 2010. In the periods divided by these years, genotypic diversity, geographic distribution and host range changed considerably. Genotypic diversity fluctuated greatly in 2000 and 2006. Since 2010, a single genotype became predominant in poultry throughout China, and the eastern coastal region became the newly identified epidemic center. Throughout their 20-year prevalence in China, H9N2 influenza viruses have emerged and adapted from aquatic birds to chickens. The minor avian species and wild birds exacerbated H9N2 genotypes by providing diversified genes, and chickens were the most prevalent vector in which the viruses evolved and expanded their prevalence. It is the necessity for surveillance and disease control on live-bird markets, poultry farms and wild-bird habitats in China.

H9N2亚型流感病毒及其重配病毒（如H7N9）对中国的禽类和人类构成日益严重的威胁。2009年至2013年期间，中国出现了多种具有H9N2原始基因的新型亚型病毒。然而，自2009年以来，中国H9N2病毒在各种宿主生物中的遗传进化尚未得到系统研究。在本研究中，我们对公共数据库中的H9N2病毒基因组进行了大规模序列分析，这些数据代表了1994年至2013年从中国的禽类、哺乳动物和人类中分离出的病毒谱，并更新了每个基因片段的分支分类。我们在730株H9N2病毒中鉴定出117种不同的基因型。我们分析了每种病毒的所有8个基因片段的序列，并发现了三个重要的时间节点：2000年、2006年和2010年。在以这些年份划分的时间段内，基因型多样性、地理分布和宿主范围发生了显著变化。基因型多样性在2000年和2006年大幅波动。自2010年以来，一种单一基因型在中国各地的家禽中占主导地位，东部沿海地区成为新确定的流行中心。在中国流行的20年中，H9N2流感病毒从水禽中出现并适应了鸡。小型禽类和野生鸟类通过提供多样化的基因加剧了H9N2基因型的复杂性，鸡是病毒进化和扩大流行的最普遍载体。在中国，对活禽市场、家禽养殖场和野生鸟类栖息地进行监测和疾病控制是必要的。