Next-generation sequencing (NGS) technologies are a valuable tool to monitor changes in viral genomes and determine the genetic heterogeneity of viruses. In this study, NGS was applied to clinical poultry samples from Jordan to detect eleven H9N2 low pathogenic avian influenza viruses (LPAIV). All of the viruses tested belonged to Middle East A genetic group of G1 lineage. Deep sequencing demonstrated a high degree of heterogeneity of glutamine and leucine residues at position 226 in the hemagglutinin (HA) gene, which increases specificity to either avian or mammalian-type receptors. Moreover, additional amino acid changes in PB1, PA, M1, M2, and NS1 were identified among the viruses tested. Compared to single gene amplification, application of NGS for surveillance and characterization of H9N2 LPAIV provides a complete genetic profile of emerging isolates and better understanding of the potential of zoonotic transmissions to mammals.

下一代测序（NGS）技术是监视病毒基因组变化并确定病毒遗传异质性的宝贵工具。在这项研究中，将NGS应用于约旦的临床家禽样品，以检测11种H9N2低致病性禽流感病毒（LPAIV）。所有测试的病毒均属于G1谱系的中东A基因组。深度测序表明，血凝素（HA）基因第226位的谷氨酰胺和亮氨酸残基具有高度的异质性，从而增加了对禽类或哺乳动物型受体的特异性。此外，在测试的病毒中还鉴定出PB1，PA，M1，M2和NS1中的其他氨基酸变化。与单基因扩增相比，