Master of Animal Biomedical Sciences, School of Veterinary and Biomedical, IPB University, Bogor, West Java, 16680, Indonesia.
Department of Microbiology, Faculty of Medicine, University of Indonesia, Jakarta, Jakarta, 10320, Indonesia.
F1000Res. 2025 Mar 5;13:571. doi: 10.12688/f1000research.150975.2. eCollection 2024.
Indonesia is one of the countries that is endemic to avian influenza virus subtype H9N2. This study aims to compare the molecular characteristics of avian influenza virus (AIV) subtype H9N2 from West Java.
Specific pathogen-free (SPF) embryonated chicken eggs were used to inoculate samples. RNA extraction and RT-qPCR confirmed the presence of H9 and N2 genes in the samples. RT-PCR was employed to amplify the H9N2-positive sample. Nucleotide sequences were obtained through Sanger sequencing and analyzed using MEGA 7. Homology comparison and phylogenetic tree analysis, utilizing the neighbor-joining tree method, assessed the recent isolate's similarity to reference isolates from GenBank. Molecular docking analysis was performed on the HA1 protein of the recent isolate and the A/Layer/Indonesia/WestJava-04/2017 isolate, comparing their interactions with the sialic acids Neu5Ac2-3Gal and Neu5Ac2-6Gal.
RT-qPCR confirmed the isolate samples as AIV subtype H9N2. The recent virus exhibited 11 amino acid residue differences compared to the A/Layer/Indonesia/WestJava-04/2017 isolate. Phylogenetically, the recent virus remains within the h9.4.2.5 subclade. Notably, at antigenic site II, the recent isolate featured an amino acid N at position 183, unlike A/Layer/Indonesia/WestJava-04/2017. Molecular docking analysis revealed a preference of HA1 from the 2017 virus for Neu5Ac2-3Gal, while the 2023 virus displayed a tendency to predominantly bind with Neu5Ac2-6Gal.
In summary, the recent isolate displayed multiple mutations and a strong affinity for Neu5Ac2-6Gal, commonly found in mammals.
印度尼西亚是 H9N2 亚型禽流感病毒的流行地区之一。本研究旨在比较来自西爪哇的 H9N2 禽流感病毒（AIV）的分子特征。
使用特定病原体无（SPF）鸡胚卵来接种样本。RNA 提取和 RT-qPCR 确认样品中存在 H9 和 N2 基因。RT-PCR 用于扩增 H9N2 阳性样本。通过 Sanger 测序获得核苷酸序列，并使用 MEGA 7 进行分析。采用邻接法构建系统进化树，分析最近分离株与 GenBank 中参考分离株的相似性。对最近分离株的 HA1 蛋白与 A/Layer/Indonesia/WestJava-04/2017 分离株进行分子对接分析，比较它们与唾液酸 Neu5Ac2-3Gal 和 Neu5Ac2-6Gal 的相互作用。
RT-qPCR 证实分离株样本为 AIV 亚型 H9N2。与 A/Layer/Indonesia/WestJava-04/2017 分离株相比，最近的病毒显示出 11 个氨基酸残基的差异。系统发育分析表明，最近的病毒仍属于 h9.4.2.5 亚分支。值得注意的是，在抗原位点 II 上，最近的分离株在位置 183 处具有氨基酸 N，而 A/Layer/Indonesia/WestJava-04/2017 则没有。分子对接分析表明，2017 年病毒的 HA1 更倾向于与 Neu5Ac2-3Gal 结合，而 2023 年病毒则更倾向于与 Neu5Ac2-6Gal 结合。
综上所述，最近的分离株显示出多个突变，并且对哺乳动物中常见的 Neu5Ac2-6Gal 具有很强的亲和力。
