Wei K, Liu X
School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China.
Transbound Emerg Dis. 2017 Apr;64(2):374-388. doi: 10.1111/tbed.12376. Epub 2015 May 19.
Highly pathogenic avian influenza (HPAI) H5N1 viruses are endemic in poultry and cause continued inter-species transmission to human in Asia, such as China and Vietnam, leading to pandemic concerns and socio-economic challenges. Phylogenetic analysis of H5N1 viruses isolated from China and Vietnam during 2001-2012 showed that several geographically distinct sublineages have become established in these two countries. Subsequently, we reassigned HPAI H5N1 viruses into three distinct groups to reveal the intrasubtype reassortment. Apart from six reassortants detected here, we found that several viral strains showed signals for homologous recombination within PB2 and PB1 genes, suggestive of the fluidity of the H5N1 virus gene pool. Furthermore, sequenced-based analyses revealed that the viral polymerase displayed a higher level of genetic polymorphism but associated with lower substitution rate when compared with those of other gene segments. In addition, the selection pressure analysis indicated that purifying selection was predominant in eight genomic segments especially in the polymerase complex. However, the site-by-site analysis helped to detect 14 positively selected sites in the PB1, PA, HA, NA, MP and NS proteins. Despite the fact that PB2 protein of H5N1 viruses was highly conserved at the amino acid level, eleven adaptive mutations were still observed in the protein. Further comparative structural analysis of the K627E mutation indicated that there were no structural differences between the variants, which possessed either PB2-627E or PB2-627K. Transcriptomic analysis suggested the non-mitochondrial PB2 protein of H5N1 virus that forms a stable complex with the mitochondrial antiviral signalling protein (MAVS, also known as IPS-1, VISA or Cardif) can induce interferon-beta (IFN-β) expression, but the substitution (PB2-K627E) is not the sole determinant of the RIG-I-like receptors (RLR) signalling components induction in Calu-3 cells.
高致病性禽流感（HPAI）H5N1病毒在家禽中呈地方流行性，在亚洲如中国和越南导致病毒持续跨物种传播给人类，引发了对大流行的担忧以及社会经济挑战。对2001年至2012年期间从中国和越南分离出的H5N1病毒进行的系统发育分析表明，在这两个国家已形成了几个地理上不同的亚谱系。随后，我们将高致病性禽流感H5N1病毒重新划分为三个不同的组，以揭示亚型内重组情况。除了在此检测到的六个重组体之外，我们发现一些病毒株在PB2和PB1基因内显示出同源重组信号，这表明H5N1病毒基因库具有流动性。此外，基于测序的分析表明，与其他基因片段相比，病毒聚合酶表现出更高水平的遗传多态性，但替换率较低。另外，选择压力分析表明，纯化选择在八个基因组片段中占主导地位，尤其是在聚合酶复合体中。然而，逐位点分析有助于在PB1、PA、HA、NA、MP和NS蛋白中检测到14个正选择位点。尽管H5N1病毒的PB2蛋白在氨基酸水平上高度保守，但在该蛋白中仍观察到11个适应性突变。对K627E突变的进一步比较结构分析表明，具有PB2 - 627E或PB2 - 627K的变体之间在结构上没有差异。转录组分析表明，H5N1病毒的非线粒体PB2蛋白与线粒体抗病毒信号蛋白（MAVS，也称为IPS - 1、VISA或Cardif）形成稳定复合体，可以诱导干扰素 - β（IFN - β）表达，但替换（PB2 - K627E）不是Calu - 3细胞中RIG - I样受体（RLR）信号成分诱导的唯一决定因素。
