The Evolutionary Pattern of Glycosylation Sites in Influenza Virus (H5N1) Hemagglutinin and Neuraminidase

Two glycoproteins, hemagglutinin (HA) and neuraminidase (NA), on the surface of influenza viruses play crucial roles in transfaunation, membrane fusion and the release of progeny virions. To explore the distribution of N-glycosylation sites (glycosites) in these two glycoproteins, we collected and aligned the amino acid sequences of all the HA and NA subtypes. Two glycosites were located at HA0 cleavage sites and fusion peptides and were strikingly conserved in all HA subtypes, while the remaining glycosites were unique to their subtypes. Two to four conserved glycosites were found in the stalk domain of NA, but these are affected by the deletion of specific stalk domain sequences. Another highly conserved glycosite appeared at the top center of tetrameric global domain, while the others glycosites were distributed around the global domain. Here we present a detailed investigation of the distribution and the evolutionary pattern of the glycosites in the envelope glycoproteins of IVs, and further focus on the H5N1 virus and conclude that the glycosites in H5N1 have become more complicated in HA and less influential in NA in the last five years.     

Glycosylation on Hemagglutinin Affects the Virulence and Pathogenicity of Pandemic H1N1/2009 Influenza A Virus in Mice

The two glycosylation sites (Asn142 and Asn177) were observed in the HA of most human seasonal influenza A/H1N1 viruses, while none in pandemic H1N1/2009 influenza A (pH1N1) viruses. We investigated the effect of the two glycosylation sites on viral virulence and pathogenicity in mice using recombinant pH1N1. The H1N1/144 and H1N1/177 mutants which gained potential glycosylation sites Asn142 and Asn177 on HA respectively were generated from A/Mexico/4486/2009(H1N1) by site-directed mutagenesis and reverse genetics, the same as the H1N1/144+177 gained both glycosylation sites Asn142 and Asn177. The biological characteristics and antigenicity of the mutants were compared with wild-type pH1N1. The virulence and pathogenicity of recombinants were also detected in mice. Our results showed that HA antigenicity and viral affinity for receptor may change with introduction of the glycosylation sites. Compared with wild-type pH1N1, the mutant H1N1/177 displayed an equivalent virus titer in chicken embryos and mice, and increased virulence and pathogenicity in mice. The H1N1/144 displayed the highest virus titer in mice lung. However, the H1N1/144+177 displayed the most serious alveolar inflammation and pathogenicity in infected mice. The introduction of the glycosylation sites Asn144 and Asn177 resulted in the enhancement on virulence and pathogenicity of pH1N1 in mice, and was also associated with the change of HA antigenicity and the viral affinity for receptor.     

禽流感病毒H5N1血凝素基因适应性进化过程中的关键位点突变规律研究

目的:寻找导致禽流感病毒H5N1血凝素(HA)适应性进化的关键突变,建立氨基酸突变评价体系,对突变作用进行评估,印证它们与病毒适应性进化的关联性。方法:计算株频率和枝频率,寻找标记分枝,向根结点回溯寻找HA进化路径上的氨基酸突变。计算各突变位点氨基酸的频率变化、有效变换及高频次突变,基于以上几个因素建立突变评价体系。结果:建立了大规模自动化寻找突变的方法,计算得到HA进化过程中的氨基酸突变435个,通过氨基酸频率图表分析这些突变可以很好地反映病毒适应性进化过程,其中79个突变是有效变换,发生的位点为正选择位点,且多数位点落在HA抗原表位上;29个突变是高频次突变,其中多数也为有效变换,因而与病毒适应性进化密切相关。结论:大规模自动化寻找突变的方法可靠,建立的突变评价体系准确性高,找到的关键突变及位点对实验有很好的指导意义。     

Inhibition of Glycosylation of the Influenza Virus Hemagglutinin

d-Glucosamine and 2-deoxy-d-glucose interfere with the biosynthesis of the hemagglutinin glycoproteins. With increasing inhibitor concentrations a progressive decrease in size of the precursor HA and the cleavage products, HA(1) and HA(2) can be observed. The shift in molecular weight is paralleled by a decrease of the carbohydrate content. This was shown by labeling studies with radioactive sugars which revealed that the inhibitors block the incorporation into glycoproteins, whereas they have no or only slight effects on the uptake and activation of sugars. Under conditions of maximal inhibition, the hemagglutinin proteins lack all or most of their carbohydrates. These findings indicate that the inhibitory effect of d-glucosamine and 2-deoxy-d-glucose is due to an impairment of glycosylation. When glycosylation is inhibited, the precursor polypeptide is synthesized at normal rates. Its cleavage products, however, are very heterogeneous. This suggests that carbohydrate protects the hemagglutinin from proteolytic degradation.     

Recombinant Parainfluenza Virus 5 Expressing Hemagglutinin of Influenza A Virus H5N1 Protected Mice against Lethal Highly Pathogenic Avian Influenza Virus H5N1 Challenge

A safe and effective vaccine is the best way to prevent large-scale highly pathogenic avian influenza virus (HPAI) H5N1 outbreaks in the human population. The current FDA-approved H5N1 vaccine has serious limitations. A more efficacious H5N1 vaccine is urgently needed. Parainfluenza virus 5 (PIV5), a paramyxovirus, is not known to cause any illness in humans. PIV5 is an attractive vaccine vector. In our studies, a single dose of a live recombinant PIV5 expressing a hemagglutinin (HA) gene of H5N1 (rPIV5-H5) from the H5N1 subtype provided sterilizing immunity against lethal doses of HPAI H5N1 infection in mice. Furthermore, we have examined the effect of insertion of H5N1 HA at different locations within the PIV5 genome on the efficacy of a PIV5-based vaccine. Interestingly, insertion of H5N1 HA between the leader sequence, the de facto promoter of PIV5, and the first viral gene, nucleoprotein (NP), did not lead to a viable virus. Insertion of H5N1 HA between NP and the next gene, V/phosphorprotein (V/P), led to a virus that was defective in growth. We have found that insertion of H5N1 HA at the junction between the small hydrophobic (SH) gene and the hemagglutinin-neuraminidase (HN) gene gave the best immunity against HPAI H5N1 challenge: a dose as low as 1,000 PFU was sufficient to protect against lethal HPAI H5N1 challenge in mice. The work suggests that recombinant PIV5 expressing H5N1 HA has great potential as an HPAI H5N1 vaccine.     

New Orf Virus (Parapoxvirus) Recombinant Expressing H5 Hemagglutinin Protects Mice against H5N1 and H1N1 Influenza A Virus

Previously we demonstrated the versatile utility of the Parapoxvirus Orf virus (ORFV) as a vector platform for the development of potent recombinant vaccines. In this study we present the generation of new ORFV recombinants expressing the hemagglutinin (HA) or nucleoprotein (NP) of the highly pathogenic avian influenza virus (HPAIV) H5N1. Correct foreign gene expression was examined in vitro by immunofluorescence, Western blotting and flow cytometry. The protective potential of both recombinants was evaluated in the mouse challenge model. Despite adequate expression of NP, the recombinant D1701-V-NPh5 completely failed to protect mice from lethal challenge. However, the H5 HA-expressing recombinant D1701-V-HAh5n mediated solid protection in a dose-dependent manner. Two intramuscular (i.m.) injections of the HA-expressing recombinant protected all animals from lethal HPAIV infection without loss of body weight. Notably, the immunized mice resisted cross-clade H5N1 and heterologous H1N1 (strain PR8) influenza virus challenge. In vivo antibody-mediated depletion of CD4-positive and/or CD8-posititve T-cell subpopulations during immunization and/or challenge infection implicated the relevance of CD4-positive T-cells for induction of protective immunity by D1701-V-HAh5n, whereas the absence of CD8-positive T-cells did not significantly influence protection. In summary, this study validates the potential of the ORFV vectored vaccines also to combat HPAIV.     

Localization Analysis of Heterophilic Antigen Epitopes of H1N1 Influenza Virus Hemagglutinin

Previous studies have indicated that two monoclonal antibodies(mAbs; A1-10 and H1-84) of the hemagglutinin(HA)antigen on the H1 N1 influenza virus cross-react with human brain tissue. It has been proposed that there are heterophilic epitopes between the HA protein and human brain tissue(Guo et al. in Immunobiology 220:941–946, 2015). However,characterisation of the two mAbs recognising the heterophilic epitope on HA has not yet been performed. In the present study, the common antigens of influenza virus HA were confirmed using indirect enzyme-linked immunosorbent assays and analysed with DNAMAN software. The epitopes were localized to nine peptides in the influenza virus HA sequence and the distribution of the peptides in the three-dimensional structure of HA was determined using PyMOL software. Key amino acids and variable sequences of the antibodies were identified using abYsis software. The results demonstrated that there were a number of common antigens among the five influenza viruses studied that were recognised by the mAbs. One of the peptides, P2(LVLWGIHHP191–199), bound both of the mAbs and was located in the head region of HA. The key amino acids of this epitope and the variable regions in the heavy and light chain sequences of the mAbs that recognised the epitope are described. A heterophilic epitope on H1 N1 influenza virus HA was also introduced. The existence of this epitope provides a novel perspective for the occurrence of nervous system diseases that could be caused by influenza virus infection, which might aid in influenza prevention and control.     

广东地区流感H3N2毒株血凝素基因特征、进化和变异分析

为揭示广东地区2007～2010年甲型H3N2毒株血凝素(HA)基因特征和变异,采用时空抽样方法抽样,检测广东2007～2010年甲型H3N2毒株HA基因核苷酸序列,同时检索全球HA基因序列作为对照,采用Lasergene 7.1和Mega 5.05软件对HA基因核苷酸序列进行比对和分析;并结合流行病学资料,对变异毒株进行进化速度分析;同时进行抗原分析。结果发现,广东2007～2010年H3N2毒株HA基因同义进化(Ks)和错义进化(Ka)速度分别为2.06×1E-3～2.23×1E-3核苷酸/年和1.05×1E-3～1.21×1E-3核苷酸/年,HA1较HA2的错义突变速率要高3.13倍。与疫苗株A/Perth/16/2009的HA基因比较,2009年广东毒株同源性达到98.8%～99.7%、2010年同源性达到98.0%～98.4%。在广东2007～2010年毒株中,HA1五个抗原表位均有氨基酸位点变异,尤其是2010年毒株B区(N160K)和D区(K174R/N)的变异;此外,广东2010年毒株受体结合部位(RBS)还发生K189E/N/Q和T228A置换变异;两个糖基化位点变异影响到抗原性;目前使用的H3N2疫苗株与目前流行毒株的抗原性有差异。广东地区2007～2010年的毒株中,血凝抑制抗体的抗原分析结果有差异。结果提示,目前广东乃至全球甲型H3N2毒株HA1B区和D区均有氨基酸位点变异,RBS的两个位点发生置换,糖基化位点变异影响到表位A区和B区抗原性;与WHO推荐2011年流感H3N2毒株疫苗株比较,目前流行毒株HA基因有抗原位点变异。     

不同特征描述下H1N1病毒血凝素蛋白序列的比较分析

在传统表征蛋白质序列的40维特征向量的基础上,依据氨基酸的种类与理化性质,将蛋白质序列40维向量分解为20维、4维和16维3种子特征向量描述。结合33条H1N1流感病毒血凝素(hemagglutinin,HA)蛋白质序列和统计学相关性分析理论,进行了蛋白质序列两两之间及每条病毒蛋白质序列对应的不同子特征向量之间的相关性分析,发现病毒蛋白质序列之间存在高度相关性,且每条病毒蛋白质序列对应的20维子特征向量与其他两种子特征向量之间均不显著相关,而4维与16维子特征向量之间显著相关。进一步依据不同的特征向量对33条HA蛋白质序列进行分类,研究发现依据40维特征向量与16维特征向量进行的分类结果高度一致。因此,在不影响表征病毒序列特性的前提下,对于已有的表征蛋白质序列的40维特征向量,可以用16维的特征向量进行代替,以减少计算复杂度。     

Antibody Recognition of the Pandemic H1N1 Influenza Virus Hemagglutinin Receptor Binding Site

Influenza virus is a global health concern due to its unpredictable pandemic potential. This potential threat was realized in 2009 when an H1N1 virus emerged that resembled the 1918 virus in antigenicity but fortunately was not nearly as deadly. 5J8 is a human antibody that potently neutralizes a broad spectrum of H1N1 viruses, including the 1918 and 2009 pandemic viruses. Here, we present the crystal structure of 5J8 Fab in complex with a bacterially expressed and refolded globular head domain from the hemagglutinin (HA) of the A/California/07/2009 (H1N1) pandemic virus. 5J8 recognizes a conserved epitope in and around the receptor binding site (RBS), and its HCDR3 closely mimics interactions of the sialic acid receptor. Electron microscopy (EM) reconstructions of 5J8 Fab in complex with an HA trimer from a 1986 H1 strain and with an engineered stabilized HA trimer from the 2009 H1 pandemic virus showed a similar mode of binding. As for other characterized RBS-targeted antibodies, 5J8 uses avidity to extend its breadth and affinity against divergent H1 strains. 5J8 selectively interacts with HA insertion residue 133a, which is conserved in pandemic H1 strains and has precluded binding of other RBS-targeted antibodies. Thus, the RBS of divergent HAs is targeted by 5J8 and adds to the growing arsenal of common recognition motifs for design of therapeutics and vaccines. Moreover, consistent with previous studies, the bacterially expressed H1 HA properly refolds, retaining its antigenic structure, and presents a low-cost and rapid alternative for engineering and manufacturing candidate flu vaccines.     

Mutations in Hemagglutinin and Polymerase Alter the Virulence of Pandemic A(H1N1) Influenza Virus

To study the pathogenicity factors of the pandemic A(H1N1) influenza virus, a number of mutant variants of the A/Hamburg/5/2009 (H1N1)pdm09 strain were obtained through passage in chicken embryos, mouse lungs, and MDCK cell culture. After 17 lung-to-lung passages of the A/Hamburg/5/2009 in mice, the minimum lethal dose of the derived variant decreased by five orders of magnitude compared to that of the parental virus. This variant differed from the original virus by nine amino acid residues in the following viral proteins: hemagglutinin (HA), neuraminidase (NA), and components of the polymerase complex. Additional passaging of the intermediate variants and cloning made it possible to obtain pairs of strains that differed by a single amino acid substitution. Comparative analysis of replicative activity, receptor specificity, and virulence of these variants revealed two mechanisms responsible for increased pathogenicity of the virus for mice. Thus, (1) substitutions in HA (Asp225Gly or Gln226Arg) and compensatory mutation decreasing the charge of HA (Lys123Asn, Lys157Asn, Gly158Glu, Asn159Asp, or Lys212Met) altered viral receptor-binding specificity and restored the functional balance between HA and NA; (2) Phe35Leu substitution in the PA protein increased viral polymerase activity.     

H5亚型禽流感重组鸡痘病毒活载体疫苗的构建及其遗传稳定性与免疫效力

以鹅源H5亚型禽流感病毒(AIV)基因组为模板,用RTPCR扩增血凝素（Hemagglutinin, HA）基因,克隆入鸡痘病毒表达载体pFG1175,转染鸡痘病毒感染的鸡胚成纤维细胞,通过蓝斑筛选和间接免疫荧光检测,获得表达HA基因的重组鸡痘病毒（Recombinant fowlpox virus, rFPVHA）。rFPVHA经鸡胚成纤维细胞连续传15代后,报告基因LacZ和HA基因可稳定表达。用103PFU和105PFU的rFPVHA免疫无特定病原体的(Specific pathogen free, SPF)鸡,免疫后22d 血凝抑制(Hemagglutinin inhibition,HI)抗体监测阳性率分别为0%和20%,但均抵御了H5亚型毒株的致死性攻击,保护率为100%。结果表明,构建了表达HA基因的重组鸡痘病毒,该重组病毒具有良好遗传稳定性,免疫鸡可提供完全保护,显示出了一定的应用前景。     

Quantitative Characterization of Glycan-Receptor Binding of H9N2 Influenza A Virus Hemagglutinin

Avian influenza subtypes such as H5, H7 and H9 are yet to adapt to the human host so as to establish airborne transmission between humans. However, lab-generated reassorted viruses possessing hemagglutinin (HA) and neuraminidase (NA) genes from an avian H9 isolate and other genes from a human-adapted (H3 or H1) subtype acquired two amino acid changes in HA and a single amino acid change in NA that confer respiratory droplet transmission in ferrets. We previously demonstrated for human-adapted H1, H2 and H3 subtypes that quantitative binding affinity of their HA to α2→6 sialylated glycan receptors correlates with respiratory droplet transmissibility of the virus in ferrets. Such a relationship remains to be established for H9 HA. In this study, we performed a quantitative biochemical characterization of glycan receptor binding properties of wild-type and mutant forms of representative H9 HAs that were previously used in context of reassorted viruses in ferret transmission studies. We demonstrate here that distinct molecular interactions in the glycan receptor-binding site of different H9 HAs affect the glycan-binding specificity and affinity. Further we show that α2→6 glycan receptor-binding affinity of a mutant H9 HA carrying Thr-189→Ala amino acid change correlates with the respiratory droplet transmission in ferrets conferred by this change. Our findings contribute to a framework for monitoring the evolution of H9 HA by understanding effects of molecular changes in HA on glycan receptor-binding properties.     

人H5N1流感病毒血凝素蛋白DNA疫苗的构建及其免疫原性研究

将我国分离的首株人H5N1亚型禽流感病毒A/Anhui/1/2005作为研究对象,扩增其HA和HA1基因片段并克隆至真核表达载体pStar,构建成真核表达质粒。通过Western blot和间接免疫荧光检测方法确认,构建的重组质粒在真核细胞中成功地表达了目的蛋白HA和HA1。将重组质粒免疫BALB/c小鼠,检测免疫后外周血中HA/HA1特异性抗体的效价,并比较HA和HA1的免疫原性。结果表明,重组质粒免疫后成功地诱导了体液免疫反应,且二者的血清抗体效价无显著性差异。     

N-Linked Glycosylation of the Hemagglutinin Protein Influences Virulence and Antigenicity of the 1918 Pandemic and Seasonal H1N1 Influenza A Viruses

The hemagglutinin (HA) protein is a major virulence determinant for the 1918 pandemic influenza virus; however, it encodes no known virulence-associated determinants. In comparison to seasonal influenza viruses of lesser virulence, the 1918 H1N1 virus has fewer glycosylation sequons on the HA globular head region. Using site-directed mutagenesis, we found that a 1918 HA recombinant virus, of high virulence, could be significantly attenuated in mice by adding two additional glycosylation sites (asparagine [Asn] 71 and Asn 286) on the side of the HA head. The 1918 HA recombinant virus was further attenuated by introducing two additional glycosylation sites on the top of the HA head at Asn 142 and Asn 172. In a reciprocal experimental approach, deletion of HA glycosylation sites (Asn 142 and Asn 177, but not Asn 71 and Asn 104) from a seasonal influenza H1N1 virus, A/Solomon Islands/2006 (SI/06), led to increased virulence in mice. The addition of glycosylation sites to 1918 HA and removal of glycosylation sites from SI/06 HA imposed constraints on the theoretical structure surrounding the glycan receptor binding sites, which in turn led to distinct glycan receptor binding properties. The modification of glycosylation sites for the 1918 and SI/06 viruses also caused changes in viral antigenicity based on cross-reactive hemagglutinin inhibition antibody titers with antisera from mice infected with wild-type or glycan mutant viruses. These results demonstrate that glycosylation patterns of the 1918 and seasonal H1N1 viruses directly contribute to differences in virulence and are partially responsible for their distinct antigenicity.     

H5N1亚型禽流感病毒血凝素蛋白单链抗体基因的克隆及表达

构建并表达H5N1亚型禽流感病毒血凝素蛋白单链抗体,为禽流感靶向治疗药物的研制制备靶向载体。从分泌血凝素单克隆抗体的杂交瘤细胞株中提取mRNA,采用RT-PCR法扩增出重链和轻链可变区基因,通过SOE-PCR法将重链和轻链通过Linker连接起来构建单链抗体基因,将获得的单链抗体基因装入原核表达载体pET28a(+)中,构建重组质粒并表达,以Western blot鉴定单链抗体的特异性。结果成功构建了单链抗体基因,全长714bp,经原核表达,所构建的单链抗体可与H5亚型禽流感病毒HA蛋白特异结合,为禽流感的靶向治疗奠定了基础。     

Properly Folded Bacterially Expressed H1N1 Hemagglutinin Globular Head and Ectodomain Vaccines Protect Ferrets against H1N1 Pandemic Influenza Virus

Background

In the face of impending influenza pandemic, a rapid vaccine production and mass vaccination is the most effective approach to prevent the large scale mortality and morbidity that was associated with the 1918 “Spanish Flu”. The traditional process of influenza vaccine production in eggs is time consuming and may not meet the demands of rapid global vaccination required to curtail influenza pandemic.

Methodology/Principal Findings

Recombinant technology can be used to express the hemagglutinin (HA) of the emerging new influenza strain in a variety of systems including mammalian, insect, and bacterial cells. In this study, two forms of HA proteins derived from the currently circulating novel H1N1 A/California/07/2009 virus, HA1 (1–330) and HA (1–480), were expressed and purified from E. coli under controlled redox refolding conditions that favoured proper protein folding. However, only the recombinant HA1 (1–330) protein formed oligomers, including functional trimers that bound receptor and caused agglutination of human red blood cells. These proteins were used to vaccinate ferrets prior to challenge with the A/California/07/2009 virus. Both proteins induced neutralizing antibodies, and reduced viral loads in nasal washes. However, the HA1 (1–330) protein that had higher content of multimeric forms provided better protection from fever and weight loss at a lower vaccine dose compared with HA (1–480). Protein yield for the HA1 (1–330) ranged around 40 mg/Liter, while the HA (1–480) yield was 0.4–0.8 mg/Liter.

Conclusions/Significance

This is the first study that describes production in bacterial system of properly folded functional globular HA1 domain trimers, lacking the HA2 transmembrane protein, that elicit potent neutralizing antibody responses following vaccination and protect ferrets from in vivo challenge. The combination of bacterial expression system with established quality control methods could provide a mechanism for rapid large scale production of influenza vaccines in the face of influenza pandemic threat.     

Computational Identification of Antigenicity-Associated Sites in the Hemagglutinin Protein of A/H1N1 Seasonal Influenza Virus

The antigenic variability of influenza viruses has always made influenza vaccine development challenging. The punctuated nature of antigenic drift of influenza virus suggests that a relatively small number of genetic changes or combinations of genetic changes may drive changes in antigenic phenotype. The present study aimed to identify antigenicity-associated sites in the hemagglutinin protein of A/H1N1 seasonal influenza virus using computational approaches. Random Forest Regression (RFR) and Support Vector Regression based on Recursive Feature Elimination (SVR-RFE) were applied to H1N1 seasonal influenza viruses and used to analyze the associations between amino acid changes in the HA1 polypeptide and antigenic variation based on hemagglutination-inhibition (HI) assay data. Twenty-three and twenty antigenicity-associated sites were identified by RFR and SVR-RFE, respectively, by considering the joint effects of amino acid residues on antigenic drift. Our proposed approaches were further validated with the H3N2 dataset. The prediction models developed in this study can quantitatively predict antigenic differences with high prediction accuracy based only on HA1 sequences. Application of the study results can increase understanding of H1N1 seasonal influenza virus antigenic evolution and accelerate the selection of vaccine strains.     

表达H5N1亚型禽流感病毒HA蛋白的重组鼠白血病病毒的特性

通过反转录 聚合酶链式反应 (RT PCR)扩增了H5N1亚型鹅源禽流感病毒 (AIV)完整的血凝素 (HA)基因并进行了克隆与鉴定。序列测定结果已经登陆GenBank ,登陆号为AY6 394 0 5。序列分析表明所扩增的HA基因开放性阅读框架 (ORF)由170 7个核苷酸组成 ,共编码 5 6 8个氨基酸 ,裂解位点的氨基酸组成为RKKR↓GLF ,含连续的碱性氨基酸 ,具有高致病性AIVHA基因裂解位点的特征。构建了含HA基因的真核表达载体pcDNA HA ,通过与鼠白血病病毒 (MuLV)假病毒构建体系的两种质粒pHIT6 0和pHIT111共转染人胚肾细胞 2 93T ,4 8h后收集假病毒上清 ,超离后通过Western blot证明HA蛋白能够在假病毒颗粒表面表达 ,表明HA能够整合到此病毒粒子表面。通过感染 2 93T、COS 7和NIH3T3三种不同的靶细胞 ,证实所构建的假病毒粒子具有感染性和泛嗜性。本研究成功构建了具有感染性的MuLV HA假病毒体系 ,为研究鹅源禽流感病毒侵入细胞的机理及其组织嗜性的变异提供一种新方法。