Recent Developments in Electrochemical-Impedimetric Biosensors for Virus Detection

Viruses, including influenza viruses, MERS-CoV (Middle East respiratory syndrome coronavirus), SARS-CoV (severe acute respiratory syndrome coronavirus), HAV (Hepatitis A virus), HBV (Hepatitis B virus), HCV (Hepatitis C virus), HIV (human immunodeficiency virus), EBOV (Ebola virus), ZIKV (Zika virus), and most recently SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), are responsible for many diseases that result in hundreds of thousands of deaths yearly. The ongoing outbreak of the COVID-19 disease has raised a global concern and intensified research on the detection of viruses and virus-related diseases. Novel methods for the sensitive, rapid, and on-site detection of pathogens, such as the recent SARS-CoV-2, are critical for diagnosing and treating infectious diseases before they spread and affect human health worldwide. In this sense, electrochemical impedimetric biosensors could be applied for virus detection on a large scale. This review focuses on the recent developments in electrochemical-impedimetric biosensors for the detection of viruses.     

流感裂解疫苗纯化及裂解工艺的优化

目的优化大规模生产的流感病毒裂解疫苗的纯化及裂解工艺。方法比较凝胶层析和蔗糖密度梯度超速离心的纯化效果,以及TritonX-100和去氧胆酸钠两种裂解剂在不同条件下的裂解效果。结果层析法纯度稍高于蔗糖密度梯度超速离心法,而蔗糖密度区带超速离心法的收率优于层析法。TritonX-100的裂解效果优于去氧胆酸钠,裂解剂浓度为0.5%或0.8%,裂解3或4h,裂解率达90%以上。疫苗在4℃保存1年后,所有检测项目均合格,4℃保存18个月和37℃保存28d后,HA含量仍保持在30μg/ml以上。结论已建立了切实可行的流感病毒裂解疫苗规模生产的纯化及裂解工艺。     

The Functional Role of Loops and Flanking Sequences of G-Quadruplex Aptamer to the Hemagglutinin of Influenza a Virus

Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is the G-quadruplex DNA aptamer RHA0385, which binds to the hemagglutinins of various influenza A virus strains. These hemagglutinins have homologous tertiary structures but moderate-to-low amino acid sequence identities. Here, the experiment was inverted, targeting the same protein using a set of related, parallel G-quadruplexes. The 5′- and 3′-flanking sequences of RHA0385 were truncated to yield parallel G-quadruplex with three propeller loops that were 7, 1, and 1 nucleotides in length. Next, a set of minimal, parallel G-quadruplexes with three single-nucleotide loops was tested. These G-quadruplexes were characterized both structurally and functionally. All parallel G-quadruplexes had affinities for both recombinant hemagglutinin and influenza virions. In summary, the parallel G-quadruplex represents a minimal core structure with functional activity that binds influenza A hemagglutinin. The flanking sequences and loops represent additional features that can be used to modulate the affinity. Thus, the RHA0385–hemagglutinin complex serves as an excellent example of the hypothesis of a core structure that is decorated with additional recognizing elements capable of improving the binding properties of the aptamer.     

Role of microRNA and Oxidative Stress in Influenza A Virus Pathogenesis

MicroRNAs (miRNAs) are non-coding RNAs that regulate diverse cellular pathways by controlling gene expression. Increasing evidence has revealed their critical involvement in influenza A virus (IAV) pathogenesis. Host–IAV interactions induce different levels of oxidative stress (OS) by disrupting the balance between reactive oxygen species (ROS) and antioxidant factors. It is thought that miRNA may regulate the expression of ROS; conversely, ROS can induce or suppress miRNA expression during IAV infection. Thus, miRNA and OS are the two key factors of IAV infection and pathogenesis. Accordingly, interactions between OS and miRNA during IAV infection might be a critical area for further research. In this review, we discuss the crosstalk between miRNAs and OS during IAV infection. Additionally, we highlight the potential of miRNAs as diagnostic markers and therapeutic targets for IAV infections. This knowledge will help us to study host–virus interactions with novel intervention strategies.     

Transportin-3 Facilitates Uncoating of Influenza A Virus

Influenza A viruses (IAVs) are a major global health threat and in the future, may cause the next pandemic. Although studies have partly uncovered the molecular mechanism of IAV–host interaction, it requires further research. In this study, we explored the roles of transportin-3 (TNPO3) in IAV infection. We found that TNPO3-deficient cells inhibited infection with four different IAV strains, whereas restoration of TNPO3 expression in knockout (KO) cells restored IAV infection. TNPO3 overexpression in wild-type (WT) cells promoted IAV infection, suggesting that TNPO3 is involved in the IAV replication. Furthermore, we found that TNPO3 depletion restrained the uncoating in the IAV life cycle, thereby inhibiting the process of viral ribonucleoprotein (vRNP) entry into the nucleus. However, KO of TNPO3 did not affect the virus attachment, endocytosis, or endosomal acidification processes. Subsequently, we found that TNPO3 can colocalize and interact with viral proteins M1 and M2. Taken together, the depletion of TNPO3 inhibits IAV uncoating, thereby inhibiting IAV replication. Our study provides new insights and potential therapeutic targets for unraveling the mechanism of IAV replication and treating influenza disease.     

Discriminating Clonotypes of Influenza A Virus Genes by Nanopore Sequencing

Influenza viruses still pose a serious threat to humans, and we have not yet been able to effectively predict future pandemic strains and prepare vaccines in advance. One of the main reasons is the high genetic diversity of influenza viruses. We do not know the individual clonotypes of a virus population because some are the majority and others make up only a small fraction of the population. First-generation (FGS) and next-generation sequencing (NGS) technologies have inherent limitations that are unable to resolve a minority clonotype’s information in the virus population. Third-generation sequencing (TGS) technologies with ultra-long reads have the potential to solve this problem but have a high error rate. Here, we evaluated emerging direct RNA sequencing and cDNA sequencing with the MinION platform and established a novel approach that combines the high accuracy of Illumina sequencing technology and long reads of nanopore sequencing technology to resolve both variants and clonotypes of influenza virus. Furthermore, a new program was written to eliminate the effect of nanopore sequencing errors for the analysis of the results. By using this pipeline, we identified 47 clonotypes in our experiment. We conclude that this approach can quickly discriminate the clonotypes of virus genes, allowing researchers to understand virus adaptation and evolution at the population level.     

The Roles of Ubiquitination in Pathogenesis of Influenza Virus Infection

The ubiquitin system denotes a potent post-translational modification machinery that is capable of activation or deactivation of target proteins through reversible linkage of a single ubiquitin or ubiquitin chains. Ubiquitination regulates major cellular functions such as protein degradation, trafficking and signaling pathways, innate immune response, antiviral defense, and virus replication. The RNA sensor RIG-I ubiquitination is specifically induced by influenza A virus (IAV) to activate type I IFN production. Influenza virus modulates the activity of major antiviral proteins in the host cell to complete its full life cycle. Its structural and non-structural proteins, matrix proteins and the polymerase complex can regulate host immunity and antiviral response. The polymerase PB1-F2 of mutated 1918 IAV, adapts a novel IFN antagonist function by sending the DDX3 into proteasomal degradation. Ultimately the fate of virus is determined by the outcome of interplay between viral components and host antiviral proteins and ubiquitination has a central role in the encounter of virus and its host cell.     

Comparison of Cell Fusions Induced by Influenza Virus and SARS-CoV-2

Virus–cell fusion is the key step for viral infection in host cells. Studies on virus binding and fusion with host cells are important for understanding the virus–host interaction and viral pathogenesis for the discovery of antiviral drugs. In this review, we focus on the virus–cell fusions induced by the two major pandemic viruses, including the influenza virus and SARS-CoV-2. We further compare the cell fusions induced by the influenza virus and SARS-CoV-2, especially the pH-dependent fusion of the influenza virus and the fusion of SARS-CoV-2 in the type-II transmembrane serine protease 2 negative (TMPRSS2^-) cells with syncytia formation. Finally, we present the development of drugs used against SARA-CoV-2 and the influenza virus through the discovery of anti-fusion drugs and the prevention of pandemic respiratory viruses.     

稳定表达甲型流感病毒血凝素蛋白的哺乳动物细胞系的建立

目的建立稳定表达甲型流感病毒血凝素(Hemagglutinin,HA)蛋白的哺乳动物细胞系。方法 PCR扩增流感病毒(A/PR/8/34)全长HA基因,并将其克隆入真核表达载体pcDNA5/FRT(pDF)中,构建重组表达质粒pDF-HA,将其与表达Flp重组酶的pOG44质粒共转染Flp-In-CHO细胞,通过体内同源重组使目的基因整合至宿主细胞染色体上。采用Hygromycin B持续压力筛选重组细胞系CHO-HA,通过间接免疫荧光法(IFA)和Western blot法检测HA蛋白的表达。重组细胞连续培养10代后,采用PCR和IFA法检测细胞中HA的基因遗传和蛋白表达的稳定性。结果重组表达质粒pDF-HA经双酶切及测序,证实构建正确;通过Hygromycin B抗性及IFA,共筛选出20株高表达HA蛋白的重组细胞株,Western blot结果进一步证实,HA蛋白在重组细胞中获得表达,并被切割成HA1和HA2蛋白;连续培养10代后,PCR与IFA方法分别检测到重组细胞HA基因和蛋白的表达。结论已成功建立了稳定表达甲型流感病毒HA蛋白的哺乳动物细胞系,为针对HA蛋白和流感病毒的免疫学检测以及HA蛋白的功能研究提供了靶细胞。     

Transient Excursions to Membrane Core as Determinants of Influenza Virus Fusion Peptide Activity

Fusion of viral and host cell membranes is a critical step in the life cycle of enveloped viruses. In the case of influenza virus, it is mediated by subunit 2 of hemagglutinin (HA) glycoprotein whose N-terminal fragments insert into the target membrane and initiate lipid exchange. These isolated fragments, known as fusion peptides (HAfp), already possess own fusogenic activity towards liposomes. Although they have long been studied with the hope to uncover the details of HA-mediated fusion, their actual mechanism of action remains elusive. Here, we use extensive molecular dynamics simulations combined with experimental studies of three HAfp variants to fully characterize their free energy landscape and interaction with lipid bilayer. In addition to customary assumed peptides localization at lipid–water interface, we characterize membrane-spanning configurations, which turn out to be metastable for active HAfps and unstable for the fusion inactive W14A mutant. We show that, while the degree of membrane perturbation by surface peptide configurations is relatively low and does not show any mutation-related differences, the effect of deeply inserted configurations is significant and correlates with insertion depth of the N-terminal amino group which is the highest for the wild type HAfp. Finally, we demonstrate the feasibility of spontaneous peptide transition to intramembrane location and the critical role of strictly conserved tryptofan residue 14 in this process.     

The Crossroads between Host Copper Metabolism and Influenza Infection

Three main approaches are used to combat severe viral respiratory infections. The first is preemptive vaccination that blocks infection. Weakened or dead viral particles, as well as genetic constructs carrying viral proteins or information about them, are used as an antigen. However, the viral genome is very evolutionary labile and changes continuously. Second, chemical agents are used during infection and inhibit the function of a number of viral proteins. However, these drugs lose their effectiveness because the virus can rapidly acquire resistance to them. The third is the search for points in the host metabolism the effect on which would suppress the replication of the virus but would not have a significant effect on the metabolism of the host. Here, we consider the possibility of using the copper metabolic system as a target to reduce the severity of influenza infection. This is facilitated by the fact that, in mammals, copper status can be rapidly reduced by silver nanoparticles and restored after their cancellation.     

禽流感病毒抗原-抗体复合物的制备及其免疫原性

目的制备禽流感病毒抗原-抗体复合物,并检测其免疫原性。方法以H5亚型禽流感病毒的HA蛋白为抗原,其病毒的高免卵黄为抗体,将抗原与抗体按不同比例混合,制备禽流感病毒抗原抗体复合物。免疫1日龄SPF仔鸡,进行保护力试验;于免疫后不同时间检测血清HI抗体水平,并与H5亚型油乳剂灭活疫苗进行比较。结果抗原与抗体比例为1∶0.6的抗原-抗体复合物在免疫仔鸡15d后,其诱导的平均抗体水平达6.5log2,与H5亚型禽流感油乳剂灭活疫苗(6.2log2)相比,差异无统计学意义;在等量病毒攻击后,二者对仔鸡的保护率相同(93.3%)。结论制备的禽流感病毒抗原-抗体复合物具有良好的免疫原性,为研制禽流感新型复合物疫苗提供了依据。     

检测禽流感病毒RT-PCR一步法的建立及H5、H9亚型的鉴定

目的建立禽流感病毒(AIV)通用型RT-PCR一步法,并鉴定AIV H5和H9亚型。方法根据流感病毒高度保守的M1基因序列,设计一套通用型引物,建立AIVRT-PCR一步法。根据H5、H9亚型HA基因序列,分别设计一套特异性引物,其上、下游引物分别位于裂解位点两侧,应用RT-PCR一步法检测AIV H5和H9亚型,并验证所建立方法的敏感性;通过检测NDV、IBV和IBDV等RNA病毒及计算机软件模拟检测,验证其特异性。结果所建立AIV系列RT-PCR检测方法具有特异、敏感、简便和快速的特点。结论该方法可用于AIV的检测,H5、H9亚型的鉴定及致病性分析。     

2005和2006年流感裂解疫苗接种人体后的反应及免疫效果

目的观察2005、2006年变更流感毒株后制备的裂解疫苗接种人体后反应及免疫效果。方法变更毒株的流感裂解疫苗于2005和2006年,分别在江西九江和河南漯河进行了接种人体后反应及免疫效果观察。结果2年的观察结果显示,生产的流感裂解疫苗接种人体后全身、局部反应轻微,并有较好的抗体应答,对有流感抗体者接种流感疫苗后,仍能促使机体产生高效抗体。结论用变更毒株生产的流感病毒裂解疫苗接种人体后反应和免疫效果均良好。     

Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment

Influenza A virus (IAV) is a member of the single-stranded RNA (ssRNA) family of viruses. The most recent global pandemic caused by the SARS-CoV-2 virus has shown the major threat that RNA viruses can pose to humanity. In comparison, influenza has an even higher pandemic potential as a result of its high rate of mutations within its relatively short (<13 kbp) genome, as well as its capability to undergo genetic reassortment. In light of this threat, and the fact that RNA structure is connected to a broad range of known biological functions, deeper investigation of viral RNA (vRNA) structures is of high interest. Here, for the first time, we propose a secondary structure for segment 8 vRNA (vRNA8) of A/California/04/2009 (H1N1) formed in the presence of cellular and viral components. This structure shows similarities with prior in vitro experiments. Additionally, we determined the location of several well-defined, conserved structural motifs of vRNA8 within IAV strains with possible functionality. These RNA motifs appear to fold independently of regional nucleoprotein (NP)-binding affinity, but a low or uneven distribution of NP in each motif region is noted. This research also highlights several accessible sites for oligonucleotide tools and small molecules in vRNA8 in a cellular environment that might be a target for influenza A virus inhibition on the RNA level.     

A Novel Prophylaxis Strategy Using Liposomal Vaccine Adjuvant CAF09b Protects against Influenza Virus Disease

The SARS-CoV-2 pandemic caused a massive health and societal crisis, although the fast development of effective vaccines reduced some of the impact. To prepare for future respiratory virus pandemics, a pan-viral prophylaxis could be used to control the initial virus outbreak in the period prior to vaccine approval. The liposomal vaccine adjuvant CAF^®09b contains the TLR3 agonist polyinosinic:polycytidylic acid, which induces a type I interferon (IFN-I) response and an antiviral state in the affected tissues. When testing CAF09b liposomes as a potential pan-viral prophylaxis, we observed that intranasal administration of CAF09b liposomes to mice resulted in an influx of innate immune cells into the nose and lungs and upregulation of IFN-I-related gene expression. When CAF09b liposomes were administered prior to challenge with mouse-adapted influenza A/Puerto Rico/8/1934 virus, it protected from severe disease, although the virus was still detectable in the lungs. However, when CAF09b liposomes were administered after influenza challenge, the mice had a similar disease course to controls. In conclusion, CAF09b may be a suitable candidate as a pan-viral prophylactic treatment for epidemic viruses, but must be administered prior to virus exposure to be effective.     

流感疫苗血凝素含量测定替代方法的建立及验证

目的建立测定流感疫苗血凝素(Haemagglutinin,HA)含量的替代方法 ,并进行验证,以解决大流行流感发生初期疫苗原液中HA定量的难题。方法优化糖苷酶处理条件,将流感疫苗原液经糖苷酶处理后,以还原SDS-PAGE方法分离样品,以灰度扫描法确定HA蛋白百分比,结合样品总蛋白数值,计算样品中HA含量。以该方法和传统的单向免疫扩散(SRID)法分别测定7批流感疫苗原液中HA含量,并进行比较。结果优化的糖苷酶处理条件为:总蛋白400μg/ml,PNGaseF加入比例为1:50。样品经糖苷酶处理后,以还原SDS-PAGE法可以清晰区分各蛋白条带,经测序后确定HA两个亚基,与预期相对分子质量一致。该方法测定7批流感疫苗原液中HA含量的结果与SRID法测定结果的符合率在87.90%~122.20%之间。结论初步建立了测定流感疫苗中HA含量的替代方法 ,在WHO参考品供应不到位时,可用于大流感发生时疫苗原液中HA之定量。     

Mass Spectrometry Analysis Coupled with de novo Sequencing Reveals Amino Acid Substitutions in Nucleocapsid Protein from Influenza A Virus

Amino acid substitutions in influenza A virus are the main reasons for both antigenic shift and virulence change, which result from non-synonymous mutations in the viral genome. Nucleocapsid protein (NP), one of the major structural proteins of influenza virus, is responsible for regulation of viral RNA synthesis and replication. In this report we used LC-MS/MS to analyze tryptic digestion of nucleocapsid protein of influenza virus (A/Puerto Rico/8/1934 H1N1), which was isolated and purified by SDS poly-acrylamide gel electrophoresis. Thus, LC-MS/MS analyses, coupled with manual de novo sequencing, allowed the determination of three substituted amino acid residues R452K, T423A and N430T in two tryptic peptides. The obtained results provided experimental evidence that amino acid substitutions resulted from non-synonymous gene mutations could be directly characterized by mass spectrometry in proteins of RNA viruses such as influenza A virus.     

Influenza A Virus NS1 Protein Structural Flexibility Analysis According to Its Structural Polymorphism Using Computational Approaches

Influenza A viruses are highly contagious RNA viruses that cause respiratory tract infections in humans and animals. Their non-structural protein NS1, a homodimer of two 230-residue chains, is the main viral factor in counteracting the antiviral defenses of the host cell. Its RNA-binding domain is an obligate dimer that is connected to each of the two effector domains by a highly flexible unstructured linker region of ten amino acids. The flexibility of NS1 is a key property that allows its effector domains and its RNA binding domain to interact with several protein partners or RNAs. The three-dimensional structures of full-length NS1 dimers revealed that the effector domains could adopt three distinct conformations as regards their mutual interactions and their orientation relative to the RNA binding domain (closed, semi-open and open). The origin of this structural polymorphism is currently being investigated and several hypotheses are proposed, among which one posits that it is a strain-specific property. In the present study, we explored through computational molecular modeling the dynamic and flexibility properties of NS1 from three important influenza virus A strains belonging to three distinct subtypes (H1N1, H6N6, H5N1), for which at least one conformation is available in the Protein Data Bank. In order to verify whether NS1 is stable in three forms for the three strains, we constructed homology models if the corresponding forms were not available in the Protein Data Bank. Molecular dynamics simulations were performed in order to predict the stability over time of the three distinct sequence variants of NS1, in each of their three distinct conformations. Our results favor the co-existence of three stable structural forms, regardless of the strain, but also suggest that the length of the linker, along with the presence of specific amino acids, modulate the dynamic properties and the flexibility of NS1.     

RNA Sequencing Demonstrates That Circular RNA Regulates Avian Influenza Virus Replication in Human Cells

Circular RNAs (circRNAs) are involved in diverse biological processes. Avian influenza virus (AIV) can cross the species barrier to infect humans. Here, we employed RNA sequencing technology to profile circRNA, microRNA, and mRNA expression in human lung carcinoma cells in response to AIV or human influenza A virus (IAV) infection at viral replication. The analysis revealed that the expression of 475 common circRNAs were significantly regulated. The 381 and 1163 up-regulated circRNAs were induced by AIV at 8 and 16 h, respectively. Subsequently, gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses were also conducted for the AIV-specific up-regulated circRNAs. Moreover, the circRNAs were characterized, of which six were verified by quantitative real-time PCR. We further confirmed that expression of the selected circRNAs only increased following AIV infection. Knocking down the selected circRNAs promoted AIV proliferation, and overexpression of three of the candidate circRNAs restricted AIV replication and proliferation. We further analyzed that AIV-specific up-regulated circRNA mechanisms might function through the ceRNA network to affect the “Endocytosis” pathway and the “Cell cycle process”. These data provide the first expression profile of AIV-specific up-regulated circRNAs and shed new light on the pathogenesis of AIV infection. Our findings also suggest that these circRNAs serve an important role in AIV infection.