Surface Glycoproteins Of Influenza Research Articles

Dually-amplified electrochemical aptasensor based on the self-linking AuPt nanoflowers for ultrasensitive determination of hemagglutinin

BackgroundInfluenza virus can spread from person to person and cause epidemics. Therefore, rapid and sensitive diagnosis of virus is essential in controlling influenza outbreaks. Conventional virus diagnostic techniques are time-consuming, labor-intensive and requires large instruments. In this work, a sandwich electrochemical assay by a pair of aptamers was developed for ultrasensitive determination of hemagglutinin (HA) protein, which is one of the two surface glycoproteins of influenza A (H1N1) virus, using dual signal amplification techniques. ResultsHA was captured and magnetically separated by Fe3O4@SiO2-NH2@Au attached to aptamer 1 (Apt1), creating a sandwich structure with AuPt nanoflowers (AuPtNFs) connected to aptamer 2 (Apt2). Herein, AuPtNFs could catalyze H2O2/hydroquinone (HQ) to generate 1,4-benzoquinone (BQ), and achieved amplification of electrochemical signal detection through differential pulse voltammetry (DPV). The constructed aptasensor expressed a wide linear range (10 pg/mL-100 ng/mL) with limit of detection (LOD) of 2.4 pg/mL. Moreover, a novel strategy for dual signal amplification was developed to further enhance sensitivity. The innovative electrochemical aptasensor could achieve secondary amplification of the detection signal with LOD of 0.3 pg/mL and linear concentration range from 0.5 pg/mL to 100 ng/mL. The secondary amplification could be achieved only through the self-linking process, which allowed for the retention of numerous AuPtNFs by simple complementary base pairing to connect more AuPtNFs onto the above-mentioned sandwich structure. SignificanceOverall, the constructed aptasensor exhibited favorable sensitivity and accuracy, indicating the potential expanded application for the clinical detection of numerous viruses.

Shrinkage-based Random Local Clocks with Scalable Inference.

Molecular clock models undergird modern methods of divergence-time estimation. Local clock models propose that the rate of molecular evolution is constant within phylogenetic subtrees. Current local clock inference procedures exhibit one or more weaknesses, namely they achieve limited scalability to trees with large numbers of taxa, impose model misspecification, or require a priori knowledge of the existence and location of clocks. To overcome these challenges, we present an autocorrelated, Bayesian model of heritable clock rate evolution that leverages heavy-tailed priors with mean zero to shrink increments of change between branch-specific clocks. We further develop an efficient Hamiltonian Monte Carlo sampler that exploits closed form gradient computations to scale our model to large trees. Inference under our shrinkage clock exhibits a speed-up compared to the popular random local clock when estimating branch-specific clock rates on a variety of simulated datasets. This speed-up increases with the size of the problem. We further show our shrinkage clock recovers known local clocks within a rodent and mammalian phylogeny. Finally, in a problem that once appeared computationally impractical, we investigate the heritable clock structure of various surface glycoproteins of influenza A virus in the absence of prior knowledge about clock placement. We implement our shrinkage clock and make it publicly available in the BEAST software package.

Influenza Virus Carrying a Codon-Reprogrammed Neuraminidase Gene as a Strategy for Live Attenuated Vaccine.

Live attenuated influenza vaccines offer broader and longer-lasting protection in comparison to inactivated influenza vaccines. The neuraminidase (NA) surface glycoprotein of influenza A virus is essential for the release and spread of progeny viral particles from infected cells. In this study, we de novo synthesized the NA gene, in which 62% of codons were synonymously changed based on mammalian codon bias usage. The codon-reprogrammed NA (repNA) gene failed to be packaged into the viral genome, which was achievable with partial restoration of wild-type NA sequence nucleotides at the 3' and 5' termini. Among a series of rescued recombinant viruses, we selected 20/13repNA, which contained 20 and 13 nucleotides of wild-type NA at the 3' and 5' termini of repNA, respectively, and evaluated its potential as a live attenuated influenza vaccine. The 20/13repNA is highly attenuated in mice, and the calculated LD50 was about 10,000-fold higher than that of the wild-type (WT) virus. Intranasal inoculation of the 20/13repNA virus in mice induced viral-specific humoral, cell-mediated, and mucosal immune responses. Mice vaccinated with the 20/13repNA virus were protected from the lethal challenge of both homologous and heterologous viruses. This strategy may provide a new method for the development of live, attenuated influenza vaccines for a better and more rapid response to influenza threats.

In vitro and computational insights revealing the potential inhibitory effect of Tanshinone IIA against influenza A virus

Seasonal human influenza is a serious respiratory infection caused by influenza viruses that can be found all over the world. Type A influenza is a contagious viral infection that, if left untreated, can lead to life-threatening consequences. Fortunately, the plant kingdom has many potent medicines with broad-spectrum antiviral activity. Herein, six plant constituents, namely Tanshinone IIA 1, Carnosic acid 2, Rosmarinic acid 3, Glycyrrhetinic acid 4, Baicalein 5, and Salvianolic acid B 6, were screened for their antiviral activities against H1N1 virus using in vitro and in silico approaches. Hence, their anti-influenza activities were tested in vitro to determine inhibitory concentration 50 (IC50) values after measuring their CC50 values using MTT assay on MDCK cells. Interestingly, Tanshinone IIA (TAN) 1 was the most promising member with CC50 = 9.678 μg/ml. Moreover, the plaque reduction assay carried on TAN 1 revealed promising viral inhibition percentages of 97.9%, 95.8%, 94.4%, and 91.7% using concentrations 0.05 μg/μl, 0.025 μg/μl, 0.0125 μg/μl, and 0.006 μg/μl, respectively. Furthermore, in silico molecular docking disclosed the superior affinities of Salvianolic acid B (SAL) 6 towards both surface glycoproteins of influenza A virus (namely, hemagglutinin (HA) and neuraminidase (NA)). The docked complexes of both SAL and TAN inside HA and NA receptor pockets were selected for 100 ns MD simulations followed by MM-GBSA binding free energy calculation to confirm the docking results and give more insights regarding the stability of both compounds inside influenza mentioned receptors, respectively. The selection criteria of the previously mentioned complexes were based on the fact that SAL showed the highest docking scores on both viral HA and NA glycoproteins whereas TAN achieved the best inhibitory activity on the other hand. Finally, we urge more advanced preclinical and clinical research, particularly for TAN, which could be used to treat the human influenza A virus effectively.

Spatial and temporal coevolution of N2 neuraminidase and H1 and H3 hemagglutinin genes of influenza A virus in US swine.

The neuraminidase (NA) and hemagglutinin (HA) are essential surface glycoproteins of influenza A virus (IAV). In this study, the evolution of subtype N2 NA paired with H1 and H3 subtype HA in swine was evaluated to understand if the genetic diversity of HA and NA were linked. Using time-scaled Bayesian phylodynamic analyses, the relationships of paired swine N2 with H1 or H3 from 2009 to 2018 were evaluated. These data demonstrated increased relative genetic diversity within the major N2 clades circulating in swine in the USA (N2.1998 between 2014 and 2017 and N2.2002 between 2010 and 2016). Preferential pairing was observed among specific NA and HA genetic clades. Gene reassortment between cocirculating influenza A strains resulted in novel pairings that persisted. The changes in genetic diversity in the NA gene were quantified using Bayesian phylodynamic analyses, and increases in diversity were observed subsequent to novel NA–HA reassortment events. The rate of evolution among NA–N2 clades and HA–H1 and HA–H3 clades were similar. Bayesian phylodynamic analyses demonstrated strong spatial patterns in N2 genetic diversity, but frequent interstate movement of rare N2 clades provided opportunity for reassortment and emergence of new N2–HA pairings. The frequent regional movement of pigs and their influenza viruses is an explanation for the documented patterns of reassortment and subsequent changes in gene diversity. The reassortment and evolution of NA and linked HA evolution may result in antigenic drift of both major surface glycoproteins, reducing vaccine efficacy, with subsequent impact on animal health.

Probing the Neuraminidase Activity of Influenza Virus Using a Cytolysin A Protein Nanopore.

Neuraminidase (NA), one of the major surface glycoproteins of influenza A virus (IAV), is an important diagnostic biomarker and antiviral therapeutic target. Cytolysin A (ClyA) is a nanopore sensor with an internal constriction of 3.3 nm, enabling the detection of protein conformations at the single-molecule level. In this study, a nanopore-based approach is developed for analysis of the enzymatic activity of NA, which facilitates rapid and highly sensitive diagnosis of IAV. Current blockade analysis of the d-glucose/d-galactose-binding protein (GBP) trapped within a type I ClyA-AS (ClyA mutant) nanopore reveals that galactose cleaved from sialyl-galactose by NA of the influenza virus can be detected in real time and at the single-molecule level. Our results show that this nanopore sensor can quantitatively measure the activity of NA with 40-80-fold higher sensitivity than those previously reported. Furthermore, the inhibition of NA is monitored using small-molecule antiviral drugs, such as zanamivir. Taken together, our results reveal that the ClyA protein nanopore can be a valuable platform for the rapid and sensitive point-of-care diagnosis of influenza and for drug screening against the NA target.

Universal anti-influenza vaccines based on viral HA2 and M2e antigens.

Aquatic birds are the main reservoir of influenza A viruses (IAVs). These viruses can infect humans repeatedly and cause acute respiratory disease with potential of spread in the form of epidemics. In addition, avian influenza viruses that overcome the interspecies barrier and adapt to humans can cause a world-wide pandemic with severe consequences to human health. Therefore, scientists are focused on the development of a "universal" vaccine with a broad protective efficacy, i.e. against different subtypes of influenza A viruses and not only against the currently co-circulating human epidemic strains. Nowadays, several new vaccine design strategies have been described. Most of them utilize the conserved stem part of influenza surface glycoprotein hemagglutinin (HA) or the ectodomain of M2 (M2e) protein with proton-channel activity. A comparison of the efficacy of novel vaccines and their protective mechanisms against influenza infection is discussed in this review and should be considered for the construction of the most effective broadly protective vaccine with minimal side effects. This is the essential goal in influenza virus research today, especially when the infection with new human coronavirus SARS-CoV-2 can interfere with the course of influenza virus infection. Keywords: influenza A virus; HA2 gp; M2 ectodomain; universal vaccine.

Characterization of Hemagglutinin Antigens on Influenza Virus and within Vaccines Using Electron Microscopy.

Influenza viruses affect millions of people worldwide on an annual basis. Although vaccines are available, influenza still causes significant human mortality and morbidity. Vaccines target the major influenza surface glycoprotein hemagglutinin (HA). However, circulating HA subtypes undergo continual variation in their dominant epitopes, requiring vaccines to be updated annually. A goal of next-generation influenza vaccine research is to produce broader protective immunity against the different types, subtypes, and strains of influenza viruses. One emerging strategy is to focus the immune response away from variable epitopes, and instead target the conserved stem region of HA. To increase the display and immunogenicity of the HA stem, nanoparticles are being developed to display epitopes in a controlled spatial arrangement to improve immunogenicity and elicit protective immune responses. Engineering of these nanoparticles requires structure-guided design to optimize the fidelity and valency of antigen presentation. Here, we review electron microscopy applied to study the 3D structures of influenza viruses and different vaccine antigens. Structure-guided information from electron microscopy should be integrated into pipelines for the development of both more efficacious seasonal and universal influenza vaccine antigens. The lessons learned from influenza vaccine electron microscopic research could aid in the development of novel vaccines for other pathogens.

NAction! How Can Neuraminidase-Based Immunity Contribute to Better Influenza Virus Vaccines?

ABSTRACTNeuraminidase is one of the two surface glycoproteins of influenza A and B viruses. It has enzymatic activity that cleaves terminal sialic acid from glycans, and that activity is essential at several points in the virus life cycle. While neuraminidase is a major target for influenza antivirals, it is largely ignored in vaccine development. Current inactivated influenza virus vaccines might contain neuraminidase, but the antigen quantity and quality are varied and not standardized. While there are data that show a protective role of anti-neuraminidase immunity, many questions remain unanswered. These questions, among others, concern the targeted epitopes or antigenic sites, the potential for antigenic drift, and, connected to that, the breadth of protection, differences in induction of immune responses by vaccination versus infection, mechanisms of protection, the role of mucosal antineuraminidase antibodies, stability, and the immunogenicity of neuraminidase in vaccine formulations. Reagents for analysis of neuraminidase-based immunity are scarce, and assays are not widely used for clinical studies evaluating vaccines. However, efforts to better understand neuraminidase-based immunity have been made recently. A neuraminidase focus group, NAction!, was formed at a Centers of Excellence for Influenza Research and Surveillance meeting at the National Institutes of Health in Bethesda, MD, to promote research that helps to understand neuraminidase-based immunity and how it can contribute to the design of better and broadly protective influenza virus vaccines. Here, we review open questions and knowledge gaps that have been identified by this group and discuss how the gaps can be addressed, with the ultimate goal of designing better influenza virus vaccines.

An Amino Acid in the Stalk Domain of N1 Neuraminidase Is Critical for Enzymatic Activity.

Neuraminidase (NA) is a sialidase that is one of the major surface glycoproteins of influenza A viruses and the target for the influenza drugs oseltamivir and zanamivir. NA is important as it releases progeny viruses from the surface of infected cells and prevents viruses becoming trapped in mucus. Mutations in the globular head domain that decrease enzymatic activity but confer resistance to NA inhibitors have been characterized; however, the importance of specific mutations in the stalk domain is unknown. We identified 66Y (N1 numbering), a highly conserved amino acid that was critical for the stability of the NA tetramer and, subsequently, for NA enzymatic activity.

Highly specific and rapid glycan based amperometric detection of influenza viruses.

Rapid and precise detection of influenza viruses in a point of care setting is critical for applying appropriate countermeasures. Current methods such as nucleic acid or antibody based techniques are expensive or suffer from low sensitivity, respectively. We have developed an assay that uses glucose test strips and a handheld potentiostat to detect the influenza virus with high specificity. Influenza surface glycoprotein neuraminidase (NA), but not bacterial NA, cleaved galactose bearing substrates, 4,7di-OMe N-acetylneuraminic acid attached to the 3 or 6 position of galactose, to release galactose. In contrast, viral and bacterial NA cleaved the natural substrate, N-acetylneuraminic acid attached to the 3 or 6 position of galactose. The released galactose was detected amperometrically using a handheld potentiostat and dehydrogenase bearing glucose test strips. The specificity for influenza was confirmed using influenza strains and different respiratory pathogens that include Streptococcus pneumoniae and Haemophilus influenzae; bacteria do not cleave these molecules. The assay was also used to detect co-infections caused by influenza and bacterial NA. Viral drug susceptibility and testing with human clinical samples was successful in 15 minutes, indicating that this assay could be used to rapidly detect influenza viruses at primary care or resource poor settings using ubiquitous glucose meters.

VIRUS-SPECIFIC HUMORAL IMMUNE RESPONSE ISOTYPIC STRUCTURE IN ADULT PATIENTS HOSPITALIZED WITH INFLUENZA A

The aim of this investigation was a comparative analysis of isotypic structure of specific antiviral systemic humoral immune response in hospitalized patients with influenza caused by virus A(H3N2) or A(H1N1), including the A(H1N1)pdm09. Paired acute and convalescent phase sera from 109 adult patients aged 18 to 67 years with laboratoryconfirmed influenza A were analyzed by ELISA. Purified surface glycoproteins of influenza A viruses of different subtypes containing the hemagglutinin and neuraminidase were used as antigen for sensitization of plates in ELISA.The absence of type-specific conserved internal proteins in antigenic material allowed to carry out a subtype-specific differentiation of antibodies against influenza viruses in ELISA. Regardless of the subtype of influenza A viruses caused the disease, the most pronounced response was observed by subtype-specific IgG1 (70–90% of seroconversions). It has been shown for the first time that low activity of virus-induced IgG2 (6–9% of seroconversions) is a peculiarity of the immune response both to primary or recurrent infections with A(H1N1)pdm09. In patients repeatedly suffered by «seasonal» influenza A(H1N1) in 2007/2008 or influenza A(H3N2) in 2012–2014 IgG2 seroconversion’s rates were 40–59% (р 0,05). Reaction virusspecific IgG3 was also weaker in patients with influenza A(H1N1)pdm09 (29–44% of seroconversions) than in subjects with influenza A(H1N1) or A(H3N2) (65% and 56% of seroconversions, respectively). Geometric mean titers of virus neutralizing antibodies identified during recovery phase in patients with primary and secondary influenza A(H1N1)pdm09 (1/28 and 1/103, respectively) were significantly lower than in patients recovered from influenza A(H1N1) or A(H3N2) (GMT were 1/594 and 1/378, respectively). It was shown that the surface glycoproteins of influenza A viruses may be an allergens. Virus-specific IgE seroconversion rates were comparable in all groups reaching 25–45%. The high activity of virus-induced serum IgA was detected in patients with influenza A(H3N2) or A(H1N1)pdm09 (60–79% of seroconversions). Thus, study of virus-specific activity of various immunoglobulin isotypes provides important information about the formation of adaptive antiviral immune response to influenza A viruses, and also estimate the contribution of its protective and immunopathogenic components to pathogenesis of the disease.

Influenza neuraminidase as a vaccine antigen.

Neuraminidase (NA) is the second most abundant influenza surface glycoprotein and contributes to virus replication in several ways, most notably by removing sialic acids from the host and viral glycoproteins, releasing newly formed virus particles from infected cells. Antibodies that block this enzyme activity restrict virus replication in vitro. This chapter describes foundational epidemiologic and human influenza challenge studies that provide evidence of an association between NA inhibiting antibodies and resistance to disease. Mouse challenge studies show that while NA immunity is infection-permissive, NA-specific antibodies attenuate infection and prevent severe disease. NA immunity is most effective against homologous viruses but there is substantial protection against viruses with a heterologous NA (different lineage within a NA subtype). Monoclonal antibodies specific for conserved antigenic domains of subtype N1 protect against seasonal and pandemic H1N1 as well as H5N1 virus challenge. Clinical studies demonstrate that licensed seasonal vaccines contain immunogenic amounts of NA, but the contribution of this immunity to vaccine efficacy is currently not known. New types of influenza vaccines could be designed to elicit NA immunity. Because NA induces heterologous immunity, it could be an important constituent of universal influenza vaccines that aim to protect against unexpected emerging viruses.

Computational investigation of interaction mechanisms between juglone and influenza virus surface glycoproteins

Surface glycoproteins of influenza virus [haemagglutinin (HA) and neuraminidase (NA)] are vital target proteins in current rational drug designs. Here, the molecular recognitions between juglone and A/H5N1 influenza virus membrane glycoproteins were studied through flexible docking and molecular dynamic simulations. The results revealed that juglone has the binding specificity to HA (H5) and NA (N1), especially the spatial match of 2-cyclohexene-1,4-dione ring. N1 rather than H5 protein is responsible for the binding, with the interaction energies of − 72.48 and − 41.91 kcal mol− 1, respectively. The residues Arg152, Arg156, Glu276, Glu277 and Arg292 of N1 protein had important roles during the binding process. Compared with other NA inhibitors, juglone is a potential source of anti-influenza ingredients, with better interaction energy and relatively smaller size. In addition, this work also pointed out how to effectively modify the functional groups of juglone. We hope that the results will aid our understanding of recognitions involving influenza surface glycoproteins with the phenolic compounds and warrant the experimental aspects to design novel anti-influenza drugs.

The specificity of the influenza B virus hemagglutinin receptor binding pocket: what does it bind to?

The influenza surface glycoprotein hemagglutinin (HA) binds to sialylglycoproteins and sialylglycolipids on the surface of host cells. These sialyl-glycans, usually linked to galactose in either α2,6 or α2,3 configurations, are the receptors for the viral HA, the binding to which promotes viral attachment, membrane fusion, and internalization of the virus. This review examines all of the available receptor binding data on the influenza B HA and provides a structure recognition perspective for the receptor binding preferences of influenza B virus HA regional and egg-adapted variants. Overall, the review serves as an up-to-date compendium of the literature binding data, and the presented discussions assist the reader in reaching a consensus understanding of the receptor specificity determinants for the influenza B HA.

Analysis of oseltamivir resistance substitutions in influenza virus glycoprotein neuraminidase using a lentivirus-based surrogate assay system

Influenza A virus poses a great threat to global health, and oseltamivir (trade marked as Tamiflu), which targets influenza surface glycoprotein neuraminidase (NA), is used clinically as a major anti-influenza treatment. However, certain substitutions in NA can render an influenza virus resistant to this drug. In this study, using a lentiviral pseudotyping system, which alleviates the safety concerns of studying highly pathogenic influenza viruses such as avian influenza H5N1, that utilizes influenza surface glycoproteins (hemagglutinin or HA, and NA) and an HIV-core combined with a luciferase reporter gene as a surrogate assay, we first assessed the functionality of NA by measuring pseudovirion release in the absence or presence of oseltamivir. We demonstrated that oseltamivir displays a dose-dependent inhibition on NA activity. In contrast, a mutant NA (H274Y) is more resistant to oseltamivir treatment. In addition, the effects of several previously reported substitution NA mutants were examined as well. Our results demonstrate that this lentivirus-based pseudotyping system provides a quick, safe, and effective way to assess resistance to neuraminidase inhibitors. And we believe that as new mutations appear in influenza isolates, their impact on the effectiveness of current and future anti-NA can be quickly and reliably evaluated by this assay.

Intrinsic Temperature Sensitivity of Influenza C Virus Hemagglutinin-Esterase-Fusion Protein

Influenza C virus replicates more efficiently at 33°C than at 37°C. To determine whether hemagglutinin-esterase-fusion protein (HEF), a surface glycoprotein of influenza C virus, is a restricting factor for this temperature sensitivity, we analyzed the biological and biochemical properties of HEF at 33°C and 37°C. We found that HEF exhibits intrinsic temperature sensitivities for surface expression and fusion activity.

Surface glycoproteins of influenza A H3N2 virus modulate virus replication in the respiratory tract of ferrets

The hemagglutinin (HA) genes of the influenza A H3N2 subtype viruses isolated from 1968 to 2010 have evolved substantially but their neuraminidase (NA) genes have been relatively less divergent. The H3N2 viruses isolated since 1995 were found to replicate in the lower respiratory tract of ferrets less efficiently than the earlier isolates. To evaluate whether the HA or/and NA or the internal protein gene segments of the H3N2 virus affected viral replication in the respiratory tract of ferrets, recombinant A/California/07/2004 (CA04) (H3N2) virus and its reassortants that contained the same CA04 internal protein gene segments and the HA and/or NA of A/Udorn/309/1972 (UD72) or A/Wuhan/359/1995 (WH95) H3N2 viruses were generated and evaluated for their replication in the respiratory tract of ferrets. All the reassortant viruses replicated efficiently in the upper respiratory tract of ferrets, but their replication in the lower respiratory tract of ferrets varied. In contrast to the UD72-HA reassortant virus that replicated efficiently in the lungs of ferrets, the virus with the WH95-HA or the CA04-HA either replicated modestly or did not replicate in the lungs of ferrets. The reassortants with the WH95-HA and UD72-NA or CA04-NA had the tendency to lose a N-linked glycosylation site at residue 246 in the HA, resulting in viral lung titer of 100-fold higher than the virus with the HA and NA from WH95. The UD72-NA had the highest neuraminidase activity and increased viral replication by up to 100-fold in tissue culture cells during early infection. Thus, our data indicate that both the HA and NA glycoproteins play important roles in viral replication of the H3N2 influenza virus in ferrets.

Comparative Analyses of N-Glycosylation Profiles of Influenza A Viruses Grown in Different Host Cells

Glycosylation of the surface glycoproteins of influenza A virus is associated with several viral properties such as receptor binding and susceptibility to neuraminidase inhibitors. In this study, we evaluated the detailed structures of N-glycans derived from the same influenza virus strain A/Memphis/1/71 (H3N2) grown in different host cells, i.e., Madin-Darby canine kidney (MDCK) cells and embryonated eggs. Although both influenza virus isolates expressed neu- tral and sulfated oligosaccharides, their detailed profiles were significantly different. In contrast, N-glycosylation profiles of the influenza virus isolate from MDCK cells were highly homologous with those of desialylated N-glycans derived from its host cells. These data demonstrate that the glycosylation of influenza viruses is governed by their host cells.

Recent Developments in Bioinformatics Analyses of Influenza A Virus Surface Glycoproteins and their Biological Relevance

Influenza A surface glycoproteins, hemagglutinin (HA) and neuraminidase (NA), are the major targets of neutralizing antibodies which necessitate their inclusion in influenza vaccines. The frequent antigenic drift and shift of these proteins are responsible for the annual epidemics and occasional pandemics of influenza. Therefore, vaccines must be reformulated annually to include the HA and NA proteins of the viral strains predicted for the upcoming flu season. There are inherent limitations in the annual vaccine preparation process since testing for effectiveness, approval by regulatory agencies and distribution of these vaccines can take approximately 6 months. These drawbacks are most pronounced in situations of pandemic influenza such as the recent swine-origin 2009 H1N1 pandemic, thus there is a critical need for the development of new antiviral and vaccine strategies. One promising new area of research is targeting the conserved regions of influenza surface glycoproteins. Recent studies have demonstrated that vaccines based on highly conserved sequences or antibodies raised against conserved epitopes can protect animals against diverse influenza A virus subtypes. In this review, we focus on the challenges associated with the two main surface glycoproteins, HA and NA, while emphasizing recent advances in bioinformatics tools and their contribution to the design of new diagnostics, vaccines and antivirals.