Differences in sialic acid-galactose linkages in the chicken egg amnion and allantois influence human influenza virus receptor specificity and variant selection

Epistasis mediates the evolution of the receptor binding mode in recent human H3N2 hemagglutinin

The receptor-binding site of influenza A virus hemagglutinin partially overlaps with major antigenic sites and constantly evolves. In this study, we observe that mutations G186D and D190N in the hemagglutinin receptor-binding site have coevolved in two recent human H3N2 clades. X-ray crystallography results show that these mutations coordinately drive the evolution of the hemagglutinin receptor binding mode. Epistasis between G186D and D190N is further demonstrated by glycan binding and thermostability analyses. Immunization and neutralization experiments using mouse and human samples indicate that the evolution of receptor binding mode is accompanied by a change in antigenicity. Besides, combinatorial mutagenesis reveals that G186D and D190N, along with other natural mutations in recent H3N2 strains, alter the compatibility with a common egg-adaptive mutation in seasonal influenza vaccines. Overall, our findings elucidate the role of epistasis in shaping the recent evolution of human H3N2 hemagglutinin and substantiate the high evolvability of its receptor-binding mode.

MAIVeSS: streamlined selection of antigenically matched, high-yield viruses for seasonal influenza vaccine production

Vaccines are the main pharmaceutical intervention used against the global public health threat posed by influenza viruses. Timely selection of optimal seed viruses with matched antigenicity between vaccine antigen and circulating viruses and with high yield underscore vaccine efficacy and supply, respectively. Current methods for selecting influenza seed vaccines are labor intensive and time-consuming. Here, we report the Machine-learning Assisted Influenza VaccinE Strain Selection framework, MAIVeSS, that enables streamlined selection of naturally circulating, antigenically matched, and high-yield influenza vaccine strains directly from clinical samples by using molecular signatures of antigenicity and yield to support optimal candidate vaccine virus selection. We apply our framework on publicly available sequences to select A(H1N1)pdm09 vaccine candidates and experimentally confirm that these candidates have optimal antigenicity and growth in cells and eggs. Our framework can potentially reduce the optimal vaccine candidate selection time from months to days and thus facilitate timely supply of seasonal vaccines.

Continued adaptation of A/H2N2 viruses during pandemic circulation in humans

Influenza A viruses of the H2N2 subtype sparked a pandemic in 1957 and circulated in humans until 1968. Because A/H2N2 viruses still circulate in wild birds worldwide and human population immunity is low, the transmissibility of six avian A/H2N2 viruses was investigated in the ferret model. None of the avian A/H2N2 viruses was transmitted between ferrets, suggesting that their pandemic risk may be low. The transmissibility, receptor binding preference and haemagglutinin (HA) stability of human A/H2N2 viruses were also investigated. Human A/H2N2 viruses from 1957 and 1958 bound to human-type α2,6-linked sialic acid receptors, but the 1958 virus had a more stable HA, indicating adaptation to replication and spread in the new host. This increased stability was caused by a previously unknown stability substitution G205S in the 1958 H2N2 HA, which became fixed in A/H2N2 viruses after 1958. Although individual substitutions were identified that affected the HA receptor binding and stability properties, they were not found to have a substantial effect on transmissibility of A/H2N2 viruses via the air in the ferret model. Our data demonstrate that A/H2N2 viruses continued to adapt during the first year of pandemic circulation in humans, similar to what was previously shown for the A/H1N1pdm09 virus.

Quantitative proteomics of differentiated primary bronchial epithelial cells from chronic obstructive pulmonary disease and control identifies potential novel host factors post-influenza A virus infection

Background

Chronic obstructive pulmonary disease (COPD) collectively refers to chronic and progressive lung diseases that cause irreversible limitations in airflow. Patients with COPD are at high risk for severe respiratory symptoms upon influenza virus infection. Airway epithelial cells provide the first-line antiviral defense, but whether or not their susceptibility and response to influenza virus infection changes in COPD have not been elucidated. Therefore, this study aimed to compare the susceptibility of COPD- and control-derived airway epithelium to the influenza virus and assess protein changes during influenza virus infection by quantitative proteomics.

Materials and methods

The presence of human- and avian-type influenza A virus receptor was assessed in control and COPD lung sections as well as in fully differentiated primary human bronchial epithelial cells (phBECs) by lectin- or antibody-based histochemical staining. PhBECs were from COPD lungs, including cells from moderate- and severe-stage diseases, and from age-, sex-, smoking, and history-matched control lung specimens. Protein profiles pre- and post-influenza virus infection in vitro were directly compared using quantitative proteomics, and selected findings were validated by qRT-PCR and immunoblotting.

Results

The human-type influenza receptor was more abundant in human airways than the avian-type influenza receptor, a property that was retained in vitro when differentiating phBECs at the air-liquid interface. Proteomics of phBECs pre- and post-influenza A virus infection with A/Puerto Rico/8/34 (PR8) revealed no significant differences between COPD and control phBECs in terms of flu receptor expression, cell type composition, virus replication, or protein profile pre- and post-infection. Independent of health state, a robust antiviral response to influenza virus infection was observed, as well as upregulation of several novel influenza virus-regulated proteins, including PLSCR1, HLA-F, CMTR1, DTX3L, and SHFL.

Conclusion

COPD- and control-derived phBECs did not differ in cell type composition, susceptibility to influenza virus infection, and proteomes pre- and post-infection. Finally, we identified novel influenza A virus-regulated proteins in bronchial epithelial cells that might serve as potential targets to modulate the pathogenicity of infection and acute exacerbations.

Serial Passaging of Seasonal H3N2 Influenza A/Singapore/G2-31.1/2014 Virus in MDCK-SIAT1 Cells and Primary Chick Embryo Cells Generates HA D457G Mutation and Other Variants in HA, NA, PB1, PB1-F2, and NS1

Influenza remains one of the most prevalent viruses circulating amongst humans and has resulted in several pandemics. The prevention and control of H3N2 influenza is complicated by its propensity for evolution, which leads to vaccine mismatch and reduced vaccine efficacies. This study employed the strategy of serial passaging to compare the evolution of the human seasonal influenza strain A/Singapore/G2-31.1/2014(H3N2) in MDCK-SIAT1 versus primary chick embryo fibroblast (CEF) cells. Genetic analysis of the HA, NS1, NA, and PB1 gene segments by Sanger sequencing revealed the presence of specific mutations and a repertoire of viral quasispecies following serial passaging. Most quasispecies were also found in PB1, which exhibited consistently high transversion-to-transition ratios in all five MDCK-SIAT1 passages. Most notably, passage 5 virus harbored the D457G substitution in the HA2 subunit, while passage 3 virus acquired K53Q and Q69H mutations in PB1-F2. An A971 variant leading to a non-synonymous R316Q substitution in PB1 was also identified in MDCK-SIAT1 passages 2 and 4. With an increasing number of passages, the proportion of D457G mutations progressively increased and was associated with larger virus plaque sizes. However, microneutralization assays revealed no significant differences in the neutralizing antibody profiles of human-influenza-immune serum samples against pre-passaged virus and passage 5 virus. In contrast, viable virus was only detected in passage 1 of CEF cells, which gave rise to multiple viral RNA quasispecies. Our findings highlight that serial passaging is able to drive differential adaptation of H3N2 influenza in different host species and may alter viral virulence. More studies are warranted to elucidate the complex relationships between H3N2 virus evolution, viral virulence changes, and low vaccine efficacy.

Egg-adaptive mutations of human influenza H3N2 virus are contingent on natural evolution

Egg-adaptive mutations in influenza hemagglutinin (HA) often emerge during the production of egg-based seasonal influenza vaccines, which contribute to the largest share in the global influenza vaccine market. While some egg-adaptive mutations have minimal impact on the HA antigenicity (e.g. G186V), others can alter it (e.g. L194P). Here, we show that the preference of egg-adaptive mutation in human H3N2 HA is strain-dependent. In particular, Thr160 and Asn190, which are found in many recent H3N2 strains, restrict the emergence of L194P but not G186V. Our results further suggest that natural amino acid variants at other HA residues also play a role in determining the preference of egg-adaptive mutation. Consistently, recent human H3N2 strains from different clades acquire different mutations during egg passaging. Overall, these results demonstrate that natural mutations in human H3N2 HA can influence the preference of egg-adaptation mutation, which has important implications in seed strain selection for egg-based influenza vaccine.

Characterization and Immunogenicity of Influenza H7N9 Vaccine Antigens Produced Using a Serum-Free Suspension MDCK Cell-Based Platform

Human infections with avian-origin H7N9 influenza A viruses were first reported in China, and an approximately 38% human mortality rate was described across six waves from February 2013 to September 2018. Vaccination is one of the most cost-effective ways to reduce morbidity and mortality during influenza epidemics and pandemics. Egg-based platforms for the production of influenza vaccines are labor-intensive and unable to meet the surging demand during pandemics. Therefore, cell culture-based technology is becoming the alternative strategy for producing influenza vaccines. The current influenza H7N9 vaccine virus (NIBRG-268), a reassortant virus from A/Anhui/1/2013 (H7N9) and egg-adapted A/PR/8/34 (H1N1) viruses, could grow efficiently in embryonated eggs but not mammalian cells. Moreover, a freezing-dry formulation of influenza H7N9 vaccines with long-term stability will be desirable for pandemic preparedness, as the occurrence of influenza H7N9 pandemics is not predictable. In this study, we adapted a serum-free anchorage-independent suspension Madin-Darby Canine Kidney (MDCK) cell line for producing influenza H7N9 vaccines and compared the biochemical characteristics and immunogenicity of three influenza H7N9 vaccine antigens produced using the suspension MDCK cell-based platform without freeze-drying (S-WO-H7N9), the suspension MDCK cell-based platform with freeze-drying (S-W-H7N9) or the egg-based platform with freeze-drying (E-W-H7N9). We demonstrated these three vaccine antigens have comparable biochemical characteristics. In addition, these three vaccine antigens induced robust and comparable neutralizing antibody (NT; geometric mean between 1016 and 4064) and hemagglutinin-inhibition antibody (HI; geometric mean between 640 and 1613) titers in mice. In conclusion, the serum-free suspension MDCK cell-derived freeze-dried influenza H7N9 vaccine is highly immunogenic in mice, and clinical development is warranted.

Are pigs overestimated as a source of zoonotic influenza viruses?

Background

Swine influenza caused by influenza A viruses (IAV) directly affects respiratory health and indirectly impairs reproduction rates in pigs causing production losses. In Europe, and elsewhere, production systems have intensified featuring fewer holdings but, in turn, increased breeding herd and litter sizes. This seems to foster swine IAV (swIAV) infections with respect to the entrenchment within and spread between holdings. Disease management of swine influenza is difficult and relies on biosecurity and vaccination measures. Recently discovered and widely proliferating forms of self-sustaining modes of swIAV infections in large swine holdings challenge these preventive concepts by generating vaccine-escape mutants in rolling circles of infection.

Main body

The most recent human IAV pandemic of 2009 rooted at least partly in IAV of porcine origin highlighting the zoonotic potential of swIAV. Pigs constitute a mixing vessel of IAV from different species including avian and human hosts. However, other host species such as turkey and quail but also humans themselves may also act in this way; thus, pigs are not essentially required for the generation of IAV reassortants with a multispecies origin. Since 1918, all human pandemic influenza viruses except the H2N2 virus of 1958 have been transmitted in a reverse zoonotic mode from human into swine populations. Swine populations act as long-term reservoirs of these viruses. Human-derived IAV constitute a major driver of swIAV epidemiology in pigs. Swine-to-human IAV transmissions occurred rarely and mainly sporadically as compared to avian-to-human spill-over events of avian IAV. Yet, new swIAV variants that harbor zoonotic components continue to be detected. This increases the risk that such components might eventually reassort into viruses with pandemic potential.

Conclusions

Domestic pig populations should not be globally stigmatized as the only or most important reservoir of potentially zoonotic IAV. The likely emergence from swine of the most recent human IAV pandemic in 2009, however, emphasized the principal risks of swine populations in which IAV circulate unimpededly. Implementation of regular and close-meshed IAV surveillance of domestic swine populations to follow the dynamics of swIAV evolution is clearly demanded. Improved algorithms for directly inferring zoonotic potential from whole IAV genome sequences as well as improved vaccines are still being sought.

Effects of Receptor Specificity and Conformational Stability of Influenza A Virus Hemagglutinin on Infection and Activation of Different Cell Types in Human PBMCs

Humans can be infected by zoonotic avian, pandemic and seasonal influenza A viruses (IAVs), which differ by receptor specificity and conformational stability of their envelope glycoprotein hemagglutinin (HA). It was shown that receptor specificity of the HA determines the tropism of IAVs to human airway epithelial cells, the primary target of IAVs in humans. Less is known about potential effects of the HA properties on viral attachment, infection and activation of human immune cells. To address this question, we studied the infection of total human peripheral blood mononuclear cells (PBMCs) and subpopulations of human PBMCs with well characterized recombinant IAVs differing by the HA and the neuraminidase (NA) but sharing all other viral proteins. Monocytes and all subpopulations of lymphocytes were significantly less susceptible to infection by IAVs with avian-like receptor specificity as compared to human-like IAVs, whereas plasmacytoid dendritic cells (pDCs) and myeloid dendritic cells were equally susceptible to IAVs with avian-like and human-like receptor specificity. This tropism correlated with the surface expression of 2-3-linked sialic acids (avian-type receptors) and 2-6-linked sialic acids (human-type receptors). Despite a reduced infectivity of avian-like IAVs for PBMCs, these viruses were not less efficient than human-like IAVs in terms of cell activation as judged by the induction of cellular mRNA of IFN-α, CCL5, RIG-I, and IL-6. Elevated levels of IFN-α mRNA were accompanied by elevated IFN-α protein secretion in primary human pDC. We found that high basal expression in monocytes of antiviral interferon-induced transmembrane protein 3 (IFITM3) limited viral infection in these cells. siRNA-mediated knockdown of IFITM3 in monocytes demonstrated that viral sensitivity to inhibition by IFITM3 correlated with the conformational stability of the HA. Our study provides new insights into the role of host- and strain-specific differences of HA in the interaction of IAVs with human immune cells and advances current understanding of the mechanisms of viral cell tropism, pathogenesis and markers of virulence.

Lectin Staining to Detect Human and Avian Influenza Virus Receptors in the Airway of Nonhuman Primates

Hemagglutinin (HA) on the surface of influenza viruses binds to sialic acids, mainly N-acetylneuraminic acid (Neu5Ac) or N-glycolylneuraminic acid. Neu5Ac and N-glycolylneuraminic acid lie at the terminal end of sugar chains on the cell surface. Human influenza viruses preferentially bind to sialic acids bound to galactose by the alpha2-6 linkage (Neu5Acα2-6Gal), abundant in the human airway. In contrast, avian influenza viruses preferentially bind to Neu5Acα2-3Gal, abundant in the intestine of ducks. Sambucus nigra lectin (SNA) and Maackia amurensis lectin (MAA) bind to Neu5Acα2-6Gal and Neu5Acα2-3Gal, respectively. These two lectins have therefore been applied to detect sialic acids on the airway epithelium of animals.

Mucin-mimetic glycan arrays integrating machine learning for analyzing receptor pattern recognition by influenza A viruses

Influenza A viruses (IAVs) exploit host glycans in airway mucosa for entry and infection. Detection of changes in IAV glycan-binding phenotype can provide early indication of transmissibility and infection potential. While zoonotic viruses are monitored for mutations, the influence of host glycan presentation on viral specificity remains obscured. Here, we describe an array platform which uses synthetic mimetics of mucin glycoproteins to model how receptor presentation and density in the mucinous glycocalyx may impact IAV recognition. H1N1 and H3N2 binding in arrays of α2,3- and α2,6-sialyllactose receptors confirmed their known sialic acid-binding specificities and revealed their different sensitivities to receptor presentation. Further, the transition of H1N1 from avian to mammalian cell culture improved the ability of the virus to recognize mucin-like displays of α2,6-sialic acid receptors. Support vector machine (SVM) learning efficiently characterized this shift in binding preference and may prove useful to study viral evolution to a new host.

Comparative Susceptibility of Madin–Darby Canine Kidney (MDCK) Derived Cell Lines for Isolation of Swine Origin Influenza A Viruses from Different Clinical Specimens

Madin–Darby canine kidney (MDCK) cells are commonly used for the isolation of mammalian influenza A viruses. The goal of this study was to compare the sensitivity and suitability of the original MDCK cell line in comparison with MDCK-derived cell lines, MDCK.2, MDCK SIAT-1 and MDCK-London for isolation of swine-origin influenza A viruses (IAV-S) from clinical specimens. One-hundred thirty clinical specimens collected from pigs in the form of nasal swabs, lung tissue and oral fluids that were positive by PCR for the presence of IAV-S RNA were inoculated in the cell cultures listed above. MDCK-SIAT1 cells yielded the highest proportion of positive IAV-S isolations from all specimen types. For nasal swabs, 58.62% of the specimens were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (36.21%), and conventional MDCK and MDCK.2 cells (27.5%). For lung specimens, 59.38% were IAV-S positive in MDCK-SIAT1 cells, followed by MDCK-London (40.63%), and conventional MDCK and MDCK.2 cells (18.75–31.25%). Oral fluids yielded the lowest number of positive virus isolation results, but MDCK-SIAT1 cells were still had the highest rate (35%) of IAV-S isolation, whereas the isolation rate in other cells ranged from 5–7.5%. Samples with lower IAV-S PCR cycle threshold (Ct) values were more suitable for culturing and isolation. The isolated IAV-S represented H1N1-β, H1N2-α, H1N1pdm and H3N2 cluster IV and cluster IVB viruses. The result of the current study demonstrated the importance of using the most appropriate MDCK cells when isolating IAV-S from clinical samples.

Sulfated glycans containing NeuAcα2-3Gal facilitate the propagation of human H1N1 influenza A viruses in eggs

When human influenza viruses are isolated and passaged in chicken embryos, variants with amino acid substitutions around the receptor binding site of hemagglutinin (HA) are selected; however, the mechanisms that underlie this phenomenon have yet to be elucidated. Here, we analyzed the receptor structures that contributed to propagation of egg-passaged human H1N1 viruses. The analysis included seasonal and 2009 pandemic strains, both of which have amino acid substitutions of HA found in strains isolated or passaged in eggs. These viruses exhibited high binding to sulfated glycans containing NeuAcα2-3Gal. In MDCK cells overexpressing the sulfotransferase that synthesize Galβ1-4(SO3--6)GlcNAc, production of human H1N1 viruses was increased up to 90-fold. Furthermore, these sulfated glycans were expressed on the allantoic and amniotic membranes of chicken embryos. These results suggest that 6-sulfo sialyl Lewis X and/or NeuAcα2-3Galβ1-4(SO3--6)GlcNAc are involved in efficient propagation of human H1N1 viruses in chicken embryos.

Evaluation of Multivalent Sialylated Polyglycerols for Resistance Induction in and Broad Antiviral Activity against Influenza A Viruses

The development of multivalent sialic acid-based inhibitors active against a variety of influenza A virus (IAV) strains has been hampered by high genetic and structural variability of the targeted viral hemagglutinin (HA). Here, we addressed this challenge by employing sialylated polyglycerols (PGs). Efficacy of prototypic PGs was restricted to a narrow spectrum of IAV strains. To understand this restriction, we selected IAV mutants resistant to a prototypic multivalent sialylated PG by serial passaging. Resistance mutations mapped to the receptor binding site of HA, which was accompanied by altered receptor binding profiles of mutant viruses as detected by glycan array analysis. Specifying the inhibitor functionalization to 2,6-α-sialyllactose (SL) and adjusting the linker yielded a rationally designed inhibitor covering an extended spectrum of inhibited IAV strains. These results highlight the importance of integrating virological data with chemical synthesis and structural data for the development of sialylated PGs toward broad anti-influenza compounds.

Dynamics of influenza A (avian influenza) virus in poultry in the Greater Accra region of Ghana amongst the production levels

This research explores, through active surveillance, influenza A prevalence at different production levels in the Greater Accra region of Ghana, a study area with previous outbreak of highly pathogenic avian influenza H5N1 virus. The prevalence of influenza A was determined by rtRTPCR. This was achieved by screening 2040 samples comprising tracheal and cloacal swabs from chicken, ducks, pigeons, guinea fowls, and turkeys. Influenza A prevalence by production levels and species was computed at 95% confidence interval (CI) using the exact binomial interval. Structured questionnaires were also administered to 50 randomly selected poultry traders in the live bird markets. The overall influenza A prevalence was 7.7% (95% CI, 6.6, 8.9). Live bird market recorded 13.5% (n = 139, 95% CI, 11.5, 15.7), backyard poultry was 1.4% (95% CI, 0.6, 2.7), and commercial poultry 2.4% (95% CI, 1.2, 4.3). There was evidence of influenza A in all the poultry species sampled except for turkey. Subtyping of the M-gene has revealed the circulation of H9 in the three production levels. Live bird market has demonstrated high prevalence coupled with low level of biosecurity consciousness among the poultry operators. This is suggestive of live bird market serving as a potential basket for genetic reassortment with unpredictable future consequences.

The effect of single amino acid substitution at position 220 in the hemagglutinin glycoprotein on avian influenza H7N9 candidate vaccine virus

Influenza vaccines represent the most effective preventive strategy to control influenza virus infections; however, adaptive mutations frequently occur in the hemagglutinin (HA) glycoprotein during the preparation of candidate vaccine virus and production of vaccine in embryonated eggs. In our previous study, we constructed candidate vaccine virus (HA-R) to match the highly pathogenic avian influenza H7N9 viruses A/Guangdong/17SF003/2016 as part of a pandemic preparedness program. However, mixed amino acids (R, G, and I) were presented at position 220 (H3 numbering) in HA during passage in embryonated eggs. The residue at position 220 is located close to the receptor-binding site and the biological characteristics of this site remain to be elucidated. Therefore, in this study, using reverse genetics, we constructed two viruses carrying the single substitution in position 220 of HA (HA-G and HA-I) and evaluated the biological effects of substitution (R with G/I) on receptor binding, neuraminidase (NA) activity, growth characteristics, genetic stability, and antigenicity. The results revealed both mutant viruses exhibited lower HA binding affinities to two receptor types (sialic acid in alpha2,3- and alpha2,6-linkage to galactose, P < 0.001) and significant better growth characteristics compared to HA-R in two cells. Moreover, under similar NA enzymatic activity, the two mutant viruses eluted more easily from agglutinated erythrocytes than HA-R. Collectively, these results implied the balance of HA and NA in mutant viruses was a stronger determinant of viral growth than the individual amino acid in the HA position 220 in HA-R without strong binding between HA and sialylated receptors. Importantly, both the substitutions conferred altered antigenicity to the mutant viruses. In conclusion, amino acid substitutions at position 220 can substantially influence viral biological properties.

Influenza Hemagglutinin Structures and Antibody Recognition

Hemagglutinin (HA) is most abundant glycoprotein on the influenza virus surface. Influenza HA promotes viral entry by engaging the receptor and mediating virus-host membrane fusion. At the same time, HA is the major antigen of the influenza virus. HA antigenic shift can result in pandemics, whereas antigenic drift allows human circulating strains to escape herd immunity. Most antibody responses against HA are strain-specific. However, antibodies that have neutralizing activities against multiple strains or even subtypes have now been discovered and characterized. These broadly neutralizing antibodies (bnAbs) target conserved regions on HA, such as the receptor-binding site and the stem domain. Structural studies of such bnAbs have provided important insight into universal influenza vaccine and therapeutic design. This review discusses the HA functions as well as HA-antibody interactions from a structural perspective.

Quadrivalent cell culture influenza virus vaccine. Comparison to egg-derived vaccine

Influenza virus infections pose a serious public health problem and vaccination is the most effective public health intervention against them. The current manufacture of influenza vaccines in embryonated chicken eggs entails significant limitations. These limitations have been overcome by producing vaccines in cell culture, which allow a faster and more flexible response to potential pandemic threats. Given the impact of influenza B virus on disease burden, the availability of quadrivalent vaccines is useful for increasing the rate of protection from disease. This paper analyzes the limitations of the current production of influenza vaccine in eggs and the advantages of vaccines developed in cell culture, as well as their safety, tolerability, efficacy and effectiveness. Additionally, we reflect on the contribution of new quadrivalent vaccines from cell culture as an alternative in seasonal vaccination campaigns against influenza.

Challenges of Making Effective Influenza Vaccines

Seasonal influenza vaccines prevent influenza-related illnesses, hospitalizations, and deaths. However, these vaccines are not as effective as other viral vaccines, and there is clearly room for improvement. Here, we review the history of seasonal influenza vaccines, describe challenges associated with producing influenza vaccine antigens, and discuss the inherent difficulties of updating influenza vaccine strains each influenza season. We argue that seasonal influenza vaccines can be dramatically improved by modernizing antigen production processes and developing models that are better at predicting viral evolution. Resources should be specifically dedicated to improving seasonal influenza vaccines while developing entirely new vaccine platforms.

Chronic exposure to arsenite enhances influenza virus infection in cultured cells

Arsenic is a ubiquitous environmental toxicant that has been associated with human respiratory diseases. In humans, arsenic exposure has been associated with increased risk of respiratory infection. Considering the existing epidemiological evidence and the well-established impact of arsenic on epithelial cell biology, we posited that the effect of arsenic exposure in epithelial cells could enhance viral infection. In this study, we characterized influenza virus A/WSN/33 (H1N1) infection in Madin-Darby Canine Kidney (MDCK) cells chronically exposed to low levels of sodium arsenite (75 ppb). We observed a 27.3-fold increase in viral matrix (M2) protein (24 hours postinfection [p.i.]), a 1.35-fold increase in viral mRNA levels, and a 126% increase in plaque area in arsenite-exposed MDCK cells (48 hours p.i.). Arsenite exposure resulted in 114% increase in virus attachment-positive cells (2 hours p.i.) and 224% increase in α-2,3 sialic acid-positive cells. Interestingly, chronic exposure to arsenite reduced the effect of the antiviral drug, oseltamivir in MDCK cells. We also found that exposure to sodium arsenite resulted in a 4.4-fold increase in viral mRNA levels and significantly increased cytotoxicity in influenza A/Udorn/72 (H3N2) infected BEAS-2B cells. This study suggests that chronic arsenite exposure could result in enhanced influenza infection in epithelial cells, and that this may be mediated through increased sialic acid binding. Finally, the decreased effectiveness of the anti-influenza drug, oseltamivir, in arsenite-exposed cells raises substantial public health concerns if this effect translates to arsenic-exposed, influenza-infected people.

Better influenza vaccines: an industry perspective

Vaccination is the most effective measure at preventing influenza virus infections. However, current seasonal influenza vaccines are only protective against closely matched circulating strains. Even with extensive monitoring and annual reformulation our efforts remain one step behind the rapidly evolving virus, often resulting in mismatches and low vaccine effectiveness. Fortunately, many next-generation influenza vaccines are currently in development, utilizing an array of innovative techniques to shorten production time and increase the breadth of protection. This review summarizes the production methods of current vaccines, recent advances that have been made in influenza vaccine research, and highlights potential challenges that are yet to be overcome. Special emphasis is put on the potential role of glycoengineering in influenza vaccine development, and the advantages of removing the glycan shield on influenza surface antigens to increase vaccine immunogenicity. The potential for future development of these novel influenza vaccine candidates is discussed from an industry perspective.

Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus

Purpose

When influenza viruses are cultured in eggs, amino acid mutations of the hemagglutinin may occur through egg adaptation. On the other hand, when influenza viruses are cultured in animal cells, no antigenic mutation occurs unlike in eggs. Therefore, we examined whether the antigenic mutations actually occurred after passage of H3N2 (A/Texas/50/2012) virus up to 15 times in eggs and MDCK-Sky3851 cells.

Materials and Methods

Prototype A/Texas/50/2012 (H3N2) influenza virus which was isolated from clinical patient, not passaged in egg, was obtained and propagated using the specific pathogen free egg and the MDCK-Sky3851 cell line up to 15 passage, and the changes in the antigen sequence of the influenza viruses were confirmed by gene sequencing and protein structure analysis.

Results

In term of the hemagglutination titer of influenza virus, the reactivity to chicken and guinea pig red blood cell showed different results between egg propagated and cell propagated viruses. In the sequence analysis results for hemagglutinin and neuraminidase, no antigenic mutation was observed throughout all passages when cultured in MDCK-Sky3851 cells. On the other hand, mutations occurred in three amino acid sequences (H156R, G186S, S219F) in hemagglutinin up to 15 passages when cultured in eggs.

Conclusion

H3N2 influenza virus cultured in eggs could lead mutations in amino acid sequence of hemagglutinin, distinct from the corresponding virus cultured in cells for which no antigenic mutation was observed. These findings suggest that cell culture is a more stable and effective way of production with lower risk of antigenic mutations for the manufacture of influenza vaccines.

Extinction and emergence of genomic haplotypes during the evolution of Avian coronavirus in chicken embryos

Avian coronavirus (AvCoV) is ubiquitously present on poultry as a multitude of virus lineages. Studies on AvCoV phenotypic traits are dependent on the isolation of field strains in chicken embryonated eggs, but the mutant spectrum on each isolate is not considered. This manuscript reports the previously unknown HTS (high throughput sequencing)-based complete genome haplotyping of AvCoV isolates after passages of two field strains in chicken embryonated eggs. For the first and third passages of strain 23/2013, virus loads were 6.699 log copies/ μL and 6 log copies/ μL and, for 38/2013, 5.699 log copies/μL and 2.699 log copies/μL of reaction, respectively. The first passage of strain 23/2013 contained no variant haplotype, while, for the third passage, five putative variant haplotypes were found, with > 99.9% full genome identity with each other and with the dominant genome. Regarding strain 38/2013, five variant haplotypes were found for the first passage, with > 99.9% full genome identity with each other and with the dominant genome, and a single variant haplotype was found. Extinction and emergence of haplotypes with polymorphisms in genes involved in receptor binding and regulation of RNA synthesis were observed, suggesting that phenotypic traits of AvCoV isolates are a result of their mutant spectrum.

Preparation and Detection of Glycan-Binding Activity of Influenza Virus

We describe a method to detect influenza virus using an evanescent-field-activated fluorescence scanner type glycan array and ELISA system. Neoglycoprotein was prepared by combination of organic chemistry and biomaterial preparation. These ligands were spotted on a glass plate or plastic well to make a glycan array and ELISA plate. We detected cultured influenza virus using glycan array and ELISA. Then, we showed that the neoglycoprotein binds to Cy3-labeled hemagglutinins (H1 and H5), a NeuAcα2,6LacNAc or NeuAcα2,3LacNAc recognized protein, as detected.

Isolation of Swine Influenza A Virus in Cell Cultures and Embryonated Chicken Eggs

Influenza virus isolation is a procedure to obtain a live and infectious virus that can be used for antigenic characterization, pathogenesis investigation, vaccine production, and so on. Embryonated chicken egg inoculation is traditionally considered the "gold standard" method for influenza virus isolation and propagation. However, many primary cells and continuous cell lines have also been examined or developed for influenza virus isolation and replication. Specifically, influenza A virus in swine (IAV-S) isolation and propagation has been attempted and compared in embryonated chicken eggs, some primary porcine cells, and a number of continuous cell lines. Currently, Madin-Darby canine kidney (MDCK) cells remain the most commonly used cell line for the isolation, propagation, and titration of IAV-S. Virus isolation in embryonated chicken eggs or in different cell lines offers alternative approaches when IAV-S isolation in MDCK cells is unsuccessful. Optimal specimens for IAV-S isolation includes nasal swabs, nasopharyngeal swabs, oral fluids, bronchoalveolar lavage, lung tissues, and so on. In this chapter, we describe the procedures of sample processing, IAV-S isolation in MDCK cells and in embryonated chicken eggs, as well as the methods used for confirming the virus isolation results.

Madin-Darby canine kidney cell sialic acid receptor modulation induced by culture medium conditions: Implications for the isolation of influenza A virus

BACKGROUND

The influenza A virus (IAV) binds to α-2,3- and α-2,6-linked sialic acid (SA) receptors expressed by Madin-Darby canine kidney (MDCK) cells. The receptor distribution may therefore be important in regulating IAV propagation. Serum-free medium (SFM) avoids variability in conventional culture medium containing fetal bovine serum (FBS), which can have variable composition and may contain endotoxins. However, little is known about the distribution of SA receptors on cells maintained in SFM.

OBJECTIVES

We assessed the influence of culture media on MDCK cell SA receptor distribution along with the effect of SA receptor distribution on IAV recovery. We hypothesized that SFM would increase the proportion of α-2,6-linked SA receptors present and alter isolate recovery.

METHODS

Madin-Darby canine kidney cells were cultured in medium containing FBS and two SFMs. Cell surface distribution of α-2,6- and α-2,3-linked receptors was determined using flow cytometry. Recovery of swine- and avian-lineage IAVs from MDCK cells maintained in each medium was quantified as TCID50 .

RESULTS

Madin-Darby canine kidney cells cultured in UltraMDCK SFM expressed both SA receptors and supported the growth of both swine- and avian-lineage IAVs. Cells maintained in other medium inconsistently expressed each receptor and the avian IAV grew to lower titers in cells cultured with FBS.

CONCLUSIONS

Medium conditions altered the distribution of SA receptors present on MDCK cells and affected IAV recovery. Culture in UltraMDCK SFM resulted in cells expressing both receptors and IAVs grew to higher titers than in the other culture condition, indicating that this medium may be useful for culturing IAV from multiple species.

A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses

The circulating avian influenza A(H7N9) has caused recurrent epidemic waves with high mortality in China since 2013, in which the alarming fifth wave crossing 2016 and 2017 was highlighted by a large number of human infections and the emergence of highly pathogenic avian influenza (HPAI) A(H7N9) strains in human cases. We generated low-pathogenic reassortant CVVs derived from the emerging A(H7N9) with improved virus replication and protein yield in both MDCK cells and eggs by introducing a single substitution, G218E, into HA, which was associated with reducing HA receptor binding and subsequently balancing HA-NA functions. The in vitro and in vivo experiments demonstrated comparable antigenicity of the G218E CVVs with that of their wild-type (WT) counterparts, and both the WT and the G218E CVVs fully protected ferrets from parental HPAI virus challenge. With high yield traits and the anticipated antigenicity, the G218E CVVs should benefit preparedness against the threat of an A(H7N9) influenza pandemic.

The potential avian influenza pandemic remains a threat to public health, as the avian-origin influenza A(H7N9) virus has caused more than 1,560 laboratory-confirmed human infections since 2013, with nearly 40% mortality. Development of low-pathogenic candidate vaccine viruses (CVVs) for vaccine production is essential for pandemic preparedness. However, the suboptimal growth of CVVs in mammalian cells and chicken eggs is often a challenge. By introducing a single adaptive substitution, G218E, into the hemagglutinin (HA), we generated reassortant A(H7N9)-G218E CVVs that were characterized by significantly enhanced growth in both cells and eggs. These G218E CVVs retained the original antigenicity, as determined by a hemagglutination inhibition assay, and effectively protected ferrets from lethal challenge with the highly pathogenic parental virus. We found that the suboptimal replication of the parental H7 CVVs was associated with impeded progeny virus release as a result of strong HA receptor binding relative to weak neuraminidase (NA) cleavage of receptors. In contrast, the G218E-mediated growth improvement was attributed to relatively balanced HA and NA functions, resulted from reduced HA binding to both human- and avian-type receptors, and thus facilitated NA-mediated virus release. Our findings revealed that a single amino acid mutation at residue 218 of the HA improved the growth of A(H7N9) influenza virus by balancing HA and NA functions, shedding light on an alternative approach for optimizing certain influenza CVVs.

IMPORTANCE The circulating avian influenza A(H7N9) has caused recurrent epidemic waves with high mortality in China since 2013, in which the alarming fifth wave crossing 2016 and 2017 was highlighted by a large number of human infections and the emergence of highly pathogenic avian influenza (HPAI) A(H7N9) strains in human cases. We generated low-pathogenic reassortant CVVs derived from the emerging A(H7N9) with improved virus replication and protein yield in both MDCK cells and eggs by introducing a single substitution, G218E, into HA, which was associated with reducing HA receptor binding and subsequently balancing HA-NA functions. The in vitro and in vivo experiments demonstrated comparable antigenicity of the G218E CVVs with that of their wild-type (WT) counterparts, and both the WT and the G218E CVVs fully protected ferrets from parental HPAI virus challenge. With high yield traits and the anticipated antigenicity, the G218E CVVs should benefit preparedness against the threat of an A(H7N9) influenza pandemic.

Semiaquatic mammals might be intermediate hosts to spread avian influenza viruses from avian to human

Avian influenza A viruses (AIVs) can occasionally transmit to mammals and lead to the development of human pandemic. A species of mammal is considered as a mixing vessel in the process of host adaptation. So far, pigs are considered as a plausible intermediate host for the generation of human pandemic strains, and are labelled ‘mixing vessels’. In this study, through the analysis of two professional databases, the Influenza Virus Resource of NCBI and the Global Initiative on Sharing Avian Influenza Data (GISAID), we found that the species of mink (Neovison vison) can be infected by more subtypes of influenza A viruses with considerably higher α-diversity related indices. It suggested that the semiaquatic mammals (riverside mammals), rather than pigs, might be the intermediate host to spread AIVs and serve as a potential mixing vessel for the interspecies transmission among birds, mammals and human. In epidemic areas, minks, possibly some other semiaquatic mammals as well, could be an important sentinel species for influenza surveillance and early warning.

Severe cases of seasonal influenza in Russia in 2017-2018

The 2017-2018 influenza epidemic season in Russia was characterized by a relatively low morbidity and mortality. We evaluated herd immunity prior to the 2017-2018 influenza season in hemagglutination inhibition assay, and performed characterization of influenza viruses isolated from severe or fatal influenza cases and from influenza cases in people vaccinated in the fall of 2017. During the 2017-2018 epidemic season, 87 influenza A and B viruses were isolated and viruses of the 75 influenza cases, including selected viral isolates and viruses analyzed directly from the original clinical material, were genetically characterized. The analyzed A(H1N1)pdm09 viruses belonged to clade 6B.1, B/Yamagata-like viruses belonged to clade 3, and B/Victoria-like viruses belonged to clade 1A and they were antigenically similar to the corresponding vaccine strains. A(H3N2) viruses belonged to clade 3C.2a and were difficult to characterize antigenically and the analysis indicated antigenic differences from the corresponding egg-grown vaccine strain. The next generation sequencing revealed the presence of D222/G/N polymorphism in the hemagglutinin gene in 32% of the analyzed A(H1N1)pdm09 lethal cases. This study demonstrated the importance of monitoring D222G/N polymorphism, including detection of minor viral variants with the mutations, in the hemagglutinin gene of A(H1N1)pdm09 for epidemiological surveillance. One strain of influenza virus A(H1N1)pdm09 was resistant to oseltamivir and had the H275Y amino acid substitution in the NA protein. All other isolates were susceptible to NA inhibitors. Prior to the 2017-2018 epidemic season, 67.4 million people were vaccinated, which accounted for 46.6% of the country's population. Just before the epidemic season 33-47% and 24-30% of blood sera samples collected within the territory of Russia showed the presence of protective antibody titers against vaccine strains of influenza A and influenza B/Victoria-like, respectively. Mass vaccination of the population had evidently reduced the severity of the flu epidemic during the 2017-2018 influenza epidemic season in Russia.

Segment 2 from influenza A(H1N1) 2009 pandemic viruses confers temperature-sensitive haemagglutinin yield on candidate vaccine virus growth in eggs that can be epistatically complemented by PB2 701D

Candidate vaccine viruses (CVVs) for seasonal influenza A virus are made by reassortment of the antigenic virus with an egg-adapted strain, typically A/Puerto Rico/8/34 (PR8). Many 2009 A(H1N1) pandemic (pdm09) high-growth reassortants (HGRs) selected this way contain pdm09 segment 2 in addition to the antigenic genes. To investigate this, we made CVV mimics by reverse genetics (RG) that were either 6 : 2 or 5 : 3 reassortants between PR8 and two pdm09 strains, A/California/7/2009 (Cal7) and A/England/195/2009, differing in the source of segment 2. The 5 : 3 viruses replicated better in MDCK-SIAT1 cells than the 6 : 2 viruses, but the 6 : 2 CVVs gave higher haemagglutinin (HA) antigen yields from eggs. This unexpected phenomenon reflected temperature sensitivity conferred by pdm09 segment 2, as the egg HA yields of the 5 : 3 viruses improved substantially when viruses were grown at 35 °C compared with 37.5 °C, whereas the 6 : 2 virus yields did not. However, the authentic 5 : 3 pdm09 HGRs, X-179A and X-181, were not markedly temperature sensitive despite their PB1 sequences being identical to that of Cal7, suggesting compensatory mutations elsewhere in the genome. Sequence comparisons of the PR8-derived backbone genes identified polymorphisms in PB2, NP, NS1 and NS2. Of these, PB2 N701D affected the temperature dependence of viral transcription and, furthermore, improved and drastically reduced the temperature sensitivity of the HA yield from the 5 : 3 CVV mimic. We conclude that the HA yield of pdm09 CVVs can be affected by an epistatic interaction between PR8 PB2 and pdm09 PB1, but that this can be minimized by ensuring that the backbones used for vaccine manufacture in eggs contain PB2 701D.

Diagnostic challenges in influenza

In 2018 there are still microbiology laboratories that do not subtype or detect influenza viruses, one of the main agents of community-acquired pneumonia. A major challenge is to introduce multiplex-type technologies into most clinical virological diagnostic laboratories, increasing the feasibility of timely etiological diagnosis of influenza and other respiratory viruses whenever required and thus limiting antibiotic treatments. Other diagnostic tools such as markers of severity and the detection of resistance are pending challenges to complete and expand. Viral culture, an essential tool in the epidemiological surveillance of viruses, has been relegated by more sensitive and affordable molecular techniques. Sequencing of the influenza virus together with the antigenic characterisation and detection techniques of antibodies against hemagglutinin and neuraminidase will, in future, be used in tandem with other techniques to detect antibodies against other structural proteins, helping to elucidate the complicated epidemiology of these viruses and the production of new vaccines and their evaluation. Supplement information: This article is part of a supplement entitled «SEIMC External Quality Control Programme. Year 2016», which is sponsored by Roche, Vircell Microbiologists, Abbott Molecular and Francisco Soria Melguizo, S.A. © 2019 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosasy Microbiología Clínica. All rights reserved.

Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus

An H9N2 avian influenza A virus (AIV), A/chicken/Korea/01310/2001 (01310-CE20), was established after 20 passages of influenza A/chicken/Korea/01310/2001 (01310-CE2) virus through embryonated chicken eggs (ECEs). As a result of this process, the virus developed highly replicative and pathogenic traits within the ECEs through adaptive mutations in hemagglutinin (HA: T133N, V216G, and E439D) and neuraminidase (NA: 18-amino acid deletion and E54D). Here, we also established that 01310-CE20 acquired resistance to innate inhibitors present in the egg white during these passages. To investigate the role of egg-adapted mutations in resistance to innate inhibitors, we generated four PR8-derived recombinant viruses using various gene combinations of HA and NA from 01310-CE2 and 01310-CE20 (rH₂N₂, rH₂N₂₀, rH₂₀N₂, and rH₂₀N₂₀). As expected, rH₂₀N₂₀ showed significantly higher replication efficiency in MDCK cells and mouse lungs, and demonstrated greater pathogenicity in mice. In addition, rH₂₀N₂₀ showed higher resistance to innate inhibitors than the other viruses. By using a loss-of-function mutant and receptor-binding assay, we demonstrated that a T133N site directed mutation created an additional N-glycosite at position 133 in rH₂₀N₂₀. Further, this mutation played a crucial role in viral replication and resistance to innate inhibitors by modulating the binding affinities to avian-like and mammalian-like receptors on the host cells and inhibitors. Thus, egg-adapted HA and NA may exacerbate the mammalian pathogenicity of AIVs by defying host innate inhibitors as well as by increasing replication efficiency in mammalian cells.

Intra-seasonal antibody repertoire analysis of a subject immunized with an MF59®-adjuvanted pandemic 2009 H1N1 vaccine

During the height of the 2009 H1N1 swine-derived influenza pandemic, a clinical trial was conducted in which seven subjects were immunized using a monovalent, MF59®-adjuvanted vaccine, developed from an egg-passaged candidate vaccine virus (CVV), A/California/07/2009 X-181. Whole blood was collected prior to immunization and at 8, 22, and 202 days post-vaccination, and subjects' serological responses were evaluated. Here, we reconstruct and examine the longitudinal, influenza-specific circulating B cell repertoire of one subject in that study. Genotypic analysis of 390 total subject-derived antibodies (Abs) revealed a total of 29 germline genes in use among immunoglobulin heavy chain variable regions (IgHV), with the majority of those sequences isolated representing memory recall responses and two major lineages dominating the early response. In vitro phenotyping showed a diverse set of binding epitopes on the surface glycoproteins hemagglutinin (HA) and neuraminidase (NA), many of which are considered subdominant. Strong correlations were found between IgHV germline usage among non-related lineages and both binding epitope and neutralization breadth. Results here highlight the potential for Ab responses to be misdirected to egg-adaptive artifacts on CVVs while simultaneously stressing the ability to mount potent, broadly neutralizing responses to mostly novel antigens via recall of subdominant memory responses, as well as the need for evaluating alternative endpoint assays and anti-NA responses following clinical trials.

Discrimination of Avian Influenza Virus Subtypes using Host-Cell Infection Fingerprinting by a Sulfinate-based Fluorescence Superoxide Probe

The current gold-standard diagnosis method for avian influenza (AI) is an embryonic egg-based hemagglutination assay followed by immunoblotting or PCR sequencing to confirm subtypes. It requires, however, specialized facilities to handle egg inoculation and incubation, and the subtyping methods relied on costly reagents. Now, the first differential sensing approach to distinguish AI subtypes is demonstrated using series of cell lines and a fluorescent sensor. Susceptibility of AI virus differs depending on genetic backgrounds of host cells. Cells were examined from different organ origins, and the infection patterns against a panel of cells were utilized for AI virus subtyping. To quantify AI infection, a highly cell-permeable fluorescent superoxide sensor was designed to visualize infection. This differential sensing strategy successfully proved discriminations of AI subtypes and demonstrated as a useful primary screening platform to monitor a large number of samples.

Influenza Virus: A Master Tactician in Innate Immune Evasion and Novel Therapeutic Interventions

Influenza is a contagion that has plagued mankind for many decades, and continues to pose concerns every year, with millions of infections globally. The frequent mutations and recombination of the influenza A virus (IAV) cast a looming threat that antigenically novel strains/subtypes will rise with unpredictable pathogenicity and fear of it evolving into a pandemic strain. There have been four major influenza pandemics, since the beginning of twentieth century, with the great 1918 pandemic being the most severe, killing more than 50 million people worldwide. The mechanisms of IAV infection, host immune responses, and how viruses evade from such defensive responses at the molecular and structural levels have been greatly investigated in the past 30 years. While this has advanced our understanding of virus–host interactions and human immunology, and has led to the development of several antiviral drugs, they have minimal impact on the clinical outcomes of infection. The heavy use of these drugs has also imposed selective pressure on IAV to evolve and develop resistance. Vaccination remains the cornerstone of public health efforts to protect against influenza; however, rapid mass-production of sufficient vaccines is unlikely to occur immediately after the beginning of a pandemic. This, therefore, requires novel therapeutic strategies against this continually emerging infectious virus with higher specificity and cross-reactivity against multiple strains/subtypes of IAVs. This review discusses essential virulence factors of IAVs that determine sustainable human-to-human transmission, the mechanisms of viral hijacking of host cells and subversion of host innate immune responses, and novel therapeutic interventions that demonstrate promising antiviral properties against IAV. This hopefully will promote discussions and investigations on novel avenues of prevention and treatment strategies of influenza, that are effective and cross-protective against multiple strains/subtypes of IAV, in preparation for the advent of future IAVs and pandemics.

The S190R mutation in the hemagglutinin protein of pandemic H1N1 2009 influenza virus increased its pathogenicity in mice

Human influenza viruses preferentially bind to sialic acid-α2,6-galactose (SAα2,6Gal) receptors, which are predominant in human upper respiratory epithelia, whereas avian influenza viruses preferentially bind to SAα2,3Gal receptors. However, variants with amino acid substitutions around the receptor-binding sites of the hemagglutinin (HA) protein can be selected after several passages of human influenza viruses from patients' respiratory samples in the allantoic cavities of embryonated chicken eggs. In this study, we detected an egg-adapted HA S190R mutation in the pandemic H1N1 virus 2009 (pdmH1N1), and evaluated the effects of this mutation on receptor binding affinity and pathogenicity in mice. Our results revealed that residue 190 is located within the pocket structure of the receptor binding site. The single mutation to arginine at position 190 slightly increased the binding affinity of the virus to the avian receptor and decreased its binding to the long human α2,6-linked sialic acid receptor. Our study demonstrated that the S190R mutation resulted in earlier death and higher weight loss in mice compared with the wild-type virus. Higher viral titers at 1 dpi (days post infection) and diffuse damage at 4 dpi were observed in the lung tissues of mice infected with the mutant virus.

A Y161F Hemagglutinin Substitution Increases Thermostability and Improves Yields of 2009 H1N1 Influenza A Virus in Cells

Vaccination is the primary strategy for influenza prevention and control. However, egg-based vaccines, the predominant production platform, have several disadvantages, including the emergence of viral antigenic variants that can be induced during egg passage. These limitations have prompted the development of cell-based vaccines, which themselves are not without issue. Most importantly, vaccine seed viruses often do not grow efficiently in mammalian cell lines. Here we aimed to identify novel high-yield signatures for influenza viruses in continuous Madin-Darby canine kidney (MDCK) and Vero cells. Using influenza A(H1N1)pdm09 virus as the testing platform and an integrating error-prone PCR-based mutagenesis strategy, we identified a Y161F mutation in hemagglutinin (HA) that not only enhanced the infectivity of the resultant virus by more than 300-fold but also increased its thermostability without changing its original antigenic properties. The vaccine produced from the Y161F mutant fully protected mice against lethal challenge with wild-type A(H1N1)pdm09. Compared with A(H1N1)pdm09, the Y161F mutant had significantly higher avidity for avian-like and human-like receptor analogs. Of note, the introduction of the Y161F mutation into HA of seasonal H3N2 influenza A virus (IAV) and canine H3N8 IAV also increased yields and thermostability in MDCK cells and chicken embryotic eggs. Thus, residue F161 plays an important role in determining viral growth and thermostability, which could be harnessed to optimize IAV vaccine seed viruses.IMPORTANCE Although a promising complement to current egg-based influenza vaccines, cell-based vaccines have one large challenge: high-yield vaccine seeds for production. In this study, we identified a molecular signature, Y161F, in hemagglutinin (HA) that resulted in increased virus growth in Madin-Darby canine kidney and Vero cells, two cell lines commonly used for influenza vaccine manufacturing. This Y161F mutation not only increased HA thermostability but also enhanced its binding affinity for α2,6- and α2,3-linked Neu5Ac. These results suggest that a vaccine strain bearing the Y161F mutation in HA could potentially increase vaccine yields in mammalian cell culture systems.

Propagation and Titration of Influenza Viruses

Influenza viruses are constantly circulating among humans, in which they cause seasonal epidemics of severe respiratory disease. Additionally, these zoonotic viruses infect different mammals and birds, from which new antigenic variants are occasionally transmitted to humans leading to devastating global pandemics. Surveillance programs, in which viruses from the main reservoir (waterfowl), intermediate hosts (like pigs and other farm animals), and other affected species are isolated and characterized, are crucial for the global influenza prevention strategy. This chapter gives an overview of the most commonly used methods for the propagation and titration of influenza viruses, which are key steps in surveillance procedures, as well as in vaccine development and basic research. Depending on the host and the viral strain, primary isolates are obtained from biological samples of different origin and subsequently amplified in embryonated chicken eggs or cell cultures. These propagation procedures are the focus of the first part of this chapter. Once the initial isolates have been amplified, virus titration methods based on particular characteristics of influenza viruses, such as their ability to agglutinate red blood cells (RBCs) or to induce cytopathic effects (CPE) in cell monolayers, are used to estimate the amount of viral particles. Such approaches, like the hemagglutination assay (HA assay), 50% tissue culture infectious dose (TCID50), or plaque assay, are included in the second part of this chapter. Although they are simple and cost-effective, some of these techniques have been partially replaced by faster and more sensitive methods based on the quantification of viral genomes, such as the quantitative real-time reverse transcription PCR (RT-qPCR), which is presented at the end of this section. The different protocols are explained in detail in order to facilitate the preparation and quantification of infectious virus stocks.

A structural explanation for the low effectiveness of the seasonal influenza H3N2 vaccine

The effectiveness of the annual influenza vaccine has declined in recent years, especially for the H3N2 component, and is a concern for global public health. A major cause for this lack in effectiveness has been attributed to the egg-based vaccine production process. Substitutions on the hemagglutinin glycoprotein (HA) often arise during virus passaging that change its antigenicity and hence vaccine effectiveness. Here, we characterize the effect of a prevalent substitution, L194P, in egg-passaged H3N2 viruses. X-ray structural analysis reveals that this substitution surprisingly increases the mobility of the 190-helix and neighboring regions in antigenic site B, which forms one side of the receptor binding site (RBS) and is immunodominant in recent human H3N2 viruses. Importantly, the L194P substitution decreases binding and neutralization by an RBS-targeted broadly neutralizing antibody by three orders of magnitude and significantly changes the HA antigenicity as measured by binding of human serum antibodies. The receptor binding mode and specificity are also altered to adapt to avian receptors during egg passaging. Overall, these findings help explain the low effectiveness of the seasonal vaccine against H3N2 viruses, and suggest that alternative approaches should be accelerated for producing influenza vaccines as well as isolating clinical isolates.

Seasonal influenza vaccine does not always confer protection in vaccinated individuals. Vaccine candidates are selected from clinical isolates based on their antigenic properties. It is common to use chicken eggs for culturing clinical isolates and for large-scale production of vaccines. However, influenza virus often mutates to adapt to being grown in chicken eggs, which can influence antigenicity and hence vaccine effectiveness. Here, we structurally characterize an egg-adaptive substitution, namely L194P, in H3N2 virus hemagglutinin. Our results reveal that the L194P substitution substantially increases the flexibility of an epitope region that is commonly targeted by antibodies. Based on the binding affinity of a broadly neutralizing antibody and a panel of human serum antibodies, we further show that the L194P substitution dramatically changes the HA antigenicity. The change of the receptor-binding mode associated with the L194P substitution provides an explanation for its ability to successfully grow in eggs. Our study describes a mechanism for the low influenza vaccine effectiveness and reaffirms the urgency for replacing the egg-based production of influenza vaccines.

Distribution of O-Acetylated Sialic Acids among Target Host Tissues for Influenza Virus

Sialic acids (Sias) are important glycans displayed on the cells and tissues of many different animals and are frequent targets for binding and modification by pathogens, including influenza viruses. Influenza virus hemagglutinins bind Sias during the infection of their normal hosts, while the encoded neuraminidases and/or esterases remove or modify the Sia to allow virion release or to prevent rebinding. Sias naturally occur in a variety of modified forms, and modified Sias can alter influenza virus host tropisms through their altered interactions with the viral glycoproteins. However, the distribution of modified Sia forms and their effects on pathogen-host interactions are still poorly understood. Here we used probes developed from viral Sia-binding proteins to detect O-acetylated (4-O-acetyl, 9-O-acetyl, and 7,9-O-acetyl) Sias displayed on the tissues of some natural or experimental hosts for influenza viruses. These modified Sias showed highly variable displays between the hosts and tissues examined. The 9-O-acetyl (and 7,9-) modified Sia forms were found on cells and tissues of many hosts, including mice, humans, ferrets, guinea pigs, pigs, horses, dogs, as well as in those of ducks and embryonated chicken egg tissues and membranes, although in variable amounts. The 4-O-acetyl Sias were found in the respiratory tissues of fewer animals, being primarily displayed in the horse and guinea pig, but were not detected in humans or pigs. The results suggest that these Sia variants may influence virus tropisms by altering and selecting their cell interactions. IMPORTANCE Sialic acids (Sias) are key glycans that control or modulate many normal cell and tissue functions while also interacting with a variety of pathogens, including many different viruses. Sias are naturally displayed in a variety of different forms, with modifications at several positions that can alter their functional interactions with pathogens. In addition, Sias are often modified or removed by enzymes such as host or pathogen esterases or sialidases (neuraminidases), and Sia modifications can alter those enzymatic activities to impact pathogen infections. Sia chemical diversity in different hosts and tissues likely alters the pathogen-host interactions and influences the outcome of infection. Here we explored the display of 4-O-acetyl, 9-O-acetyl, and 7,9-O-acetyl modified Sia forms in some target tissues for influenza virus infection in mice, humans, birds, guinea pigs, ferrets, swine, horses, and dogs, which encompass many natural and laboratory hosts of those viruses.

Rapid screening for specific glycosylation and pathogen interactions on a 78 species avian egg white glycoprotein microarray

There is an urgent need for discovery of novel antimicrobials and carbohydrate-based anti-adhesive strategies are desirable as they may not promote resistance. Discovery of novel anti-adhesive molecules from natural product libraries will require the use of a high throughput screening platform. Avian egg white (EW) provides nutrition for the embryo and protects against infection, with glycosylation responsible for binding certain pathogens. In this study, a microarray platform of 78 species of avian EWs was developed and profiled for glycosylation using a lectin panel with a wide range of carbohydrate specificities. The dominating linkages of sialic acid in EWs were determined for the first time using the lectins MAA and SNA-I. EW glycosylation similarity among the different orders of birds did not strictly depend on phylogenetic relationship. The interactions of five strains of bacterial pathogens, including Escherichia coli, Staphylococcus aureus and Vibrio cholera, identified a number of EWs as potential anti-adhesives, with some as strain- or species-specific. Of the two bacterial toxins examined, shiga-like toxin 1 subunit B bound to ten EWs with similar glycosylation more intensely than pigeon EW. This study provides a unique platform for high throughput screening of natural products for specific glycosylation and pathogen interactions. This platform may provide a useful platform in the future for discovery of anti-adhesives targeted for strain and species specificity.

Distinct susceptibility and applicability of MDCK derivatives for influenza virus research

Madin-Darby Canine Kidney (MDCK) cells are widely utilized as a substrate for influenza virus isolation and propagation due to the high yields of virus. Here we compared the conventional MDCK cell line, MDCK-SIAT1 and MDCK-London for viral production, cell survival, and suitability in testing antivirals using six influenza strains including two H1N1 (pandemic and epidemic strains), three H3N2 and one influenza B strain. Overall our results suggest that MDCK-London cell line is superior for virus culturing and quantification, and hence an ideal platform to evaluate antiviral drug efficacy against multiple strains of influenza. Our data also suggests that while virus titers determined by the hemagglutination assay (HA) and neuraminidase activity (NA) are widely used to indicate viral load, there is a poor correlation between these measurements and the infectious titer obtained by plaque assay.

Pathogenicity and transmission of triple reassortant H3N2 swine influenza A viruses is attenuated following Turkey embryo propagation

Genetic lineages of swine influenza A viruses (SIVs) have recently been established in Turkeys in the United States. To identify molecular determinants that are involved in virulence and transmission of SIVs to Turkeys, we sequentially passaged two triple reassortant H3N2 SIV isolates from Minnesota in ten day old specific-pathogen free (SPF) Turkey embryos and tested them in seven-day old Turkey poults. We found that SIV replication in Turkey embryos led to minimal mutations in and around the receptor binding and antigenic sites of the HA molecule, while other gene segments were unchanged. The predominant changes associated with Turkey embryo passage were A223V, V226A and T248I mutations in the receptor-binding and glycosylation sites of the HA molecule. Furthermore, Turkey embryo propagation altered receptor specificity in SIV strain 07-1145. Embryo passaged 07-1145 virus showed a decrease in α2, 6 sialic acid receptor binding compared to the wild type virus. Intranasal infection of wild type SIVs in one-week-old Turkey poults resulted in persistent diarrhea and all the infected birds seroconverted at ten days post infection. The 07-1145 wild type virus also transmitted to age matched in-contact birds introduced one-day post infection. Turkeys infected with embryo passaged viruses displayed no clinical signs and were not transmitted to in-contact poults. Our results suggest that Turkey embryo propagation attenuates recent TR SIVs for infectivity and transmission in one week old Turkeys. Our findings will have important implications in identifying molecular determinants that control the transmission and virulence of TR SIVs in Turkeys and other species.

Influenza immunization elicits antibodies specific for an egg-adapted vaccine strain

For broad protection against infection by viruses such as influenza or HIV, vaccines should elicit antibodies that bind conserved viral epitopes, such as the receptor-binding site (RBS). RBS-directed antibodies have been described for both HIV and influenza virus, and the design of immunogens to elicit them is a goal of vaccine research in both fields. Residues in the RBS of influenza virus hemagglutinin (HA) determine a preference for the avian or human receptor, α-2,3-linked sialic acid and α-2,6-linked sialic acid, respectively. Transmission of an avian-origin virus between humans generally requires one or more mutations in the sequences encoding the influenza virus RBS to change the preferred receptor from avian to human, but passage of a human-derived vaccine candidate in chicken eggs can select for reversion to avian receptor preference. For example, the X-181 strain of the 2009 new pandemic H1N1 influenza virus, derived from the A/California/07/2009 isolate and used in essentially all vaccines since 2009, has arginine at position 226, a residue known to confer preference for an α-2,3 linkage in H1 subtype viruses; the wild-type A/California/07/2009 isolate, like most circulating human H1N1 viruses, has glutamine at position 226. We describe, from three different individuals, RBS-directed antibodies that recognize the avian-adapted H1 strain in current influenza vaccines but not the circulating new pandemic 2009 virus; Arg226 in the vaccine-strain RBS accounts for the restriction. The polyclonal sera of the three donors also reflect this preference. Therefore, when vaccines produced from strains that are never passaged in avian cells become widely available, they may prove more capable of eliciting RBS-directed, broadly neutralizing antibodies than those produced from egg-adapted viruses, extending the established benefits of current seasonal influenza immunizations.

Cellular Microbiology of Mycoplasma canis

Mycoplasma canis can infect many mammalian hosts but is best known as a commensal or opportunistic pathogen of dogs. The unexpected presence of M. canis in brains of dogs with idiopathic meningoencephalitis prompted new in vitro studies to help fill the void of basic knowledge about the organism's candidate virulence factors, the host responses that it elicits, and its potential roles in pathogenesis. Secretion of reactive oxygen species and sialidase varied quantitatively (P < 0.01) among strains of M. canis isolated from canine brain tissue or mucosal surfaces. All strains colonized the surface of canine MDCK epithelial and DH82 histiocyte cells and murine C8-D1A astrocytes. Transit through MDCK and DH82 cells was demonstrated by gentamicin protection assays and three-dimensional immunofluorescence imaging. Strains further varied (P < 0.01) in the extents to which they influenced the secretion of tumor necrosis factor alpha (TNF-α) and the neuroendocrine regulatory peptide endothelin-1 by DH82 cells. Inoculation with M. canis also decreased major histocompatibility complex class II (MHC-II) antigen expression by DH82 cells (P < 0.01), while secretion of gamma interferon (IFN-γ), interleukin-6 (IL-6), interleukin-10 (IL-10), and complement factor H was unaffected. The basis for differences in the responses elicited by these strains was not obvious in their genome sequences. No acute cytopathic effects on any homogeneous cell line, or consistent patterns of M. canis polyvalent antigen distribution in canine meningoencephalitis case brain tissues, were apparent. Thus, while it is not likely a primary neuropathogen, M. canis has the capacity to influence meningoencephalitis through complex interactions within the multicellular and neurochemical in vivo milieu.

Antigenic characterization of influenza viruses produced using synthetic DNA and novel backbones

The global system for manufacturing seasonal influenza vaccines has been developed to respond to the natural evolution of influenza viruses, but the problem of antigenic mismatch continues to be a challenge in certain years. In some years, mismatches arise naturally due to the antigenic drift of circulating viruses after vaccine strain selection has already been made. In other years, antigenic differences between the vaccine virus and circulating viruses are introduced as part of the current system, which relies on the use of egg-adapted isolates as a starting material for candidate vaccine viruses (CVVs). Improving the current process for making vaccine viruses can provide great value. We have previously established a synthetic approach for rapidly generating influenza viruses in a vaccine-approved Madin Darby canine kidney (MDCK) cell line using novel, high-growth backbones that increase virus rescue efficiency and antigen yield. This technology also has the potential to produce viruses that maintain antigenic similarity to the intended reference viruses, depending on the hemagglutinin (HA) and neuraminidase (NA) sequences used for gene synthesis. To demonstrate this utility, we generated a panel of synthetic viruses using HA and NA sequences from recent isolates and showed by hemagglutination inhibition (HI) tests that all synthetic viruses were antigenically-like their conventional egg- or cell-propagated reference strains and there was no impact of the novel backbones on antigenicity. This synthetic approach can be used for the efficient production of CVVs that may be more representative of circulating viruses and may be used for both egg- and cell-based vaccine manufacturing platforms. When combined with mammalian cell culture technology for antigen production, synthetic viruses generated using HA and NA sequences from a non-egg-adapted prototype can help to reduce the potential impact of antigenic differences between vaccine virus and circulating viruses on vaccine effectiveness.

Expression of interferon-inducible transmembrane proteins in the chicken and possible role in prevention of viral infections

In mammals, interferon-inducible transmembrane proteins (IFITMs) prevent infections by various enveloped viruses. The expression of IFITMs in chicken was herein examined in the adult and embryonic organs using a quantitative reverse-transcription-polymerase chain reaction. The results obtained revealed that IFITM3 was expressed at a higher level than IFITM1, 2 and 5, in both embryonic and adult organs. However, the expression levels of IFITMs in embryonic organs were less than 5 % of those in adult lungs. Among the embryonic tissues examined, primordial germ cells (PGCs) at day 2.5 expressed relatively higher levels of IFITM3. IFITM3 expression levels were 1.5-fold higher in the chicken cell line DF-1 than in PGCs. The knockdown of IFITM3 in DF-1 cells by siRNA increased the infectivity of a vesicular stomatitis virus G protein-pseudotyped lentiviral vector, suggesting that lower levels of IFITM3 are still sufficient to restrict this viral vector.

Analyses of chicken sialyltransferases related to O-glycosylation

The chicken β-galactoside α2,3-sialyltransferase 1, 2, and 5 (ST3Gal1, 2, and 5) genes were cloned, and their enzymes were expressed in 293FT cells. ST3Gal1 and 2 exhibited enzymatic activities toward galactose-β1,3-N-acetylgalactosamine and galactose-β1,3-N-acetylglucosamine. ST3Gal5 only exhibited activity toward lactosylceramide. ST3Gal1 and 2 and previously cloned ST3Gal3 and 6 transferred CMP-sialic acid to asialofetuin. Reverse-transcription-quantitative PCR indicated that ST3Gal1 was expressed at higher levels in the trachea, lung, spleen, and magnum, and the strong expression of ST3Gal5 was observed in the spleen, magnum, and small and large intestines. ST3Gal1, 5, and 6 were also expressed in the tubular gland cells of the magnum, which secretes egg-white proteins. ST3Gal1, 5, and 6 were expressed in the egg chorioallantoic membrane, in which influenza viruses are propagated for the production of vaccines.