Influenza virus infects the human population worldwide and causes acute respiratory disease. Currently, the primary strategy for preventing influenza is seasonal vaccination which is capable of providing protection in most populations. However, seasonal vaccines are less efficacious to immunize the elderly and poorly induce cross-protective immunity against the reassorted pandemic virus in the recipients. Neuraminidase (NA) inhibitors have also been widely utilized to limit disease outcome. The currently used NA inhibitors, nonetheless, generate the drug-resistant progeny viruses; moreover, they are unable to directly target the host immune responses which cause immunopathology in severe cases. Therefore, new strategies that provide more effective immunogenicity, cross-protection and therapies against influenza infection must be developed. In this thesis, the adjuvanticity of CpG oligodeoxynucleotide (ODN), type I interferon (IFN) and Complete Freund’s adjuvant (CFA) when coadministered with seasonal influenza vaccines in ferrets is presented. It has been found that the adjuvanted vaccines are efficacious to induce neutralizing antibody responses. Several common and distinguished signaling pathways leading to dendritic cell (DC) maturation and B cell activation have been discovered from their adjuvanticity. Furthermore, it was determined that seasonal H1N1 prior infection more effectively induces cross-protection against the newly emerged 2009 pandemic H1N1 (H1N1pdm) virus in ferrets and mice than the seasonal vaccines. The prior infection-induced cross-reactive but non-neutralizing antibodies are capable of providing substantial protection in the H1N1pdm infected mice when CD8 T cells are absent. Lastly, function of different vaccine adjuvants for controlling H1N1pdm infection in mice has been investigated. Unlike other adjuvants, CFA is capable of protecting the mice from infection through enhancement of Treg cell suppressive molecules galectin-1 and CTLA-4 which downregulated DC costimulation and effector T cell responses. Overall, this thesis has provided novel mechanistic insights for developing protective strategies against influenza infection.

Influenza virus infects the human population worldwide and causes acute respiratory disease. Currently, the primary strategy for preventing influenza is seasonal vaccination which is capable of providing protection in most populations. However, seasonal vaccines are less efficacious to immunize the elderly and poorly induce cross-protective immunity against the reassorted pandemic virus in the recipients. Neuraminidase (NA) inhibitors have also been widely utilized to limit disease outcome. The currently used NA inhibitors, nonetheless, generate the drug-resistant progeny viruses; moreover, they are unable to directly target the host immune responses which cause immunopathology in severe cases. Therefore, new strategies that provide more effective immunogenicity, cross-protection and therapies against influenza infection must be developed. In this thesis, the adjuvanticity of CpG oligodeoxynucleotide (ODN), type I interferon (IFN) and Complete Freund’s adjuvant (CFA) when coadministered with seasonal influenza vaccines in ferrets is presented. It has been found that the adjuvanted vaccines are efficacious to induce neutralizing antibody responses. Several common and distinguished signaling pathways leading to dendritic cell (DC) maturation and B cell activation have been discovered from their adjuvanticity. Furthermore, it was determined that seasonal H1N1 prior infection more effectively induces cross-protection against the newly emerged 2009 pandemic H1N1 (H1N1pdm) virus in ferrets and mice than the seasonal vaccines. The prior infection-induced cross-reactive but non-neutralizing antibodies are capable of providing substantial protection in the H1N1pdm infected mice when CD8 T cells are absent. Lastly, function of different vaccine adjuvants for controlling H1N1pdm infection in mice has been investigated. Unlike other adjuvants, CFA is capable of protecting the mice from infection through enhancement of Treg cell suppressive molecules galectin-1 and CTLA-4 which downregulated DC costimulation and effector T cell responses. Overall, this thesis has provided novel mechanistic insights for developing protective strategies against influenza infection.

Le génome des virus influenza de type A est composé de huit segments de gènes (ARNv) de polarité négative retrouvés sous la forme de complexes ribonucléiques (RNPv). L'incorporation sélective des huit RNPv dans les particules virales néosynthétisées se fait par un mécanisme moléculaire qui fait intervenir des signaux d'encapsidation dites « région de packaging ». Nous avons montré que les segments de gènes interagissaient entre eux via des interactions de type ARN/ARN permettant la formation d'un réseau d'interactions. Nous avons de plus montré que les régions de packaging décrites dans la littérature semblent héberger les régions impliquées dans la mise en place du réseau d'interactions. Cette étude a été réalisée pour le virus humain H3N2 et le virus aviaire H5N2. Le mécanisme d'incorporation sélective des segments de gènes semble également réguler le réassortiment génétique, processus génétique responsable de l'émergence de virus réassortants. Nous avons montré qu'une restriction génomique impliquant les régions de packaging semble être responsable du taux de réassortiment génétique faible observé in-vitro et in-vivo. La modulation du réseau d'interactions ARN/ARN semble être nécessaire pour l'incorporation de segments aviaire dans le fond génétique du virus humain. Pour finir, nous avons montré que la composition génomique des virus réassortants vaccinaux joue un rôle central dans la réplication virale et dans la production des antigènes vaccinaux. Par une stratégie de cryo-microscopie, nous avons montré que la protéine PB1 joue un rôle central dans l'optimisation de la production des antigènes de surface / The genome of the influenza A virus (IAV) comprises eight single-stranded negativesense RNA segments (vRNAs). All eight vRNAs are selectively packaged into each progeny virion via packaging signal sequences that are located at both ends of the vRNAs. How these signals ensure packaging of all eight vRNAs remains unclear. It was hypothesized that selective packaging might be driven by direct interactions between vRNAs. Combination of biochemical and reverse genetic approaches allowed us to identify short nucleotide regions on vRNAs interacting with each other in vitro. Here, we demonstrated the importance of these interactions in the packaging process of the human H3N2 and avian H5N2 viral genomes. Furthermore, our results suggest that the packaging process could regulate genetic reassortment. Indeed, we observed that the genetic reassortment between H3N2 and H5N2 viruses is restricted as the avian vRNA HA cannot be incorporated into the human genetic background. Our investigations indicated that (i) the packaging signals are crucial for genetic reassortment and (ii) the modulation of the vRNAs interaction network may be required for the incorporation of the avian HA gene into the human genetic background. Characterization of seed viruses showed that the genetic composition is important for both high growth ability and antigen production. Indeed, cryo-electronic microscopy observations of reassortant virus indicated that the PB1 gene can strongly influence the antigen glycoprotein spike density

Although seasonal influenza epidemics represent a significant threat to public health, their treatment options remain limited. With deaths from the 1918 influenza pandemic estimated at >50,000,000 worldwide and future pandemics predicted, the need for a potent broad-spectrum influenza therapy is critical. In this thesis, I describe the use of a structurally modified zanamivir, an influenza neuraminidase inhibitor that blocks the release of nascent virus, to deliver attached therapeutic agents specifically to the surfaces of viruses and virus-infected cells, leading to simultaneous inhibition of virus release and immune-mediated destruction of both free virus and virus-infected cells. Chapter 1 describes the major characteristics of the influenza virus, the morbidity and mortality associated with annual infections by current strains of the virus, and the treatments available to reduce the disease burden associated with these infections. Chapter 2 describes the design, synthesis, and evaluation of a zanamivir-related targeting ligand and its conjugation to two orthogonal imaging agents which are then used to characterize the binding specificity and biodistribution of the targeting ligand in influenza virus-infected cells and in infected mice. Chapter 3 describes the development of an influenza virus-targeted immunotherapy, where a zanamivir-targeted hapten is exploited to redirect the immune system to destroy influenza virus and virus-infected cells. When tested in vivo, this immunotherapy is shown to be significantly superior to zanamivir in protecting mice from lethal influenza virus infections. Finally, both a zanamivir-targeted chemotherapy and a CAR-T cell therapy with different mechanisms of cytotoxicity against neuraminidase expressing cells are introduced in Chapter 4.

Influenza is a severe disease in humans and animals, causing upwards of 40,000 deaths every year in America alone. Influenza A virus (IAV) also causes periodic pandemics every 10 to 50 years, killing millions of people. Despite this, very few effective therapies are available. All strains of IAV are prone to developing resistance to antibodies due to the high mutation rate in the viral genome. Because of this mutation rate, a yearly vaccine must be generated before every flu season, and efficacy varies year to year. IAV has also mutated to escape several of the clinically-approved small molecule inhibitors. A therapeutic agent that targets a highly conserved region of the virus could bypass resistance and also be effective against multiple strains of IAV. IAV attachment is mediated by many individually weak hemagglutinin–sialic acid interactions that all together make a strong attachment to a host cell. Polymerized sialic acid analogs can recreate these interactions and block infection. However, they are not ideal therapeutics due to solubility issues and in vivo toxicity. We used liposomes as a novel means for delivery of the sialic acid-containing glycan, sialylneolacto-N-tetraose c (LSTc). LSTcbearing decoy liposomes form multivalent, polymer-like interactions with IAV. Decoy liposomes competitively bind IAV in hemagglutination inhibition assays and inhibit infection of target cells in a dose-dependent manner. LSTc decoy liposomes co-localize with IAV, while control liposomes do not. Inhibition is specific, as inhibition of Sendai virus and respiratory syncytial virus is not observed. In contrast, monovalent LSTc does not bind IAV or inhibit infectivity. LSTc decoy liposomes prevent the spread of IAV during multiple rounds of replication in vitro and extend survival of mice challenged with a lethal dose of virus. Considering the conservation of the hemagglutinin binding pocket and the ability of decoy liposomes to form high-avidity interactions with IAV hemagglutinin, our decoy liposomes have potential as a new therapeutic agent against emerging strains.

While memory CD4 T cells are critical for effective immunity to pathogens, the mechanisms underlying their generation are poorly defined. Although extensive work has been done to examine the role of antigen (Ag) in shaping memory formation, most studies focus on the requirements during the first few days of the response known as the priming phase. Little is known about whether or not Ag re-encounter by effector T cells (late Ag) alters CD4 memory T cell formation. Since influenza infection produces a large, heterogeneous, protective CD4 memory T cell population, I used this model to examine the role of late Ag in promoting CD4 memory T cell formation. In the experiments presented in this thesis, I demonstrate that late Ag is required to rescue responding CD4 T cells from default apoptosis and to program the transition to long-lived memory. Responding cells that failed to re-encounter Ag had decreased memory marker expression and failed to produce multiple cytokines upon re-stimulation. Ag recognition is required at a defined stage, as short-term Ag presentation provided 6 days after infection is able to restore canonical memory formation even in the absence of viral infection. Finally, I find that memory CD4 T cell formation following cold-adapted influenza vaccination is boosted when Ag is administered at this stage. These findings imply that persistence of viral Ag presentation into the effector phase is the key factor that determines the efficiency of memory generation. They also suggest that administering Ag during the effector stage may improve vaccine efficacy.

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