Influenza is a contagious respiratory disease that has caused at least four pandemics and countless epidemics since the 20th century, impacted millions of people worldwide and the global economy. To date, the predominant influenza species circulating in humans are influenza A and B. Influenza may cause serious illness in all age groups but individuals such as the newborns and senior population whose immune systems are compromised are at higher risk for severe disease. Interestingly, during the outbreak of pandemic 2009 H1N1 (H1N1pdm), it was found that the elderly had the lowest hospitalization rate and an increased proportion of healthy adults developed severe disease. Furthermore, several clinical studies have demonstrated that most H1N1pdm infected children experienced mild to moderate illness and led to the least mortality. The difference of disease outcome in age groups between different influenza infections may be due to several factors, which include differing pathogenicity between the viruses, differential immune status and composition among the age groups, and pre-existing immunity from previous encounter(s) with a similar virus. Since the human clinical data are often complicated by secondary factors such as co-morbidities, I used the ferret model to address these questions. I first compared the clinical and pathological patterns among the pandemic and seasonal influenza strains and found H1N1pdm caused the most severe illness to healthy ferrets. Importantly, the disease severity did not correlate with viral burden but immunopathology. To study the age effect, I found that H1N1pdm infected young ferrets with mild clinical symptoms developed specialized ectopic lymphoid structures and a distinct cytokine expression profile in the lungs, which were absent in adult ferrets with severe illness. I also examined antigenic change in historical H1N1s and anti-H1 responses to explain the pre-existing immunity of H1N1pdm found in the elderly. However, low similarity was found between historical H1N1s and H1N1pdm. Lastly, I conducted a detailed influenza B comparative study. I observed the pathogenic B strain was capable to cause lower respiratory tract infection and pathology like the influenza A viruses. Overall, this thesis provides novel insights for developing therapeutic and prophylactic strategies against influenza infection.

Introdução: A Imunodeficiência Comum Variável (ICV) faz parte de um grupo de imunodeficiências primárias na qual os pacientes apresentam defeitos na maturação e diferenciação dos linfócitos B (LB), resultando em distúrbios funcionais além de alterações na distribuição de seus subtipos. Consequentemente, estes pacientes apresentam hipogamaglobulinemia, susceptibilidade a infecções e ausência de produção de anticorpos a antígenos específicos. Na tentativa de reduzir os episódios de infecções recorrentes, alguns trabalhos têm recomendado a vacinação com patógenos mortos ou subunidades e em trabalho anterior demonstramos a eficácia clínica da vacinação de pacientes com ICV, porém, a experiência com a administração de vacinas em imunocomprometidos é limitada. Objetivos: Avaliar a cinética da distribuição das subpopulações de linfócitos B antes e após a vacinação com antígenos proteicos e polissacarídicos em pacientes com ICV acompanhados no Ambulatório de Imunodeficiências Primárias do Hospital das Clínicas, FMUSP, além da produção de anticorpos específicos aos antígenos vacinais. Pacientes e Métodos: Um grupo de 35 pacientes com ICV e 16 controles foram vacinados contra Influenza, H1N1 e S. pneumoniae. Após as coletas nos tempos pré e pós 1, 3 e 6 meses foram realizados a separação de PBMC e cultura de linfócitos com lisado viral e hemaglutinina de Influenza, além da citometria de fluxo para identificação das subpopulações de LB naive, zona marginal (MZB), memória com troca de isotipo (SMB) e plasmoblastos (PBL). Foram dosados os anticorpos específicos e no grupo dos pacientes foi aplicado um score de sintomas antes e após a imunização. Resultados: Apesar da redução significativa na pontuação do score de sintomas, a maioria dos pacientes não produziu anticorpos específicos para Influenza, H1N1 e S. pneumoniae. A análise da cinética das subpopulações de LB revelou que em indivíduos saudáveis, a resposta contra Influenza apresentou duração de 6 meses, observada por meio da redução da subpopulação naive e aumento gradual da frequência de SMB a partir do primeiro mês. Observamos também redução da população de memória por volta do 3º mês, com aumento da população de PBL que permaneceu elevada até o 6º mês. Por outro lado, a despeito de os pacientes apresentarem aumento de SMB no primeiro mês após a vacinação, sua frequência foi inferior ao observado nos controles, decaindo ao terceiro mês. A população de PBL apresentou aumento precoce no primeiro mês após a vacinação, também muito menor do que observado nos controles, não sendo mantido no terceiro mês. Ainda, observamos uma correlação entre o aumento da expressão destas duas subpopulações no primeiro mês. Apenas a população de MZB apresentou aumento significativo no terceiro mês nos pacientes quando comparados aos controles. Ao dividirmos os pacientes de acordo com a expressão de SMB e PBL após 1 mês da administração das vacinas, observamos que os pacientes que apresentaram aumento na expressão de células B de memória foram os que exibiram uma melhora clínica mais expressiva, soroconverteram e desenvolveram soroproteção para H1N1.Conclusões: Apesar de não apresentarem eficaz diferenciação em células de memória e efetoras, resultando na resposta precoce e de curta duração, observamos que os pacientes foram capazes de reconhecer e responder às vacinas. Além disso, a elevada expressão de MZB no terceiro mês após a vacinação pode sugerir a atuação desta subpopulação na apresentação para os LT. Estes achados reforçam a necessidade de uma melhor compreensão da ativação do sistema imune em pacientes com ICV, para uma adequada subdivisão de acordo com o perfil de resposta após a vacinação / Introduction: Common Variable Immunodeficiency (CVID) is a primary antibody deficiency characterized by defects in B lymphocyte maturation, resulting in disturbed differentiation, distribution and functional variations on its subtypes. As a result , CVID patients have hypogammaglobulinemia and poor antibody response to specific antigens with increased susceptibility to infections. In an effort to minimize the recurrent episodes of infections, some studies have recommended immunization with inactivated pathogens or subunits and in a former study we have shown the clinical improvement determined by immunization in CVID patients, but the experience with vaccines\' administration to immunodeficient patients is limited. Objectives: To evaluate the changes in distribution of B cell subtypes before and after vaccination of CVID patients followed at the Division of Clinical Immunology and Allergy of University of São Paulo Medical School with protein and polysaccharide antigens, as well as specific antibody production . Methods: A group of 35 CVID patients and 16 controls were vaccinated against Influenza, H1N1 and S. pneumoniae vaccines. Blood samples were collected before and 1, 3 and 6 months post vaccination. PBMCs were stimulated with Influenza viral lysate and hemagglutinin peptide. Flow cytometry was performed to identify naïve B cells, marginal zone (MZB), switched memory B cells (SMB) and plasmablasts (PBL). Specific antibody production was measured and a symptoms score was applied for clinical evaluation before and after immunization. Results: In spite of the significant reduction in symptoms score after vaccination, most patients didn\'t produce specific antibodies to Influenza, H1N1 and S. pneumoniae. The analyzes of B cell subtypes changes in healthy individuals upon in vitro Influenza stimulation showed that the response endured up to 6 months post immunization. We observed a reduction in naïve B cell frequency while gradual increase in SMB frequency occurred already at 1 month after vaccination. Moreover, as the memory cell population declined, PBL population increased at the third month post vaccination until the sixth month. Although patients had an increase of SMB on the first month after vaccination, it was lower than that observed in controls, decreasing by the third month post vaccination. Plasmablast frequency had an early increase on the first month, also much lower than the observed in controls decreasing by the third month. In addition, we observed a correlation between the increased expression of SMB and PBL on the first month post vaccination. In patients, only MZB subtype presented a significant increase on the third month when compared to controls. We divided the patients according SMB and PBL expression after 1 month post vaccination and we observed that patients who were able to produce memory B cells showed a better clinical improvement, developed H1N1 seroconversion and seroprotection. Conclusion: Despite the defect on differentiation into memory and effector B cells resulting in early response with lowduration, we observed that patients were able to recognize and respond to vaccines. In addition, the over expression of MZB on the third month after vaccination may suggest the role of this subpopulation as an antigen presenting cell for T cells. These findings reinforce the need of a better understanding of immune system activation and response in CVID patients to propose a division according to vaccine (antigen) responders and non responders

Introdução: A Imunodeficiência Comum Variável (ICV) faz parte de um grupo de imunodeficiências primárias na qual os pacientes apresentam defeitos na maturação e diferenciação dos linfócitos B (LB), resultando em distúrbios funcionais além de alterações na distribuição de seus subtipos. Consequentemente, estes pacientes apresentam hipogamaglobulinemia, susceptibilidade a infecções e ausência de produção de anticorpos a antígenos específicos. Na tentativa de reduzir os episódios de infecções recorrentes, alguns trabalhos têm recomendado a vacinação com patógenos mortos ou subunidades e em trabalho anterior demonstramos a eficácia clínica da vacinação de pacientes com ICV, porém, a experiência com a administração de vacinas em imunocomprometidos é limitada. Objetivos: Avaliar a cinética da distribuição das subpopulações de linfócitos B antes e após a vacinação com antígenos proteicos e polissacarídicos em pacientes com ICV acompanhados no Ambulatório de Imunodeficiências Primárias do Hospital das Clínicas, FMUSP, além da produção de anticorpos específicos aos antígenos vacinais. Pacientes e Métodos: Um grupo de 35 pacientes com ICV e 16 controles foram vacinados contra Influenza, H1N1 e S. pneumoniae. Após as coletas nos tempos pré e pós 1, 3 e 6 meses foram realizados a separação de PBMC e cultura de linfócitos com lisado viral e hemaglutinina de Influenza, além da citometria de fluxo para identificação das subpopulações de LB naive, zona marginal (MZB), memória com troca de isotipo (SMB) e plasmoblastos (PBL). Foram dosados os anticorpos específicos e no grupo dos pacientes foi aplicado um score de sintomas antes e após a imunização. Resultados: Apesar da redução significativa na pontuação do score de sintomas, a maioria dos pacientes não produziu anticorpos específicos para Influenza, H1N1 e S. pneumoniae. A análise da cinética das subpopulações de LB revelou que em indivíduos saudáveis, a resposta contra Influenza apresentou duração de 6 meses, observada por meio da redução da subpopulação naive e aumento gradual da frequência de SMB a partir do primeiro mês. Observamos também redução da população de memória por volta do 3º mês, com aumento da população de PBL que permaneceu elevada até o 6º mês. Por outro lado, a despeito de os pacientes apresentarem aumento de SMB no primeiro mês após a vacinação, sua frequência foi inferior ao observado nos controles, decaindo ao terceiro mês. A população de PBL apresentou aumento precoce no primeiro mês após a vacinação, também muito menor do que observado nos controles, não sendo mantido no terceiro mês. Ainda, observamos uma correlação entre o aumento da expressão destas duas subpopulações no primeiro mês. Apenas a população de MZB apresentou aumento significativo no terceiro mês nos pacientes quando comparados aos controles. Ao dividirmos os pacientes de acordo com a expressão de SMB e PBL após 1 mês da administração das vacinas, observamos que os pacientes que apresentaram aumento na expressão de células B de memória foram os que exibiram uma melhora clínica mais expressiva, soroconverteram e desenvolveram soroproteção para H1N1.Conclusões: Apesar de não apresentarem eficaz diferenciação em células de memória e efetoras, resultando na resposta precoce e de curta duração, observamos que os pacientes foram capazes de reconhecer e responder às vacinas. Além disso, a elevada expressão de MZB no terceiro mês após a vacinação pode sugerir a atuação desta subpopulação na apresentação para os LT. Estes achados reforçam a necessidade de uma melhor compreensão da ativação do sistema imune em pacientes com ICV, para uma adequada subdivisão de acordo com o perfil de resposta após a vacinação / Introduction: Common Variable Immunodeficiency (CVID) is a primary antibody deficiency characterized by defects in B lymphocyte maturation, resulting in disturbed differentiation, distribution and functional variations on its subtypes. As a result , CVID patients have hypogammaglobulinemia and poor antibody response to specific antigens with increased susceptibility to infections. In an effort to minimize the recurrent episodes of infections, some studies have recommended immunization with inactivated pathogens or subunits and in a former study we have shown the clinical improvement determined by immunization in CVID patients, but the experience with vaccines\' administration to immunodeficient patients is limited. Objectives: To evaluate the changes in distribution of B cell subtypes before and after vaccination of CVID patients followed at the Division of Clinical Immunology and Allergy of University of São Paulo Medical School with protein and polysaccharide antigens, as well as specific antibody production . Methods: A group of 35 CVID patients and 16 controls were vaccinated against Influenza, H1N1 and S. pneumoniae vaccines. Blood samples were collected before and 1, 3 and 6 months post vaccination. PBMCs were stimulated with Influenza viral lysate and hemagglutinin peptide. Flow cytometry was performed to identify naïve B cells, marginal zone (MZB), switched memory B cells (SMB) and plasmablasts (PBL). Specific antibody production was measured and a symptoms score was applied for clinical evaluation before and after immunization. Results: In spite of the significant reduction in symptoms score after vaccination, most patients didn\'t produce specific antibodies to Influenza, H1N1 and S. pneumoniae. The analyzes of B cell subtypes changes in healthy individuals upon in vitro Influenza stimulation showed that the response endured up to 6 months post immunization. We observed a reduction in naïve B cell frequency while gradual increase in SMB frequency occurred already at 1 month after vaccination. Moreover, as the memory cell population declined, PBL population increased at the third month post vaccination until the sixth month. Although patients had an increase of SMB on the first month after vaccination, it was lower than that observed in controls, decreasing by the third month post vaccination. Plasmablast frequency had an early increase on the first month, also much lower than the observed in controls decreasing by the third month. In addition, we observed a correlation between the increased expression of SMB and PBL on the first month post vaccination. In patients, only MZB subtype presented a significant increase on the third month when compared to controls. We divided the patients according SMB and PBL expression after 1 month post vaccination and we observed that patients who were able to produce memory B cells showed a better clinical improvement, developed H1N1 seroconversion and seroprotection. Conclusion: Despite the defect on differentiation into memory and effector B cells resulting in early response with lowduration, we observed that patients were able to recognize and respond to vaccines. In addition, the over expression of MZB on the third month after vaccination may suggest the role of this subpopulation as an antigen presenting cell for T cells. These findings reinforce the need of a better understanding of immune system activation and response in CVID patients to propose a division according to vaccine (antigen) responders and non responders

A ce jour, les données génétiques et moléculaires se rapportant aux virus influenza de type A (VIs) présents dans la population porcine au Québec sont relativement rares. Pourtant, ces informations sont essentielles pour la compréhension de de l'évolution des VIs à grande échelle de 2011 à 2015. Afin de remédier à ce manque de données, différents échantillons (pulmonaires, salivaires et nasaux) ont été prélevés à partir de 24 foyers dans lesquelles les animaux présentaient des signes cliniques. Ensuite, les souches virales ont été isolées en culture cellulaire (MDCK) ou sur oeufs embryonnés. Les 8 segments génomiques des VIs de 18 souches virales ont par la suite été séquencés et analysés intégralement. La résistance aux drogues antivirales telles que l’oseltamivir (GS4071) carboxylate, le zanamivir (GS167) et l’amantadine hydrochloride a également été évaluée par des tests d'inhibition de la neuraminidase (INAs) ainsi que par un test de réduction sur plaque. Deux sous-types viraux H3N2 et H1N1 ont été identifiés dans la population porcine au Québec. Douze souches des VIs de sous-type trH3N2 ont été génétiquement liées au Cluster IV, avec au moins 6 profils de réassortiment différents. D'autre part, 6 souches virales ont été trouvées génétiquement liées au virus pandémique A(H1N1)pdm09 avec au moins trois profils de réassortiment génétique différents. Le sous-type trH3N2 des VIs est le plus répandu dans la population porcine au Québec (66,7%). La cartographie d'épitope de la protéine HA de sous-type H3 a présenté la plus forte variabilité avec 21 substitutions d’acides aminés sur 5 sites antigéniques A (5), B (8), C (5), D (1), et E (2). Toutefois, la protéine HA du sous-type H1 avait seulement 5 substitutions d'aa sur les 3 sites antigéniques Sb (1), Ca1 (2) et Ca2 (2). Un isolat H1N1 (1/6 = 16,7%) et 1 autre trH3N2 (1/12 = 8,3%) ont été trouvés comme étant résistants à l'oseltamivir. En revanche, 2 isolats du H1N1 (2/6 = 33,3%) et 2 autres du trH3N2 (2/12 = 16,7%) ont révélé être résistants au zanamivir. Dans l'ensemble, le taux de résistance aux INAs et à l’amantadine était compris entre 33,3% et 100%. La présence des VIs résistants aux drogues antivirales chez les porcs ainsi que l'émergence possible de nouvelles souches virales constituent des préoccupations majeures en la santé publique et animale justifiant ainsi la surveillance continue des VIs dans la population porcine au Québec. / Data about genomic variability of swine influenza A viruses (SIV) in Quebec herds are scarce. Yet, this information is important for understanding virus evolution in Quebec from until 2015. Different clinical samples were obtained from 24 outbreaks of swine flu in which animals were experiencing respiratory disease. Samples including lung tissues, saliva and nasal swabs were collected and virus isolation was attempted in MDCK cells and embryonated eggs. All eight gene segments of the 18 isolated SIV strains were sequenced and analysed. Antiviral drugs resistance against oseltamivir carboxylate (GS4071), zanamivir (GS167) and amantadine hydrochloride was evaluated by neuraminidase inhibition assays (NAIs) and plaque reduction assay. Two subtypes of SIV, H3N2 and H1N1, were identified in Quebec pig herds. Twelve SIV strains were genetically related to trH3N2 Cluster IV and at least 6 different reassortment profiles were identified. On the other hand, 6 Quebec SIV strains were found to be genetically related to the pandemic virus A(H1N1)pdm09 and from which three reassortment profiles were identified. Overall, the trH3N2 was the most prevalent subtype (66.7%) found in Quebec swine herds. The epitope mapping of HA indicated that the H3 subtype was the most variable with a possibility of 21 amino acids (aa) substitutions within the 5 antigenic sites A(5), B(8), C(5), D(1) and E(2). However, the HA protein of the H1 subtype had only 5 aa substitutions within 3 antigenic sites Sb(1), Ca1(2) and Ca2(2). One H1N1 (1/6 = 16.7%) and one trH3N2 (1/12 = 8.3%) were identified as strains resistant against oseltamivir. In contrast, two H1N1 (2/6 = 33.3%) and two trH3N2 (2/12 = 16.7%) strains were found to be resistant against zanamivir. Overall, the SIV resistance against antiviral neuraminidase inhibitor drugs was (33.3%). All strains were resistant against the M2 inhibitor antiviral drug, amantadine. The presence of antiviral drug resistance in Quebec swine herds and the possible emergence of new SIVs strains are public health concerns supporting the surveillance of SIVs.