Introdução: Durante o inverno de 2009, o vírus influenza A(H1N1)09pdm surgiu e se espalhou globalmente. A infecção por este vírus pode induzir a síndrome do desconforto respiratório agudo (SDRA) em alguns pacientes. O dano alveolar difuso (DAD), padrão histopatológico principal da SDRA, tem etiologia multifatorial, sendo possível que a imunopatologia seja diferente nas várias apresentações do DAD. Objetivo: Descrever, quantificar e comparar a imunopatologia viral (influenza A (H1N1) pdm09) e não-viral em casos de autópsia com dano alveolar difuso. Métodos: Foram analisados tecidos pulmonares de autopsia de 44 pacientes, sendo divididos em 3 grupos: grupo H1N1 (n=15), caracterizado por DAD secundário à influenza A(H1N1)pdm09; grupo SDRA (n=13), caracterizado por pacientes com DAD exsudativo de causas não-pulmonares; e o grupo de controle (n=16) com indivíduos que faleceram de causas não-pulmonares. Foram utilizadas as técnicas de imunohistoquímica e análise de imagem para quantificar, no parênquima pulmonar e nas pequenas vias aéreas, os marcadores de células imunes. Resultados: Foi observada uma elevada densidade celular de linfócitos T CD4+ e T CD8+, células Natural Killer CD57+, células dendríticas CD83+ e granzima A+ no parênquima pulmonar do grupo H1N1 (p < 0,05) em relação aos outros grupos. Na análise das pequenas vias aéreas, observou-se uma menor densidade célular de mastócitos (triptase), células dendríticas (CD207), e um aumento de IL-17 nos grupos H1N1 e SDRA, além de um aumento do número de granzimas A+ e diminuição de celulas dendríticas (CD83) apenas no grupo H1N1 (p < 0,05). Conclusão: O DAD causado pelo vírus influenza A (H1N1) pdm09 está associado com um fenótipo citotóxico inflamatório diferente do DAD de causas não-virais, com uma resposta parcialmente divergente no parênquima pulmonar em relação às pequenas vias aéreas / Rationale: The pandemic influenza A (H1N1) virus emerged in 2009 and spread globally. This virus infection can induce acute respiratory distress syndrome (ARDS) in some patients. Diffuse alveolar damage (DAD), which is the histological surrogate for ARDS, has a multifactorial etiology. Therefore, it is possible that the immunopathology differs among the various presentations of DAD. Objectives: To compare the lung immunopathology of viral (influenza A(H1N1)pdm09) to non-viral, extrapulmonary etiologies in autopsy cases with DAD. Methods: The lung tissue of 44 patients, was divided into 3 groups: the H1N1 group (n=15) characterized by DAD due to influenza A(H1N1)pdm09 infection; the ARDS group (n=13), characterized by patients with exudative DAD due to non-pulmonary causes; and the control group (n=16), consisting of patients with non-pulmonary causes of death. Measurements and main results: Immunohistochemistry and image analysis were used to quantify, in the lung parenchyma and small airways, several immune cell markers. There was higher expression of CD4+ and CD8+ T lymphocytes, CD83+ dendritic cells, granzyme A+ and natural killer+ cell density in the lung parenchyma of the H1N1 group (p < 0,05). In the small airways, there was a lower cell density of tryptase+ mast cells and dendritic+ cells and an increase of IL-17 in both DAD groups, with an increased number of granzyme A in H1N1 group (p < 0,05). Conclusion: DAD due to viral A(H1N1)pdm09 is associated with a cytotoxic inflammatory phenotype that is different from non-viral causes of DAD, with partially divergent responses in the parenchyma relative to the small airways.

A atenção à saúde compreende múltiplas formas de prestação de serviços, sendo o hospital a instituição nuclear para os sistemas de saúde. Em maio de 2009 iniciou-se uma epidemia que evoluiu para escala mundial, com novo subtipo de vírus influenza identificado como Influenza A (H1N1)09pdm, caracterizado pela alta demanda de consultas e internações hospitalares, o que impactou na gestão e custos do serviço. O objetivo da pesquisa foi estudar o consumo de serviços hospitalares dos casos suspeitos e confirmados de Influenza A(H1N1)09pdm no Instituto Central do Hospital das Clínicas da FMUSP (ICHC-HCFMUSP), entre maio e dezembro de 2009. Tomando como informação inicial os registros do banco de notificações e do de saídas hospitalares do Núcleo de Informação em Saúde do HCFMUSP, foram selecionados 430 indivíduos que preencheram os critérios de inclusão da pesquisa e que levaram à 632 internações hospitalares. Em 26% (n=112) das pessoas e em 22,3% (n=141) das internações foi confirmada a suspeita para infecção por H1N1. Nas internações de casos suspeitos, a mediana de duração da internação foi de 5+17 (0-161) dias e 23,4% (n=148) foram admitidos nas UTIs, com mediana de internação 4,5+7,8 (0-46) dias. Nos casos confirmados, a mediana foi de 5+19,1 (0- 161) dias de internação e 26,9% (n=38) de internações em UTI com 5+8,3 (0-31) dias. O pico de notificações de casos suspeitos e confirmados foi no mês de agosto, com 31,6% (n=200 das 632) internações de casos suspeitos e 44% (n=62 das 141) internações de casos confirmados. A Influenza A(H1N1)09pdm impactou o consumo de serviços, mostrando-se presente em muitas enfermarias do ICHC, o que implicou grande consumo de procedimentos diagnósticos e terapêuticos / Healt care comprises multiple ways of services, where hospitals are the nuclear reference institution of health services. In may 2009, a new pandemic influenza vírus subtype was identified as Influenza A(H1N1)09pdm, wich was characterized by high demand for hospital visits and hospitalizations. This research aimed to study the hospital service expenditure on confirmed and non-confirmed hospitalizations associated with Influenza A(H1N1)09pdm at Instituto Central do Hospital das Clínicas FMUSP (ICHC - HCFMUSP), between May and December of 2009. It was analyzed the registers from the notification database and output hospital database from the Information Health Department. According to inclusion criteria, it was found 430 people with 632 hospitalizations with 26% (n=112) patients and 22,3% (n=141) hospitalization for confirmed cases. For non confirmed hospitalizations, the median length of stay was 5+17 (0-161) days with 23,4% (n=148) of ICU admissions with median length of stay 4,5+7,8 (0-46) days. For confirmed cases, the hospitalization length of stay was 5+19,1 (0-161) days with 26,9% (n=38) on ICU admissions with median length of stay 5+8,3 (0-31) days. The notification peak was on August with 31,6% (n=200 from 632) hospitalizations form non-confirmed cases and 44% (n=62 from 141) confirmed cases hospitalization. The Influenza A(H1N1)09pdm impacted on service expenditure, because of its distribution in several wards from ICHC wich implied high expenditure of diagnosis and therapeutic proceeds

Carcinomas de mama são heterogêneos e consistem de diversos tipos celulares. Perfis de expressão gênica usando DNA microarrays identificaram quatro subtipos moleculares fundamentais baseados na expressão de receptores hormonais (estrógeno e progesterona) e de fator de crescimento epidérmico (HER2) (luminal tipo A, luminal tipo B, tumores expressando somente HER2 e triplos negativos) refletindo a heterogeneidade molecular dos carcinomas. Sugeriu-se que esta heterogeneidade advém da presença de células tronco tumorais com a capacidade de se diferenciar ao longo de vias divergentes e outros estudos sugeriram que a presença destas células tronco tumorais pode ser evidenciada pela análise fenotípica de CD44 e CD24. Nosso objetivo foi detectar a freqüência de CD24 e CD44 isolados ou combinados, analisados por imunoistoquímica e sua associação com os subtipos moleculares e com diversos marcadores biológicos em 95 casos de carcinoma ductal infiltrativo organizados em um microarranjo tissular (TMA). Realizamos determinações imunoistoquímicas de CD44, CD24, citoqueratinas (CK5, CK6, CK18), claudina 7 e Ki67. Subgrupos moleculares foram definidos pela expressão imunoistoquímica de RE, RP e HER2. Resultados: Os tumores apresentaram uma maior freqüência dos grupos luminais (49,5%) atribuído à alta expressão de RP ou RE (47,4%), e freqüência menor de tumores triplo negativos (21,5%) e HER2 (9,5%). Os fenótipos CD44+CD24- e CD44-/CD24+ estavam respectivamente presentes em 8,4% e 16,8% dos tumores e o fenótipo duplamente positivo foi predominante (45,3%). Ausência de ambas as proteínas foi evidente em 6,3% dos tumores. Tumores com fenótipo CD44+CD24- (definido como um marcador de células tronco tumorais por estudos in vitro) foram mais comuns em tumores triplos negativos mas não demonstraram nenhum tipo de associação com características clinico-patológicas e demais marcadores. Este fenótipo não foi expresso nos tumores HER2 positivos. O fenótipo duplamente positivo CD44+CD24+ mostrou-se mais freqüente nos subtipos luminais ou com alta expressão de HER2. Os fenótipos (CD44-CD24+ e CD44-CD24-) não mostraram associação com os subgrupos. Tumores expressando CD24+ isolado, com grande freqüência deste marcador (74,7%), mostraram significativa associação com positividade do RE, RP e Ki67 e uma significância marginal com marcadores de diferenciação luminal (CK18 e claudina 7, p = 0,14). Nenhuma associação foi observada com tumores CD44+ quando analisado isoladamente. A expressão de claudina 7 e Ki67 não mostrou associação com os subgrupos e a expressão de CK5 apresentou uma tendência a uma maior negatividade nos subtipos luminais e uma freqüência maior de positividade nos tumores HER2 e triplo negativos. De outro lado, associação da freqüência da expressão positiva de CK18 nos subgrupos luminais foi estatisticamente significativa (p = 0,003). Para se determinar se CD24+ e CD44+ e seus subtipos combinados poderiam afetar a sobrevida global e o intervalo livre da doença preparamos curvas de sobrevida de acordo com Kaplan-Meier que foram analisadas estatisticamente (log rank test). A mediana do período de seguimento das pacientes do nosso estudo foi de 4,8 anos (0,36 10,9 anos). Estas análises não demostraram influência dos fenótipos CD44+CD24- ou CD44+ sobre a sobrevida global ou intervalo livre de doença, mas observamos uma tendência a um prognóstico mais favorável. Interessantemente tumores HER2 positivos não expressaram este fenótipo, sugerindo que outros marcadores de células tronco caracterizam estes tumores. O fenótipo CD44-CD24+ mostrou-se mais freqüente nos tumores luminais, mas não apresentou correlação com marcadores clínico-patológicos ou biológicos analisados. Não houve diferenças significativas com respeito a sobrevida global ou intervalo livre de doença . A expressão de CD24+ isolado associou-se a expressão dos marcadores de diferenciação celular e a uma diminuição do intervalo livre de doença. A sobrevida livre de doença (10 anos) indicou uma percentagem de 94,1% para CD24- e 72,1% para os pacientes CD24+ enquanto a sobrevida global foi de 84,2% para os pacientes CD24- e 72,1% para os pacientes CD24+. Citoqueratinas (CK5, CK18) e Ki67 não influenciaram a sobrevida e o intervalo livre de doença. No entanto a expressão positiva de claudina 7, embora não associada à sobrevida global, foi estatisticamente associada ao decréscimo do intervalo livre da doença (p = 0,05). Conclusão: As características dos tumores CD44+CD24- e sua tendência a associação um prognóstico mais favorável parecem não estar de acordo com as propriedades descritas na literatura para células tronco e enfatizam a necessidade de outros marcadores. A determinação da freqüência de CD44+ e claudina 7 positiva pode contribuir para a análise do prognóstico em carcinoma de mama / Background: Breast carcinomas consist phenotypically of diverse cells and exhibit intra tumoral heterogeneity being stratified in several subgroups based in gene expression profiles or histochemical biomarkers. It was suggested that this heterogeneity is derived in part from the transformation of different subsets of cancer stem cells (CSC) in each intrinsic subgroup. The presence of CSC can be evidenced by phenotypic analysis of CD44 e CD24. This study aimed to identify the CD24 and CD44 immunophenotype within invasive ductal breast carcinoma (IDC) subtypes and determine its influence on prognosis as well as its association with the expression of Ki67, citokeratins (CK5, CK6 and CK18) and claudin-7. Methods: Immuno expression of CD44 and CD24 alone or in combination was investigated in 95 IDC cases arranged in a tissue microarray (TMA). The association with intrinsic subgroups defined as luminal A (ER+, PR+, HER2-), luminal B (ER and or PR+, HER2+), HER2 subtype (ER-, PR-, HER2+) and triple negative (ER-, PR-, HER2-), and the other markers and prognosis was analyzed. Results: CD44+CD24- and CD44-CD24+ were respectively presents in 8.4% and 16.8% of the tumors, a lack of both proteins was detected in 6.3%, while CD44+CD24+ was determined in 45.3% of the tumors. Although there was no significant correlation between subgroups and different phenotypes, the CD44+CD24- phenotype was more common in the basal subgroups but the frequency of this subtype has not been associated with clinical characteristic or biological markers. The phenotype was absent in HER2 tumors whereas luminal tumors are enriched in CD44-CD24+ and CD44+CD24+ cells which did not show associations with clinical/biological markers features. There was also no significant association of the subtypes with the event free (DFS) and overall survival (OS) but the CD44+CD24- phenotype showed a more favorable prognostic as compared to CD44-CD44+ phenotype that showed a worse prognosis (p = 0.26) (median follow up, 4.8 years) CD44+ alone was evident in 57.9%, while CD24+ was positive in 74.7% of the tumors, the latter showing a significant association with ER, PR and Ki67 and a marginal association with CK18 and claudin-7. Expression of claudin-7 and Ki67 did not associate with the cancer subgroups, while a positive association between CK18 and the luminal subgroups was found. CD44+ was not significantly associated with OS (p = 0.684) and DFS (p = 0.386) whereas CD24+ expression was also no significantly associated with OS (p = 0.32) but was associated with a decrease in DFS (p = 0.07). CK5, CK18 and Ki67 expression had no influence in OS or DFS, however claudin-7 positive although not statistically associated with OS, was associated with reduced DFS (p = 0.05). Conclusions: The heterogeneity of cells with several CD44CD24 expression may indicate the presence of different stem cell populations. Ocurrence of CD44+CD24- phenotype is more common in triple negative tumors and lower in tumors of luminal type and absent in HER2 tumors. Although not associated significantly with patho-biological markers or OS and DFS, the CD44+CD24- phenotype has a tendency to be a favorable prognostic marker in breast cancer raising the possibilty that the putative tumorigenic ability may no be restricted to cells of this phenotype. The presence of CD44-CD24+ may indicat a worse prognosis. CD24+ was associated with ER, PR, Ki67and showed a marginal association with CK18 and claudin-7. CD24 and Claudin-7 positivity were the only biological markers associated with reduced DFS. These two investigated markers can be used to improve the assessement of prognosis in breast cancer

MSc (Microbiology) / Department of Microbiology / Background: Antiretroviral treatment (ART) has grown to be one of the most effective tool in the fight to control HIV/AIDS morbidity and mortality worldwide. However, due to the emergence of drug resistant HIV, ART efficacy can be jeopardized. Drug resistant HIV strain has a potential of becoming a major public threat, as its limit treatment options on people living with HIV. With several findings worldwide reporting drug resistant HIV to be currently being transmitted to ART-naïve persons, measures have been taken to genotype drug resistant HIV prior to treatment initiation. However, in resource limited countries such measures are not executed especially in public sectors due to the costs associated with the required assays for genotyping. Objective: The objectives of the study was to establish a deep sequencing protocol (Next Generation Sequencing-NGS) using an Illumina MiniSeq Platform and subsequently apply it to genotype HIV in chronically infected drug naïve persons for resistance mutations and viral genotypes Methods: HIV positive Individuals without any exposure to ART (Treatment-naive) were recruited. Partial pol fragment (complete protease and ~1104bp reverse transcriptase) were amplified and purified. Libraries were prepared using Nextera XT library preparation kit, fragmented, tagmented, pooled and denatured then sequenced with Illumina MiniSeq instrument. Consensus sequences were derived, aligned and phylogenetically analysed. The Stanford HIV Drug Resistance Algorithm was used to infer the presence of drug resistant mutants, at the viral minority and majority population levels. Results and discussion: An NGS protocol to generate nucleotide sequences for drug resistance inference was established. No major drug resistance mutations were detected against protease, reverse transcriptase inhibitors in the study subjects investigated. Nevertheless, V179D change was observed in one patient (8.3%). V179D has been shown to impact a low-level resistance to NNRTI. On the other hand, several secondary and unusual mutations at known drug sites were detected even at minority threshold level of <20%. Conclusion: No major drug resistance mutations was detected in the drug naïve study population. This finding suggests that there is no risk of treatment failure to the investigated subjects, however it is important to assess the potential phenotypic v | P a g e significance of the identified secondary resistance mutations in the context of HIV-1 subtype C. The established NGS protocol should be applied in subsequent HIV drug resistance studies. / NRF

TRPA1 is a thermosensitive ion channel from the ankyrin subfamily of Transient Receptor Potential (TRP) receptors. These proteins play essential roles in the transduction of wide variety of environmental and endogenous signals. TRPA1, which is abundantly expressed in primary nociceptive neurons, is an important transducer of various noxious and irritant stimuli and is also involved in the detection of temperature changes. Similarly to other TRP channels, TRPA1 is comprised of four subunits, each with six transmembrane segments (S1-S6), flanked by the cytoplasmic N- and C-terminal ends. In native tissues, TRPA1 is supposed to be regulated by multiple phosphorylation sites that underlie TRPA1 activity under physiological and various pathophysiological conditions. Using mutational approach, we predicted and explored the role of potential phosphorylation sites for protein kinase C in TRPA1 functioning. Our results identify candidate residues, at which phosho-mimicking mutations affected the channel's ability to respond to voltage and chemical stimuli, whereas the phospho-null mutations to alanine or glycine did not affect the channel activation. Particularly, we identify the serine 602 within the N-terminal ankyrin repeat domain 16, the substitution of which to aspartate completely abolished the TRPA1...

Disease subtyping has been a critical aim of precision and personalized medicine. With the potential to improve patient outcomes, unsupervised and semi-supervised methods for determining phenotypes of subtypes have emerged with a recent focus on matrix and tensor factorization. However, interpretability of proposed models is debatable. Principal component analysis (PCA), a traditional method of dimensionality reduction, does not impose non-negativity constraints. Thus coefficients of the principal components are, in cases, difficult to translate to real physical units. Non-negative matrix factorization (NMF) constrains the factorization to positive numbers such that representative types resulting from the factorization are additive. Archetypal analysis (AA) extends this idea and seeks to identify pure types, archetypes, at the extremes of the data from which all other data can be expressed as a convex combination, or by proportion, of the archetypes. Using AA, this study sought to evaluate the sufficiency of AKI staging criteria through unsupervised subtyping. Archetype analysis failed to find a direct 1:1 mapping of archetypes to physician staging and also did not provide additional insight into patient outcomes. Several factors of the analysis such as quality of the data source and the difficulty in selecting features contributed to the outcome. Additionally, after performing feature selection with lasso across data subsets, it was determined that current staging criteria is sufficient to determine patient phenotype with serum creatinine at time of diagnosis to be a necessary factor.

In Anbetracht der enormen Verbesserung der HCV-Therapie durch die Entwicklung hochwirksamer und direkt wirkender Virostatika (DAA) dient diese Studie der Analyse von HCV-Koinfektionen unter den gemeldeten HIV-Neudiagnosen in Deutschland. Zunächst wurde die Eignung zweier kommerzieller HCV Ag/Ab ELISAs, dem Murex (Abbott) und dem Monolisa (Bio-Rad), zum Nachweis von HCV in getrockneten Serumspots (DSS) verglichen. Der Murex-ELISA zeigte sich sensitiver bei Antigen-positiven Plasma-HCV-Serokonversionsproben während der Monolisa eine höhere Sensitivität bei HCV-Antikörper-positiven DSS-Eluaten. Des Weiteren wurde ein Aviditätstest zur Unterscheidung von neuen und bereits länger bestehenden Infektionen bei einem Aviditätsindex Cut-off von 40% und einem Zeitraum von 364 Tagen etabliert. Von den insgesamt 6.097 untersuchten Proben der Jahre 2015-2017 waren 396 HCV-ELISA-reaktiv (6,5%). Von diesen wurden 256 (64,6%) als aktive und 140 (35,4%) als ausgeheilte Infektionen identifiziert. Ein hoher Anteil der HCV-Koinfektionen wurde bei intra-venösen Drogenkonsumenten (77,8%, n=168/216), in der Altersgruppe der 30-39 Jährigen (9%, n=179/1.978) und bei Menschen osteuropäischer Herkunft (38,3%, n=124/324) beobachtet. Im Vergleich zum Jahr 2016 hat sich der Anteil der ausgeheilten Infektionen im Jahr 2017 bei der Gesamtzahl der Patienten (p<0,01) sowie insbesondere bei Personen ausländischer (p<0,01) und osteuropäischer (p<0,05) Herkunft erhöht. Die HCV Subtypen (St)-1a, St-3a und St-1b waren mit 33,9% (n=79/233), 33,5% (n=78/233) und 23,3% (n=52/233) vorherrschend. Der Anteil der St-1a- und St-1b-Proben, deren HCV-Sequenz gegen DAAs resistent ist, war in allen untersuchten Jahren hoch (25%-42,9%). Der beobachtete Anstieg des Anteils der ausgeheilten HCV-Koinfektionen kann auf die DAA-Therapie zurückgeführt werden. Es sind jedoch weitere Anstrengungen erforderlich, damit Gruppen mit weiterhin hoher HCV-Prävalenz von dieser Behandlung profitieren. / In light of the major shift in HCV therapy resulting from the availability of highly potent direct acting antivirals (DAA), this study performed a surveillance of HCV coinfections among reported HIV new diagnoses in Germany. First the suitability of two HCV Ag/Ab ELISAs, Murex (Abbott) and Monolisa (Bio-Rad) for dried serum spots (DSS) was compared. The Murex was more sensitive in antigen positive plasma HCV seroconversion samples while the Monolisa showed a higher sensitivity in HCV antibody positive DSS eluates. Furthermore, an avidity test was established to distinguish between new and already longer existing infections at an avidity index cut-off of 40% and a period of 364 days. Of the total of 6,097 samples examined for the years 2015-2017, 396 were HCV ELISA reactive (6.5%). Of these, 256 (64.6%) were identified as active and 140 (35.4%) as resolved infections. A high proportion of HCV coinfections were observed in intravenous drug users (77.8%, n=168/216), in the age group 30-39 years (9%, n=179/1,978) and in people of Eastern European origin (38.3%, n=124/324). Compared to 2016, the proportion of resolved infections in 2017 has increased in the total number of patients (p<0.01) and especially in people of foreign (p<0.01) and Eastern European (p<0.05) origin. HCV subtypes (St)-1a, St-3a, and St-1b were predominant with 33.9% (n=79/233), 33.5% (n=78/233) and 23.3% (n=52/233), respectively. The proportion of St-1a and St-1b samples whose HCV sequence has resistance to DAAs was high in all diagnoses years (25%-42.9%). The observed increase in the proportion of resolved HCV coinfections can be attributed to DAA therapy. However, further efforts are needed to ensure that groups with continued high HCV prevalence benefit from this treatment.

No description available.

Chong, Ka Chun. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 125-141). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Cette thèse traite de la résistance du VIH-1 aux antirétroviraux, en particulier de l'activité antivirale de plusieurs inhibiteurs non nucléosidiques de la transcriptase inverse (INNTI) ainsi que des inhibiteurs de protéase (IP). Nous avons exploré l’émergence et la spécificité des voies de mutations qui confèrent la résistance contre plusieurs nouveaux INNTI (étravirine (ETR) et rilpivirine (RPV)) (chapitres 2 et 3). En outre, le profil de résistance et le potentiel antirétroviral d'un nouvel IP, PL-100, est présenté dans les chapitres 4 et 5. Pour le premier projet, nous avons utilisé des sous-types B et non-B du VIH-1 pour sélectionner des virus résistants à ETR, et ainsi montré que ETR favorise l’émergence des mutations V90I, K101Q, E138K, V179D/E/F, Y181C, V189I, G190E, H221H/Y et M230L, et ce, en 18 semaines. Fait intéressant, E138K a été la première mutation à émerger dans la plupart des cas. Les clones viraux contenant E138K ont montré un faible niveau de résistance phénotypique à ETR (3,8 fois) et une diminution modeste de la capacité de réplication (2 fois) par rapport au virus de type sauvage. Nous avons également examiné les profils de résistance à ETR et RPV dans les virus contenant des mutations de résistance aux INNTI au début de la sélection. Dans le cas du virus de type sauvage et du virus contenant la mutation unique K103N, les premières mutations à apparaître en présence d’ETR ou de RPV ont été E138K ou E138G suivies d’autres mutations de résistance aux INNTI. À l’inverse, dans les mêmes conditions, le virus avec la mutation Y181C a évolué pour produire les mutations V179I/F ou A62V/A, mais pas E138K/G. L'ajout de mutations à la position 138 en présence de Y181C n'augmente pas les niveaux de résistance à ETR ou RPV. Nous avons également observé que la combinaison de Y181C et E138K peut conduire à un virus moins adapté par rapport au virus contenant uniquement Y181C. Sur la base de ces résultats, nous suggérons que les mutations Y181C et E138K peuvent être antagonistes. L’analyse de la résistance au PL-100 des virus de sous-type C et CRF01_AE dans les cellules en culture est décrite dans le chapitre 4. Le PL-100 sélectionne pour des mutations de résistance utilisant deux voies distinctes, l'une avec les mutations V82A et L90M et l'autre avec T80I, suivi de l’addition des mutations M46I/L, I54M, K55R, L76F, P81S et I85V. Une accumulation d'au moins trois mutations dans le rabat protéique et dans le site actif est requise dans chaque cas pour qu’un haut niveau de résistance soit atteint, ce qui démontre que le PL-100 dispose d'une barrière génétique élevée contre le développement de la résistance. Dans le chapitre 5, nous avons évalué le potentiel du PL-100 en tant qu’inhibiteur de protéase de deuxième génération. Les virus résistants au PL-100 émergent en 8-48 semaines alors qu’aucune mutation n’apparaît avec le darunavir (DRV) sur une période de 40 semaines. La modélisation moléculaire montre que la haute barrière génétique du DRV est due à de multiples interactions avec la protéase dont des liaison hydrogènes entre les groupes di-tétrahydrofuranne (THF) et les atomes d'oxygène des acides aminés A28, D29 et D30, tandis que la liaison de PL-100 est principalement basée sur des interactions polaires et hydrophobes délocalisées à travers ses groupes diphényle. Nos données suggèrent que les contacts de liaison hydrogène et le groupe di-THF dans le DRV, ainsi que le caractère hydrophobe du PL-100, contribuent à la liaison à la protéase ainsi qu’à la haute barrière génétique contre la résistance et que la refonte de la structure de PL-100 pour inclure un groupe di-THF pourrait améliorer l’activité antivirale et le profil de résistance. / This thesis focuses on HIV-1 drug resistance and on the antiviral activity of several non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs). We have explored the mutational pathways and resistance patterns of several new NNRTIs (etravirine (ETR) and rilpivirine (RPV)) (Chapters 2 and 3). In addition, the drug resistance profile and potential of a novel protease inhibitor (PI) PL-100 is presented in Chapters 4 and 5. In the first project, we used both B and non-B subtypes of HIV-1 to select for ETR resistance and showed that ETR selected for mutations at positions V90I, K101Q, E138K, V179D/E/F, Y181C, V189I, G190E, H221H/Y and M230L within 18 weeks of commencing drug pressure. Interestingly, E138K was the first mutation to emerge in most instances. Viral clones containing E138K displayed low-level phenotypic resistance to ETR (3.8-fold) and modestly impaired replication capacity (2-fold) compared to wild-type virus. We also examined resistance patterns to ETR and RPV in viruses containing NNRTI mutations at baseline. In wild-type (wt) viruses and viruses containing K103N alone, E138K or E138G mutations were observed in the presence of either ETR or RPV drug pressure followed by the appearance of other NNRTI resistance mutations. Alternatively, subtype B viruses containing Y181C generated V179I/F or A62V/A on exposure to ETR or RPV drug pressure, respectively, but not E138K. The addition of mutations at position 138 to Y181C did not significantly enhance levels of resistance to ETR or RPV. We also observed that the combination of Y181C and E138K may lead to a less fit virus compared to virus containing Y181C alone. Based on these findings, we suggest that Y181C may be antagonistic to E138K. The tissue culture drug resistance analysis of PL-100 in subtype C and CRF01_AE viruses is described in Chapter 4. PL-100 selected for PI resistance mutations along either of two distinct pathways, one of which involved resistance mutations at positions V82A and L90M while the other involved a mutation at position T80I, with other mutations being observed at positions M46I/L, I54M, K55R, L76F, P81S and I85V. An accumulation of at least three mutations in the protease flap and enzyme active sites were required in each case for high-level resistance to occur, demonstrating that PL-100 has a high genetic barrier against the development of drug resistance. In Chapter 5, we evaluated the potential of PL-100 as a second generation HIV-1 protease inhibitor. PL-100 resistant variants emerged within 8-48 weeks while darunavir (DRV) did not select for resistance mutations over a period of 40 weeks. Structural modeling demonstrated that the high genetic barrier of DRV is due to numerous interactions with protease that include hydrogen-bonding to PR backbone oxygens at amino acid positions A28, D29 and D30 via di-tetrahydrofuran (THF) groups, while binding of PL-100 was predominantly based on polar interactions and delocalized hydrophobic interactions through its diphenyl groups. Our data suggest that hydrogen bonding contacts and the di-THF group in DRV, as well as the hydrophobic nature of PL-100, contribute to PI binding and a high genetic barrier for resistance and that redesigning the structure of PL-100 to include a di-THF group might improve it antiviral potency and drug resistance profile.