In early 2020 the World Health Organization (WHO) declared a COVID-19 pandemic outbreak. As of March 2023, the Kingdom of Saudi Arabia has reported over 829 thousand cases and over 9 thousand deaths. Due to the public health emergency, the wild-type SARS-CoV-2 genome was fully sequenced early on the pandemic course. Afterward, different viral variants emerged around the world. The variant prevalence fluctuates over time, with some strains presenting increased transmissibility, changes in disease severity, and decreased efficacy of containment measures. In this respect, genomic surveillance and timely data sharing to public repositories represent a tool to track and detect emerging changes that require addressing with public health measurements. However, the Kingdom's genome contribution to the GISAID database represents merely 0.27% of the reported cases. To address this gap, we incorporated whole genome sequencing and the available metadata, to track the circulating viral lineages and identify the variants of concern (VOC) and variants of interest (VOI) over 14 months, from December 2021 to January 2023. We sequenced 581 genomes using the MinION MK1C platform of Oxford Nanopore Technologies (ONT) and assigned the viral lineages, the data primarily derived from COVID-19-positive patients from the city of Jeddah. The VOC Omicron was the principal circulating variant in the country (~99%), which aligns with the global trend. Our report included the sublineages BA.2.75, BQ.1, CH.1.1, XBB, and XBB.1.5, which are under WHO monitoring. We also reported the VOC Delta and the recombinant strains XF, XZ, and XPB. Finally, to validate the use of ONT for genomic surveillance, we compared the data quality of 93 samples sequenced in both ONT MinION and Illumina NaovaSeq platforms. There was 90% correspondence in the Nextstrain clade assignment (84/93) and 78% correspondence in the Pangolin sublineage assignment (73/93). MinION offered a shorter turnaround time, while Illumina produced a consistently higher breadth of genome coverage. In conclusion, the continued viral evolution patterns are reflected in the Kingdom's variant prevalence, where only Omicron circulated by January 2023. Likewise, current Variants Under Monitoring (VUM) were already identified in KSA, highlighting the need for increased genomic surveillance.

Le Gallid herpesvirus 2 (GaHV-2), responsable de lymphomes T du poulet, est contrôlé par le vaccin CVI988/Rispens. Mes travaux de thèse ont montré que le vaccin était composé, au contraire des souches virulentes, d’une population dynamique de variants viraux majoritairement délétés de la région promotrice et d’une partie variable de l’extrémité 5’ du gène LAT codant des microARN et associé à la latence virale. Dans une approche vaccinale, un virus recombinant correspondant à l’un des variants majoritaires du vaccin CVI988/Rispens a été généré à partir d’une souche GaHV-2 hypervirulente, clonée en bacmide. Nous avons montré que ce recombinant, présentant une perte de pathogénicité presque totale, était capable de protéger significativement les poulets lors d’une épreuve avec des souches GaHV-2 hypervirulentes. Ces travaux posent les bases du développement de nouveaux vaccins à partir de souches hypervirulentes émergentes. / Gallid herpesvirus 2 (GaHV-2), responsible for T-cell lymphomas chicken, is controlled by the vaccine CVI988/Rispens. My work has shown that the vaccine contains, unlike virulent strain, a viral variants population mostly deleted from the promoter region and a variable portion of the 5' end of the gene LAT encoding microRNA and associated with viral latency. In a vaccine approach, a recombinant virus corresponding to a majority variant of the CVI988/Rispens vaccine was generated from a hypervirulent strain GaHV-2, cloned as bacmid. We showed that recombinant, with an almost total loss of pathogenicity, was able to significantly protect chickens against challenge with virulent strains GaHV-2. This work lays the basis for the development of new vaccines from emerging virulent strains.

A raiva é uma zoonose quase sempre fatal, que causa milhares de mortes humanas por ano em todo mundo. Essa enfermidade manifesta-se nos mamíferos em duas formas clínicas: furiosa e paralítica. Distinções em relação à evolução, manifestações clínicas, lesões, distribuição e respectiva carga viral no Sistema Nervoso Central (SNC) podem estar relacionadas às características de neuroinvasividade e neuropatogenicidade das diferentes variantes do vírus da raiva (RABV). O objetivo deste projeto foi estabelecer um modelo para o estudo da patogênese da raiva em camundongos inoculados com vírus fixo CVS/31 e variantes de rua do RABV originárias de bovino (variante 3 compatível com isolados de morcegos hematófagos) e de canídeo silvestre (variante compatível com isolados de canídeo silvestre). Para estabelecer o modelo murino, 24 camundongos isogênicos da linhagem BALB/c, de três semanas de idade foram inoculados com 103 DLIC50/0,03mL por via intracerebral (IC) para confirmar a neurovirulência das diferentes variantes do RABV. De modo concomitante, 32 camundongos desta mesma linhagem e faixa etária, foram inoculados com 105 DLIC50/0,03mL pela via coxim plantar (CP) com o intuito de mimetizar a progressão da infecção natural. Para o estudo da patogênese do RABV foram analisados durante um período de trinta dias após a inoculação (DPI) em camundongos pela via CP os seguintes parâmetros: manifestações clínicas, alterações histopatológicas, distribuição antigênica viral pela técnica de imuno-histoquímica (IHQ) e distribuição de RNA viral pela técnica da reação em cadeia da polimerase em tempo real precedida pela transcrição reversa (RT-qPCR) - sistema SYBR Green em diversos segmentos do SNC. Todos os camundongos inoculados com as três amostras do RABV apresentaram sintomas compatíveis com a forma paralítica da doença, tais como: piloereção, perda de peso, postura arqueada, prostração e paresia dos membros posteriores. Apesar de não ser possível observar diferenças de neuropatogenicidade entre as variantes virais, detectaram-se diversidade de virulência entre essas estirpes, demonstrado pelas distinções de período de incubação e taxa de letalidade. Ao analisar os resultados, também foi possível observar diferenças entre a neurovirulência e a neuroinvasividade das diferentes variantes do RABV. Nos camundongos inoculados com CVS/31 pela via CP, no 6º DPI, observaram-se predomínio de manguitos perivasculares na medula espinhal e degeneração neuronal em córtex e intensa distribuição antigênica de RABV no tronco encefálico. Nos camundongos inoculados via CP com amostras do RABV originárias de bovino, no 8º DPI, apresentaram moderada distribuição de manguitos perivasculares na medula e córtex e intensa distribuição antigênica no tálamo. Já nos animais inoculados com a amostra de canídeo silvestre, no 9ºDPI, relataram-se moderada distribuição de manguitos perivasculares no tronco encefálico e moderada distribuição antigênica no córtex. Além disso, foi observado discrepâncias na comparação entre a intensidade e distribuição de marcações antigênicas pela IHQ e inferência semi-quantitativa de distribuição de RNA viral analisada pelo RT-qPCR-sistema SYBR Green no SNC de camundongos / Rabies is a zoonotic disease usually fatal, causing thousands of human deaths each year worldwide. This disease manifests itself in mammals in two clinical forms: furious and paralytic. Distinctions regarding the evolution, clinical manifestations, injuries, distribution and their viral load on the central nervous system (CNS) may be related to the characteristics of neuroinvasiveness and neuropathogenicity of different variants of rabies virus (RABV). The objective of this project was to establish a model to study the pathogenesis of rabies in mice inoculated with fixed virus CVS / 31 and RABV Street variants originating from bovine (variant 3 - compatible with isolates from vampire bats) and wild canid (variant supports isolated from wild canid). To establish the mouse model, 24 mice of the inbred strain BALB/c, three weeks old were inoculated with 103DLIC50/0,03mL intracerebrally (IC) to confirm the neurovirulence of the different variants of RABV. Concomitantly, 32 mice of the same lineage and age were inoculated with 105DLIC50/0,03mL via footpad (CP) in order to mimic the natural progression of the infection. To study the pathogenesis of RABV CP the following parameters were analyzed over a period of thirty days after inoculation (DPI) in mice via CP: clinical, histopathological changes, viral antigen distribution by the technique of immunohistochemistry (IHC) and distribution of RNA by real-time polymerase chain reaction technique preceded by reverse transcription (RT-qPCR) - SYBR Green system in various segments of the CNS. All mice inoculated with the three RABV samples showed symptoms consistent with the paralytic form of the disease, such as ruffled fur, weight loss, hunched, prostration and paresis of the hind limbs. Although it is not possible to observe neuropathogenicity differences between viral variants, the virulence diversity is detected between these strains demonstrated by distinctions incubation period and fatality rate. When analyzing the results, it was also possible to observe differences between neurovirulence and neuroinvasiveness of different variants of RABV. In mice inoculated with CVS/31 via CP on the 6th DPI, there were predominance of perivascular cuffing in spinal cord and neuronal degeneration in cortex and intense antigenic distribution of the RABV in the brainstem. Mice inoculated via CP with RABV samples originating from bovine on the 8thDPI had moderate distribution of perivascular cuffing in the medulla and cortex and intense antigenic distribution in the thalamus. The animals inoculated with the sample of wild canid in 9thDPI reported a moderate perivascular cuffing distribution in the brainstem and moderate antigenic distribution in the cortex. Additionally, discrepancies were observed when comparing the intensity and distribution of antigenic tags by IHC, semi-quantitative inference viral RNA distribution analyzed by RT-qPCR using SYBR Green system in the mouse CNS

A raiva é uma zoonose quase sempre fatal, que causa milhares de mortes humanas por ano em todo mundo. Essa enfermidade manifesta-se nos mamíferos em duas formas clínicas: furiosa e paralítica. Distinções em relação à evolução, manifestações clínicas, lesões, distribuição e respectiva carga viral no Sistema Nervoso Central (SNC) podem estar relacionadas às características de neuroinvasividade e neuropatogenicidade das diferentes variantes do vírus da raiva (RABV). O objetivo deste projeto foi estabelecer um modelo para o estudo da patogênese da raiva em camundongos inoculados com vírus fixo CVS/31 e variantes de rua do RABV originárias de bovino (variante 3 compatível com isolados de morcegos hematófagos) e de canídeo silvestre (variante compatível com isolados de canídeo silvestre). Para estabelecer o modelo murino, 24 camundongos isogênicos da linhagem BALB/c, de três semanas de idade foram inoculados com 103 DLIC50/0,03mL por via intracerebral (IC) para confirmar a neurovirulência das diferentes variantes do RABV. De modo concomitante, 32 camundongos desta mesma linhagem e faixa etária, foram inoculados com 105 DLIC50/0,03mL pela via coxim plantar (CP) com o intuito de mimetizar a progressão da infecção natural. Para o estudo da patogênese do RABV foram analisados durante um período de trinta dias após a inoculação (DPI) em camundongos pela via CP os seguintes parâmetros: manifestações clínicas, alterações histopatológicas, distribuição antigênica viral pela técnica de imuno-histoquímica (IHQ) e distribuição de RNA viral pela técnica da reação em cadeia da polimerase em tempo real precedida pela transcrição reversa (RT-qPCR) - sistema SYBR Green em diversos segmentos do SNC. Todos os camundongos inoculados com as três amostras do RABV apresentaram sintomas compatíveis com a forma paralítica da doença, tais como: piloereção, perda de peso, postura arqueada, prostração e paresia dos membros posteriores. Apesar de não ser possível observar diferenças de neuropatogenicidade entre as variantes virais, detectaram-se diversidade de virulência entre essas estirpes, demonstrado pelas distinções de período de incubação e taxa de letalidade. Ao analisar os resultados, também foi possível observar diferenças entre a neurovirulência e a neuroinvasividade das diferentes variantes do RABV. Nos camundongos inoculados com CVS/31 pela via CP, no 6º DPI, observaram-se predomínio de manguitos perivasculares na medula espinhal e degeneração neuronal em córtex e intensa distribuição antigênica de RABV no tronco encefálico. Nos camundongos inoculados via CP com amostras do RABV originárias de bovino, no 8º DPI, apresentaram moderada distribuição de manguitos perivasculares na medula e córtex e intensa distribuição antigênica no tálamo. Já nos animais inoculados com a amostra de canídeo silvestre, no 9ºDPI, relataram-se moderada distribuição de manguitos perivasculares no tronco encefálico e moderada distribuição antigênica no córtex. Além disso, foi observado discrepâncias na comparação entre a intensidade e distribuição de marcações antigênicas pela IHQ e inferência semi-quantitativa de distribuição de RNA viral analisada pelo RT-qPCR-sistema SYBR Green no SNC de camundongos / Rabies is a zoonotic disease usually fatal, causing thousands of human deaths each year worldwide. This disease manifests itself in mammals in two clinical forms: furious and paralytic. Distinctions regarding the evolution, clinical manifestations, injuries, distribution and their viral load on the central nervous system (CNS) may be related to the characteristics of neuroinvasiveness and neuropathogenicity of different variants of rabies virus (RABV). The objective of this project was to establish a model to study the pathogenesis of rabies in mice inoculated with fixed virus CVS / 31 and RABV Street variants originating from bovine (variant 3 - compatible with isolates from vampire bats) and wild canid (variant supports isolated from wild canid). To establish the mouse model, 24 mice of the inbred strain BALB/c, three weeks old were inoculated with 103DLIC50/0,03mL intracerebrally (IC) to confirm the neurovirulence of the different variants of RABV. Concomitantly, 32 mice of the same lineage and age were inoculated with 105DLIC50/0,03mL via footpad (CP) in order to mimic the natural progression of the infection. To study the pathogenesis of RABV CP the following parameters were analyzed over a period of thirty days after inoculation (DPI) in mice via CP: clinical, histopathological changes, viral antigen distribution by the technique of immunohistochemistry (IHC) and distribution of RNA by real-time polymerase chain reaction technique preceded by reverse transcription (RT-qPCR) - SYBR Green system in various segments of the CNS. All mice inoculated with the three RABV samples showed symptoms consistent with the paralytic form of the disease, such as ruffled fur, weight loss, hunched, prostration and paresis of the hind limbs. Although it is not possible to observe neuropathogenicity differences between viral variants, the virulence diversity is detected between these strains demonstrated by distinctions incubation period and fatality rate. When analyzing the results, it was also possible to observe differences between neurovirulence and neuroinvasiveness of different variants of RABV. In mice inoculated with CVS/31 via CP on the 6th DPI, there were predominance of perivascular cuffing in spinal cord and neuronal degeneration in cortex and intense antigenic distribution of the RABV in the brainstem. Mice inoculated via CP with RABV samples originating from bovine on the 8thDPI had moderate distribution of perivascular cuffing in the medulla and cortex and intense antigenic distribution in the thalamus. The animals inoculated with the sample of wild canid in 9thDPI reported a moderate perivascular cuffing distribution in the brainstem and moderate antigenic distribution in the cortex. Additionally, discrepancies were observed when comparing the intensity and distribution of antigenic tags by IHC, semi-quantitative inference viral RNA distribution analyzed by RT-qPCR using SYBR Green system in the mouse CNS

Made available in DSpace on 2016-08-15T20:31:10Z (GMT). No. of bitstreams: 1 WanessaBM_DISSERT.pdf: 2965999 bytes, checksum: 15229eda004f6eb0eefb1d93516bce41 (MD5) Previous issue date: 2013-08-29 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Rabies is a viral disease that affects the central nervous system, causing encephalitis and almost 100% lethality once the signs and symptoms start. This study describes the genetic characterization of rabies virus strains isolated in samples from domestic and wild animals acquired in the states of Rio Grande do Norte, Paraíba and Pernambuco in the period of 2001 to 2012, aiming to contribute to the understanding of the molecular epidemiology of rabies. Eighty fivesamplespositivethrough direct immunofluorescenceandbiological test,provided by theCentral Laboratoryof Public Healthof RioGrande do Norte(LACEN-RN) and theRabies Laboratoryof the Federal Universityof CampinaGrande(UFCG-Campos Patos) were analyzed, and underwent RT-PCR directedto thenucleoprotein geneand subsequentlysequencing was performed.In this study67% ofsampleswere positiveinRT-PCR and 40% presented viablesequences. Theaggregation patternobtainedin the phylogenetic treeresulted in the formationof the main expectedgroupsof rabies virussamples, i.e., antigenic variants2, 3; insectivorous batvariant;andfixed sample(CVS).The study andconstant monitoringof these variantsare extremely important, sincegenetic changescanlead toproteinmodifications, andwith itvaccineinefficiency / A raiva é uma enfermidade de origem viral, que afeta o sistema nervoso central, ocasionando encefalite e praticamente 100% de letalidade uma vez iniciados os sinais e sintomas. Este estudo descreve a caracterização genética das cepas de vírus rábico isoladas de amostras de animais domésticos e silvestres nos Estados do Rio Grande do Norte, Paraíba e Pernambuco no período de 2001 a 20012 visando contribuir para o entendimento da epidemiologia molecular da raiva. Foram analisadas 85 amostras positivas pela imunofluorescência direta e prova biológica cedida pelo Laboratório Central de Saúde Pública do Rio Grande do Norte (LACEN-RN) e o Laboratório de Raiva da Universidade Federal de Campina Grande (UFCG-Campus Patos) e submetidas a RT-PCR direcionada ao gene da nucleoproteína e posterior sequenciamento.No presente estudo 67% da amostras apresentaram positividade na RT-PCR e 40% apresentaram sequencias viáveis. O padrão de agregação obtido na árvore filogenética resultou na formação dos principais grupos esperados de amostras do vírus da raiva, ou seja, variante antigênica 2, 3 e variante de morcego insetívoro e amostra fixa (CVS). O estudo e a monitoração constante dessas variantes são de extrema importância, pois alterações genéticas podem levar a modificações protéicas, e com isso ineficiência vacinal

L’épidémie du VIH-1 dure maintenant depuis plus de 25 ans. La grande diversité génétique de ce virus est un obstacle majeur en vue de l’éradication de cette pandémie. Au cours des années, le VIH-1 a évolué en plus de cinquante sous-types ou formes recombinantes. Cette diversité génétique est influencée par diverses pressions de sélection, incluant les pressions du système immunitaire de l’hôte et les agents antirétroviraux (ARV). En effet, bien que les ARV aient considérablement réduit les taux de morbidité et de mortalité, en plus d’améliorer la qualité et l’espérance de vie des personnes atteintes du VIH-1, ces traitements sont complexes, dispendieux et amènent leur lot de toxicité pouvant mener à des concentrations plasmatiques sous-optimales pour contrôler la réplication virale. Ceci va permettre l’émergence de variantes virales portant des mutations de résistance aux ARV. Ce phénomène est encore plus complexe lorsque l’on prend en considération l’immense diversité génétique des différents sous-types. De plus, le virus du VIH est capable de persister sous forme latente dans diverses populations cellulaires, rendant ainsi son éradication extrêmement difficile. Des stratégies pouvant restreindre la diversité virale ont donc été préconisées dans le but de favoriser les réponses immunes de l’hôte pour le contrôle de l’infection et d’identifier des variantes virales offrant une meilleure cible pour des stratégies vaccinales ou immunothérapeutiques. Dans cet esprit, nous avons donc étudié, chez des sujets infectés récemment par le VIH-1, l’effet du traitement ARV précoce sur la diversité virale de la région C2V5 du gène enveloppe ainsi que sur la taille des réservoirs. En deuxième lieu, nous avons caractérisé la pression de sélection des ARV sur des souches virales de sous types variés non-B, chez des patients du Mali et du Burkina Faso afin d’évaluer les voies d’échappement viral dans un fond génétique différent du sous-type B largement prévalent en Amérique du Nord. Notre étude a démontré la présence d’une population virale très homogène et peu diversifiée dans les premières semaines suivant l’infection, qui évolue pour atteindre une diversification de +0,23% à la fin de la première année. Cette diversification est plus importante chez les sujets n’ayant pas initié de traitement. De plus, ceci s’accompagne d’un plus grand nombre de particules virales infectieuses dans les réservoirs viraux des cellules mononucléées du sang périphérique (PBMC) chez ces sujets. Ces résultats suggèrent que l’initiation précoce du traitement pourrait avoir un effet bénéfique en retardant l’évolution virale ainsi que la taille des réservoirs, ce qui pourrait supporter une réponse immune mieux ciblée et potentiellement des stratégies immunothérapeutiques permettant d’éradiquer le virus. Nous avons également suivi 801 sujets infectés par des sous-types non-B sur le point de débuter un traitement antirétroviral. Bien que la majorité des sujets ait été à un stade avancé de la maladie, plus de 75% des individus ont obtenu une charge virale indétectable après 6 mois d’ARV, témoignant de l’efficacité comparable des ARV sur les sous-types non-B et B. Toutefois, contrairement aux virus de sous-type B, nous avons observé différentes voies moléculaires de résistance chez les sous type non-B, particulièrement chez les sous-types AGK/AK/K pour lesquels les voies de résistances étaient associées de façon prédominante aux TAM2. De plus, bien que la divergence entre les virus retrouvés chez les patients d’une même région soit faible, nos analyses phylogénétiques ont permis de conclure que ces mutations de résistance se sont produites de novo et non à partir d’un ancêtre commun porteur de résistance. Cependant, notre dernière étude au Mali nous a permis d’évaluer la résistance primaire à près de 10% et des études phylogénétiques seront effectuées afin d’évaluer la circulation de ces souches résistantes dans la population. Ces études suggèrent qu’un contrôle de la réplication virale par les ARV peut freiner la diversité du VIH et ainsi ouvrir la voie à un contrôle immunologique ciblé, utilisant de nouvelles stratégies vaccinales ou immunothérapeutiques. Toutefois, une thérapie antirétrovirale sous-optimale (adhérence, toxicité) peut conduire à l’échappement virologique en favorisant l’émergence et la dissémination de souches résistantes. / The HIV epidemic has been ongoing for 25 years. The striking genetic diversity of this virus is a formidable obstacle to the eradication of the pandemic. Throughout the years, HIV-1 has evolved in more than fifty subtypes and circulating recombinants forms. This evolution is shaped by selective pressures including the host immune responses and sub-optimal HAART treatment. In the era of HAART, HIV associated morbidity and mortality has decreased dramatically and significantly improved the life expectancy of infected individuals. However, treatments are complex, expensive and are associated with toxicity. When viral replication is not fully contained, drug mutations arise which further complicate treatment options. This phenomenon is even more complex when taking into account the great genetic diversity of various HIV-1 subtypes. HIV also has the capacity to persist in different cellular population and thus eradication is extremely difficult to achieve. Strategies aiming at limiting viral diversity and improving the host immune responses to control HIV replication are needed. The identification of conserved viral variants could ultimately be useful in vaccine design or as an immunotherapeutic target. Thus, we have studied the effects early HAART during primary HIV infection has on viral diversity in the C2V5 region of the env gene and on the size of viral reservoir. We then characterized the selective pressure of ARV on non-B subtype and evaluated drug resistance pathways in non-B HIV genetic background in infected subjects from Mali and Burkina Faso as they initiated treatment. Our study demonstrated a homogenous viral population during the first weeks post infection. Viral diversity did increase during the first year to reach +0.23% at the end of the first year post infection. Patients not initiating treatment exhibited a higher magnitude of viral diversity, and the size of their viral reservoir as determined by the number of infectious units per million PBMC’s also reached higher values. Our results suggest that early treatment, by slowing viral evolution and size of viral reservoir, could permit strong immune system responses against contemporaneous viruses and could help achieved eradication. In another study, we followed 801 patients infected with non-B subtype who were about to start antiretroviral therapy. The majority of these patients were at advanced stages of the infection. Nevertheless, more than 75% achieved undetectable viral load after 6 months of therapy. This very encouraging result led us to conclude that antiretroviral therapy was efficient in controlling replication in non-B subtype infection at similar level than in subtype B infection. In contrast to subtype B infection, we observed different molecular resistance pathways in non-B subtypes, particularly in the AGK/AK/K subtype for which mutations were predominantly associated with the TAM2 pathway. Although our phylogenetic analysis showed a very closely related viral population in our population, we were able to determine that those mutations were not from a common ancestral virus transmitted in this population but rather were emerging de novo in those patients. We conducted another study in Mali and our results showed a primary drug resistance frequency of 10%. We are now conducting phlylogenetic studies to evaluate the prevalence of drug resistance virus transmission in this population. Our studies suggest that controlling viral replication by treatment could delay viral evolution. A slower viral diversity could have a beneficial effect on the immune system and could lead to the development of new vaccines or immunotherapeutics strategies. However, sub-optimal drugs concentrations (poor adherence, toxicitiy) could lead to viral escape and emergence of virus bearing drug resistance mutations which could further be disseminated in the population.

L’épidémie du VIH-1 dure maintenant depuis plus de 25 ans. La grande diversité génétique de ce virus est un obstacle majeur en vue de l’éradication de cette pandémie. Au cours des années, le VIH-1 a évolué en plus de cinquante sous-types ou formes recombinantes. Cette diversité génétique est influencée par diverses pressions de sélection, incluant les pressions du système immunitaire de l’hôte et les agents antirétroviraux (ARV). En effet, bien que les ARV aient considérablement réduit les taux de morbidité et de mortalité, en plus d’améliorer la qualité et l’espérance de vie des personnes atteintes du VIH-1, ces traitements sont complexes, dispendieux et amènent leur lot de toxicité pouvant mener à des concentrations plasmatiques sous-optimales pour contrôler la réplication virale. Ceci va permettre l’émergence de variantes virales portant des mutations de résistance aux ARV. Ce phénomène est encore plus complexe lorsque l’on prend en considération l’immense diversité génétique des différents sous-types. De plus, le virus du VIH est capable de persister sous forme latente dans diverses populations cellulaires, rendant ainsi son éradication extrêmement difficile. Des stratégies pouvant restreindre la diversité virale ont donc été préconisées dans le but de favoriser les réponses immunes de l’hôte pour le contrôle de l’infection et d’identifier des variantes virales offrant une meilleure cible pour des stratégies vaccinales ou immunothérapeutiques. Dans cet esprit, nous avons donc étudié, chez des sujets infectés récemment par le VIH-1, l’effet du traitement ARV précoce sur la diversité virale de la région C2V5 du gène enveloppe ainsi que sur la taille des réservoirs. En deuxième lieu, nous avons caractérisé la pression de sélection des ARV sur des souches virales de sous types variés non-B, chez des patients du Mali et du Burkina Faso afin d’évaluer les voies d’échappement viral dans un fond génétique différent du sous-type B largement prévalent en Amérique du Nord. Notre étude a démontré la présence d’une population virale très homogène et peu diversifiée dans les premières semaines suivant l’infection, qui évolue pour atteindre une diversification de +0,23% à la fin de la première année. Cette diversification est plus importante chez les sujets n’ayant pas initié de traitement. De plus, ceci s’accompagne d’un plus grand nombre de particules virales infectieuses dans les réservoirs viraux des cellules mononucléées du sang périphérique (PBMC) chez ces sujets. Ces résultats suggèrent que l’initiation précoce du traitement pourrait avoir un effet bénéfique en retardant l’évolution virale ainsi que la taille des réservoirs, ce qui pourrait supporter une réponse immune mieux ciblée et potentiellement des stratégies immunothérapeutiques permettant d’éradiquer le virus. Nous avons également suivi 801 sujets infectés par des sous-types non-B sur le point de débuter un traitement antirétroviral. Bien que la majorité des sujets ait été à un stade avancé de la maladie, plus de 75% des individus ont obtenu une charge virale indétectable après 6 mois d’ARV, témoignant de l’efficacité comparable des ARV sur les sous-types non-B et B. Toutefois, contrairement aux virus de sous-type B, nous avons observé différentes voies moléculaires de résistance chez les sous type non-B, particulièrement chez les sous-types AGK/AK/K pour lesquels les voies de résistances étaient associées de façon prédominante aux TAM2. De plus, bien que la divergence entre les virus retrouvés chez les patients d’une même région soit faible, nos analyses phylogénétiques ont permis de conclure que ces mutations de résistance se sont produites de novo et non à partir d’un ancêtre commun porteur de résistance. Cependant, notre dernière étude au Mali nous a permis d’évaluer la résistance primaire à près de 10% et des études phylogénétiques seront effectuées afin d’évaluer la circulation de ces souches résistantes dans la population. Ces études suggèrent qu’un contrôle de la réplication virale par les ARV peut freiner la diversité du VIH et ainsi ouvrir la voie à un contrôle immunologique ciblé, utilisant de nouvelles stratégies vaccinales ou immunothérapeutiques. Toutefois, une thérapie antirétrovirale sous-optimale (adhérence, toxicité) peut conduire à l’échappement virologique en favorisant l’émergence et la dissémination de souches résistantes. / The HIV epidemic has been ongoing for 25 years. The striking genetic diversity of this virus is a formidable obstacle to the eradication of the pandemic. Throughout the years, HIV-1 has evolved in more than fifty subtypes and circulating recombinants forms. This evolution is shaped by selective pressures including the host immune responses and sub-optimal HAART treatment. In the era of HAART, HIV associated morbidity and mortality has decreased dramatically and significantly improved the life expectancy of infected individuals. However, treatments are complex, expensive and are associated with toxicity. When viral replication is not fully contained, drug mutations arise which further complicate treatment options. This phenomenon is even more complex when taking into account the great genetic diversity of various HIV-1 subtypes. HIV also has the capacity to persist in different cellular population and thus eradication is extremely difficult to achieve. Strategies aiming at limiting viral diversity and improving the host immune responses to control HIV replication are needed. The identification of conserved viral variants could ultimately be useful in vaccine design or as an immunotherapeutic target. Thus, we have studied the effects early HAART during primary HIV infection has on viral diversity in the C2V5 region of the env gene and on the size of viral reservoir. We then characterized the selective pressure of ARV on non-B subtype and evaluated drug resistance pathways in non-B HIV genetic background in infected subjects from Mali and Burkina Faso as they initiated treatment. Our study demonstrated a homogenous viral population during the first weeks post infection. Viral diversity did increase during the first year to reach +0.23% at the end of the first year post infection. Patients not initiating treatment exhibited a higher magnitude of viral diversity, and the size of their viral reservoir as determined by the number of infectious units per million PBMC’s also reached higher values. Our results suggest that early treatment, by slowing viral evolution and size of viral reservoir, could permit strong immune system responses against contemporaneous viruses and could help achieved eradication. In another study, we followed 801 patients infected with non-B subtype who were about to start antiretroviral therapy. The majority of these patients were at advanced stages of the infection. Nevertheless, more than 75% achieved undetectable viral load after 6 months of therapy. This very encouraging result led us to conclude that antiretroviral therapy was efficient in controlling replication in non-B subtype infection at similar level than in subtype B infection. In contrast to subtype B infection, we observed different molecular resistance pathways in non-B subtypes, particularly in the AGK/AK/K subtype for which mutations were predominantly associated with the TAM2 pathway. Although our phylogenetic analysis showed a very closely related viral population in our population, we were able to determine that those mutations were not from a common ancestral virus transmitted in this population but rather were emerging de novo in those patients. We conducted another study in Mali and our results showed a primary drug resistance frequency of 10%. We are now conducting phlylogenetic studies to evaluate the prevalence of drug resistance virus transmission in this population. Our studies suggest that controlling viral replication by treatment could delay viral evolution. A slower viral diversity could have a beneficial effect on the immune system and could lead to the development of new vaccines or immunotherapeutics strategies. However, sub-optimal drugs concentrations (poor adherence, toxicitiy) could lead to viral escape and emergence of virus bearing drug resistance mutations which could further be disseminated in the population.