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Projeto de investigação
Gene therapy for HIV cure using RNA replicons.
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Epidemic history of hepatitis C virus genotypes and subtypes in Portugal
Publication . Palladino, Claudia; Ezeonwumelu, Ifeanyi Jude; Marcelino, Rute; Briz, Verónica; Moranguinho, Inês; Serejo, Fátima; Velosa, José Fernando; Marinho, Rui Tato; Borrego, Pedro; Taveira, Nuno
Any successful strategy to prevent and control HCV infection requires an understanding of the epidemic behaviour among the different genotypes. Here, we performed the first characterization of the epidemic history and transmission dynamics of HCV subtypes in Portugal. Direct sequencing of NS5B was performed on 230 direct-acting antiviral drugs (DAA)-treatment naïve patients in Lisbon. Phylogenetic analysis was used for subtyping and transmission cluster identification. Bayesian methods were used to reconstruct the epidemic history of HCV subtypes. Sequences were analysed for resistance-associated substitutions (RAS). The majority of strains were HCV-GT1 (62.6%), GT3 (18.3%, all subtype 3a) and GT4 (16.1%). Among GT1, the most frequent were subtypes 1a (75.5%) and 1b (24.5%). Polyphyletic patterns were found in all but 12 lineages suggesting multiple introductions of the different subtypes in this population. Five distinct epidemics were identified. The first significant HCV epidemic in Portugal occurred between 1930s and 1960s, was caused almost exclusively by GT1b and was likely associated with blood transfusions. Rapid expansion of GT3a occurred in the 1960s and GT1a in the 1980s, associated with intravenous drug use. The most recent epidemics were caused by GT4a and GT4d and seem to be associated with the resurgence of opioid use. The C316N substitution was found in 31.4% of GT1b-patients. Close surveillance of patients bearing this mutation and undergoing dasabuvir-based regimens will be important to determine its impact on treatment outcome.
Treatment and cure of HIV infection : available drugs, resistance pathways, and promising new compounds
Publication . Moura, Ines; Taveira, Nuno Eduardo Moura dos Santos da Costa; Sousa, Ana Espada de; Gonçalves, João Manuel Braz
Human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) are the cause of acquired immunodeficiency syndrome (AIDS). What was once a death sentence has become a chronically manageable condition with the introduction of antiretroviral therapy (ART). Although HIV-2 infection has a much lower prevalence than HIV-1 infection, its intrinsic resistance to specific classes of antiretroviral drugs (ARVs) presents substantial challenges in the treatment of affected individuals. Recognizing the importance of addressing these challenges, our research focuses on the identification of drug resistance mutations and the exploration of novel compounds to devise more potent treatment strategies tailored specifically to HIV-2 infection. In the initial segment of this thesis, we present two key projects: The first project involves identifying resistance mutations in people living with HIV-2 experiencing treatment failure in Cape Verde. The second project aims to analyze the efficacy of integrase inhibitors and a new spiro-β-lactam compound against both naïve and raltegravir (RAL)-resistant isolates from Portuguese HIV-2-infected individuals. The initial project outcomes revealed a high prevalence (76.5%) of resistance mutations in people from Cape Verde living with HIV-2 experiencing virological failure. These mutations, located in the reverse transcriptase (RT) and protease (PR), confer resistance against the majority of RT and PR inhibitors. This underscores the imperative for incorporating integrase inhibitors into treatment regimens to effectively address this resistance. In the second project, the results confirmed the robust efficacy of integrase inhibitors, specifically RAL and DTG, against HIV-2 isolates. This aligns with the established clinical efficacy of RAL and DTG in managing HIV-2 infection. The compelling activity observed with the new integrase inhibitor BIC and the novel spiro-β-lactam BSS-730A, even in the face of multi-drug resistant isolates, holds promising prospects for the clinical application of these drugs. While ART has undeniably transformed the landscape of HIV management, the pursuit of an HIV cure remains a crucial endeavor to alleviate the enduring burden of lifelong therapy. Achieving a cure necessitates the elimination of latent virus reservoirs, making a functional cure a more pragmatic goal. Consequently, the second segment of this thesis encompasses two projects dedicated to advancing our understanding and contributing to the cure of HIV infection. The first project entails the development and antiviral evaluation of a compound, Apsi510, which combines an anti-integrase aptamer (T30695) with a small interfering RNA (siRNA) targeting the TAR/poly A region of HIV-1. Notably, the Apsi510 compound exhibited potent antiviral activity against HIV-1, with a remarkable inhibition of over 95% of viral replication observed at a concentration of 50 nM. The siRNA, designed to target the TAR/poly A region, demonstrated efficacy in inhibiting viral transcription, suggesting its potential application in a functional cure approach. In the second project, the investigation into the role of FUBP3 in the regulation of HIV transcription revealed promising findings. Depletion of FUBP3 resulted in a substantial reduction in viral messenger RNA and p24 protein, indicating a significant inhibition of HIV replication. This inhibition persisted even in the presence of an HIV transcription activator compound. Furthermore, the results underscored that the inhibition of FUBP3 protein expression led to a diminished recruitment of RNA polymerase II to the HIV-1 promoter, emphasizing the pivotal role of FUBP3 in the regulation of HIV transcription. As such, these findings position FUBP3 as a compelling candidate for consideration as a potential target in functional cure strategies, particularly through the block-and-lock approach. In summary, our data significantly contributes to the ongoing development of advanced algorithms aimed at predicting treatment susceptibility for HIV-2 infection. Additionally, our research introduces novel compounds that hold promise for the treatment of HIV-2 infection. Furthermore, we present a novel and potent HIV-1 antiviral compound that has potential implications for advancing strategies towards the cure of HIV-1 infection. Concurrently, our work underscores the viability of FUBP3 as a target for functional cure strategies in HIV infection. It is imperative to acknowledge that the ultimate goal in the battle against HIV infection lies in a comprehensive approach, combining multiple strategies and the judicious use of ART. Furthermore, recognizing the unique characteristics of HIV-2, including its lower infectivity and propensity for latency, underscores the importance of tailoring strategies specifically to HIV-2. Insights derived from such tailored approaches may prove instrumental in the development of effective functional cure strategies.
Epidemic history of hepatitis C virus genotypes and subtypes in Portugal
Publication . Palladino, Claudia; Ezeonwumelu, Ifeanyi J.; Marcelino, Rute; Briz, Verónica; Moranguinho, Inês; Serejo, Fátima; Velosa, José Fernando; Marinho, Rui; Borrego, Pedro; Taveira, Nuno
Any successful strategy to prevent and control HCV infection requires an understanding of the epidemic behaviour among the different genotypes. Here, we performed the first characterization of the epidemic history and transmission dynamics of HCV subtypes in Portugal. Direct sequencing of NS5B was performed on 230 direct-acting antiviral drugs (DAA)-treatment naïve patients in Lisbon. Phylogenetic analysis was used for subtyping and transmission cluster identification. Bayesian methods were used to reconstruct the epidemic history of HCV subtypes. Sequences were analysed for resistance-associated substitutions (RAS). The majority of strains were HCV-GT1 (62.6%), GT3 (18.3%, all subtype 3a) and GT4 (16.1%). Among GT1, the most frequent were subtypes 1a (75.5%) and 1b (24.5%). Polyphyletic patterns were found in all but 12 lineages suggesting multiple introductions of the different subtypes in this population. Five distinct epidemics were identified. The first significant HCV epidemic in Portugal occurred between 1930s and 1960s, was caused almost exclusively by GT1b and was likely associated with blood transfusions. Rapid expansion of GT3a occurred in the 1960s and GT1a in the 1980s, associated with intravenous drug use. The most recent epidemics were caused by GT4a and GT4d and seem to be associated with the resurgence of opioid use. The C316N substitution was found in 31.4% of GT1b-patients. Close surveillance of patients bearing this mutation and undergoing dasabuvir-based regimens will be important to determine its impact on treatment outcome.
Antiretroviral Treatment of HIV-2 Infection: Available Drugs, Resistance Pathways, and Promising New Compounds
Publication . Moranguinho, Inês; Taveira, Nuno; Bártolo, Inês
Currently, it is estimated that 1–2 million people worldwide are infected with HIV-2, accounting for 3–5% of the global burden of HIV. The course of HIV-2 infection is longer compared to HIV-1 infection, but without effective antiretroviral therapy (ART), a substantial proportion of infected patients will progress to AIDS and die. Antiretroviral drugs in clinical use were designed for HIV-1 and, unfortunately, some do not work as well, or do not work at all, for HIV-2. This is the case for non-nucleoside reverse transcriptase inhibitors (NNRTIs), the fusion inhibitor enfuvirtide (T-20), most protease inhibitors (PIs), the attachment inhibitor fostemsavir and most broadly neutralizing antibodies. Integrase inhibitors work well against HIV-2 and are included in first-line therapeutic regimens for HIV-2-infected patients. However, rapid emergence of drug resistance and cross-resistance within each drug class dramatically reduces second-line treatment options. New drugs are needed to treat infection with drug-resistant isolates. Here, we review the therapeutic armamentarium available to treat HIV-2-infected patients, as well as promising drugs in development. We also review HIV-2 drug resistance mutations and resistance pathways that develop in HIV-2-infected patients under treatment.
High Instantaneous Inhibitory Potential of Bictegravir and the New Spiro-ß-Lactam BSS-730A for HIV-2 Isolates from RAL-Naïve and RAL-Failing Patients
Publication . Bártolo, Inês; Moranguinho, Inês; Gonçalves, Paloma; Ana Rita Diniz; Borrego, Pedro; Martin, Francisco; Figueiredo, Inês; Gomes, Perpetua; Gonçalves, Maria Fátima; Alves, Américo; Alves, Nuno; Caixas, Umbelina; Vaz-Pinto, Inês; Barahona, Isabel; Melo, Teresa M. V. D. Pinho E; Taveira, Nuno
Integrase inhibitors (INIs) are an important class of drugs for treating HIV-2 infection, given the limited number of drugs active against this virus. While the clinical efficacy of raltegravir and dolutegravir is well established, the clinical efficacy of bictegravir for treating HIV-2 infected patients has not been determined. Little information is available regarding the activity of bictegravir against HIV-2 isolates from patients failing raltegravir-based therapy. In this study, we examined the phenotypic and matched genotypic susceptibility of HIV-2 primary isolates from raltegravir-naïve and raltegravir-failing patients to raltegravir, dolutegravir, and bictegravir, and to the new spiro-β-lactam BSS-730A. The instantaneous inhibitory potential (IIP) was calculated to help predict the clinical activity of bictegravir and BSS-730A. Isolates from raltegravir-naïve patients were highly sensitive to all INIs and BSS-730A. Combined integrase mutations E92A and Q148K conferred high-level resistance to raltegravir, and E92Q and T97A conferred resistance to raltegravir and dolutegravir. The antiviral activity of bictegravir and BSS-730A was not affected by these mutations. BSS-730A displayed strong antiviral synergism with raltegravir. Mean IIP values at Cmax were similar for all INIs and were not significantly affected by resistance mutations. IIP values were significantly higher for BSS-730A than for INIs. The high IIP values of bictegravir and BSS-730A for raltegravir-naïve and raltegravir-resistant HIV-2 isolates highlight their potential value for treating HIV-2 infection. Overall, the results are consistent with the high clinical efficacy of raltegravir and dolutegravir for HIV-2 infection and suggest a promising clinical profile for bictegravir and BSS-730A.
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Fundação para a Ciência e a Tecnologia
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SFRH/BD/131062/2017