Publications by authors named "Nuno Taveira"

69 Publications

Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis.

Diagnostics (Basel) 2021 Feb 21;11(2). Epub 2021 Feb 21.

Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz-Cooperativa de Ensino Superior CRL, Campus Universitário, Quinta da Granja, 2829-511 Caparica, Portugal.

The rapid and accurate testing of SARS-CoV-2 infection is still crucial to mitigate, and eventually halt, the spread of this disease. Currently, nasopharyngeal swab (NPS) and oropharyngeal swab (OPS) are the recommended standard sampling techniques, yet, these have some limitations such as the complexity of collection. Hence, several other types of specimens that are easier to obtain are being tested as alternatives to nasal/throat swabs in nucleic acid assays for SARS-CoV-2 detection. This study aims to critically appraise and compare the clinical performance of RT-PCR tests using oral saliva, deep-throat saliva/posterior oropharyngeal saliva (DTS/POS), sputum, urine, feces, and tears/conjunctival swab (CS) against standard specimens (NPS, OPS, or a combination of both). In this systematic review and meta-analysis, five databases (PubMed, Scopus, Web of Science, ClinicalTrial.gov and NIPH Clinical Trial) were searched up to the 30th of December, 2020. Case-control and cohort studies on the detection of SARS-CoV-2 were included. The methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2). We identified 1560 entries, 33 of which (1.1%) met all required criteria and were included for the quantitative data analysis. Saliva presented the higher accuracy, 92.1% (95% CI: 70.0-98.3), with an estimated sensitivity of 83.9% (95% CI: 77.4-88.8) and specificity of 96.4% (95% CI: 89.5-98.8). DTS/POS samples had an overall accuracy of 79.7% (95% CI: 43.3-95.3), with an estimated sensitivity of 90.1% (95% CI: 83.3-96.9) and specificity of 63.1% (95% CI: 36.8-89.3). The remaining index specimens could not be adequately assessed given the lack of studies available. Our meta-analysis shows that saliva samples from the oral region provide a high sensitivity and specificity; therefore, these appear to be the best candidates for alternative specimens to NPS/OPS in SARS-CoV-2 detection, with suitable protocols for swab-free sample collection to be determined and validated in the future. The distinction between oral and extra-oral salivary samples will be crucial, since DTS/POS samples may induce a higher rate of false positives. Urine, feces, tears/CS and sputum seem unreliable for diagnosis. Saliva testing may increase testing capacity, ultimately promoting the implementation of truly deployable COVID-19 tests, which could either work at the point-of-care (e.g. hospitals, clinics) or at outbreak control spots (e.g., schools, airports, and nursing homes).
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http://dx.doi.org/10.3390/diagnostics11020363DOI Listing
February 2021

Computational Modulation of the V3 Region of Glycoprotein gp125 of HIV-2.

Int J Mol Sci 2021 Feb 16;22(4). Epub 2021 Feb 16.

Department of Pharmaceutical Sciences and Medicines and Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Avenida Professor Gama Pinto, 1649-003 Lisboa, Portugal.

HIV-2 infection is frequently neglected in HIV/AIDS campaigns. However, a special emphasis must be given to HIV-2 as an untreated infection that also leads to AIDS and death, and for which the efficacy of most available drugs is limited against HIV-2. HIV envelope glycoproteins mediate binding to the receptor CD4 and co-receptors at the surface of the target cell, enabling fusion with the cell membrane and viral entry. Here, we developed and optimized a computer-assisted drug design approach of an important HIV-2 glycoprotein that allows us to explore and gain further insights at the molecular level into protein structures and interactions crucial for the inhibition of HIV-2 cell entry. The 3D structure of a key HIV-2ROD gp125 region was generated by a homology modeling campaign. To disclose the importance of the main structural features and compare them with experimental results, 3D-models of six mutants were also generated. These mutations revealed the selective impact on the behavior of the protein. Furthermore, molecular dynamics simulations were performed to optimize the models, and the dynamic behavior was tackled to account for structure flexibility and interactions network formation. Structurally, the mutations studied lead to a loss of aromatic features, which is very important for the establishment of π-π interactions and could induce a structural preference by a specific coreceptor. These new insights into the structure-function relationship of HIV-2 gp125 V3 and surrounding regions will help in the design of better models and the design of new small molecules capable to inhibit the attachment and binding of HIV with host cells.
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http://dx.doi.org/10.3390/ijms22041948DOI Listing
February 2021

Spiro-β-lactam BSS-730A Displays Potent Activity against HIV and Plasmodium.

ACS Infect Dis 2021 02 4;7(2):421-434. Epub 2021 Jan 4.

Instituto de investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal.

The high burden of malaria and HIV/AIDS prevents economic and social progress in developing countries. A continuing need exists for development of novel drugs and treatment regimens for both diseases in order to address the tolerability and long-term safety concerns associated with current treatment options and the emergence of drug resistance. We describe new spiro-β-lactam derivatives with potent (nM) activity against HIV and and no activity against bacteria and yeast. The best performing molecule of the series, BSS-730A, inhibited both HIV-1 and HIV-2 replication with an IC of 13 ± 9.59 nM and hepatic infection with an IC of 0.55 ± 0.14 μM with a clear impact on parasite development. BSS-730A was also active against the erythrocytic stages of , with an estimated IC of 0.43 ± 0.04 μM. Time-of-addition studies showed that BSS-730A potentially affects all stages of the HIV replicative cycle, suggesting a complex mechanism of action. BSS-730A was active against multidrug-resistant HIV isolates, with a median 2.4-fold higher IC relative to control isolates. BSS-730A was equally active against R5 and X4 HIV isolates and displayed strong synergism with the entry inhibitor AMD3100. BSS-730A is a promising candidate for development as a potential therapeutic and/or prophylactic agent against HIV and .
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http://dx.doi.org/10.1021/acsinfecdis.0c00768DOI Listing
February 2021

Anti-HIV-1 Activity of pepRF1, a Proteolysis-Resistant CXCR4 Antagonist Derived from Dengue Virus Capsid Protein.

ACS Infect Dis 2021 01 15;7(1):6-22. Epub 2020 Dec 15.

Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal.

There is an urgent need for the development of new anti-HIV drugs that can complement existing medicines to be used against resistant strains. Here, we report the anti-HIV-1 peptide pepRF1, a human serum-resistant peptide derived from the Dengue virus capsid protein. , pepRF1 shows a 50% inhibitory concentration of 1.5 nM with a potential therapeutic window higher than 53 000. This peptide is specific for CXCR4-tropic strains, preventing viral entry into target cells by binding to the viral coreceptor CXCR4, acting as an antagonist of this receptor. pepRF1 is more effective than T20, the only peptide-based HIV-1 entry inhibitor approved, and excels in inhibiting a HIV-1 strain resistant to T20. Potentially, pepRF1 can be used alone or in combination with other anti-HIV drugs. Furthermore, one can also envisage its use as a novel therapeutic strategy for other CXCR4-related diseases.
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http://dx.doi.org/10.1021/acsinfecdis.9b00507DOI Listing
January 2021

Predicting the evolution and control of the COVID-19 pandemic in Portugal.

F1000Res 2020 23;9:283. Epub 2020 Apr 23.

Centro de investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, 2829-511, Portugal.

Coronavirus disease 2019 (COVID-19) is a worldwide pandemic that has been affecting Portugal since 2 March 2020. The Portuguese government has been making efforts to contradict the exponential growth through lockdown, social distancing and the usage of masks. However, these measures have been implemented without controlling the compliance degree and how much is necessary to achieve an effective control. To address this issue, we developed a mathematical model to estimate the strength of Government-Imposed Measures (GIM) and predict the impact of the degree of compliance on the number of infected cases and peak of infection. We estimate the peak to be around 650 thousand infected cases with 53 thousand requiring hospital care by the beginning of May if no measures were taken. The model shows that the population compliance of the GIM was gradual between   30% to 75%, contributing to a significant reduction on the infection peak and mortality. Importantly, our simulations show that the infection burden could have been further reduced if the population followed the GIM immediately after their release on 18 March.
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http://dx.doi.org/10.12688/f1000research.23401.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7503179PMC
October 2020

Epidemic history and baseline resistance to NS5A-specific direct acting drugs of hepatitis C virus in Spain.

Sci Rep 2020 08 3;10(1):13024. Epub 2020 Aug 3.

Laboratory of Viral Hepatitis, National Center for Microbiology, Institute of Health Carlos III, Carretera Majadahonda-Pozuelo km 2.2, Majadahonda, 28220, Madrid, Spain.

Hepatitis C virus (HCV) infection remains a global health problem. Previously, the prevalence of NS5A resistance-associated substitutions (RASs) to elbasvir, a new direct-acting antiviral (DAA) against the NS5A viral protein was assessed by our group before its introduction into clinical use in Spain. However, the origin, epidemic history, transmission dynamics, diversity and baseline RASs to NS5A direct-acting agents of HCV-GT1a in Spain remain unknown. A nationwide cross-sectional survey of individuals chronically-infected with HCV-G1a and DAAs-naïve was performed. HCV population sequencing, phylogenetic analysis and Bayesian methods were used. GT1a clade II was more prevalent than clade I (82.3% vs. 17.7%; P < 0.001) and older (estimated origin in 1912 vs. 1952). Clade II epidemic is currently declining whereas clade I epidemic has reached equilibrium. A total of 58 single RASs were identified, which account for the moderate level (10%) of baseline resistance observed. When considering the regional data, marked differences were observed, with thirteen regions showing an intermediate level (5-15%) and one a high level (20%) of resistance. Current HCV-GT1a epidemic in Spain is driven by clade I which seem to have different dissemination routes relative to clade II. A moderate level of baseline RASs to NS5A-DAAs with marked differences among regions was observed. Close surveillance of response to treatment with DAAs will be important.
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http://dx.doi.org/10.1038/s41598-020-69692-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7398927PMC
August 2020

Pyromellitic dianhydride crosslinked soluble cyclodextrin polymers: Synthesis, lopinavir release from sub-micron sized particles and anti-HIV-1 activity.

Int J Pharm 2020 Jun 20;583:119356. Epub 2020 Apr 20.

Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal. Electronic address:

We report the synthesis of water soluble cyclodextrin (CD) polymers prepared by crosslinking pyromellitic dianhydride (PMDA) with two CD derivatives (methyl-β-CD - MβCD and (2-hydroxy)propyl-β-CD - HPβCD) and their evaluation as functional sub-micron sized carriers in the development of antiretroviral drug delivery systems. Using the protease inhibitor lopinavir (LPV) as model drug, LPV loaded CD polymers (pHPβCD and pMβCD) were prepared and fully characterized. The physicochemical characterization and in vitro drug release confirmed the successful synthesis of pHPβCD and pMβCD, the formation of sub-micron sized particles and a 12-14 fold increase in LPV solubility. Cytotoxicity assays indicated that both pHPβCD and pMβCD were able to improve the safety profile of LPV while the viral infectivity assay revealed a concentration independent anti-HIV-1 effect for both pHPβCD and pMβCD with a maximum percentage inhibition (MPI) of 79 and 91% respectively. After LPV loading, the antiviral profile of pHPβCD was reversed to the sigmoidal dose-response profile of LPV, while pMβCD maintained its dose-independent profile followed by a LPV mediated increase in viral inhibition. Overall, both pHPβCD and pMβCD demonstrated anti-HIV-1 activity, while drug loaded pMβCD indicated its potential as functional sub-micron sized drug delivery polymers for achieving synergistic anti-HIV activity.
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http://dx.doi.org/10.1016/j.ijpharm.2020.119356DOI Listing
June 2020

A Prime-Boost Immunization Strategy with Vaccinia Virus Expressing Novel gp120 Envelope Glycoprotein from a CRF02_AG Isolate Elicits Cross-Clade Tier 2 HIV-1 Neutralizing Antibodies.

Vaccines (Basel) 2020 Apr 7;8(2). Epub 2020 Apr 7.

Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal.

Development of new immunogens eliciting broadly neutralizing antibodies (bNAbs) is a main priority for the HIV-1 vaccine field. Envelope glycoproteins from non-B-non-C HIV-1clades have not been fully explored as components of a vaccine. We produced Vaccinia viruses expressing a truncated version of gp120 (gp120t) from HIV-1 clades CRF02_AG, H, J, B, and C and examined their immunogenicity in mice and rabbits. Mice primed with the recombinant Vaccinia viruses and boosted with the homologous gp120t or C2V3C3 polypeptides developed antibodies that bind potently to homologous and heterologous envelope glycoproteins. Notably, a subset of mice immunized with the CRF02_AG-based envelope immunogens developed a cross-reactive neutralizing response against tier 2 HIV-1 Env-pseudoviruses and primary isolates. Rabbits vaccinated with the CRF02_AG-based envelope immunogens also generated potent binding antibodies, and one animal elicited antibodies that neutralized almost all (13 of 16, 81.3%) tier 2 HIV-1 isolates tested. Overall, the results suggest that the novel CRF02_AG-based envelope immunogens and prime-boost immunization strategy elicit the type of immune responses required for a preventive HIV-1 vaccine.
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http://dx.doi.org/10.3390/vaccines8020171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7349027PMC
April 2020

Expanded Spectrum of Antiretroviral-Selected Mutations in Human Immunodeficiency Virus Type 2.

J Infect Dis 2020 06;221(12):1962-1972

Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA.

Background: HIV-1 and HIV-2 differ in their antiretroviral (ARV) susceptibilities and drug resistance mutations (DRMs).

Methods: We analyzed published HIV-2 pol sequences to identify HIV-2 treatment-selected mutations (TSMs). Mutation prevalences were determined by HIV-2 group and ARV status. Nonpolymorphic mutations were those in <1% of ARV-naive persons. TSMs were those associated with ARV therapy after multiple comparisons adjustment.

Results: We analyzed protease (PR) sequences from 483 PR inhibitor (PI)-naive and 232 PI-treated persons; RT sequences from 333 nucleoside RT inhibitor (NRTI)-naive and 252 NRTI-treated persons; and integrase (IN) sequences from 236 IN inhibitor (INSTI)-naive and 60 INSTI-treated persons. In PR, 12 nonpolymorphic TSMs occurred in ≥11 persons: V33I, K45R, V47A, I50V, I54M, T56V, V62A, A73G, I82F, I84V, F85L, L90M. In RT, 9 nonpolymorphic TSMs occurred in ≥10 persons: K40R, A62V, K70R, Y115F, Q151M, M184VI, S215Y. In IN, 11 nonpolymorphic TSMs occurred in ≥4 persons: Q91R, E92AQ, T97A, G140S, Y143G, Q148R, A153G, N155H, H156R, R231 5-amino acid insertions. Nine of 32 nonpolymorphic TSMs were previously unreported.

Conclusions: This meta-analysis confirmed the ARV association of previously reported HIV-2 DRMs and identified novel TSMs. Genotypic and phenotypic studies of HIV-2 TSMs will improve approaches to predicting HIV-2 ARV susceptibility and treating HIV-2-infected persons.
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http://dx.doi.org/10.1093/infdis/jiaa026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7289557PMC
June 2020

Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance.

Nat Microbiol 2020 03 13;5(3):443-454. Epub 2020 Jan 13.

Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.

Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use.
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http://dx.doi.org/10.1038/s41564-019-0637-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7047537PMC
March 2020

Genotypic resistance profiles of HIV-2-infected patients from Cape Verde failing first-line antiretroviral therapy.

AIDS 2020 03;34(3):483-486

Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa.

: The pol gene from HIV-2-infected patients from Cape Verde experiencing virologic failure was sequenced and drug resistance mutations were determined. Most patients were taking a first-line regimen of zidovudine (AZT), lamivudine (3TC) and lopinavir/ritonavir (LPV/r). Resistance mutations were found in most patients (11/17; 64.7%) especially I82F (4/7; 57.1%) and M184V (10/17; 58.8%). Resistance to all reverse transcriptase and protease inhibitors was found in 58.8% (10/17) of the patients. Integrase inhibitors are warranted to treat these patients.
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http://dx.doi.org/10.1097/QAD.0000000000002431DOI Listing
March 2020

Spiro-Lactams as Novel Antimicrobial Agents.

Curr Top Med Chem 2020 ;20(2):140-152

CQC and Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.

Introduction: Structural modulation of previously identified lead spiro-β-lactams with antimicrobial activity was carried out.

Objective: The main objective of this work was to synthesize and evaluate the biological activity of novel spiro-lactams based on previously identified lead compounds with antimicrobial activity.

Methods: The target chiral spiro-γ-lactams were synthesized through 1,3-dipolar cycloaddition reaction of a diazo-γ-lactam with electron-deficient dipolarophiles. In vitro activity against HIV and Plasmodium of a wide range of spiro-β-lactams and spiro-γ-lactams was evaluated. Among these compounds, one derivative with good anti-HIV activity and two with promising antiplasmodial activity (IC50 < 3.5 µM) were identified.

Results: A novel synthetic route to chiral spiro-γ-lactams has been established. The studied β- and γ- lactams were not cytotoxic, and three compounds with promising antimicrobial activity were identified, whose structural modulation may lead to new and more potent drugs.

Conclusion: The designed structural modulation of biologically active spiro-β-lactams involved the replacement of the four-membered β-lactam ring by a five-membered γ-lactam ring. Although conformational and superimposition computational studies revealed no significant differences between β- and γ- lactam pharmacophoric features, the studied structural modulation did not lead to compounds with a similar biological profile. The observed results suggest that the β-lactamic core is a requirement for the activity against both HIV and Plasmodium.
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http://dx.doi.org/10.2174/1568026619666191105110049DOI Listing
April 2020

Inhibition of HIV replication through siRNA carried by CXCR4-targeted chimeric nanobody.

Cell Mol Life Sci 2020 Jul 22;77(14):2859-2870. Epub 2019 Oct 22.

Molecular Microbiology and Biotechnology Department, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal.

Small interfering RNA (siRNA) application in therapy still faces a major challenge with the lack of an efficient and specific delivery system. Current vehicles are often responsible for poor efficacy, safety concerns, and burden costs of siRNA-based therapeutics. Here, we describe a novel strategy for targeted delivery of siRNA molecules to inhibit human immunodeficiency virus (HIV) infection. Specific membrane translocation of siRNA inhibitor was addressed by an engineered nanobody targeting the HIV co-receptor CXCR4 (NbCXCR4) in fusion with a single-chain variable fragment (4M5.3) that carried the FITC-conjugated siRNA. 4M5.3-NbCXCR4 conjugate (4M5.3X4) efficiently targeted CXCR4 T lymphocytes, specifically translocating siRNA by receptor-mediated endocytosis. Targeted delivery of siRNA directed to the mRNA of HIV transactivator tat silenced Tat-driven viral transcription and inhibited the replication of distinct virus clades. In summary, we have shown that the engineered nanobody chimera developed in this study constitutes an efficient and specific delivery method of siRNAs through CXCR4 receptor.
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http://dx.doi.org/10.1007/s00018-019-03334-8DOI Listing
July 2020

Mapping 123 million neonatal, infant and child deaths between 2000 and 2017.

Authors:
Roy Burstein Nathaniel J Henry Michael L Collison Laurie B Marczak Amber Sligar Stefanie Watson Neal Marquez Mahdieh Abbasalizad-Farhangi Masoumeh Abbasi Foad Abd-Allah Amir Abdoli Mohammad Abdollahi Ibrahim Abdollahpour Rizwan Suliankatchi Abdulkader Michael R M Abrigo Dilaram Acharya Oladimeji M Adebayo Victor Adekanmbi Davoud Adham Mahdi Afshari Mohammad Aghaali Keivan Ahmadi Mehdi Ahmadi Ehsan Ahmadpour Rushdia Ahmed Chalachew Genet Akal Joshua O Akinyemi Fares Alahdab Noore Alam Genet Melak Alamene Kefyalew Addis Alene Mehran Alijanzadeh Cyrus Alinia Vahid Alipour Syed Mohamed Aljunid Mohammed J Almalki Hesham M Al-Mekhlafi Khalid Altirkawi Nelson Alvis-Guzman Adeladza Kofi Amegah Saeed Amini Arianna Maever Loreche Amit Zohreh Anbari Sofia Androudi Mina Anjomshoa Fereshteh Ansari Carl Abelardo T Antonio Jalal Arabloo Zohreh Arefi Olatunde Aremu Bahram Armoon Amit Arora Al Artaman Anvar Asadi Mehran Asadi-Aliabadi Amir Ashraf-Ganjouei Reza Assadi Bahar Ataeinia Sachin R Atre Beatriz Paulina Ayala Quintanilla Martin Amogre Ayanore Samad Azari Ebrahim Babaee Arefeh Babazadeh Alaa Badawi Soghra Bagheri Mojtaba Bagherzadeh Nafiseh Baheiraei Abbas Balouchi Aleksandra Barac Quique Bassat Bernhard T Baune Mohsen Bayati Neeraj Bedi Ettore Beghi Masoud Behzadifar Meysam Behzadifar Yared Belete Belay Brent Bell Michelle L Bell Dessalegn Ajema Berbada Robert S Bernstein Natalia V Bhattacharjee Suraj Bhattarai Zulfiqar A Bhutta Ali Bijani Somayeh Bohlouli Nicholas J K Breitborde Gabrielle Britton Annie J Browne Sharath Burugina Nagaraja Reinhard Busse Zahid A Butt Josip Car Rosario Cárdenas Carlos A Castañeda-Orjuela Ester Cerin Wagaye Fentahun Chanie Pranab Chatterjee Dinh-Toi Chu Cyrus Cooper Vera M Costa Koustuv Dalal Lalit Dandona Rakhi Dandona Farah Daoud Ahmad Daryani Rajat Das Gupta Ian Davis Nicole Davis Weaver Dragos Virgil Davitoiu Jan-Walter De Neve Feleke Mekonnen Demeke Gebre Teklemariam Demoz Kebede Deribe Rupak Desai Aniruddha Deshpande Hanna Demelash Desyibelew Sagnik Dey Samath Dhamminda Dharmaratne Meghnath Dhimal Daniel Diaz Leila Doshmangir Andre R Duraes Laura Dwyer-Lindgren Lucas Earl Roya Ebrahimi Soheil Ebrahimpour Andem Effiong Aziz Eftekhari Elham Ehsani-Chimeh Iman El Sayed Maysaa El Sayed Zaki Maha El Tantawi Ziad El-Khatib Mohammad Hassan Emamian Shymaa Enany Sharareh Eskandarieh Oghenowede Eyawo Maha Ezalarab Mahbobeh Faramarzi Mohammad Fareed Roghiyeh Faridnia Andre Faro Ali Akbar Fazaeli Mehdi Fazlzadeh Netsanet Fentahun Seyed-Mohammad Fereshtehnejad João C Fernandes Irina Filip Florian Fischer Nataliya A Foigt Masoud Foroutan Joel Msafiri Francis Takeshi Fukumoto Nancy Fullman Silvano Gallus Destallem Gebremedhin Gebre Tsegaye Tewelde Gebrehiwot Gebreamlak Gebremedhn Gebremeskel Bradford D Gessner Birhanu Geta Peter W Gething Reza Ghadimi Keyghobad Ghadiri Mahsa Ghajarzadeh Ahmad Ghashghaee Paramjit Singh Gill Tiffany K Gill Nick Golding Nelson G M Gomes Philimon N Gona Sameer Vali Gopalani Giuseppe Gorini Bárbara Niegia Garcia Goulart Nicholas Graetz Felix Greaves Manfred S Green Yuming Guo Arvin Haj-Mirzaian Arya Haj-Mirzaian Brian James Hall Samer Hamidi Hamidreza Haririan Josep Maria Haro Milad Hasankhani Edris Hasanpoor Amir Hasanzadeh Hadi Hassankhani Hamid Yimam Hassen Mohamed I Hegazy Delia Hendrie Fatemeh Heydarpour Thomas R Hird Chi Linh Hoang Gillian Hollerich Enayatollah Homaie Rad Mojtaba Hoseini-Ghahfarokhi Naznin Hossain Mostafa Hosseini Mehdi Hosseinzadeh Mihaela Hostiuc Sorin Hostiuc Mowafa Househ Mohamed Hsairi Olayinka Stephen Ilesanmi Mohammad Hasan Imani-Nasab Usman Iqbal Seyed Sina Naghibi Irvani Nazrul Islam Sheikh Mohammed Shariful Islam Mikk Jürisson Nader Jafari Balalami Amir Jalali Javad Javidnia Achala Upendra Jayatilleke Ensiyeh Jenabi John S Ji Yash B Jobanputra Kimberly Johnson Jost B Jonas Zahra Jorjoran Shushtari Jacek Jerzy Jozwiak Ali Kabir Amaha Kahsay Hamed Kalani Rohollah Kalhor Manoochehr Karami Surendra Karki Amir Kasaeian Nicholas J Kassebaum Peter Njenga Keiyoro Grant Rodgers Kemp Roghayeh Khabiri Yousef Saleh Khader Morteza Abdullatif Khafaie Ejaz Ahmad Khan Junaid Khan Muhammad Shahzeb Khan Young-Ho Khang Khaled Khatab Amir Khater Mona M Khater Alireza Khatony Mohammad Khazaei Salman Khazaei Maryam Khazaei-Pool Jagdish Khubchandani Neda Kianipour Yun Jin Kim Ruth W Kimokoti Damaris K Kinyoki Adnan Kisa Sezer Kisa Tufa Kolola Soewarta Kosen Parvaiz A Koul Ai Koyanagi Moritz U G Kraemer Kewal Krishan Kris J Krohn Nuworza Kugbey G Anil Kumar Manasi Kumar Pushpendra Kumar Desmond Kuupiel Ben Lacey Sheetal D Lad Faris Hasan Lami Anders O Larsson Paul H Lee Mostafa Leili Aubrey J Levine Shanshan Li Lee-Ling Lim Stefan Listl Joshua Longbottom Jaifred Christian F Lopez Stefan Lorkowski Sameh Magdeldin Hassan Magdy Abd El Razek Muhammed Magdy Abd El Razek Azeem Majeed Afshin Maleki Reza Malekzadeh Deborah Carvalho Malta Abdullah A Mamun Navid Manafi Ana-Laura Manda Morteza Mansourian Francisco Rogerlândio Martins-Melo Anthony Masaka Benjamin Ballard Massenburg Pallab K Maulik Benjamin K Mayala Mohsen Mazidi Martin McKee Ravi Mehrotra Kala M Mehta Gebrekiros Gebremichael Meles Walter Mendoza Ritesh G Menezes Atte Meretoja Tuomo J Meretoja Tomislav Mestrovic Ted R Miller Molly K Miller-Petrie Edward J Mills George J Milne G K Mini Seyed Mostafa Mir Hamed Mirjalali Erkin M Mirrakhimov Efat Mohamadi Dara K Mohammad Aso Mohammad Darwesh Naser Mohammad Gholi Mezerji Ammas Siraj Mohammed Shafiu Mohammed Ali H Mokdad Mariam Molokhia Lorenzo Monasta Yoshan Moodley Mahmood Moosazadeh Ghobad Moradi Masoud Moradi Yousef Moradi Maziar Moradi-Lakeh Mehdi Moradinazar Paula Moraga Lidia Morawska Abbas Mosapour Seyyed Meysam Mousavi Ulrich Otto Mueller Atalay Goshu Muluneh Ghulam Mustafa Behnam Nabavizadeh Mehdi Naderi Ahamarshan Jayaraman Nagarajan Azin Nahvijou Farid Najafi Vinay Nangia Duduzile Edith Ndwandwe Nahid Neamati Ionut Negoi Ruxandra Irina Negoi Josephine W Ngunjiri Huong Lan Thi Nguyen Long Hoang Nguyen Son Hoang Nguyen Katie R Nielsen Dina Nur Anggraini Ningrum Yirga Legesse Nirayo Molly R Nixon Chukwudi A Nnaji Marzieh Nojomi Mehdi Noroozi Shirin Nosratnejad Jean Jacques Noubiap Soraya Nouraei Motlagh Richard Ofori-Asenso Felix Akpojene Ogbo Kelechi E Oladimeji Andrew T Olagunju Meysam Olfatifar Solomon Olum Bolajoko Olubukunola Olusanya Mojisola Morenike Oluwasanu Obinna E Onwujekwe Eyal Oren Doris D V Ortega-Altamirano Alberto Ortiz Osayomwanbo Osarenotor Frank B Osei Aaron E Osgood-Zimmerman Stanislav S Otstavnov Mayowa Ojo Owolabi Mahesh P A Abdol Sattar Pagheh Smita Pakhale Songhomitra Panda-Jonas Animika Pandey Eun-Kee Park Hadi Parsian Tahereh Pashaei Sangram Kishor Patel Veincent Christian Filipino Pepito Alexandre Pereira Samantha Perkins Brandon V Pickering Thomas Pilgrim Majid Pirestani Bakhtiar Piroozi Meghdad Pirsaheb Oleguer Plana-Ripoll Hadi Pourjafar Parul Puri Mostafa Qorbani Hedley Quintana Mohammad Rabiee Navid Rabiee Amir Radfar Alireza Rafiei Fakher Rahim Zohreh Rahimi Vafa Rahimi-Movaghar Shadi Rahimzadeh Fatemeh Rajati Sree Bhushan Raju Azra Ramezankhani Chhabi Lal Ranabhat Davide Rasella Vahid Rashedi Lal Rawal Robert C Reiner Andre M N Renzaho Satar Rezaei Aziz Rezapour Seyed Mohammad Riahi Ana Isabel Ribeiro Leonardo Roever Elias Merdassa Roro Max Roser Gholamreza Roshandel Daem Roshani Ali Rostami Enrico Rubagotti Salvatore Rubino Siamak Sabour Nafis Sadat Ehsan Sadeghi Reza Saeedi Yahya Safari Roya Safari-Faramani Mahdi Safdarian Amirhossein Sahebkar Mohammad Reza Salahshoor Nasir Salam Payman Salamati Farkhonde Salehi Saleh Salehi Zahabi Yahya Salimi Hamideh Salimzadeh Joshua A Salomon Evanson Zondani Sambala Abdallah M Samy Milena M Santric Milicevic Bruno Piassi Sao Jose Sivan Yegnanarayana Iyer Saraswathy Rodrigo Sarmiento-Suárez Benn Sartorius Brijesh Sathian Sonia Saxena Alyssa N Sbarra Lauren E Schaeffer David C Schwebel Sadaf G Sepanlou Seyedmojtaba Seyedmousavi Faramarz Shaahmadi Masood Ali Shaikh Mehran Shams-Beyranvand Amir Shamshirian Morteza Shamsizadeh Kiomars Sharafi Mehdi Sharif Mahdi Sharif-Alhoseini Hamid Sharifi Jayendra Sharma Rajesh Sharma Aziz Sheikh Chloe Shields Mika Shigematsu Rahman Shiri Ivy Shiue Kerem Shuval Tariq J Siddiqi João Pedro Silva Jasvinder A Singh Dhirendra Narain Sinha Malede Mequanent Sisay Solomon Sisay Karen Sliwa David L Smith Ranjani Somayaji Moslem Soofi Joan B Soriano Chandrashekhar T Sreeramareddy Agus Sudaryanto Mu'awiyyah Babale Sufiyan Bryan L Sykes P N Sylaja Rafael Tabarés-Seisdedos Karen M Tabb Takahiro Tabuchi Nuno Taveira Mohamad-Hani Temsah Abdullah Sulieman Terkawi Zemenu Tadesse Tessema Kavumpurathu Raman Thankappan Sathish Thirunavukkarasu Quyen G To Marcos Roberto Tovani-Palone Bach Xuan Tran Khanh Bao Tran Irfan Ullah Muhammad Shariq Usman Olalekan A Uthman Amir Vahedian-Azimi Pascual R Valdez Job F M van Boven Tommi Juhani Vasankari Yasser Vasseghian Yousef Veisani Narayanaswamy Venketasubramanian Francesco S Violante Sergey Konstantinovitch Vladimirov Vasily Vlassov Theo Vos Giang Thu Vu Isidora S Vujcic Yasir Waheed Jon Wakefield Haidong Wang Yafeng Wang Yuan-Pang Wang Joseph L Ward Robert G Weintraub Kidu Gidey Weldegwergs Girmay Teklay Weldesamuel Ronny Westerman Charles Shey Wiysonge Dawit Zewdu Wondafrash Lauren Woyczynski Ai-Min Wu Gelin Xu Abbas Yadegar Tomohide Yamada Vahid Yazdi-Feyzabadi Christopher Sabo Yilgwan Paul Yip Naohiro Yonemoto Javad Yoosefi Lebni Mustafa Z Younis Mahmoud Yousefifard Hebat-Allah Salah A Yousof Chuanhua Yu Hasan Yusefzadeh Erfan Zabeh Telma Zahirian Moghadam Sojib Bin Zaman Mohammad Zamani Hamed Zandian Alireza Zangeneh Taddese Alemu Zerfu Yunquan Zhang Arash Ziapour Sanjay Zodpey Christopher J L Murray Simon I Hay

Nature 2019 10 16;574(7778):353-358. Epub 2019 Oct 16.

Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.

Since 2000, many countries have achieved considerable success in improving child survival, but localized progress remains unclear. To inform efforts towards United Nations Sustainable Development Goal 3.2-to end preventable child deaths by 2030-we need consistently estimated data at the subnational level regarding child mortality rates and trends. Here we quantified, for the period 2000-2017, the subnational variation in mortality rates and number of deaths of neonates, infants and children under 5 years of age within 99 low- and middle-income countries using a geostatistical survival model. We estimated that 32% of children under 5 in these countries lived in districts that had attained rates of 25 or fewer child deaths per 1,000 live births by 2017, and that 58% of child deaths between 2000 and 2017 in these countries could have been averted in the absence of geographical inequality. This study enables the identification of high-mortality clusters, patterns of progress and geographical inequalities to inform appropriate investments and implementations that will help to improve the health of all populations.
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http://dx.doi.org/10.1038/s41586-019-1545-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800389PMC
October 2019

Mitochondrial DNA in human identification: a review.

PeerJ 2019 13;7:e7314. Epub 2019 Aug 13.

Instituto Universitário Egas Moniz (IUEM), Almada, Portugal.

Mitochondrial DNA (mtDNA) presents several characteristics useful for forensic studies, especially related to the lack of recombination, to a high copy number, and to matrilineal inheritance. mtDNA typing based on sequences of the control region or full genomic sequences analysis is used to analyze a variety of forensic samples such as old bones, teeth and hair, as well as other biological samples where the DNA content is low. Evaluation and reporting of the results requires careful consideration of biological issues as well as other issues such as nomenclature and reference population databases. In this work we review mitochondrial DNA profiling methods used for human identification and present their use in the main cases of humanidentification focusing on the most relevant issues for forensics.
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http://dx.doi.org/10.7717/peerj.7314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697116PMC
August 2019

In vitro evaluation of novel reverse transcriptase inhibitors TAF (tenofovir alafenamide) and OBP-601 (2,3-didehydro-3-deoxy-4-ethynylthymidine) against multi-drug resistant primary isolates of HIV-2.

Antiviral Res 2019 01 2;161:85-89. Epub 2018 Nov 2.

Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Avenida Professor Gama Pinto, 1649-003, Lisboa, Portugal; Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz (IUEM), Campus Universitário, Quinta da Granja Monte de Caparica, 2829 - 511, Caparica, Portugal. Electronic address:

New antiretroviral drugs are needed to treat HIV-2 infected patients failing therapy. Herein, we evaluate the activity of novel reverse transcriptase inhibitors tenofovir alafenamide (TAF) and OBP-601(2,3-didehydro-3-deoxy-4-ethynylthymidine) against primary isolates from HIV-2 infected patients experiencing virologic failure. TAF and OBP-601 were tested against twelve primary isolates obtained from nine drug-experienced patients failing therapy and three drug naïve patients using a single-round infectivity assay in TZM-bl cells. The RT-coding region of pol was sequenced and the GRADE algorithm was used to identify resistance profiles and mutations. TAF and OBP-601 inhibited the replication of almost all isolates at a median EC of 0.27 nM and 6.83 nM, respectively. Two isolates showed moderate-level resistance to OBP-601 or TAF and two other isolates showed high-level resistance to OBP-601 or to both drugs. With one exception, all resistant viruses had canonical nucleoside reverse transcriptase inhibitors (NRTIs)-associated resistance mutations (K65R, N69S, V111I, Y115F, Q151M and M184V). Our results show that TAF has potent activity against most multi-drug resistant HIV-2 isolates and should be considered for the treatment of HIV-2 infected patients failing therapy.
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http://dx.doi.org/10.1016/j.antiviral.2018.10.018DOI Listing
January 2019

Noncovalent PEG Coating of Nanoparticle Drug Carriers Improves the Local Pharmacokinetics of Rectal Anti-HIV Microbicides.

ACS Appl Mater Interfaces 2018 Oct 4;10(41):34942-34953. Epub 2018 Oct 4.

CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde , Gandra 4585-116 , Portugal.

Antiretroviral drug nanocarriers hold great promise for developing anti-human immunodeficiency virus (HIV) rectal microbicides. However, challenges remain, namely, concerning which properties are more suited for enhancing colorectal distribution and retention of microbicide compounds. In this work, we developed and assessed the in vitro and in vivo performance of poly(lactic- co-glycolic acid) (PLGA)-based nanoparticles (NPs) as carriers for the model drug efavirenz (EFV). We particularly focused on the effect of noncovalent poly(ethylene glycol) coating of PLGA NPs (PEG-PLGA NPs) conferring a mucus-diffusive behavior on the pharmacokinetics (PK) of EFV following rectal administration to mice. Drug-loaded PLGA NPs and PEG-PLGA NPs (200-225 nm) were obtained by nanoprecipitation. Both types of systems were able to retain native antiretroviral activity of EFV in vitro, while featuring lower cytotoxicity against different epithelial cell lines and HIV target cells. Also, PLGA NPs and PEG-PLGA NPs were readily taken up by colorectal cell lines and mildly reduced EFV permeation while increasing membrane retention in Caco-2 and Caco-2/HT29-MTX cell monolayer models. When administered intrarectally to CD-1 mice in phosphate-buffered saline (pH 7.4), EFV-loaded PEG-PLGA NPs consistently provided higher drug levels in colorectal tissues and lavages, as compared to free EFV or drug-loaded PLGA NPs. Mean values for the area-under-the-curve between 15 min and 12 h following administration were particularly higher for PEG-PLGA NPs in distal and middle colorectal tissues, with relative bioavailability values of 3.7 and 29, respectively, as compared to free EFV (2.2 and 6.0 over PLGA NPs, respectively). Systemic exposure to EFV was reduced for all treatments. NPs were further shown safe after once-daily administration for 14 days, as assessed by histological analysis of colorectal tissues and chemokine/cytokine assay of rectal lavages. Overall, PEG-PLGA NPs demonstrated to be safe carriers for rectal microbicide drug delivery and able to provide enhanced local PK that could be valuable in preventing rectal HIV transmission.
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http://dx.doi.org/10.1021/acsami.8b12214DOI Listing
October 2018

Epidemic history of hepatitis C virus genotypes and subtypes in Portugal.

Sci Rep 2018 08 16;8(1):12266. Epub 2018 Aug 16.

Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.

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.
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http://dx.doi.org/10.1038/s41598-018-30528-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095915PMC
August 2018

Accidental Father-to-Son HIV-1 Transmission During the Seroconversion Period.

AIDS Res Hum Retroviruses 2018 10 20;34(10):857-862. Epub 2018 Sep 20.

1 HIV Evolution, Epidemiology and Prevention, Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal .

A 4-year-old child born to an HIV-1 seronegative mother was diagnosed with HIV-1, the main risk factor being transmission from the child's father who was seroconverting at the time of the child's birth. In the context of a forensic investigation, we aimed to identify the source of infection of the child and date of the transmission event. Samples were collected from the father and child at two time points about 4 years after the child's birth. Partial segments of three HIV-1 genes (gag, pol, and env) were sequenced and maximum likelihood (ML) and Bayesian methods were used to determine direction and estimate date of transmission. Neutralizing antibodies were determined using a single cycle assay. Bayesian trees displayed a paraphyletic-monophyletic topology in all three genomic regions, with the father's host label at the root, which is consistent with father-to-son transmission. ML trees found similar topologies in gag and pol and a monophyletic-monophyletic topology in env. Analysis of the time of the most recent common ancestor of each HIV-1 gene population indicated that the child was infected shortly after the father. Consistent with the infection history, both father and son developed broad and potent HIV-specific neutralizing antibody responses. In conclusion, the direction of transmission implicated the father as the source of transmission. Transmission occurred during the seroconversion period when the father was unaware of the infection and was likely accidental. This case shows how genetic, phylogenetic, and serological data can contribute for the forensic investigation of HIV transmission.
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http://dx.doi.org/10.1089/AID.2018.0060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6204557PMC
October 2018

Evaluation of the fusion inhibitor P3 peptide as a potential microbicide to prevent HIV transmission in women.

PLoS One 2018 18;13(4):e0195744. Epub 2018 Apr 18.

Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Lisboa, Portugal.

Microbicides are an important strategy for preventing the sexual transmission of HIV but, so far, the most advanced tenofovir-based microbicides have had modest efficacy. This has been related to adherence problems and high prevalence of tenofovir-resistant HIV-1 strains. P3 is a new peptide with potent activity against HIV that may be a good microbicide candidate. In this work P3 was formulated in a gel of hydroxyethyl cellulose and its activity, stability and safety profile in Balb/c mice were evaluated. HIV infection was fully blocked by a 1.5% gel containing P3 at the IC90 (366.4 nM) concentration. The antiviral activity did not change at 4°C during 4 months and at 25, 37 and 65°C for 1 week. P3 was stable and fully functional at acidic pH up to 24h, under different concentrations of hydrogen peroxide and in the presence of genital fluids up to 48h. P3 had no antibacterial activity and did not affect sperm motility and vitality. Finally, P3 didn't cause significant alterations in the vaginal epithelium of Balb/c mice at 0.06 (456.8 μM) and 0.2 mg/day (1522.7 μM) doses. These findings indicate that P3 is an excellent candidate for further development as a microbicide gel for the prevention of HIV transmission in women.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0195744PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905968PMC
July 2018

Clonal expansion across the seas as seen through CPLP-TB database: A joint effort in cataloguing Mycobacterium tuberculosis genetic diversity in Portuguese-speaking countries.

Infect Genet Evol 2019 08 17;72:44-58. Epub 2018 Mar 17.

iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal. Electronic address:

Tuberculosis (TB) remains a major health problem within the Community of Portuguese Language Speaking Countries (CPLP). Despite the marked variation in TB incidence across its member-states and continued human migratory flux between countries, a considerable gap in the knowledge on the Mycobacterium tuberculosis population structure and strain circulation between the countries still exists. To address this, we have assembled and analysed the largest CPLP M. tuberculosis molecular and drug susceptibility dataset, comprised by a total of 1447 clinical isolates, including 423 multidrug-resistant isolates, from five CPLP countries. The data herein presented reinforces Latin American and Mediterranean (LAM) strains as the hallmark of M. tuberculosis populational structure in the CPLP coupled with country-specific differential prevalence of minor clades. Moreover, using high-resolution typing by 24-loci MIRU-VNTR, six cross-border genetic clusters were detected, thus supporting recent clonal expansion across the Lusophone space. To make this data available to the scientific community and public health authorities we developed CPLP-TB (available at http://cplp-tb.ff.ulisboa.pt), an online database coupled with web-based tools for exploratory data analysis. As a public health tool, it is expected to contribute to improved knowledge on the M. tuberculosis population structure and strain circulation within the CPLP, thus supporting the risk assessment of strain-specific trends.
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http://dx.doi.org/10.1016/j.meegid.2018.03.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6598853PMC
August 2019

Potency of HIV-2-specific antibodies increase in direct association with loss of memory B cells.

AIDS 2017 11;31(17):2431-2433

aHIV Evolution, Epidemiology and Prevention, Research Institute for Medicines/Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal bInstituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon cCentro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Almada dInstituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (IHMT, UNL), Lisbon, Portugal eDivision of Infection and Immunity, UCL Institute of Immunity and Transplantation, London, UK fServiço de Doenças Infecciosas, Faculdade de Medicina, Centro Hospitalar Lisboa Norte, Clínica Universitária de Doenças Infecciosas, Hospital de Santa Maria, Universidade de Lisboa, Lisbon, Portugal.

: Potent HIV-neutralizing antibodies are critical for vaccination and viral reservoir control. High levels of neutralizing antibodies characterize HIV-2 infection, a naturally occurring model of attenuated HIV disease with low-to-undectable viremia. We found that HIV-2-specific antibody potency increased in direct association with the loss of both switched and unswitched memory B cells in untreated HIV-2 infection. Thus, HIV antibody affinity maturation is linked to memory B-cell exhaustion even in reduced viremia settings.
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http://dx.doi.org/10.1097/QAD.0000000000001661DOI Listing
November 2017

Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation.

Genetics 2017 11 14;207(3):1089-1101. Epub 2017 Sep 14.

Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico 87545.

Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections, there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods, and the reconstruction of epidemiologic histories. To infer who-infected-whom, and to compute the probability of alternative transmission scenarios while explicitly taking phylogenetic uncertainty into account, we created an approximate Bayesian computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity. We applied our method to a suspected heterosexual transmission case involving three individuals, showing a complex monophyletic-paraphyletic-polyphyletic phylogenetic topology. We detected that seven phylogenetic lineages had been transmitted between two of the individuals based on the available samples, implying that many more unsampled lineages had also been transmitted. Testing whether the lineages had been transmitted at one time or over some length of time suggested that an ongoing superinfection process over several years was most likely. While one individual was found unlinked to the other two, surprisingly, when evaluating two competing epidemiological priors, the donor of the two that did infect each other was not identified by the host root-label, and was also not the primary suspect in that transmission. This highlights that it is important to take epidemiological information into account when analyzing support for one transmission hypothesis over another, as results may be nonintuitive and sensitive to details about sampling dates relative to possible infection dates. Our study provides a formal inference framework to include information on infection and sampling times, and to investigate ancestral node-label states, transmission direction, transmitted genetic diversity, and frequency of transmission.
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http://dx.doi.org/10.1534/genetics.117.300284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676238PMC
November 2017

Early infant diagnosis of HIV-1 infection in Luanda, Angola, using a new DNA PCR assay and dried blood spots.

PLoS One 2017 17;12(7):e0181352. Epub 2017 Jul 17.

Research Institute for Medicines (iMed.Ulisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal.

Background: Early diagnosis and treatment reduces HIV-1-related mortality, morbidity and size of viral reservoirs in infants infected perinatally. Commercial molecular tests enable the early diagnosis of infection in infants but the high cost and low sensitivity with dried blood spots (DBS) limit their use in sub-Saharan Africa.

Objectives: To develop and validate a sensitive and cheap qualitative proviral DNA PCR-based assay for early infant diagnosis (EID) in HIV-1-exposed infants using DBS samples.

Study Design: Chelex-based method was used to extract DNA from DBS samples followed by a nested PCR assay using primers for the HIV-1 integrase gene. Limit of detection (LoD) was determined by Probit regression using limiting dilutions of newly produced recombinant plasmids with the integrase gene of all HIV-1 subtypes and ACH-2 cells. Clinical sensitivity and specificity were evaluated on 100 HIV-1 infected adults; 5 infected infants; 50 healthy volunteers; 139 HIV-1-exposed infants of the Angolan Pediatric HIV Cohort (APEHC) with serology at 18 months of life.

Results: All subtypes and CRF02_AG were amplified with a LoD of 14 copies. HIV-1 infection in infants was detected at month 1 of life. Sensitivity rate in adults varied with viral load, while diagnostic specificity was 100%. The percentage of HIV-1 MTCT cases between January 2012 and October 2014 was 2.2%. The cost per test was 8-10 USD which is 2- to 4-fold lower in comparison to commercial assays.

Conclusions: The new PCR assay enables early and accurate EID. The simplicity and low-cost of the assay make it suitable for generalized implementation in Angola and other resource-constrained countries.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0181352PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5513534PMC
October 2017

Assessment of the Cavidi ExaVir Load Assay for Monitoring Plasma Viral Load in HIV-2-Infected Patients.

J Clin Microbiol 2017 08 17;55(8):2367-2379. Epub 2017 May 17.

Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal

HIV plasma viral load is an established marker of disease progression and of response to antiretroviral therapy, but currently there is no commercial assay validated for the quantification of viral load in HIV-2-infected individuals. We sought to make the first clinical evaluation of Cavidi ExaVir Load (version 3) in HIV-2-infected patients. Samples were collected from a total of 102 individuals living in Cape Verde, and the HIV-2 viral load was quantified by both ExaVir Load and a reference in-house real-time quantitative PCR (qPCR) used in Portugal in 91 samples. The associations between viral load and clinical prognostic variables (CD4 T cell counts and antiretroviral therapy status) were similar for measurements obtained using ExaVir Load and qPCR. There was no difference between the two methods in the capacity to discriminate between nonquantifiable and quantifiable HIV-2 in the plasma. In samples with an HIV-2 viral load quantifiable by both methods ( = 27), the measurements were highly correlated (Pearson = 0.908), but the ExaVir Load values were systematically higher relative to those determined by qPCR (median difference, 0.942 log copies/ml). A regression model was derived that enables the conversion of ExaVir Load results to those that would have been obtained by the reference qPCR. In conclusion, ExaVir Load version 3 is a reliable commercial assay to measure viral load in HIV-2-infected patients and therefore a valuable alternative to the in-house assays in current use.
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http://dx.doi.org/10.1128/JCM.00235-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5527414PMC
August 2017

Genetic diversity, transmission dynamics and drug resistance of Mycobacterium tuberculosis in Angola.

Sci Rep 2017 02 23;7:42814. Epub 2017 Feb 23.

iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.

Tuberculosis (TB) poses a serious public health problem in Angola. No surveillance data on drug resistance is available and nothing is known regarding the genetic diversity and population structure of circulating Mycobacterium tuberculosis strains. Here, we have genotyped and evaluated drug susceptibility of 89 Mycobacterium tuberculosis clinical isolates from Luanda. Thirty-three different spoligotype profiles corresponding to 24 different Shared International Types (SIT) and 9 orphan profiles were detected. SIT 20 (LAM1) was the most prevalent (n = 16, 18.2%) followed by SIT 42 (LAM9; n = 15, 17.1%). Overall, the M. tuberculosis population structure in this sample was dominated by LAM (64.8%) and T (33.0%) strains. Twenty-four-loci MIRU-VNTR analysis revealed that a total of 13 isolates were grouped in 5 distinct clusters. Drug susceptibility data showed that 22 (24.7%) of the 89 clinical isolates were resistant to one or more antibacillary drugs of which 4 (4.5%) were multidrug resistant. In conclusion, this study demonstrates a high predominance of LAM strains circulating in the Luanda setting and the presence of recent transmission events. The rate and the emergence dynamics of drug resistant TB found in this sample are significant and highlight the need of further studies specifically focused on MDR-TB transmission.
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http://dx.doi.org/10.1038/srep42814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5322374PMC
February 2017

Genetic diversity, transmission dynamics, and drug resistance of Mycobacterium tuberculosis in Luanda, Angola.

Int J Mycobacteriol 2016 Dec 12;5 Suppl 1:S38-S39. Epub 2016 Nov 12.

iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal. Electronic address:

Objective/background: Despite the important role that the African region plays in a global tuberculosis (TB) epidemiological context, many countries in the region still lack data on the prevalence of specific Mycobacterium tuberculosis strains and drug resistance. This is the case for Angola, which presently lacks any data concerning drug-resistance rates and prevalence of specific M. tuberculosis genotypes and respective population structure. In this study, we made the first characterization of the genetic diversity and drug resistance of M. tuberculosis complex strains circulating in Luanda, Angola's most important setting concerning TB epidemiology.

Methods: We have analyzed 89 M. tuberculosis isolates recovered from the same number of patients. All clinical isolates were genotyped by spoligotyping and 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTRs). First-line drug-susceptibility testing was performed by the standard BACTEC 960 Mycobacteria Growth Indicator Tube (MGIT) procedure.

Results: We have detected 33 different spoligotype profiles corresponding to 24 different shared international types (SITs) and nine orphan profiles. SIT 20 (LAM1) was the most prevalent (n=16, 18.2%) followed by SIT 42 (LAM9; n=15, 17.1%). Overall, the M. tuberculosis population structure in this sample was dominated by LAM (64.8%) and T (33.0%) strains. Twenty-four-loci MIRU-VNTR analysis revealed that a total of 13 isolates were grouped into five distinct clusters. Drug-susceptibility testing revealed a worrying situation concerning resistance rates. Drug-susceptibility data showed that 22 (24.7%) of the 89 clinical isolates were resistant to one or more antibacillary drugs of which four (4.5%) were multidrug resistant (MDR). Drug-resistant isolates were found across distinct clades and MIRU-VNTR clusters.

Conclusion: This first cross-sectional study conducted in Luanda, Angola, provides a framework for future studies and programmatic management of TB in Angola. We provide sufficient evidence for cluster-based transmission with a high predominance of LAM strains, with differential geographic dispersion. The moderate rate of MDR-TB found in this sample has major public health implications and highlights the need for further studies specifically focused on MDR-TB transmission.
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http://dx.doi.org/10.1016/j.ijmyco.2016.09.050DOI Listing
December 2016