Fostensavir trometamol 600 mg para o tratamento de indivíduos adultos vivendo com HIV multirresistentes aos antirretrovirais / Fostensavir trometamol 600 mg for the treatment of individuals adults living with multidrug-resistant HIV

INTRODUÇÃO: O HIV-1 é um vírus que apresenta em seu envelope viral a glicoproteína gp120, capaz de se ligar aos receptores CD4+ dos linfócitos T do hospedeiro, inviabilizando o funcionamento normal ou levando à destruição das células do sistema imune da pessoa vivendo com esse agente infeccioso. No contexto do tratamento contra o vírus, as quasispécies de HIV-1 podem sofrer uma ou mais mutações genéticas que afetam a atividade de um ou mais ARVs que já foram efetivos anteriormente, processo que é denominado resistência. Segundo a Organização Mundial de Saúde (OMS), observa-se em diversos países que a resistência atinge mais de 10% dos indivíduos em início ou reinício do tratamento contra o HIV. PERGUNTA: Fostensavir 600 mg é eficaz, custo-efetivo e seguro no tratamento de pessoas adultas vivendo com HIV-1 multirresistente aos ARVs? EVIDÊNCIAS CLÍNICAS: A partir da pergunta de pesquisa, foi desenvolvida estratégia de busca nas bases de dados MEDLINE via PubMed e EMBASE. A busca realizada resultou em 318 publicações. Foram inicialmente excluídas 72 por serem duplicatas. Posteriormente, foram excluídas outras 220 após triagem. Após leitura dos textos completos, chegou-se ao resultado de cinco publicações elegíveis, todas fruto do ensaio clínico randomizado de fase III, BRIGHTE. Foram relatados os desfechos de média de redução de carga viral, resposta virológica, falha virológica, variação média de linfócitos T CD4+, eventos adversos, morte, qualidade de vida e adesão ao tratamento. Em geral, o nível de certeza das evidências foi classificado como baixo, com risco de viés grave. AVALIAÇÃO ECONÔMICA: Utilizando um modelo de árvore de decisão, foi realizada uma análise para estimar a razão de custo-efetividade incremental (RCEI) do fostensavir 600 mg para pessoas vivendo com HIV-Aids, adultos e com multirresistência a pelo menos quatro classes terapêuticas de antirretrovirais desde que combinado a pelo menos um ARV totalmente ativo para um ano. O modelo comparou o fostensavir à terapia de base otimizada (TBO) apresentada no estudo pivotal BRIGHTE. ANÁLISE DE IMPACTO ORÇAMENTÁRIO: Foram projetados dois cenários de incorporação para a difusão do fostensavir: conservador e moderado. No cenário de difusão conservador (market share 10% ao ano), o impacto da incorporação do fostensavir em cinco anos variou entre R$ 10.975.053,60 e R$ 65.109.874,58, de 2024 a 2028 respectivamente. O impacto orçamentário acumulado em cinco anos no cenário conservador foi R$ 185.241.468,80. No cenário de difusão moderado (market share 20% ao ano), o impacto da incorporação em cinco anos variou entre R$ 10.975.053,60 e R$ 117.197.774,25, de 2024 a 2028. O impacto orçamentário acumulado em cinco anos no cenário de difusão moderado foi R$ 310.435.446,95. Monitoramento do horizonte tecnológico: Foram identificadas duas tecnologias para o tratamento de pessoas adultas convivendo com HIV multirresistente. Lenacapavir, que está registrado nas agências EMA e FDA, e ibalizumabe, com registro na FDA. PERSPECTIVA DO PACIENTE: A chamada pública nº 30/2023 ficou aberta entre 14 e 24 de agosto de 2023. Duas pessoas se inscreveram. O representante titular contou que tem 50 anos e há 25 vive com HIV. Acredita já ter usado todas as classes de medicamentos por conta da multirresistência do HIV aos ARV, chegando a ficar sem opção terapêutica por cinco ou seis anos. Atualmente utiliza a combinação maraviroque, dolutegravir, tenofovir, lamivudina, darunavir e ritonavir, com a qual consegue obter a supressão da carga viral. Ressaltou que quem vive com HIV há muito tempo corre o risco de ficar sem opção de medicamentos e que a incorporação de novas tecnologias pode beneficiar pessoas como ele. RECOMENDAÇÃO PRELIMINAR DA CONITEC: Os membros do Comitê de Medicamentos presentes na 125ª Reunião Ordinária, realizada no dia 6 de dezembro de 2023, deliberaram, por unanimidade, encaminhar o tema para consulta pública com recomendação preliminar favorável à incorporação do fostensavir trometamol 600 mg para o tratamento de pessoas vivendo com HIV-Aids multirresistentes a terapia antirretroviral. Considerou-se a oportunidade de uma opção terapêutica aos indivíduos multirresitentes, a capacidade das Câmaras Técnicas Estaduais e da área técnica do Ministério da Saúde no monitoramento dos benefícios clínicos e dos eventos adversos do fostensavir e a expectativa de uma nova proposta de preço encaminhada pela empresa durante a consulta pública. CONSULTA PÚBLICA: A consulta pública (CP) nº 69/2023 foi realizada entre os dias 29/12/2023 e 17/01/2024. Foram recebidas 11 contribuições, sendo sete pelo formulário para contribuições técnico-científico e quatro pelo formulário pra contribuições sobre experiência ou opinião de pacientes, familiares, amigos ou cuidadores de pacientes, profissionais de saúde ou pessoas interessadas no tema. Sobre as contribuições técnicas, todas foram favoráveis às recomendações preliminares da Conitec e uma possuía referencial teórico para a abordagem técnico-científica. Entretanto, não se identificou nenhuma evidência científica adicional que pudesse modificar o entendimento preliminar da Conitec. Nas contribuições de experiência ou opinião, todos os participantes manifestaram-se favoráveis à recomendação preliminar da tecnologia avaliada. Os argumentos relevantes foram classificados em "Sobrevida do paciente", uma vez que a abordagem foi especificamente quanto às falhas terapêuticas do uso de outros antirretrovirais e a evolução para complicações e óbito. Metade dos respondedores apontaram ter experiência com o fostensavir. No que diz respeito à experiência com outras tecnologias, um dos três respondentes, o paciente, mencionou o uso de medicamentos, como tenofovir, lamivudina, efavirenz e dolutegravir e apontou como evento negativo os seus efeitos colaterais. Além disso, destacaram o valor elevado da aquisição do fostensavir como uma das principais dificuldades para acesso a este tratamento. NOVA PROPOSTA COMERCIAL: Foi submetida ao DGITS/SECTICS/MS o valor de USD 38,67 por comprimido, com uma quantidade mínima de aquisição estabelecida em 360.000 (trezentos e sessenta mil) unidades. Considerando o novo valor proposto, o custo mensal do tratamento será de R$ 11.513,40, representando aproximadamente 65,59% de desconto em relação ao preço CMED PMVG 18% e uma redução de 1,66% em relação à proposta apresentada em 2023. Ainda com base no novo valor proposto, atualizou-se a avaliação econômica e a AIO. Os critérios considerados englobam os termos da recente proposta comercial e a taxa de câmbio do dólar no dia 15 de fevereiro de 2024, fixada em 1 USD = R$ 4,9624. A RCEI foi estimada em R$ 257.370,65, apresentando uma efetividade incremental de 0,54. No cenário conservador da nova AIO, levando em consideração uma participação de mercado de 10% ao ano, o impacto orçamentário incremental em cinco anos foi R$ 100.714.577,75. Já no cenário moderado, com um aumento de 20% após o primeiro ano, o impacto orçamentário acumulado em cinco anos foi R$ 247.300.234,85. RECOMENDAÇÃO FINAL DA CONITEC: Os membros do Comitê de Medicamentos presentes na 127ª Reunião Ordinária, realizada no dia 6 de março de 2024, deliberaram, por unanimidade, recomendar a incorporação do fostensavir trometamol 600 mg para o tratamento de indivíduos adultos vivendo com HIV multirresistentes aos antirretrovirais, conforme Protocolo Clínico do Ministério da Saúde. Considerou-se as expectativas da ampliação das opções terapêuticas e da redução da carga viral aos pacientes multirresistentes. Foi assinado o Registro de Deliberação nº 881/2024. DECISÃO: incorporar, no âmbito do Sistema Único de Saúde - SUS, o fostensavir trometamol 600 mg para o tratamento de indivíduos adultos vivendo com HIV multirresistente aos antirretrovirais, conforme Protocolo Clínico do Ministério da Saúde, publicada no Diário Oficial da União nº 77, seção 1, página 177, em 22 de abril de 2024.

CD4-binding obstacles in conformational transitions and allosteric communications of HIV gp120.

As the only exposed viral protein at the membrane surface of HIV, envelope glycoprotein gp120 is responsible for recognizing host cells and mediating virus-cell membrane fusion. Available structures of gp120 indicate that it exhibits two distinct conformational states, called closed and open states. Although experimental data demonstrates that CD4 binding stabilizes open state of gp120, detailed structural dynamics and kinetics of gp120 during this process remain elusive. Here, two open-state gp120 simulation systems, one without any ligands (ligand-free) and the other complexed with CD4 (CD4-bound), were subjected to microsecond-scale molecular dynamics simulations following the conformational transitions and allosteric pathways of gp120 evaluated by using the Markov state model and a network-based method, respectively. Our results provide an atomic-resolution description of gp120 conformational transitions, suggesting that gp120 is intrinsically dynamic from the open state to closed state, whereas CD4 binding blocks these transitions. Consistent with experimental structures, five metastable conformations with different orientations of the V1/V2 region and V3 loop have been extracted. The binding of CD4 significantly enhances allosteric communications from the CD4-binding site to V3 loop and ß20-21 hairpin, resulting in high-affinity interactions with coreceptors and activation of the conformational transitions switcher, respectively. This study will facilitate the structural understanding of the CD4-binding effects on conformational transitions and allosteric pathways of gp120.

A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses.

The identification of transmission clusters (TCs) of HIV-1 using phylogenetic analyses can provide insights into viral transmission network and help improve prevention strategies. We compared the use of partial HIV-1 envelope fragment of 1,070 bp with its loop 3 (108 bp) to determine its utility in inferring HIV-1 transmission clustering. Serum samples of recently (n = 106) and chronically (n = 156) HIV-1-infected patients with status confirmed were sequenced. HIV-1 envelope nucleotide-based phylogenetic analyses were used to infer HIV-1 TCs. Those were constructed using ClusterPickerGUI_1.2.3 considering a pairwise genetic distance of ≤10% threshold. Logistic regression analyses were used to examine the relationship between the demographic factors that were likely associated with HIV-1 clustering. Ninety-eight distinct consensus envelope sequences were subjected to phylogenetic analyses. Using a partial envelope fragment sequence, 42 sequences were grouped into 15 distinct small TCs while the V3 loop reproduces 10 clusters. The agreement between the partial envelope and the V3 loop fragments was significantly moderate with a Cohen's kappa (κ) coefficient of 0.59, p < .00001. The mean age (<38.8 years) and HIV-1 B subtype are two factors identified that were significantly associated with HIV-1 transmission clustering in the cohort, odds ratio (OR) = 0.25, 95% confidence interval (CI, 0.04-0.66), p = .002 and OR: 0.17, 95% CI (0.10-0.61), p = .011, respectively. The present study confirms that a partial fragment of the HIV-1 envelope sequence is a better predictor of transmission clustering. However, the loop 3 segment may be useful in screening purposes and may be more amenable to integration in surveillance programs.

HIV-1 tropism prediction by the XGboost and HMM methods.

Human Immunodeficiency Virus 1 (HIV-1) co-receptor usage, called tropism, is associated with disease progression towards AIDS. Furthermore, the recently developed and developing drugs against co-receptors CCR5 or CXCR4 open a new thought for HIV-1 therapy. Thus, knowledge about tropism is critical for illness diagnosis and regimen prescription. To improve tropism prediction accuracy, we developed two novel methods, the extreme gradient boosting based XGBpred and the hidden Markov model based HMMpred. Both XGBpred and HMMpred achieved higher specificities (72.56% and 72.09%) than the state-of-the-art methods Geno2pheno (61.6%) and G2p_str (68.60%) in a 10-fold cross validation test at the same sensitivity of 93.73%. Moreover, XGBpred had more outstanding performances (with AUCs 0.9483, 0.9464) than HMMpred (0.8829, 0.8774) on the Hivcopred and Newdb (created in this work) datasets containing larger proportions of hard-to-predict dual tropic samples in the X4-using tropic samples. Therefore, we recommend the use of our novel method XGBpred to predict tropism. The two methods and datasets are available via http://spg.med.tsinghua.edu.cn:23334/XGBpred/. In addition, our models identified that positions 5, 11, 13, 18, 22, 24, and 25 were correlated with HIV-1 tropism.

Transmission patterns of HIV-1 non-R5 strains in Poland.

HIV-1 env sequencing enables predictions of viral coreceptor tropism and phylogenetic investigations of transmission events. The aim of the study was to estimate the contribution of non-R5 strains to the viral spread in Poland. Partial proviral env sequences were retrieved from baseline blood samples of patients with newly diagnosed HIV-1 infection between 2008-2014, including 46 patients with recent HIV-1 infection (RHI), and 246 individuals with long-term infection (LTHI). These sequences were subjected to the genotypic coreceptor tropism predictions and phylogenetic analyses to identify transmission clusters. Overall, 27 clusters with 57 sequences (19.5%) were detected, including 15 sequences (26.3%) from patients with RHI. The proportion of non-R5 strains among all study participants was 23.3% (68/292), and was comparable between patients with RHI and LTHI (11/46, 23.9% vs 57/246, 23.2%; p = 1.000). All 11 patients with non-R5 strains and RHI were men having sex with men (MSM). Among these patients, 4 had viral sequences grouped within phylogenetic cluster with another sequence of non-R5 strain obtained from patient with LTHI, indicating potential acquisition of non-R5 HIV-1 for at least 4/46 (8.7%) patients with RHI. We were unable to confirm the contribution of patients with RHI to the forward transmission of non-R5 strains, but a relatively high proportion of non-R5 strains among them deserves attention due to the limited susceptibility to CCR5 antagonists.

In vitro assessment of biological activity and stability of the ALVAC-HIV vaccine.

The first evidence in humans that a safe and effective preventive vaccine for HIV is possible came from the phase III HIV clinical trial RV144 in Thailand. This trial was based on a prime/boost combination of a recombinant canarypox vaccine and two glycoprotein 120 proteins (ALVAC-HIV and AIDSVAX B/E). A pivotal phase IIb/III trial has recently commenced in the Republic of South Africa, for which the infectious titer assay was applied as the quantitative release test for the ALVAC-HIV vaccine. The infectious titer assay measures the ability of the vaccine vector to infect target permissive cells, but does not indicate if the vaccine transgenes are expressed. We have developed a high-throughput biological activity assay that provides results in agreement with the infectious titer assay. This assay uses flow cytometry to quantify expression of ALVAC-HIV encoded proteins gp120 and p24 in human cells. This transgene expression is detected by two cross-clade-reactive, biologically functional human anti-gp120 monoclonal antibodies isolated from clinical trial participants and a commercial mouse anti-p24 monoclonal antibody. The relative biological activity of the vaccine test sample is calculated by comparison of the test sample dose-response curve against that of a reference standard. We show that the novel biological activity assay is specific, accurate, precise, stability-indicating, and robust. The assay is being used for characterization of ALVAC-HIV (vCP2438) product, the efficacy of which is being evaluated in the pivotal phase IIb/III clinical trial HVTN702. The biological activity assay has the potential to indicate vaccine consistency and quality as a complement to the infectious titer assay.

Quantitative Assessment of Molecular Dynamics Sampling for Flexible Systems.

Molecular dynamics (MD) simulation is a natural method for the study of flexible molecules but at the same time is limited by the large size of the conformational space of these molecules. We ask by how much the MD sampling quality for flexible molecules can be improved by two means: the use of diverse sets of trajectories starting from different initial conformations to detect deviations between samples and sampling with enhanced methods such as accelerated MD (aMD) or scaled MD (sMD) that distort the energy landscape in controlled ways. To this end, we test the effects of these approaches on MD simulations of two flexible biomolecules in aqueous solution, Met-Enkephalin (5 amino acids) and HIV-1 gp120 V3 (a cycle of 35 amino acids). We assess the convergence of the sampling quantitatively with known, extensive measures of cluster number Nc and cluster distribution entropy Sc and with two new quantities, conformational overlap Oconf and density overlap Odens, both conveniently ranging from 0 to 1. These new overlap measures quantify self-consistency of sampling in multitrajectory MD experiments, a necessary condition for converged sampling. A comprehensive assessment of sampling quality of MD experiments identifies the combination of diverse trajectory sets and aMD as the most efficient approach among those tested. However, analysis of Odens between conventional and aMD trajectories also reveals that we have not completely corrected aMD sampling for the distorted energy landscape. Moreover, for V3, the courses of Nc and Odens indicate that much higher resources than those generally invested today will probably be needed to achieve convergence. The comparative analysis also shows that conventional MD simulations with insufficient sampling can be easily misinterpreted as being converged.

The Low-Cost Compound Lignosulfonic Acid (LA) Exhibits Broad-Spectrum Anti-HIV and Anti-HSV Activity and Has Potential for Microbicidal Applications.

OBJECTIVES: Lignosulfonic acid (LA), a low-cost lignin-derived polyanionic macromolecule, was extensively studied for its anti-HIV and anti-HSV activity in various cellular assays, its mechanism of viral inhibition and safety profile as potential microbicide. RESULTS: LA demonstrated potent inhibitory activity of HIV replication against a wide range of R5 and X4 HIV strains and prevented the uptake of HIV by bystander CD4+ T cells from persistently infected T cells in vitro (IC50: 0.07 - 0.34 µM). LA also inhibited HSV-2 replication in vitro in different cell types (IC50: 0.42 - 1.1 µM) and in rodents in vivo. Furthermore, LA neutralized the HIV-1 and HSV-2 DC-SIGN-mediated viral transfer to CD4+ T cells (IC50: ~1 µM). In addition, dual HIV-1/HSV-2 infection in T cells was potently blocked by LA (IC50: 0.71 µM). No antiviral activity was observed against the non-enveloped viruses Coxsackie type B4 and Reovirus type 1. LA is defined as a HIV entry inhibitor since it interfered with gp120 binding to the cell surface of T cells. Pretreatment of PBMCs with LA neither increased expression levels of cellular activation markers (CD69, CD25 and HLA-DR), nor enhanced HIV-1 replication. Furthermore, we found that LA had non-antagonistic effects with acyclovir, PRO2000 or LabyA1 (combination index (CI): 0.46 - 1.03) in its anti-HSV-2 activity and synergized with tenofovir (CI: 0.59) in its anti-HIV-1 activity. To identify mechanisms of LA resistance, we generated in vitro a mutant HIV-1 NL4.3LAresistant virus, which acquired seven mutations in the HIV-1 envelope glycoproteins: S160N, V170N, Q280H and R389T in gp120 and K77Q, N113D and H132Y in gp41. Additionally, HIV-1 NL4.3LAresistant virus showed cross-resistance with feglymycin, enfuvirtide, PRO2000 and mAb b12, four well-described HIV binding/fusion inhibitors. Importantly, LA did not affect the growth of vaginal Lactobacilli strains. CONCLUSION: Overall, these data highlight LA as a potential and unique low-cost microbicide displaying broad anti-HIV and anti-HSV activity.

HIV-1 Coreceptor Usage Assessment by Ultra-Deep Pyrosequencing and Response to Maraviroc.

BACKGROUND: Maraviroc is an HIV entry inhibitor that alters the conformation of CCR5 and is poorly efficient in patients infected by viruses that use CXCR4 as an entry coreceptor. The goal of this study was to assess the capacity of ultra-deep pyrosequencing (UDPS) and different data analysis approaches to characterize HIV tropism at baseline and predict the therapeutic outcome on maraviroc treatment. METHODS: 113 patients with detectable HIV-1 RNA on HAART were treated with maraviroc. The virological response was assessed at months 1, 3 and 6. The sequence of the HIV V3 loop was determined at baseline and prediction of maraviroc response by different software and interpretation algorithms was analyzed. RESULTS: UDPS followed by analysis with the Pyrotrop software or geno2pheno algorithm provided better prediction of the response to maraviroc than Sanger sequencing. We also found that the H34Y/S substitution in the V3 loop was the strongest individual predictor of maraviroc response, stronger than substitutions at positions 11 or 25 classically used in interpretation algorithms. CONCLUSIONS: UDPS is a powerful tool that can be used with confidence to predict maraviroc response in HIV-1-infected patients. Improvement of the predictive value of interpretation algorithms is possible and our results suggest that adding the H34S/Y substitution would substantially improve the performance of the 11/25/charge rule.

Generative models of conformational dynamics.

Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods for learning generative models from atomistic simulation data. Here, the term 'generative' refers to a model of the joint probability distribution over the behaviors of the constituent atoms. In the context of molecular modeling, generative models reveal the correlation structure between the atoms, and may be used to predict how the system will respond to structural perturbations. We begin by discussing traditional methods, which produce multivariate Gaussian models. We then discuss GAMELAN (GRAPHICAL MODELS OF ENERGY LANDSCAPES), which produces generative models of complex, non-Gaussian conformational dynamics (e.g., allostery, binding, folding, etc.) from long timescale simulation data.

Prediction of virological response and assessment of resistance emergence to the HIV-1 attachment inhibitor BMS-626529 during 8-day monotherapy with its prodrug BMS-663068.

BACKGROUND: BMS-663068 is the phosphonooxymethyl prodrug of BMS-626529, a small-molecule attachment inhibitor that targets the HIV-1 envelope glycoprotein gp120 preventing it from binding to CD4 T cells. In vitro investigations have demonstrated considerable variation in susceptibility of different HIV-1 isolates to BMS-626529. BMS-663068 monotherapy in HIV-1-infected subjects produced a mean maximum change from baseline of -1.64 log10 copies per milliliter, but the response was variable. METHODS: In this analysis, baseline and day 8 samples were analyzed for susceptibility to BMS-626529 and the presence of known HIV-1 attachment inhibitor resistance mutations. In addition, predictors of virological response (maximal HIV-1 RNA decline ≥1 log10 copies per milliliter) and resistance selection were investigated. RESULTS: The only factor associated with reduced virological response was low baseline susceptibility to BMS-626529. There was no apparent relationship between virological response and baseline treatment experience, coreceptor tropism, plasma HIV-1 RNA level, or CD4 T-cell count. Examination of all positions with known BMS-626529 resistance mutations based on in vitro selection studies showed that gp120 M426L was the primary substitution most clearly associated with nonresponse to BMS-663068. There was minimal change in susceptibility to BMS-626529 over the course of the study and no clear evidence of emergence of a known HIV-1 attachment inhibitor resistance mutation in the majority of subjects as measured by standard population-based phenotypic and genotypic approaches. CONCLUSIONS: Nonresponse to BMS-663068 was associated with low baseline susceptibility to BMS-626529 and the presence of M426L. In this short-term trial, there was minimal evidence of selection for BMS-626529 high-level resistance over 8 days of monotherapy with BMS-663068 by population-based approaches.

Human immunodeficiency virus type-1 (HIV-1) continues to evolve in presence of broadly neutralizing antibodies more than ten years after infection.

BACKGROUND: The evolution of HIV-1 and its immune escape to autologous neutralizing antibodies (Nabs) during the acute/early phases of infection have been analyzed in depth in many studies. In contrast, little is known about neither the long-term evolution of the virus in patients who developed broadly Nabs (bNabs) or the mechanism of escape in presence of these bNabs. RESULTS: We have studied the viral population infecting a long term non progressor HIV-1 infected patient who had developed broadly neutralizing antibodies toward all tier 2/3 viruses (6 clades) tested, 9 years after infection, and was then followed up over 7 years. The autologous neutralization titers of the sequential sera toward env variants representative of the viral population significantly increased during the follow-up period. The most resistant pseudotyped virus was identified at the last visit suggesting that it represented a late emerging escape variant. We identified 5 amino acids substitutions that appeared associated with escape to broadly neutralizing antibodies. They were V319I/S, R/K355T, R/W429G, Q460E and G/T463E, in V3, C3 and V5 regions. CONCLUSION: This study showed that HIV-1 may continue to evolve in presence of both broadly neutralizing antibodies and increasing autologous neutralizing activity more than 10 years post-infection.

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction.

UNLABELLED: We describe handalign, a software package for Bayesian reconstruction of phylogenetic history. The underlying model of sequence evolution describes indels and substitutions. Alignments, trees and model parameters are all treated as jointly dependent random variables and sampled via Metropolis-Hastings Markov chain Monte Carlo (MCMC), enabling systematic statistical parameter inference and hypothesis testing. handalign implements several different MCMC proposal kernels, allows sampling from arbitrary target distributions via Hastings ratios, and uses standard file formats for trees, alignments and models. AVAILABILITY AND IMPLEMENTATION: Installation and usage instructions are at http://biowiki.org/HandAlign.

Quantitative assessment of masking of neutralization epitopes in HIV-1.

Despite the frequent observation of masking of HIV-1 neutralization epitopes, its extent has not been previously systematically assessed either for multiple epitopes presented by individual viruses or for individual epitopes across multiple viral strains. Using a recently developed method to identify amino acid sequence motifs required for recognition by HIV-1-neutralizing monoclonal antibodies (mAbs), we visualized the patterns of masking of specific epitopes targeted by mAbs in a diverse panel of HIV-1 isolates. We also calculated a specific masking intensity score for each virus based on the observed neutralization activity of mAbs against the epitopes in the virus. Finally, we combined these data with estimates of the conservation of each mAb-targeted epitope in circulating HIV-1 strains to estimate the effective neutralization potential (E(N)) for each mAb. Focusing on the V3 loop of gp120 as a prototype neutralization domain, we found that the V3 loop epitope targeted by mAb 2219 is one of the least masked mAbs and it has the highest E(N). Interestingly, although the V3 loop epitope targeted by mAb 3074 is present in over 87% of all viruses, it is 82.2% masked, so its E(N) is lower than that for mAb 2219. Notably, 50% of the viruses that mAb 3074 is able to neutralize are classified as subtype C viruses, while 70% or more of the viruses neutralized by mAbs 2219, 2557 or 447-52D are classified as subtype B. Thus, neutralization epitopes (in this case, in the V3 loop) have differential patterns of masking and also display distinct patterns of distribution among circulating HIV-1 viruses. Both factors combine to contribute to the practical vaccine value of any single epitope/mAb. Here we have developed a quantitative score for this value. These results have important implications for rational design of vaccines designed to induce neutralizing Abs by revealing epitopes that are minimally masked and maximally reactive with neutralizing Abs.

Assessment of immunologically relevant dynamic tertiary structural features of the HIV-1 V3 loop crown R2 sequence by ab initio folding.

The antigenic diversity of HIV-1 has long been an obstacle to vaccine design, and this variability is especially pronounced in the V3 loop of the virus' surface envelope glycoprotein. We previously proposed that the crown of the V3 loop, although dynamic and sequence variable, is constrained throughout the population of HIV-1 viruses to an immunologically relevant ß-hairpin tertiary structure. Importantly, there are thousands of different V3 loop crown sequences in circulating HIV-1 viruses, making 3D structural characterization of trends across the diversity of viruses difficult or impossible by crystallography or NMR. Our previous successful studies with folding of the V3 crown used the ab initio algorithm accessible in the ICM-Pro molecular modeling software package (Molsoft LLC, La Jolla, CA) and suggested that the crown of the V3 loop, specifically from positions 10 to 22, benefits sufficiently from the flexibility and length of its flanking stems to behave to a large degree as if it were an unconstrained peptide freely folding in solution. As such, rapid ab initio folding of just this portion of the V3 loop of any individual strain of the 60,000+ circulating HIV-1 strains can be informative. Here, we folded the V3 loop of the R2 strain to gain insight into the structural basis of its unique properties. R2 bears a rare V3 loop sequence thought to be responsible for the exquisite sensitivity of this strain to neutralization by patient sera and monoclonal antibodies. The strain mediates CD4-independent infection and appears to elicit broadly neutralizing antibodies. We demonstrate how evaluation of the results of the folding can be informative for associating observed structures in the folding with the immunological activities observed for R2.

Organization of cellular receptors into a nanoscale junction during HIV-1 adhesion.

The fusion of the human immunodeficiency virus type 1 (HIV-1) with its host cell is the target for new antiretroviral therapies. Viral particles interact with the flexible plasma membrane via viral surface protein gp120 which binds its primary cellular receptor CD4 and subsequently the coreceptor CCR5. However, whether and how these receptors become organized at the adhesive junction between cell and virion are unknown. Here, stochastic modeling predicts that, regarding binding to gp120, cellular receptors CD4 and CCR5 form an organized, ring-like, nanoscale structure beneath the virion, which locally deforms the plasma membrane. This organized adhesive junction between cell and virion, which we name the viral junction, is reminiscent of the well-characterized immunological synapse, albeit at much smaller length scales. The formation of an organized viral junction under multiple physiopathologically relevant conditions may represent a novel intermediate step in productive infection.

Quantum dot-based HIV capture and imaging in a microfluidic channel.

Globally, over 33.2 million people who mostly live in developing countries with limited access to the appropriate medical care suffer from the human immunodeficiency virus (HIV) infection. We developed an on-chip HIV capture and imaging method using quantum dots (Qdots) from fingerprick volume (10 microl) of unprocessed HIV-infected patient whole blood in anti-gp120 antibody-immobilized microfluidic chip. Two-color Qdots (Qdot525 and Qdot655 streptavidin conjugates) were used to identify the captured HIV by simultaneous labeling the envelope gp120 glycoprotein and its high-mannose glycans. This dual-stain imaging technique using Qdots provides a new and effective tool for accurate identification of HIV particles from patient whole blood without any pre-processing. This on-chip HIV capture and imaging platform creates new avenues for point-of-care diagnostics and monitoring applications of infectious diseases.

Genetic characterization of HIV-1 BC recombinants and evolutionary history of the CRF31_BC in Southern Brazil.

To evaluate the recombination profiles and evolutionary history of HIV-1 BC recombinants in Southern Brazil, 81 isolates collected in the city of Porto Alegre (Rio Grande do Sul State) from 1998 to 2006 previously subtyped as C (env-gp120/C2V3) were screened in the protease-reverse transcriptase (pr/rt), integrase and gp41 genomic regions. Detailed phylogenetic, bootscan and informative site analyses were performed to trace the subtype classification. The evolutionary rate and divergence time of the Brazilian CRF31_BC epidemic were estimated using a Bayesian Markov Chain Monte Carlo framework. Analysis of the four target regions identified: 43 isolates as "pure" subtype C, 23 as CRF31_BC, and 15 as unique BC recombinant forms (URFs_BC). Recombination breakpoints were mainly localized in the rt gene and 100% of the recombinant samples could be detected analyzing only this region. Most URFs_BC (86.7%) contained small subtype B fragments (

Two-dimensional gel-based approaches for the assessment of N-Linked and O-GlcNAc glycosylation in human and simian immunodeficiency viruses.

The glycosylation state of envelope glycoproteins in human and simian immunodeficiency viruses (HIV/SIV) is critical to viral infectivity and tropism, viral protein processing, and in virus evasion of the immune system. Using a rapid fluorescent 2-D gel-based method coupled with enzymatic pre-treatment of virus with PNGase F (Peptide: N-Glycosidase F) and fluorescent 2-D gels or 2-D gel Western blotting, we show significant differences in the glycosylation patterns of two SIV strains widely used in animal models of HIV disease and vaccine studies. We also demonstrate the modification of a host protein important in HIV biology (HLA-DR) by O-GlcNAc. Further, this experimental pipeline allows for the identification of the modified protein and the site of N-linked glycosylation by fluorescent 2-DE coupled with MS and the qualitative and semi-quantitative assessment of viral glycosylation. The method is fully compatible with downstream glycomics analysis. This approach will permit correlation of virus glycosylation status with pathological severity and may serve as a rapid screen of viruses from physiological samples for further study by more advanced MS methodology.

Analysis of the neutralization breadth of the anti-V3 antibody F425-B4e8 and re-assessment of its epitope fine specificity by scanning mutagenesis.

The identification of cross-neutralizing antibodies to HIV-1 is important for designing antigens aimed at eliciting similar antibodies upon immunization. The monoclonal antibody (mAb) F425-B4e8 had been suggested previously to bind an epitope at the base of V3 and shown to neutralize two primary HIV isolates. Here, we have assessed the neutralization breadth of mAb F425-B4e8 using a 40-member panel of primary HIV-1 and determined the epitope specificity of the mAb. The antibody was able to neutralize 8 clade B viruses (n=16), 1 clade C virus (n=11), and 2 clade D viruses (n=6), thus placing it among the more broadly neutralizing anti-V3 antibodies described so far. Contrary to an initial report, results from our scanning mutagenesis of the V3 region suggest that mAb F425-B4e8 interacts primarily with the crown/tip of V3, notably Ile(309), Arg(315), and Phe(317). Despite the somewhat limited neutralization breadth of mAb F425-B4e8, the results presented here, along with analyses from other cross-neutralizing anti-V3 mAbs, may facilitate the template-based design of antigens that target V3 and permit neutralization of HIV-1 strains in which the V3 region is accessible to antibodies.