Search Results (491)

The molecular epidemiology and antiretroviral (ARV) drug resistance of human immunodeficiency virus type 1 (HIV-1) remain incompletely outlined in the Middle East and North Africa (MENA). The aim of this retrospective molecular epidemiology study was to analyze MENA HIV-1 sequences for phylogenetic clustering and to delineate surveillance drug-resistance mutations (SDRMs) for nucleoside reverse-transcriptase inhibitors (NRTIs), non-nucleoside reverse-transcriptase inhibitors (NNRTIs), and protease inhibitors (PIs) across various periods, locations, and subtypes/circulating recombinant forms (CRFs). Viral sequences were retrieved from the Los Alamos HIV Sequence Database as of 15 April 2026. Analyses were done using multiple sub-gene regions (two env regions (n = 224 and n = 60) and PR (n = 2413) and RT (n = 2103) of the pol gene). Phylogeny construction was conducted using maximum-likelihood estimation, while ARV drug resistance analysis was conducted using the Stanford HIVdb algorithm. The HIV-1 MENA sequences showed a remarkable genetic diversity, with co-circulation of multiple subtypes/CRFs, including subtype B in the Maghreb, Levant, and Egypt sub-regions, subtypes A1, G, CRF01_AE, and CRF02_AG in the Gulf Cooperation Council (GCC) and Yemen sub-region, and subtypes C and D in the Horn of Africa and Sudan sub-region. The percentage of MENA HIV-1 sequences in clusters was 10.3% for env1, 8.3% for env2, 22.0% for PR and 37.2% for RT. Phylogenetic reconstruction hinted at a structured epidemic dominated by small transmission units, with most clusters comprising dyads (n = 260) or networks (n = 142) and a limited number of large clusters (n = 8) that were largely confined within national boundaries, with only occasional cross-border linkages (n = 8). Overall SDRM prevalence was 3.2% in the PR region and 14.9% in the RT region, with a higher percentage of NNRTI-associated mutations (10.0%) than NRTI-associated mutations (9.1%) and dual-class resistance observed in 4.1% of sequences. Phylogenetic clustering was not associated with the probability of harboring SDRMs; however, negative binomial models showed that non-clustered sequences had a greater burden of NRTI-associated mutations, whereas no such association was observed for NNRTI- or PI-associated mutations. The findings showed predominantly localized and fragmented MENA HIV-1 transmission dynamics. Heterogeneous ARV drug resistance dynamics indicated that resistance emergence might be shaped by broader epidemiologic and treatment-related factors rather than ongoing clustered transmission. There is a need for coordinated molecular surveillance and optimized ART strategies across the MENA countries. Full article

Background/Objectives: Transfusion-transmitted infections (TTIs) remain an important concern in blood safety. Nucleic acid amplification testing (NAT) shortens the diagnostic window period relative to conventional serological assays. This study aimed to determine the prevalence of Hepatitis B virus(HBV), Hepatitis C virus (HCV), and Human immunodeficiency virus (HIV) among blood donors and to evaluate concordance between NAT and conventional serological screening methods. Methods: A retrospective cross-sectional study was conducted at Riyadh Regional Laboratory from May 2021 to May 2022 and included 48,901 blood donors. Donor samples were tested for HBV, HCV, and HIV using serological assays (chemiluminescent immunoassays on the Abbott Alinity s system) and NAT. Data were analyzed using SPSS. Results: The prevalence of HCV was 0.149% by serological testing and 0.061% by NAT. HBV prevalence was 0.252% by serology and 0.264% by NAT, while HIV prevalence was 0.041% and 0.037%, respectively. NAT identified 25 seronegative but NAT-reactive donations, including 13 HBV, 11 HCV, and 1 HIV donation. A statistically significant difference between NAT and serology was observed for HCV (p < 0.001, McNemar’s test), but not for HBV (p = 0.180) or HIV (p = 0.317). Conclusions: The prevalence of major viral TTIs among blood donors was low, with HBV being the most frequently detected infectious agent. NAT and serological assays provide complementary information and support the continued use of combined screening strategies to enhance transfusion safety. Full article

Human viral entry receptor mouse models exist to overcome a fundamental experimental barrier: many clinically important viruses bind their human entry factors far more efficiently than the corresponding murine orthologs, leaving conventional mice unable to support authentic infection, physiological tissue tropism, or meaningful countermeasure evaluation. This review is organized around the receptor-humanization concept rather than around a single coronavirus model. Engineering strategies compared here include random transgenesis, endogenous-locus knock-in, minimal receptor-interface humanization, conditional and inducible expression, and transient vector-mediated delivery. Receptor systems covered span human angiotensin-converting enzyme 2 (hACE2)-dependent sarbecoviruses, human dipeptidyl peptidase 4 (hDPP4)-dependent Middle East respiratory syndrome coronavirus (MERS-CoV), human cluster of differentiation 4/human C-C chemokine receptor type 5 (hCD4/hCCR5)-dependentt human immunodeficiency virus type 1 (HIV-1), adenovirus receptor models, human intercellular adhesion molecule 1 (hICAM-1) rhinovirus systems, hepatitis C virus (HCV), hepatitis B virus (HBV), and hepatitis D virus (HDV) entry-factor models, measles receptor models, poliovirus receptor/CD155 (PVR/CD155) models, human scavenger receptor class B member 2 (hSCARB2) enterovirus systems, and human transferrin receptor 1 (hTfR1) arenavirus models. We then discuss how these platforms support antibody evaluation, Fc-effector analysis, vaccine protection, variant benchmarking, and safety assessment. These models yield the most reliable data when the experimental question is explicitly entry-dependent and when receptor expression level, anatomical distribution, pathology window, and immune context have all been independently validated. They are least informative when receptor expression is non-physiological, when disease readouts are driven by promoter artifacts, or when post-entry species barriers remain the dominant bottleneck. A validation-centered framework is therefore proposed to guide the selection of each model for the specific antiviral antibody or vaccine question it can legitimately answer. Full article

Retroviruses induce immunosuppression in their infected hosts. This phenomenon is well described for the immunodeficiency viruses, with human immunodeficiency virus type 1 (HIV-1) representing the best-studied example, but it also occurs in other retroviral infections. Immunosuppressive properties were first characterized in murine leukemia viruses (MuLV). Additional well-studied examples include feline leukemia virus (FeLV) and koala retrovirus (KoRV). Investigations into the mechanisms underlying retrovirus-induced immunosuppression revealed that not only inactivated viral particles but also their purified transmembrane (TM) envelope proteins exhibit immunosuppressive activity. However, in certain retroviral infections, additional viral proteins contribute to the immunosuppression in vivo. Within the TM envelope proteins, a highly conserved region—designated the immunosuppressive (isu) domain—was identified. Synthetic peptides corresponding to this domain suppress a wide range of in vitro immune responses, possibly by regulating Ras-Raf-MEK-MAPK and PI3K-AKT-mTOR pathways. They modulate cytokine release and alter gene expression in immune cells, mirroring the activity of the corresponding TM envelope protein. Mutations in the sequence abrogate the effect. Numerous TM envelope proteins have demonstrated immunosuppressive activity in vivo in a tumor rejection model, and mutations within the isu domain also abrogate this function. These studies have important implications for reproduction, particularly through the immunosuppressive syncytins in the placenta, for tumor development, where similar mechanisms may protect cancer cells from the host immune system, and for vaccine development and xenotransplantation. Notably, immunization with TM envelope proteins carrying mutations in the isu domain elicits stronger immune responses compared with the wild-type proteins. Finally, the potential of retroviral TM envelope proteins to protect xenotransplants from immune rejection will be discussed. Full article

Over a decade of advances in Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9 (Cas9)-based technologies have culminated in the first-ever FDA-approved CRISPR/Cas-based therapy. Aside from this approved therapy for sickle cell anemia, several CRISPR/Cas-based therapies are currently under development or testing for a range of chronic diseases, including viral diseases like human immunodeficiency virus type 1 (HIV-1) infection, genetic diseases like familial hypercholesterolemia, and cancer. The success of these therapies hinges on the effective delivery of CRISPR/Cas9 components to target regions, efficient Cas endonuclease editing, repair profiles generated, and their resulting outcomes. Here, we discuss the factors that influence the generation of CRISPR/Cas9-generated repair edits, the overall profiles, and outcome prediction(s), as well as the analytical tools that have been developed to date. Finally, how this technology has been used towards a functional HIV-1 cure is discussed. Full article

Human immunodeficiency virus type 1 exhibits extensive genetic diversity, which has important implications for molecular epidemiology, recombinant-pattern assessment, and antiretroviral resistance surveillance. In Mexico, HIV-1 molecular surveillance has historically relied mainly on partial pol gene sequencing, limiting the ability to compare lineage assignments across gag, pol, and env regions. We analyzed plasma samples from 40 treatment-naïve adults receiving care at a tertiary-care hospital in Mexico using a commercial amplicon-based multiregion HIV-1 genomic sequencing workflow. DeepChek^® was used as the primary workflow for read processing, mutation calling, region-level subtype assignment, and antiretroviral resistance interpretation. Resistance interpretation was restricted to antiretroviral target regions with sufficient coverage, mainly reverse transcriptase, protease, integrase, and capsid, when available. Drug resistance mutations were identified in 6/40 participants (15.0%) when mutation-level resistance findings in RT, PR, and IN were considered; one additional sample showed a capsid inhibitor-nonsusceptible NGS call. NNRTI-associated findings were identified in 2/40 patients (5.0%), whereas NRTI- and PI-associated findings were identified in 1/40 patients (2.5%). Accessory or secondary INSTI-associated substitutions were detected in 2/40 patients (5.0%). Region-level subtype analysis revealed frequent discordant assignments across amplified segments, which is consistent with complex mosaic profiles; however, these findings are interpreted as region-level subtypes and recombinant-pattern assignments rather than continuous whole-genome recombination maps. One sample had insufficient RT/PROT/INT coverage for drug resistance interpretation in the complete DeepChek report and was retained only for regions meeting quality thresholds. These findings support the value of multiregion HIV-1 sequencing for local molecular surveillance while emphasizing the need for transparent region-level coverage reporting, cautious interpretation of recombinant-pattern calls, and transparent repository reporting. Full article

HP1090 is a short, cationic, amphipathic peptide derived from scorpion venom and previously described as a membrane-active antiviral compound. Here, we primarily characterize the antiviral activity of HP1090 and assess whether additional antibacterial effects are consistent with membrane-disruptive properties. Chemically synthesized HP1090 exhibited dose-dependent virucidal activity against multiple enveloped viruses, including herpes simplex virus type 1 and 2 (HSV-1, HSV-2), human immunodeficiency virus type 1 (HIV-1), and Zika virus (ZIKV), with IC₅₀ values ranging from 14.7 to 56.1 µg/mL. No activity was observed against the non-enveloped human rhinovirus 14 (HRV14), suggesting strict dependence on a viral lipid envelope. Consistent with a membrane-targeting mechanism, HP1090 induced rapid and concentration-dependent permeabilization of virus-like liposomes. HP1090 also displayed antibacterial activity against selected clinically relevant pathogens in agar-based growth inhibition assays. However, antibacterial effects required substantially higher concentrations (>125 µg/mL) and varied between bacterial species, with some strains showing little or no susceptibility. Membrane permeabilization assays in Listeria monocytogenes demonstrated disruption of bacterial membrane integrity as a contributing mechanism. No cytotoxicity was observed on mammalian cell lines at effective antiviral concentrations. Together, these findings establish HP1090 as a membrane-active venom peptide and, by linking envelope-dependent viral inactivation with bacterial membrane permeabilization, support a shared biophysical mode of action relevant to the development of membrane-targeting anti-infectives. Full article

The extraordinary genetic diversity of human immunodeficiency virus type 1 (HIV-1), driven by high mutation and recombination rates, poses significant challenges for diagnostics, therapy, and vaccine development. While variable regions enable immune escape, hyperconserved regions are critical for viral function and represent promising targets for novel therapeutic interventions. This study aimed to develop and validate a bioinformatic algorithm for quantitative assessment of sequence conservation and automated identification of functionally significant conserved regions across all major HIV-1 proteins. A total of 1119 full-length HIV-1 genome sequences representing major subtypes (A1, A2, A6, B, C, D, F1, F2, G, H, J, K) were analyzed. Normalized Shannon entropy (S-index) was calculated for each alignment column. Statistical thresholds for conserved regions were established using 95% confidence intervals derived from bootstrap resampling. Two complementary algorithms, clustering and local maxima detection, were applied to identify conserved regions, which were subsequently mapped to known functional domains based on literature data. Protein conservation varied markedly, with S_m values ranging from 0.784 (Vpu) to 0.920 (Pol). Gag, Pol, and Vpr demonstrated the highest overall conservation, while Env, Rev, Tat, and Vpu exhibited pronounced variability interspersed with conserved domains. In total, 25 conserved regions in Gag, 49 in Pol, 28 in Env, and 6–4 regions in accessory proteins (Vif, Vpr, Rev, Tat, Nef, Vpu) were identified. These regions corresponded to critical functional elements including enzyme catalytic centers, zinc fingers, receptor-binding sites, protein interaction interfaces, and membrane-anchoring domains. The developed computational framework enables statistically grounded identification of evolutionarily constrained regions across analyzed HIV-1 subtypes. The identified conserved regions represent candidate sites for further investigation and may inform downstream studies focused on antiviral target prioritization, immunogen design, and diagnostic assay development. However, their translational applicability requires additional analytical, structural, and experimental validation. Full article

Background: Among the complications caused directly or indirectly by the Human Immunodeficiency Virus (HIV) are alterations in the auditory system. Children who are HIV-exposed but uninfected (HEU) appear to have a higher risk of hearing loss (HL) compared to their unexposed peers, but a lower risk than those infected with HIV. However, the literature remains inconclusive regarding this association. This study aims to evaluate the hearing function of HEU infants during the first months of life and to correlate these findings with maternal, gestational, and neonatal variables. Methods: This prospective cohort study included all HIV-exposed infants born in a quaternary hospital in southern Brazil between 2021 and 2023. Maternal, gestational, and neonatal data were collected, as well as the results of neonatal auditory screening. At approximately 6 months of age, otolaryngological and audiological assessments were performed, including wideband tympanometry and electrophysiological evaluation using Auditory Brainstem Response with frequency-specific stimuli. The prevalence of hearing loss refers to the number of infants affected. Results: Thirty-eight infants, with a mean age of 8 months (±3.3), completed the study. Of these, 1 (2.6%) presented with bilateral sensorineural HL, and 13 (34.2%) presented with conductive HL, with 6 cases being unilateral and 7 bilateral. No associations were found between hearing loss and maternal, gestational, or neonatal variables, except for maternal CD4 count, where higher CD4 cell counts were associated with an increased risk of conductive HL. Conclusion: The findings provide relevant data on auditory alterations in HEU infants, demonstrating a high prevalence of conductive HL. These results highlight the importance of monitoring the hearing of these children during the first years of life. Full article

The prevalence of chronic conditions such as hypertension, diabetes, and Human Immunodeficiency Virus (HIV) is rising globally, yet access to continuous care remains limited, particularly in rural low- and middle-income countries. This study evaluated the acceptability and psychosocial predictors of retention in a linkage-to-care (LTC) intervention for patients with chronic conditions in rural South Africa. We conducted a cross-sectional analytical study with a retrospective cohort component among 1673 patients diagnosed with hypertension, diabetes, and/or HIV in Limpopo Province, South Africa. Acceptability and psychosocial factors were assessed cross-sectionally using a theory-informed, interviewer-administered questionnaire between January and June 2024. Retention in care over the preceding six months (July–December 2023) was extracted from routine clinic records and classified as consistent (no gaps > 6 months between visits) or inconsistent (≥1 gap > 6 months. Logistic regression examined associations between psychosocial factors and retention outcomes, adjusting for age, gender, marital status, and diagnostic category. Overall, 25.1% of participants maintained consistent retention over six months, while 74.9% were retained inconsistently. Acceptability of the LTC intervention varied significantly by diagnosis (p < 0.001): 79.5% of participants with multimorbidity rated the intervention as acceptable compared to 54.9% with hypertension, 64.5% with diabetes, and 46.8% with HIV. However, only 12.8% of multimorbid participants agreed that intervention activities fit well with their daily lives. In adjusted analyses, participants who were not happy to participate had 85% lower odds of consistent retention (adjusted odds ratio [AOR] = 0.15, 95% CI: 0.09–0.22) and 7.2 times higher odds of inconsistent retention (AOR = 7.2, 95% CI: 4.8–10.9). Most participants supported de-identified data sharing, though privacy concerns were elevated among those with multimorbidity. Acceptability of LTC interventions differs by diagnosis, with multimorbid patients reporting poorer alignment with daily routines. Retention is strongly associated with emotional engagement and self-efficacy, suggesting that LTC interventions should integrate psychosocial support and be contextually adapted for multimorbid patients in rural settings. Full article

Natural bioactive polysaccharides have been investigated for their ability to modulate antiviral immune responses. Polysaccharide peptide (PSP) from Coriolus versicolor previously restricted human immunodeficiency virus type 1 (HIV-1) entry into monocytic cells through a protein kinase R (PKR)-dependent cytoskeletal mechanism. However, its impact on antiviral signaling in adaptive cluster of differentiation 4 (CD4)+ T-cell models remains incompletely defined. Here, we evaluated concentration- and time-dependent effects of PSP (50–1000 µg/mL) in Jurkat T cells over 3 and 6 days. Cell viability was assessed by MTT, trypan blue exclusion, and viable cell density analysis. Immunoblotting and reverse transcription quantitative polymerase chain reaction (RT-qPCR) were performed to examine Toll-like receptor 4 (TLR4), nuclear factor kappa B (NF-κB), signal transducer and activator of transcription 1 and 2 (STAT1/STAT2), PKR, interferon gamma (IFN-γ), and cofilin-1 signaling. PSP did not induce cytotoxicity at any concentration. Instead, PSP promoted dose- and time-dependent upregulation of intracellular TLR4, PKR, phospho-PKR (Thr446), Cofilin-1, phospho-Cofilin-1 (Ser3), phospho-STAT1 (Tyr701), phospho-STAT2 (Tyr690), phospho-NF-κB (Ser536), and IFN-γ, with amplified responses at Day 6. These changes were paralleled by transcriptional induction of antiviral-associated genes. Collectively, PSP induces coordinated interferon (IFN)-associated and cytoskeletal regulatory signaling in Jurkat T cells without cytotoxicity, providing a mechanistic framework for future evaluation of viral permissiveness and antiviral responses in adaptive immune models. Full article

The block-and-lock strategy aims to achieve a functional cure for human immunodeficiency virus type 1 (HIV-1) infection by enforcing durable, drug-independent silencing of proviral transcription. Several latency-promoting agents have been described that effectively limit viral reactivation in vitro or in animal models. However, most approaches induce only partial or reversible transcriptional repression and have not yet been translated into safe and effective clinical interventions. This review summarizes the molecular mechanisms underlying block-and-lock strategies and critically evaluates the limitations of current candidate compounds. We highlight recent advances in understanding HIV-1 integration site selection, focusing on the roles of lens epithelium-derived growth factor p75 (LEDGF/p75) and cleavage and polyadenylation specificity factor subunit 6 (CPSF6) in directing proviral integration toward gene-dense, transcriptionally active chromatin. Pharmacological disruption of the LEDGF/p75–integrase interaction by LEDGF/p75 inhibitors (LEDGINs) redirects proviral integration toward less transcriptionally active genomic regions that are more resistant to reactivation. Recent tandem knockout experiments, however, demonstrate that CPSF6 plays a dominant role in guiding HIV-1 integration toward gene-dense, transcriptionally active chromatin. LEDGIN treatment has been linked to the preferential targeting of proviruses to heterochromatin-rich regions within the nuclear interior. By contrast, CPSF6 knockout redirects integration toward peripheral heterochromatin, especially lamina-associated domains (LADs), genomic regions typically exhibiting stronger and more stable transcriptional repression than interior heterochromatin. These findings suggest that therapeutic modulation of CPSF6 may exert a more profound and durable effect on proviral silencing within a block-and-lock framework. Nevertheless, complete CPSF6 ablation is associated with severe cellular toxicity. The challenges associated with CPSF6-related adverse effects and potential strategies to overcome these limitations are discussed. Full article

Six 1,4-disubstituted pyrazoles linked to a benzenesulfonamide and a benzodioxane unit have been synthesized through a copper(I)-catalyzed formal [3+2] cycloaddition (32CA) reaction of alkynes with 3-arylsydnones. The Cu-catalyzed sydnone–alkyne cycloaddition (CuSAC) procedure has been optimized to promote the formation of the pyrazole ring and to deliver in three steps the six target compounds 5a–f, fully characterized by ¹H/¹³C-NMR and mass spectrometry (EIMS). Ten solvent conditions were evaluated. The reaction proceeded most efficiently in the presence of copper(II) sulfate pentahydrate in aqueous t-butanol in the presence sodium acetate, to reach a yield of 96%. The mechanism of the Cu(I)-catalyzed reaction has been studied within the Molecular Electron Density Theory (MEDT). This rection is a domino process that consists in a Cu(I)-catalyzed formal [3+2] cycloaddition followed of an extrusion of CO₂ yielding the final pyrazole. The capacity of heterocyclic compounds 5a–f to interact with human cyclophilin A (Cyp A), which is a host cofactor for hepatitis C virus (HCV) and human immunodeficiency virus 1 (HIV-1), and with the HIV-1 protein gp120-CD4 was evaluated using molecular docking. Compounds 5a,b,d,f showed a satisfactory protein binding capacity. The physicochemical and metabolic properties of the compounds were also evaluated in silico. These predictions provide important information to guide future design in this series of potential antiviral agents. Full article

Despite the remarkable success of antiretroviral therapy (ART) in suppressing human immunodeficiency virus type 1 (HIV-1) replication, viral persistence remains a major barrier to cure. This persistence is sustained by heterogeneous cellular reservoirs in which viral expression is tightly regulated by host-dependent molecular mechanisms. Beyond the canonical cluster of differentiation 4 (CD4+) T-cell reservoirs, HIV-1 establishes long-lived infection in myeloid cells, glial populations within the central nervous system (CNS), and additional non-canonical cellular niches, each characterized by distinct transcriptional, epigenetic, and immune environments. In this review, we synthesize recent advances in understanding how HIV-1 expression, latency, and reactivation are shaped across diverse susceptible cell types. We highlight cell-type-specific mechanisms governing viral integration, chromatin organization, transcriptional elongation, innate immune sensing, host restriction factors, and cytoskeletal regulation. Particular emphasis is placed on how host signaling pathways and immune microenvironments contribute to reservoir stability and heterogeneity, complicating eradication strategies. We further discuss immunomodulatory approaches that seek to modulate viral expression without exacerbating immune activation. By integrating molecular, cellular, and immunological perspectives, this review provides a framework for understanding HIV-1 persistence as a context-dependent process and underscores the need for cell-type-tailored strategies in HIV cure research. Full article

Human Immunodeficiency Virus Type 1 (HIV-1), the causative agent of the acquired immune deficiency syndrome (AIDS), originated from zoonotic transmissions of simian immunodeficiency viruses (SIVs) infecting African great apes, following complex cross-species transmission events and virus–host co-evolution. These processes were accompanied by multiple viral adaptations, particularly within structural and accessory genes, enabling evasion of host restriction factors and long-term viral persistence. In 1988, an antisense open reading frame (ORF) overlapping the env gene was proposed and subsequently confirmed by the identification of antisense transcripts and the antisense protein (ASP). An “intact” ASP ORF (defined as >150 codons) is predominantly conserved in pandemic HIV-1 group M viruses and shows evidence of positive selection, suggesting a selective advantage. Increasing evidence supports the hypothesis that the asp gene emerged de novo during the evolution of group M and contributed to viral adaptation and global spread in humans. This review combines a narrative review of the literature with original in silico analyses of HIV-1 and SIV sequences retrieved from the Los Alamos National Laboratory database. We systematically reassessed the distribution, length variability and conservation of the ASP ORF across HIV-1 groups (M, N, O, P), subtypes, circulating recombinant forms (CRFs), unique recombinant forms (URFs) and related SIV lineages. Our updated analyses confirmed the strong association between the presence of an “intact” ASP ORF and pandemic HIV-1 group M lineages, while revealing rare but notable antisense ORFs in selected SIVcpz and SIVgor strains. By integrating evolutionary, epidemiological and sequence-based evidence, we aim to clarify the origin and maintenance of the ASP ORF and to contextualize its emergence within the broader framework of overlapping gene evolution, de novo gene birth and the selective pressures shaping viral fitness and pandemic potential. Full article