Search Results (302)

Human immunodeficiency virus (HIV) remains a major global health challenge, requiring accurate diagnostic testing for early detection. Chemiluminescent immunoassay screening, particularly the Architect HIV Ag/Ab Combo assay, followed by immunoblot confirmation using INNO-LIA™ has traditionally been used in many diagnostic workflows. To address these limitations, the U.S. Centers for Disease Control and Prevention (CDC) recommends the use of an HIV-1/2 antibody differentiation immunoassay, such as the Geenius HIV-1/2 Supplemental Assay, as part of the confirmatory testing algorithm. This study evaluates the performance of two rapid HIV-1/2 confirmatory assays—the Multisure HIV-1/2 Confirmatory Test and the Bio-Rad Geenius HIV-1/2 Supplemental Assay—within a CDC-aligned diagnostic framework, with the aim of assessing Multisure as a potential alternative differentiation assay. A total of 224 archived serum samples were analyzed, including true positives (n = 38), true negatives (n = 139), false positives (n = 20), and INNO-LIA™ indeterminate samples (n = 27), as defined by Architect HIV and INNO-LIA™ results. Samples were initially screened using the Architect HIV Ag/Ab Combo assay, confirmed by INNO-LIA™ and PCR, and subsequently re-tested using Multisure HIV-1/2 and Geenius HIV-1/2 assays. Diagnostic performance metrics were evaluated. Both rapid assays demonstrated 100% sensitivity and specificity when compared with INNO-LIA™. Among INNO-LIA™ indeterminate samples, Multisure HIV-1/2 classified 81.5% as negative compared with 55.6% using Geenius HIV-1/2. When compared with PCR, Multisure demonstrated higher specificity (89.2%) and positive predictive value (89.5%) than Geenius (82.9% and 84.6%). No confirmed HIV-2 infections were identified in the analyzed dataset, and HIV-1 subtype information was not available for the archived samples; therefore, conclusions regarding HIV-1/2 differentiation are based primarily on assay design and antigenic targets. Multisure HIV-1/2 demonstrated strong diagnostic performance comparable to established differentiation assays and may represent a practical alternative rapid confirmatory option within CDC-aligned HIV diagnostic workflows. Further studies including larger datasets and confirmed HIV-2 infections are warranted to further validate its clinical utility. 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

Macrophages differentiated with macrophage colony-stimulating factor (M-CSF) (M-Mac) are widely used as an experimental model. Interleukin 27 (IL-27)-polarized M-Mac (27M-Mac) suppresses HIV replication; however, the effects of IL-27 polarization on granulocyte-macrophage colony-stimulating factor (GM-CSF)-induced macrophages (GM-Mac) remain less investigation. Here, we compare multiple functional properties and gene expression profiles of 27M-Mac and IL-27-polarized GM-Mac (27GM-Mac). M-Mac and GM-Mac were generated from monocytes of healthy donors and subsequently treated with IL-27 for three days. HIV replication in 27M-Mac, GM-Mac, and 27GM-Mac was suppressed to nearly 10% of that in M-Mac; however, single-cell RNA sequencing showed that M-Mac clustered with GM-Mac, and 27M-Mac clustered with 27GM-Mac. Expression of CD38 and secretion of CXCL9 and C1q were significantly increased in 27M-Mac and 27GM-Mac compared with M-Mac and GM-Mac. Although CD16 and CD64 expression increased in 27M-Mac and 27GM-Mac relative to their respective controls, phagocytic activity in 27M-Mac and 27GM-Mac was 30% of that in M-Mac. Autophagy was promoted 3.7-fold more strongly in 27M-Mac than in M-Mac, reaching levels comparable to those in GM-Mac and 27GM-Mac. Collectively, these findings indicate that IL-27 polarizes M-Mac and GM-Mac toward transcriptionally and functionally similar subtypes, providing insight into the role of IL-27 in macrophage polarization and plasticity. Full article

Objective: Population mobility complicates the prevention and control of HIV. To address these challenges, this study explored the molecular epidemiology of HIV among migrant populations in Hangzhou. Methods: People newly diagnosed with HIV/AIDS from 2020 to 2023 were divided into permanent migrant population (PMP), temporary migrant population (TMP), and non-migrant population (NMP). HIV-1 pol gene sequencing was performed to calculate genetic distance. Sample pairs with genetic distances ≤0.005 were used to construct the molecular transmission network. Results: PMP comprised people living with HIV in Hangzhou, characterized by younger age, higher education, and predominantly homosexual transmission. This population forms multiple large molecular clusters together with NMP. TMP accounted for the highest proportion of females and people infected through heterosexual contact, but the education level was the lowest. NMP had the fewest people living with HIV. The main subtypes identified were CRF01_AE, CRF07_BC, CRF08_BC and CRF55_01B. Drug resistance prevalence did not differ significantly among the populations. The molecular transmission network included 833 cases forming 275 clusters, with an overall sample inclusion rate of 23.04%. PMP, TMP and NMP inclusion rates were 27.10%, 19.03% and 21.4%, respectively. All molecular clusters involved migrant populations. Factors associated with inclusion in the network for migrants included current residence, household registration, STD history, sample source, and stage at diagnosis. Conclusions: Migrant populations play a major role in ongoing HIV transmission. Prevention and control measures should be strengthened according to population-specific characteristics. Molecular transmission networks are useful tools for assisting precise control. Full article

Background: In Pakistan, the number of Human immunodeficiency virus (HIV) cases is increasing significantly, attributed to risk factors such as injection drug use, sexual transmission, etc. However, transmission through hemodialysis units is not well documented. In 2024, an outbreak of HIV cases in Multan, Pakistan, drew alarm from local health authorities due to reports linking it to a large public hospital in South Punjab. Here, we report the molecular epidemiological investigation of the outbreak. Methods: Twenty-five hemodialysis patients identified during the outbreak were enrolled. Blood samples were subjected to DNA extraction and polymerase chain reaction (PCR) amplification. Phylogenetic analysis was conducted using the maximum-likelihood approach in IQ-TREE. For dating phylogenetics, a maximum clade credibility tree (MCC) was constructed using the BEAST tool. The MCC tree was constructed using the Bayesian Skyline model with an uncorrelated lognormal relaxed clock. The VESPA program was used to identify amino acid signatures unique to outbreak sequences compared with Pakistani reference sequences. Results: A total of 25 patients (identified as part of the HIV outbreak) were enrolled. 96% (24 out of 25) also tested positive for Hepatitis C, while none tested positive for Hepatitis B. The age range of patients in the study was 23 to 72 years (median age: 44.88 years). In terms of gender distribution, 13 out of 25 were male. All the sequences were identified as HIV subtype CRF02_AG. Phylogenetic analysis revealed that Multan sequences formed a well-supported monophyletic cluster, indicating shared recent origin. Signature pattern analysis identified a unique molecular fingerprint at 26 nucleotide positions, whereas molecular dating placed the emergence of the cluster between 2023 and 2024, consistent with the outbreak timing. Conclusions: Findings provide biologically plausible evidence of a point-source HIV outbreak linked to lapses in infection prevention and control practices at the hemodialysis unit. Full article

mRNA vaccines represent a revolutionary advance in vaccinology, boasting advantages like rapid development, robust immunogenicity and flexible antigen design over traditional vaccines. This review systematically summarizes the core research progress of mRNA vaccines, including their structural composition with five functional elements and novel subtypes (linear mRNA, self-amplifying RNA, circular RNA) with unique biological characteristics and application value. It elaborates on the immune activation mechanism of mRNA vaccines, which mimic natural viral infection to trigger both innate and adaptive immunity, and analyzes mainstream delivery systems (lipid nanoparticles, dendritic cells, protamine, exosomes, polymers) with their respective performance, advantages and bottlenecks. This review also details the clinical application status of mRNA vaccines in infectious diseases (influenza, rabies, monkeypox, SARS-CoV-2, HIV, parasites) and cancer therapy, highlighting promising preclinical and clinical results of candidate vaccines and combined therapeutic regimens. Additionally, it addresses the current limitations of mRNA vaccines, such as delivery inefficiency, production costs, and cold chain constraints. Finally, this review prospects the future development direction, emphasizing that the optimization of delivery systems, antigen design and production processes will further promote the clinical translation and diversified application of mRNA vaccines in disease prevention and treatment. Full article

HIV-1 diversified for decades within the Democratic Republic of the Congo (DRC) before spreading globally in the early 1980s. Thus, the DRC is home to some of the most ancestral and diverse HIV-1 strains. Recent serosurveys conducted from 2017 to 2019 in Kinshasa, DRC, indicated high prevalence of HIV-1, yet sequence data is lacking from this period. Given the history of circulating rare HIV-1 subtypes in the DRC, a viral whole-genome sequencing study was conducted to determine current diversity in the greater Kinshasa area. Next-generation sequencing (NGS) through metagenomic and target enrichment methods was conducted on 197 specimens collected from 2017 to 2019. A large array of HIV subtypes (A, B, C, D, F1, G, H, J, and K), circulating recombinant forms (CRF01_AE, CRF02_AG, CRF05_DF, CRF11_cpx, CRF13_cpx, CRF25_cpx, CRF 45_cpx, and CRF92_C2U), unique recombinant forms, and unclassifiable sequences were observed, with many branching in basal positions within, or outside of, many subtypes on phylogenetic trees. Incorporating these new sequences into Bayesian inference of phylogeny pushes back the dates of the most recent common ancestors of HIV-1 group M and the rare subtypes G, H, and J by between 3 and 7 years each. The DRC continues to harbor diverse and rare HIV-1 subtypes that could challenge diagnostic tests, treatments, and vaccines. In addition to shifting subtype emergence dates, the sequences from our study are evidence that rare strains continue to circulate and should be regularly monitored. Full article

The persistence of latent HIV-1 reservoirs in individuals on antiretroviral therapy (ART) remains a major barrier to cure, necessitating strategies such as “shock and kill” using latency-reversing agents (LRAs). However, current LRAs show limited clinical efficacy, highlighting the need for novel interventions. This study evaluated the in vitro latency-reversing potential of Product Nkabinde (PN) and Gnidia sericocephala using J-Lat A2 (subtype B) and J-Lat C clones T66 and T17 (subtype C) cells. Cell viability was assessed using flow cytometry with Live/Dead dye. Reactivation potential was further tested in combination with established LRAs: panobinostat, SAHA, and TNF-α. G. sericocephala induced dose-dependent latency reversal, with 26.1% of J-Lat A2 and 15.8% of J-Lat T66 cells GFP-positive at 106 µg/mL (p = 0.0001). Co-treatment with LRAs enhanced reactivation—34.6% with SAHA and 87.2% with TNF-α in J-Lat A2 cells, and 56.9% with SAHA and 65.4% with TNF-α in J-Lat T66 cells (p = 0.0001)—while maintaining cell viability above 90%. PN showed minimal activity (≤1.3% GFP-positive) and no effect in combination assays. Fractional inhibitory concentration index analysis revealed no synergistic interactions. Ex vivo, PN and G. sericocephala induced limited increases in HIV-1 gag RNA without substantial cytotoxicity. These findings demonstrate that G. sericocephala effectively reverses HIV-1 latency and potentiates TNF-α-induced reactivation, supporting its potential as a plant-derived LRA for future “shock and kill” HIV-1 cure strategies. Full article

We present the single-cell transcriptomic analysis of peripheral blood mononuclear cells (PBMC) from individuals during acute HIV-1 infection caused by viral strains circulating in Russia and the Former Soviet Union (FSU) countries. Using 10x Genomics single-cell RNA sequencing (scRNA-seq) on the Illumina NextSeq 550 platform, we have analyzed scRNA-seq data from three treatment-naive patients (viral load > 1 × 10⁶ copies/mL, estimated infection duration ≤ 4 weeks) and three healthy donors. Data integration (Seurat, Harmony), automated cell-type annotation (CellTypist), and GeneOntology (GO) enrichment analysis for highly expressed and low-expressed genes revealed a profound reorganization of transcriptional programs across key immune populations, including memory CD4⁺ and CD8⁺ T cells, non-classical monocytes and natural killer cells (NK-cells). We observed signatures of hyperactivation of pro-inflammatory pathways (NF-kB, TNF, and type I/II interferon signaling), upregulation of genes associated with cellular migration (CXCR4, CCR7) and metabolic adaptation (oxidative phosphorylation components), alongside a mixed pro- and anti-apoptotic expression profile. Notably, our data pointed to a pronounced dysregulation of the TGF-β and mTOR signaling cascades, disrupted intercellular communication networks—particularly between cytotoxic cells and their regulators—altered expression of genes implicated in disease progression (OLR1, SERPINB2, COPS9) and viral persistence control (NEAT1, NAF1). This work provides an initial single-cell transcriptional atlas characterizing early immune responses to HIV-1 sub-subtypes A6 and CRF63_02A6, the predominant drivers of the HIV epidemic across the FSU region. Full article

The first major HIV outbreak in the Eastern Europe and Central Asia (EECA) region was registered. Phylogeographic analysis revealed that the main exporters of the virus were Donetsk and Lugansk, from which most migration events occurred, and the predominant genetic variant in Donetsk was subtype A. However, despite a relatively high level of understanding of HIV genetic diversity, data on resistance mutations remain limited. The aim of this study is to assess HIV genetic diversity and drug resistance in Donetsk, Luhansk and Zaporizhzhia regions. A comprehensive examination was conducted, encompassing 392 sequences covering the integrase-coding region of the HIV-1 pol gene. Subtyping was achieved through various programs, including COMET, the Stanford Database, BLAST and REGA. The study also involved phylogenetic analysis to clarify HIV genovariants. The profiles and levels of drug resistance were determined. The overall prevalence of drug resistance mutations to the integrase strand transfer inhibitors (INSTIs) among the studied patients was 3.6% (95% CI, 1.7–5.4%). The most commonly detected major DRMs for INSTIs were G140R (4, 28.6%) and Y143R (3, 21.4%), followed by R263K (2, 14.3%), G140RG (2, 14.3%), Y143YS (2, 14.3%), Y143YC (1, 7.1%) and Q148QR (1, 7.1%). A high-level resistance was observed for RAL—8/14 (57.1%), CAB—6/14 (42.9%) and EVG—2/14 (14.3%). The results presented are part of a further larger study and are preliminary. The results of this study suggest a moderate HIV-1 resistance situation in the Donetsk, Luhansk and Zaporizhzhia regions, but require further monitoring. Full article

Studying the incidence of Kaposi sarcoma in relation to key variables can guide targeted research and subtype-specific clinical interventions. We reviewed the records of all patients who visited our hospital’s dermatology outpatient clinic, and patients who were clinically and histopathologically diagnosed with Kaposi sarcoma were included in the study. The age, gender, lesion location, anti-HIV test results, and comorbidities of the patients were recorded. Thirty-three patients with Kaposi sarcoma were identified. The male/female ratio was 2.7:1. The Kaposi sarcoma lesions were statistically significantly more prevalent in the lower extremities of HIV-negative patients (p = 0.005). Receiver operating characteristic (ROC) curve analysis identified 59 years as the optimal age cutoff for distinguishing between HIV-positive and HIV-negative patients. Anti-HIV positivity was significantly higher in individuals aged 59 and younger compared to those aged 60 and older (p < 0.001). To the best of our knowledge, this is the first study to demonstrate a statistically significant higher prevalence of lower extremity lesions among HIV-negative patients and to identify 59 years as the optimal age cutoff for distinguishing between HIV-positive and HIV-negative Kaposi sarcoma patients using ROC curve analysis. The age-related patterns observed in this study warrant further investigation. Full article

The HIV epidemic in Romania started in the late eighties with a large cohort of children nosocomially infected with subtype F1 strains, in parallel with sexual transmission. The purpose of the present study was to investigate the transmitted drug resistance (TDR), subtype distribution, and transmission clusters among persons diagnosed with HIV between 2019 and 2022 in Romania. The prototype of a person recently diagnosed with HIV in Romania is male, 20–50 years old, a late presenter, infected with F1, B, or A subtype. The rate of TDR varied over time, from 5% in 2019 to 15% in 2022. TDR affected mainly the first generation of NNRTIs and the PI class. The rate of late presentation was almost 60%, with 35% of persons qualifying as very late presenters. Subtype F1 is still preponderant in Romania, whereas other subtypes (B, A) and recombinants account for a quarter of HIV-1 new cases. Several transmission networks were identified in the study population, two of them associated with TDR in subtypes F1 and A1. The largest cluster consisted of 26 sequences, originating from Western Romania and introduced around 2007. Molecular clock analysis indicated different origin time points for different clusters, with the most recent in subtypes A1 and B, and the oldest in subtype F1. In conclusion, the HIV-1 epidemic in Romania is currently driven by sexual transmission, with MSM contribution continuously rising in recent years; there are also increases in TDR and the circulation of HIV-1 strains other than F1 (subtype B, A, recombinants). Full article

Vif and Vpr are HIV-1 accessory proteins that create optimal conditions for viral replication. They are considered as potential targets for the development of therapeutic agents. Natural amino acid substitutions in these proteins have previously been associated with disease progression. The aim of this study was to analyze the genetic diversity of Vif and Vpr in HIV-1 group M clades. A total of 5286 sequences were downloaded and analyzed. For 37 clades in group M, the consensus sequences, amino acid natural variation, and clade-specific amino acid residue substitutions (CSSs) were evaluated. Structural analysis and modeling of consensus sequences were performed for subtypes A1, B, C, and D. The average conservation degree in the HIV-1 group M was 86.4% for Vif and 91.3% for Vpr. In both proteins, the lowest amino acid diversity was observed in sub-subtype A6, and the highest in subtype B. In consensus sequences, the substitutions, which might influence pathogenesis, have been determined: in Vif—22H (11_cpx, 91_cpx) and 136P (A6, 01_AE, 15_01B, 59_01B, 89_BF1, 103_01B, 111_01C, 133_A6B), in Vpr—41N (06_cpx) and 55A (B, 07_BC, 35_01D, 56_cpx, 66_cpx, 66_BF1, 71_BF1, 85_BC, 137_0107). In functional motifs, CSSs associated with changes in the chemical properties of amino acid residues were noted. These findings could be taken into account for the development of therapeutic drugs in the future. No correlation was observed between the subtypes and the spatial organization of the oligomeric structures of Vif and Vpr. Using the structural analysis and modeling, it has been shown for the first time that Vif can interact with APOBEC3G as an oligomer. Full article

Human immunodeficiency virus type 1 (HIV-1) continues to be a major global health burden. Combination antiretroviral therapy (cART) effectively abrogates HIV-1 replication and has transformed HIV-1 infection from a fatal to chronic disease. While ART can suppress viremia to undetectable levels in people living with HIV-1 (PWH), a small reservoir of cells infected with replication-competent HIV-1 persists and can lead to viral rebound upon ART interruption. This persistent HIV-1 reservoir can be quantified and characterized by measuring replication of infectious HIV-1 using a quantitative viral outgrowth assay (qVOA), or by measuring HIV-1 DNA, RNA, or protein levels as a proxy for the reservoir. Tools to quantify the reservoir in these distinct molecular compartments have been developed for HIV-1 subtype B, which is predominant in the Global North. However, non-B subtypes constitute the majority of HIV-1 infections worldwide. Here, we discuss the wide range of reservoir quantitation and characterization tools, explore their limitations, and, where applicable, their adaptations to non-B subtypes. We conclude that standardized tools should be used to characterize reservoir dynamics of HIV-1 B and non-B subtypes. These tests should be well-validated and accessible to all laboratories world-wide to be able to draw conclusions about subtype-specific reservoir dynamics. Full article

Circulating recombinant forms (CRFs) are important components of the HIV-1 pandemic. Previous studies have reported the propagation of diverse HIV-1 CRFs of South American origin in Europe. Here, through protease-reverse transcriptase (Pr-RT) and integrase sequence analyses, we identify a Spanish cluster (BC3) branching with a Brazilian virus (10BR_RJ009) previously classified as CRF146_BC. In Pr-RT, BC3 comprised 14 viruses and was nested within a larger cluster, comprising 22 Brazilian viruses and 1 Spanish virus branching outside of BC3. Near full-length genome analyses of five BC3 viruses revealed mosaic structures identical to 10BR_RJ009, with two breakpoints delimiting a ~0.3 kb subtype B fragment within an otherwise subtype C genome. Two other Brazilian viruses previously classified as CRF146_BC (10BR_RJ039 and 01_BR_RGS69) had one and two additional short subtype B fragments, respectively, and failed to group with the 10BR_RJ009/BC3 cluster in subtype C fragments. Based on these results, we contend that 10BR_RJ009 and BC3 viruses, but not 10BR_RJ039 and 01_BR_RGS69, should be classified as CRF146_BC. Bayesian analyses estimated the CRF146_BC emergence in Brazil to be around 1999 and its introduction in Europe around 2011. CRF146_BC is the 10th CRF of South American origin reported to circulate in Europe, reflecting the relationship between South American and European HIV-1 epidemics. Full article