Search Results (192)

Historically, mpox was thought to be a geographically constrained ‘disease of poverty,’ leading to decades of neglect by global health actors. Waning population immunity from the cessation of smallpox vaccination and prolonged scientific neglect created conditions that enabled the monkeypox virus (MPXV) to adapt cryptically. This ultimately contributed to the emergence of unprecedented global public health crises. This review aims to systematically trace the history, epidemiology, genomic evolution, and reservoir ecology of mpox in West Africa from 1970 to 2025. Following PRISMA guidelines, 110 articles met the inclusion criteria and were synthesized to map the virus’s trajectory. For nearly four decades, an “Era of Silence” (1970–2016) masked the silent enzootic circulation of MPXV within West African wildlife, primarily rodents and small mammals. This epidemiological quiescence ended with the 2017 re-emergence in Nigeria, which signaled a fundamental paradigm shift. The disease profile transitioned from sporadic, rural paediatric infections to sustained, urban and secondary transmission among young adult males. This shift was often associated with sexual networks, especially among men who have sex with men, and was characterized by novel clinical presentations, including genital and perianal lesions. Genomic analyses revealed that clade II diverged from clade I approximately 3500 years ago and is uniquely defined by the deletion of virulence factors, such as the complement-binding protein. Importantly, the clade IIb lineage, which triggered the 2022 global outbreak, exhibits accelerated microevolution consistent with APOBEC3-mediated hypermutation. This host-driven mutational signature provides genomic evidence supporting the hypothesis that clade IIb circulated cryptically within human-to-human transmission chains in West Africa as early as 2014. Ecologically, while no definitive reservoir has yet been identified, evidence suggests diverse rodents and an expanding host range. The transformation of mpox from a rare zoonosis to a global threat underscores the severe consequences of delayed intervention, demanding robust, integrated “One Health” surveillance. Full article

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) evolution has been marked by the rapid accumulation of mutations, among which cytosine-to-uracil (C-to-U) transitions represent a major proportion of observed genomic changes. These mutations have been proposed to result from the activity of host APOBEC3 cytidine deaminases, innate immune enzymes capable of editing viral RNA. However, the molecular mechanisms underlying APOBEC3 involvement in SARS-CoV-2 biology remain poorly understood. Here, we systematically investigated physical interactions between APOBEC family members and the SARS-CoV-2 proteins using a Gaussia princeps protein complementation assay. Screening of APOBEC family proteins against the viral proteome identified specific interactions between APOBEC3G (A3G) and APOBEC3H (A3H) with the viral nucleocapsid (N) protein. These interactions were validated by co-immunoprecipitation and were found to be conserved across nucleocapsid proteins from all seven human coronaviruses, suggesting conserved structural determinants. Mechanistic analyses revealed that the RNA-binding and oligomerization capacities of A3G and A3H are key for their interaction with the SARS-CoV-2 nucleocapsid. Mapping experiments further showed that the C-terminal domain of N constitutes the minimal interacting region, with stronger binding observed in larger constructs encompassing adjacent regions, indicating cooperative stabilization. Further work will be needed to determine whether A3G and/or A3H can restrict viral replication and whether their interaction with the nucleocapsid allows them to access and mutate the viral genome. Full article

Cyclin-dependent kinase 4/6 inhibitors have fundamentally changed the management of hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancer. However, these drugs are not interchangeable and the field is moving away from the notion of a uniform “class effect.” In early breast cancer, adjuvant abemaciclib and ribociclib improve invasive disease-free survival in patients at a high risk of recurrence, whereas palbociclib does not. This difference likely stems from agent-specific pharmacological profiles, differences in trial design, and patient selection, rather than simply dosing nuances. In metastatic breast cancer, all three agents prolong progression-free survival when combined with endocrine therapy, but only ribociclib and potentially abemaciclib have shown an overall survival advantage. In addition, resistance remains a major obstacle in clinical practice. We propose that resistance mechanisms can be meaningfully grouped into two categories: target-driven (e.g., RB1 loss, CDK6 amplification) and bypass-driven (e.g., ESR1 mutations, PI3K/AKT pathway activation, APOBEC3-mediated mutagenesis). Distinguishing between these classes helps in the design of rational sequencing algorithms and combinatorial regimens. Emerging strategies, such as next-generation protein degraders, oral selective estrogen receptor degraders, antibody–drug conjugates, and inhibition of autophagy, are promising methods for overcoming resistance. Moving forward, the greatest need in breast cancer treatment will be not simply developing additional agents but using current therapies more intelligently by refining biomarker-guided patient selection, tailoring treatment duration, and ensuring broad global access. Full article

The human APOBEC3 (A3) family of cytidine deaminases, including A3G, A3F, and A3H, participates in cellular anti-retroviral immunity. In contrast, to antagonize the anti-retroviral activities of these A3 family proteins, HIV-1 produces its gene product called viral infectivity factor (Vif) in infected cells. Vif is a pleiotropic hub protein that specifically binds to various A3 proteins with the aid of host core-binding factor subunit β (CBF-β) and mediates their proteasomal degradation. To date, numerous biological and structural studies have been performed to understand the arms race between A3 and Vif. Previous extensive mutagenesis and structural analyses have suggested that there are three distinct types of Vif-binding interfaces among human A3s and three largely nonoverlapping interfaces on Vif for binding with these A3s. Moreover, recent cryo-electron microscopy (cryo-EM) structural analyses have clarified further details of the different intermolecular interactions of Vif with each of three human A3s (A3G, A3F, and A3H) and have proposed a possible mechanism by which one Vif molecule can recognize all three types of A3s. In this review, we summarize the current understanding of the structural basis of the interaction between A3 and Vif. This information may be helpful for developing drugs targeting these interfaces. Full article

The MUCIN 1 (MUC1) gene evolved in eutherian mammals in association with the marked expansion of endogenous retroviruses (ERVs). MUC1 encodes the MUC1-C/M1C protein that protects barrier epithelia from exogenous viruses. Activation of M1C in response to loss of homeostasis induces STAT1 and the type I interferon (IFN-I) pathway. Studies in cancer cells have found that M1C regulates human ERV (HERV) expression by a STAT1-mediated mechanism. These discoveries have uncovered new insights into M1C-induced regulation of HERVs and other retrotransposons, such as LINE-1 (L1) and Alu. M1C signaling integrates retrotransposon transcription with induction of the counteracting apolipoprotein B mRNA-editing catalytic 3 (APOBEC3) genes that, like MUC1, first appeared in placental mammals. Activation of retrotransposons induces viral mimicry characterized as an IFN-I response that promotes innate anti-tumor immunity. Conversely, M1C protects cancer cells by sustained induction of the IFN-I pathway and immune evasion. This review posits that M1C-dependent regulation of retrotransposon and APOBEC3 expression represents an adaptive response exploited by cancer cells that promotes malignant progression. Full article

Lung adenocarcinoma (LUAD) remains the leading cause of mortality worldwide, while asthma is the most prevalent chronic disease affecting individuals of all ages. The shared airway involvement in these global health concerns results in exposure to common risk factors, suggesting a potential overlap in their genetic background. Given the roles oxidative stress and chronic inflammation play in both LUAD and asthma, we aimed to investigate similarities in their molecular mechanisms and to explore whether these shared transcriptomic signatures may prove useful for potential drug repurposing hypotheses by analyzing relevant transcriptomic datasets. This analysis identified a set of genes and co-expression interactions shared between asthma and LUAD, suggesting potential common molecular mechanisms underlying both diseases. Specifically, DNAJC3, APOBEC3G, and PRDX4 were highlighted as potential common molecular mediators underlying both diseases, offering correlative evidence for shared pathways. These genes may represent key molecular links connecting the pathogenic processes of asthma and LUAD. The transcriptomic profiles of asthma and lung cancer datasets reveal common molecular interactions, suggesting potential shared biological mechanisms between the two diseases. These findings provide a computational framework that may guide future studies investigating therapeutic associations and possible drug–gene relationships in lung adenocarcinoma and asthma. Full article

Babesia microti is the primary agent of human babesiosis, an emerging tick-borne disease with limited treatment options and growing evidence of drug resistance. Deubiquitinases (DUBs) play critical roles in protein homeostasis and host–pathogen interactions, yet none have been characterized in B. microti. Here, we report the first molecular cloning, expression, and functional characterization of an OTU-like cysteine protease from B. microti (bm-OTU). The recombinant bm-OTU protein (~22 kDa) was expressed in E. coli, purified to high homogeneity, and exhibited ~93% solubility under native conditions. In vitro fluorogenic assays confirmed its deubiquitinase activity. Expression of bm-OTU in HEK293T cells was associated with reduced ubiquitination in cells and increased apoptosis in this overexpression model, as demonstrated by flow cytometry and Western blot analyses. Furthermore, transcriptomic analysis revealed that bm-OTU modulates host immune pathways, notably suppressing the expression of interferon-stimulated genes (APOBEC3G, G1P2) while upregulating the pro-apoptotic gene BAK and the inflammasome sensor AIM2. These findings establish bm-OTU as a functional deubiquitinase and a potential virulence factor that may contribute to immune evasion and pathogenesis in babesiosis and may represent a potential target, pending further validation. Full article

Background/Objectives: Bisulfite-based cell-free DNA (cfDNA) methylation assays enable the detection of clinically valuable epigenetic biomarkers but often cause DNA degradation and inconsistent conversion efficiency, limiting performance in low-input liquid biopsy samples. We aimed to develop and evaluate a fully enzymatic cfDNA methylation workflow that preserves DNA integrity and supports quantitative clinical detection. Methods: The assay integrates TET2-mediated oxidation and APOBEC3A deamination with RNase H2-guided primer design, uracil-DNA glycosylase error suppression, and dual-probe detection compatible with quantitative PCR (qPCR) and digital PCR (dPCR). Performance was assessed using serial dilutions of methylated HT29 DNA, unmethylated controls, and plasma cfDNA from colorectal cancer (CRC) patients and healthy donors. Analytical sensitivity, linearity, and concordance between platforms were evaluated. Results: The 40-marker panel demonstrated higher cumulative methylation scores and more frequent methylation-positive signals in CRC cfDNA compared to controls. dPCR confirmed single-molecule resolution and clear discrimination between methylated and unmethylated templates, with occasional double-positive partitions consistent with mixed allelic methylation. Signal intensity across the dilution series followed a four-parameter logistic model, achieving detection sensitivity below 0.2% methylated DNA. qPCR and dPCR results showed strong correlation across the HT29 dilution series (R² = 0.80) and high concordance in classifying CRC and healthy samples. Conclusions: This TET2–APOBEC-based enzymatic cfDNA assay enables sensitive, quantitative, sequencing-free methylation detection under gentle conditions, supporting its application in early colorectal cancer screening and routine clinical liquid biopsy workflows. Full article

The membrane fusion process, mediated by the entry fusion complex (EFC) of the monkeypox virus (MPXV), is crucial for host cell invasion. Apolipoprotein B mRNA Editing Catalytic Polypeptide-like 3 (APOBEC3)-driven mutation bias is a key factor in MPXV’s adaptive evolution during its global spread. However, how these mutations affect the structure and function of EFC proteins remains poorly understood. To address this, we performed genomic mutation analysis on globally circulating MPXV clades Ib and IIb, combined with protein monomer, binary, and quaternary complex structure modeling based on AlphaFold 3 and experimental validation by ELISA. We first delineated the mutational spectra of all 11 EFC proteins, revealing that although EFC proteins in clade Ib are highly conserved, lineage IIb B exhibits extensive APOBEC3-driven mutations and the G9 M142I mutation is identified as a lineage-associated APOBEC3-type mutation of lineage IIb B. Structural predictions revealed that while the M142I mutation does not alter G9 monomer folding, it induces a conformational shift in the G9/A16 subcomplex. Furthermore, within the predicted G9/A16/A56/K2 quaternary complex, this mutation enlarges the interfacial gap and reduces docking stability between the G9/A16 subcomplex and A56/K2. Experimental validation demonstrated that the M142I mutation significantly reduces the binding affinity of G9 for A16 and impairs the recruitment of A56/K2 to the quaternary complex, confirming the computationally predicted mechanism of interface destabilization. These findings highlight a dynamic interplay between APOBEC3-driven evolution and EFC protein structure, demonstrating that the M142I mutation alters EFC complex assembly dynamics and may shift the regulatory balance of the membrane fusion system. These structural changes provide molecular insights into MPXV lineage differentiation, though direct functional assays are required to determine the net effect on viral entry efficiency. Full article

Lumpy skin disease virus (LSDV) is a large DNA capripoxvirus that causes LSD, a disease that has major economic impact. Since 1989, several sporadic outbreaks were reported in Israel, with the latest outbreaks in 2012, 2019 and 2023. Although considered genetically stable, LSDV shows a high degree of genetic recombination events and genetic variations. In particular, in-frame nonsense mutations were suggested to act as one of the main evolutionary drivers of outbreaks. Whole-genome sequencing of LSDV isolates from the 2019 and 2023 outbreaks was used for genomic analysis using various bioinformatics tools to characterize the genomic evolution, recombination events and micro-evolutionary forces shaping LSDV in Israel by comparing isolates. Comparative genomic analysis revealed substantial nucleotide substitutions in the 2019 and 2023 isolates relative to the 2012 isolate. Specifically, increased nucleotide mismatches, inter-genic deletion, enhanced APOBEC editing signatures and elevated codon usage. Additionally, numerous mutations were recognized, leading to structural disruptions in specific viral proteins and possible RNA instability. In conclusion, this analysis supports that nucleotide substitutions, codon selection pressure and APOBEC-associated editing had driven local microevolution of LSDV during the years between outbreaks despite the absence of clinical indications and major vaccination campaigns. Furthermore, genomic evidences of recombination events between the 2012 and 2019 isolates suggests that these processes may have contributed to the emergence of the variant identified during the 2023 outbreak. Full article

The APOBEC family of cytidine deaminases is part of the innate immune response to infections by multiple RNA- and DNA-containing viruses. Since the activity of these enzymes, typically APOBEC3, often involves mutations that inhibit or block viral replication, viruses have evolved antagonists that limit APOBEC function. The retrovirus mouse mammary tumor virus (MMTV) encodes an APOBEC antagonist, Rem. Surprisingly, Rem appears to inhibit APOBEC3 through proteasomal degradation of a different APOBEC enzyme, AID. Full article

Apolipoprotein B mRNA editing enzyme catalytic polypeptide 3s (APOBEC3s, A3s) are single-stranded DNA cytidine deaminases with antiviral activity against diverse DNA and RNA viruses. The human APOBEC3 locus encodes seven members: A3A, A3B, A3C, A3D, A3F, A3G, and A3H. Of these, A3C, A3D, A3F, A3G, and A3H are packaged into HIV-1, lacking the viral infectivity factor (VIF, HIV-1Δvif), while A3D, A3F, A3G, and A3H hap II exhibit strong antiviral activity. Packaging of A3s into virions is critical for viral restriction, yet the underlying mechanisms remain incompletely understood. A3 incorporation requires interactions with the GAG polyprotein, especially the matrix (MA) and nucleocapsid (NC) domains, and binding to cellular or viral RNAs. Specific amino acid residues within A3 proteins mediate these contacts, and A3G localization to lipid rafts facilitates packaging. While A3F and A3G incorporation have been extensively characterized, mechanisms for other A3s remain poorly defined. This review synthesizes current knowledge on A3 packaging, emphasizing the interplay of protein, RNA, and membrane determinants in efficient virion incorporation. Full article

Despite increasing reports of zoonotic simian foamy virus (SFV) infections globally, knowledge of its genetic adaptation in humans and impact on viral transmission and pathogenicity remains limited. We obtained complete SFV genomes using metagenomics analysis of viral isolates from peripheral blood lymphocytes (PBLs) and throat specimens from a worker (Case 6) and source chimpanzee (B1) that bit him. We analyzed viral diversity in three genomic regions (LTR, tas, and bet) involved in replication and latency using longitudinal specimens (PBLs, throat, saliva, urine, and semen) from Case 6 over five years, and PBLs from B1 and five additional chimpanzees over three years. Proviral loads were measured using a validated qPCR assay. Phylogenetic analysis revealed nearly identical SFV genomes in Case 6 and B1. Overall, bet sequences exhibited high genetic stability across body compartments and over time, with evidence of compartmentalization in Case 6 urine and semen specimens. G→A substitutions in GG and GA motifs in bet indicated heterogeneous APOBEC-associated editing across hosts and anatomical compartments following zoonotic transmission. Case 6 had significant deletions in the LTR region that were absent in B1 and other chimpanzees. Length variation in tas, including truncated forms, was observed across longitudinal specimens from Case 6, B1, and other chimpanzees. Proviral loads were consistently low and undetectable in most Case 6 urine specimens. Together, analysis of this SFV transmission pair identifies genomic changes likely to affect viral replication and persistence, highlighting mechanisms that may limit secondary transmission and pathogenicity of SFV in humans. Full article

Since 2022, global outbreaks of monkeypox virus (MPXV) have been repeatedly designated by the World Health Organization (WHO) as a public health emergency of international concern (PHEIC), underscoring the urgent need to elucidate the multidimensional mechanisms underlying viral evolution and transmission. Current understanding remains largely focused on genomic variation, while the critical role of epigenetic regulation has been considerably overlooked. To address this gap, this study integrates high-throughput evolutionary genomic analysis with whole-genome DNA methylation profiling. Using parallel Illumina and Nanopore sequencing platforms, we comprehensively characterized two clinically derived MPXV isolates collected locally. The results revealed that both isolates belonged to the C.1.1 ancestral lineage, diverging into distinct clades (E.3 and E.4, respectively, supporting the presence of at least two independent viral introduction events into the region, each followed by limited local transmission. They had accrued a considerable number of single-nucleotide polymorphisms (SNPs), with APOBEC3-associated substitutions constituting 84.8% and 77.6% of all observed mutations. Furthermore, both 5-hydroxymethylcytosine (5hmC) and N6-methyladenine (6mA) modifications were identified and found to be preferentially enriched within the inverted terminal repeats (ITRs) regions of MPXV genome in both viral strains; moreover, the E.4 lineage viral strain exhibits a markedly more intricate and compositionally diversified modification landscape, a pattern that indicates appreciable epigenetic heterogeneity among MPXV lineages. Our study furnishes a multi-omics framework that presents a systematic evolutionary feature of two clinical MPXV isolates and their genomic DNA 5hmC and 6mA modification topologies, and enhances our understanding of MPXV viral adaptation and diversification. Full article

Viruses of the family Anelloviridae represent a predominant component of the human virome across various anatomical sites, yet their clinical significance remains poorly understood. This review summarizes current data on the dynamics and functional interactions of anelloviruses with the immune system in the context of human immune deficiency virus (HIV) infection. Existing studies indicate that an individual’s complement of anelloviruses (their “anellome”) serves as a highly sensitive indicator of immunocompetence. In the absence of antiretroviral therapy (ART), the viral load and taxonomic diversity of anelloviruses (genera Alphatorquevirus, Betatorquevirus, and Gammatorquevirus) demonstrate a rapid increase, correlating with HIV viral load, a decline in CD4+ T-lymphocyte count, and the CD4/CD8 ratio, reflecting weakened immune surveillance. Upon initiation of antiretroviral therapy (ART), a decrease in anellovirus viral load is observed; however, it likely does not revert to the pre-HIV infection baseline. At the same time, a high baseline level of Torque teno virus (TTV) is associated with incomplete immune recovery and the risk of ART non-response. Anelloviruses exhibit a dual role as both activators of the immune system (via APOBEC3, antibody production, and pro-inflammatory cytokines resulting from Toll-like receptor (TLR) activation) and disruptors of certain signaling pathways (through micro-RNAs and proteins encoded by ORF2). Thus, monitoring the anellome represents a promising non-invasive approach for assessing immune status, risk stratification, and personalizing therapy in patients with HIV infection. Future research should focus on the practical application of anellovirus viral load and diversity as markers of immune status and on clarifying the consequences of the aggregate interaction between HIV modulator proteins and anelloviruses during co-infection. Full article