Search Results (3,115)

A 19 nt fragment that spans the SARS-CoV-2 furin cleavage site (FCS) is identical to the reverse complement of a proprietary human DNA repair gene sequence. Rather than interpreting this overlap as evidence of a laboratory event, this article uses it as a theoretical springboard to explore underappreciated biorisk concerns, specifically in the context of cancer research. Although they are RNA viruses, coronaviruses are capable of hijacking host DNA damage response (DDR) pathways, exploiting nuclear functions to enhance replication and evade innate immunity. Under selective pressures (antivirals, DDR antagonists, or large-scale siRNA libraries designed to silence critical host genes), escape mutants may arise with fitness advantages. Parallel observations involving in vivo RNA interference via chimeric viruses lend plausibility to some of the key aspects underlying unappreciated biorisks. The mechanistic insights that incorporate DNA repair mechanisms, CoVs in the nucleus, specifics of viruses in cancer research, anticancer drugs, automated gene silencing experiments, and gene sequence overlaps identify gaps in biorisk policies, even those unaccounted for by the potent “Sequences of Concern” paradigm. Key concerning attributes, including genome multifunctionality, such as NLS/FCS in SARS-CoV-2, antisense sequences, and their combination, are further described in more general terms. The article concludes with recommendations pairing modern technical safeguards with enduring ethical principles. Full article

The development of cancer immunotherapies has transformed cancer treatment paradigms, yet durable and tumour-specific responses remain elusive for many patients. Neoantigens, immunogenic peptides arising from tumour-specific genomic alterations, have emerged as promising cancer vaccine targets. Early-phase clinical trials using different vaccine platforms, including mRNA, peptide, DNA, and viral vector-based personalised cancer vaccines, have demonstrated the feasibility of targeting neoantigens, with early signals of prolonged survival in some patients. Most current vaccine strategies focus on canonical neoantigens, typically derived from exonic single-nucleotide variants (SNVs) and small insertions/deletions (INDELs), yet this represents only a fraction of the potential neoantigen repertoire. Evidence now shows that non-canonical neoantigens, arising mostly from alternative splicing, intron retention, translation of non-coding RNAs, gene fusions, and retroelement activation, broaden the antigenic landscape, with the potential for increasing tumour specificity and immunogenicity. In this review, we explore the biology of non-canonical neoantigens, the technological advances that now enable their systematic detection, and their potential to inform next-generation personalised cancer vaccines. Full article

Background: Vietnam faces a hyperendemic burden of hepatitis B virus (HBV) infection, but the prevalence of occult HBV infection (OBI) and its underlying molecular mechanisms in healthy populations remain poorly understood. This study aimed to characterize the serological and molecular HBV profile of a healthy Vietnamese adult cohort in Southern Vietnam. We assessed the prevalence of occult HBV infection (OBI) and HBsAg-positivity (serving as a proxy for probable chronic infection). Methods: In this cross-sectional study, 397 healthy adults from Southern Vietnam underwent serological screening for HBsAg, anti-HBs, and anti-HBc. All participants were screened for HBV DNA using a high-sensitivity PCR assay (LOD ≥ 5 IU/mL). For all viremic cases, the full Pre-S/S region was sequenced to determine genotype and characterize escape mutations. Results: We uncovered a high prevalence of both HBsAg-positivity (17.6%) and OBI (9.3% HBsAg-negative, HBV DNA-positive). Serological analysis revealed a massive, age-dependent reservoir of past exposure (63.7% anti-HBc) characterized by a high and increasing prevalence of the anti-HBc only profile (31.5%), a key serological marker for OBI. This trend contrasted sharply with a steep age-related decline in protective anti-HBs. The viral landscape was dominated by genotypes B (73.8%) and C (26.2%), with sub-genotypes B4 and C1 being the most prevalent. Critically, individuals with OBI carried a significantly higher burden of S gene escape mutations compared to those with HBsAg-positivity (p < 0.001). Canonical escape variants, including sG145R (21.6%), sK141R/T/E/Q (24.3%), and sT116N/A/I/S (18.9%), were exclusively or highly enriched in the OBI group. A LASSO-logistic model based on this mutational profile successfully predicted occult infection with high accuracy (AUC = 0.83). Conclusions: A substantial hidden reservoir of occult HBV infection exists within the healthy adult population of Vietnam, driven by a high burden of S gene escape mutations. These findings highlight the significant limitations of conventional HBsAg-only screening. They also underscore the need for comprehensive molecular surveillance to address the true scope of HBV viremia, hopefully enabling a reduction in hidden transmission of clinically significant viral variants. Full article

Introduction: The health care burden of chronic hepatitis B virus (CHB) infection can be reduced by appropriate workup, treatment, and monitoring. Methods: As a primary objective, we determined whether adequate initial hepatitis B virus (HBV) laboratory workup in CHB patients is associated with improved CHB complications risk. Secondary outcomes assessed included: mortality, hospitalization, emergency department, and liver specialist visits. We conducted a retrospective cohort study from 1 January 2012 to 31 December 2018. Participants were followed from 12 months post index event until outcome occurrence, death, loss of eligibility, or 31 March 2023. Health administrative data from Ontario, Canada was utilized. The study cohort included individuals with at least one positive result of either hepatitis B surface antigen, hepatitis B e antigen, or HBV DNA viral load documented during the study window. The exposure of interest was defined as adequate laboratory workup, defined as having subsequent quantitative HBV DNA, and alanine aminotransferase testing completed within 12 months of the index event. CHB-related complications were assessed using previously validated diagnostic codes. Modified Poisson regression modelling was used to estimate relative risks. Results: The study cohort consisted of 30,794 CHB patients, with a mean age 45.7 years. The majority were male (53.5%) and within the lowest two income quintiles (50.2%). In total, 68.0% underwent adequate workup. Individuals with adequate workup were more likely to be older, male, urban based, and of the highest racialized and newcomer populations quintile. The risk for CHB complications was 1.50 (95% CI 1.36–1.65) times greater among those with adequate workup. By multivariable analysis, adequate workup was associated with a lower risk of mortality (RR 0.78; 95% CI 0.69–0.87), all-cause hospitalizations (RR 0.77; 95% CI 0.74–0.80), all-cause (RR 0.77; 95% CI 0.75–0.78), and liver-related (RR 0.67; 95% CI 0.60–0.75) ED visits. Conclusions: Adequate CHB clinical workup is associated with improved patient outcomes. Our findings advocate for the comprehensive evaluation of CHB patients using key laboratory tests to optimize clinical management and improve long-term health outcomes. We identified gaps in the workup of young adults, females, and those residing in rural settings, which should be addressed to ensure equity of HBV care. Full article

Background: Congenital cytomegalovirus (cCMV) infection is a leading cause of neonatal morbidity. This retrospective study aimed to evaluate the efficacy of valacyclovir in reducing vertical transmission after primary maternal CMV infection and to assess the diagnostic performance of amniocentesis and prenatal imaging. Methods: Eighty-two pregnant women with confirmed primary CMV infection were included. Maternal CMV serology and viral DNA were assessed in blood and urine, with standardized prenatal care including serial ultrasound examinations and fetal MRI when indicated. Amniocentesis was offered to confirm fetal infection. Valacyclovir (8 g/day) was administered before 24 weeks’ gestation, and neonatal infection was diagnosed by CMV DNA detection in urine at birth. Statistical analyses were performed using SPSS version 27.0. Results: Most infections (62.2%) were diagnosed in the first trimester. Valacyclovir was administered in 97.6% of cases, and amniocentesis was performed in 81.7%, with CMV DNA detected in 19.4%. Among 74 live births, 23% of neonates were CMV-positive and 6.8% symptomatic. Seven infected neonates had negative amniocentesis (false-negative rate, 13.2%). Prenatal ultrasound and MRI failed to detect abnormalities in symptomatic cases. Conclusions: Valacyclovir may reduce, but does not eliminate, the risk of cCMV transmission. Negative amniocentesis does not fully exclude fetal infection, highlighting postnatal follow-up. Full article

Torque Teno Virus (TTV), a common and genetically diverse component of the human virome, is not linked to any known disease but reflects immune status. Its plasma viral load has shown clinical relevance in solid organ transplant recipients, correlating it with immunosuppression when present at high levels. However, the clinical significance of TTV viral load in hematopoietic stem cell transplantation (HSCT) recipients is less understood. This systematic review aims to evaluate whether plasma TTV DNA load directly correlates with the degree of T-cell immune reconstitution after HSCT, supporting its potential role as a biomarker for immune competence. The study protocol was registered in the PROSPERO International Prospective Register of Systematic Reviews (CRD420251116208) and followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Twenty-one studies were included. The results showed concordant data about TTV kinetics with peak levels reaching approximately between +90 to +120 days after transplantation. Contradictory results have instead been found for the association of TTV load with immune parameters (lymphocyte counts, viral opportunistic infection, and development of acute graft versus host diseases). Even if a low-risk bias assessment was classified in most studies (67%), it was possible to identify important clinical and methodological differences between them, which might account for the different findings observed. Therefore, future larger studies with standardized protocols are needed to assess whether TTV viral load can serve as a reliable tool for guiding clinical decisions in the context of HSCT. Full article

Several studies have demonstrated that methionine supplementation in fish diets enhances immune status, inflammatory response, and resistance to bacterial infections by modulating for DNA methylation, aminopropylation, and transsulfuration pathways. However, the immunomodulatory effects of methionine in viral infections remain unexplored. This study aimed to evaluate the effect of methionine supplementation on immune modulation and resistance to the viral haemorrhagic septicaemia virus (VHSV) in rainbow trout (Oncorhynchus mykiss). Two diets were formulated and fed to juvenile rainbow trout for four weeks: a control diet (CTRL) with all nutritional requirements, including the amino acid profile required for the species, and a methionine-supplemented diet (MET), containing twice the normal requirement of DL-methionine. After feeding, fish were bath-infected with VHSV, while control fish were exposed to a virus-free bath. Samples were collected at 0 (after feeding trial), 24, 72, and 120 h post-infection for the haematological profile, humoral immune response, oxidative stress, viral load, RNAseq, and gene expression analysis. In both diets, results showed a peak in viral activity at 72 h, followed by a reduction in viral load at 120 h, indicating immune recovery. During the peak of infection, leukocytes, thrombocytes, and monocytes migrated to the infection site, while oxidative stress biomarkers (superoxide dismutase glutathione S-transferase, and glutathione redox ratio) suggested a compromised ability to manage cellular imbalance due to intense viral activity. At 120 h, immune recovery and homeostasis were observed due to an increase in the amount of nitric oxide, GSH/GSSG levels, leukocyte replacement, monocyte influx, and a reduction in the viral load. When focusing on the infection peak, gene ontology (GO) analysis showed several exclusively enriched pathways in the skin and gills of MET-fed fish, driven by the upregulation of several key genes. Genes involved in recognition/signalling, inflammatory response, and other genes with direct antiviral activity, such as TLR3, MYD88, TRAF2, NF-κB, STING, IRF3, -7, VIG1, caspases, cathepsins, and TNF, were observed. Notably, VIG1 (viperin), a key antiviral protein, was significantly upregulated in gills, confirming the modulatory role of methionine in inducing its transcription. Viperin, which harbours an S-adenosyl-L-methionine (SAM) radical domain, is directly related to methionine biosynthesis and plays a critical role in the innate immune response to VHSV infection in rainbow trout. In summary, this study suggests that dietary methionine supplementation can enhance a more robust fish immune response to viral infections, with viperin as a crucial mediator. The improved antiviral readiness observed in MET-fed fish underscores the potential of targeted nutritional adjustments to sustain fish health and welfare in aquaculture. Full article

Evidence on the contribution of human papillomaviruses (HPVs) to the development of esophageal papillomas is still controversial. Esophageal papillomatosis (EP) is considered an exceedingly rare, but distinct entity within esophageal proliferations, with about 57 cases published so far. Tissues derived from an EP case and from non-EP esophageal papillomas were investigated for the presence of HPVs and virus-positive specimens were subsequently analyzed for transcriptional activity and surrogate markers of infection. Low-risk type HPV6 DNA was detected in a subset of the esophageal papillomatous tissues, including EP, and a variant isolate belonging to lineage A. In the EP tissue, the abundant expression of the viral E6/E7 mRNA and the presence of HPV6-specific E1^E4 transcripts, the latter indicative of productive viral infection, were detected. An analysis of HPV-specific neutralizing antibodies in sera obtained from the EP case during natural infection as well as after HPV vaccination revealed that, despite extensive manifestation, HPV6-specific antibodies were absent during natural infection and only elicited after repeated HPV immunizations. Although limited by a small sample size, this exploratory study suggests a possible involvement of HPV6 in the development of EP. Furthermore, this study may contribute to the evidence distinguishing EP from less extensive forms of non-EP esophageal squamous papillomas. 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

Cervical cancer remains a major global public health concern, with persistent infection by high-risk human papillomavirus (hrHPV) types recognized as the primary etiological factor. This review explores the multifactorial nature of the disease, focusing on the complex interplay between host genetic susceptibility and epigenetic alterations that drive cervical carcinogenesis. Evidence from genome-wide association studies (GWAS) is discussed, highlighting the contribution of specific genetic loci, predominantly within the HLA region, to susceptibility to HPV infection and disease progression. In parallel, the review examines the molecular mechanisms by which the viral oncoproteins E6 and E7 promote genetic instability and epigenetic reprogramming, including histone modifications and dysregulation of non-coding RNAs. Particular emphasis is placed on DNA methylation, affecting both the viral genome and host genes such as FAM19A4, CADM1, PAX1, and MAL, as a promising biomarker for triage and detection of high-grade intraepithelial lesions (CIN2+). Finally, the review evaluates currently available methylation-based assays and self-sampling devices, highlighting their potential to enhance diagnostic accuracy and increase participation in cervical cancer screening programs. Full article

The SARS-CoV-2 nucleocapsid protein (Np) is essential for viral RNA replication and genomic RNA packaging. Phosphorylation of Np within its central Ser-Arg-rich (SRR) linker is proposed to modulate these functions. To gain mechanistic insights into these distinct roles, we performed in vitro biophysical and biochemical studies using recombinantly expressed ancestral Np and phosphomimetic SRR variants. Limited-proteolysis showed minor cleavage differences between wild-type (WT) and phosphomimetic Np, but no major structure or stability changes in the N- and C-terminal domains were observed by circular dichroism spectroscopy and differential scanning fluorimetry, respectively. Mass photometry (MP) revealed that WT Np dimerized more readily than phosphomimetic variants. Crosslinking-MP showed that WT Np formed discrete complexes on viral 5′ UTR stem-loop (SL) 5 RNA, whereas phosphomimetic Np assembled preferentially on SL1–4. WT Np bound non-specifically to all RNAs tested primarily via hydrophobic interactions, whereas phosphomimetic Np showed selectivity for SARS-CoV-2-derived RNAs despite binding more electrostatically. A major difference was observed in the binding kinetics; WT Np compacted and irreversibly bound single-stranded DNA, whereas phosphomimetic Np displayed reduced compaction and fast on/off binding kinetics. These mechanistic insights support a model where phosphorylated Np functions in RNA replication and chaperoning, while non-phosphorylated Np facilitates genomic RNA packaging. The findings also help to explain infectivity differences and clinical outcomes associated with SRR linker variants. Full article

RNA viruses are major pathogens in fish, causing high mortality and substantial economic losses in aquaculture. To uncover conserved antiviral mechanisms, we investigated the response of turbot (Scophthalmus maximus) to viral hemorrhagic septicemia virus (VHSV), infectious pancreatic necrosis virus (IPNV), and red-spotted grouper nervous necrosis virus (RGNNV) using a comparative proteomic approach complemented by in vivo and in vitro functional assays. Proteomic analyses revealed the central, conserved role of proteins involved in reactive oxygen species (ROS) production and redox homeostasis during early infection. Functional assays using head kidney-derived leukocytes identified neutrophils and macrophages as the primary ROS producers and showed that the modulation of cytoplasmic and mitochondrial ROS, as well as ROS-dependent DNA release, follows virus-specific patterns. The pharmacological inhibition of NADPH oxidase and mitochondrial ROS significantly affected viral replication, demonstrating the direct role of ROS in viral pathogenicity. Collectively, these findings highlight redox modulation as a conserved host response in teleost fish during RNA virus infection, linking oxidative stress regulation to viral progression. This knowledge provides a foundation for developing broad-spectrum therapeutic or preventive strategies to enhance disease resistance and promote sustainable aquaculture. Full article

Background and Objectives: Kidney transplant recipients (KTRs) face increased susceptibility to persistent viral infections due to prolonged immunosuppression. While high-risk human papillomavirus (HR-HPV) infection is known to be more prevalent in this population, little is known about the co-occurrence of HPV with human herpesviruses (HHVs) infection in the female genital tract. This study aimed to investigate the presence, dynamics, and potential interactions between HR-HPV and HHVs infections—including HSV-1, HSV-2, EBV, CMV, HHV-6, and HHV-7—in female KTRs during the first year after transplantation. Materials and Methods: A total of 39 female KTRs and 79 age-matched healthy controls were enrolled in the study. Cervicovaginal swabs from recipients were obtained at three time points: two weeks, six months, and one year post-transplantation. HPV DNA was screened using PCR, followed by high-risk HPV genotyping and quantitative viral load assessment using two commercial PCR kits. HHVs were detected using a multiplex PCR assay. Results: HPV DNA was detected in 98% of the KTRs at least once during follow-up, which was significantly greater than in the controls (38%). HR-HPV was identified in 46% of the recipients over the study period, with the highest viral load at one year post-transplantation. HHVs were detected in 72% of the KTRs but not in 43% of the controls (p < 0.01), with EBV and CMV being the most common. Coinfection with HR-HPV and HHVs occurred in 46% of the recipients but not in the controls. Samples containing both EBV and CMV had significantly higher HR-HPV viral loads than samples with no HHVs or with single/other HHV combinations (p < 0.01). All cervical intraepithelial neoplasia patients were found to have combined HPV and HHV infection. Conclusions: Female KTRs present a high burden of both HR-HPV and herpesviruses infections, with increased HPV viral loads. These findings suggest a potential synergistic interaction between HR-HPV and herpesviruses in the immunosuppressed setting. Full article

Background: Efficient nucleic acid extraction is essential for reliable viral load testing, yet performance can differ widely depending on the extraction system and sample type. We compared three automated platforms, QIAcube, EZ1 Advanced, and Maxwell RSC, for their ability to recover cytomegalovirus (CMV) DNA and West Nile virus (WNV) RNA from common clinical matrices. Methods: Mock specimens were prepared using whole blood, plasma, serum, and urine collected from two donors. Samples were spiked with CMV or WNV culture material and extracted in triplicate on each platform according to the manufacturers’ protocols. Viral loads were measured using ELITech ELITE MGB assays on the InGenius system. Whole blood samples were also tested after a 1:4 dilution. Matrix-specific standard curves were applied, and viral loads were compared using Wilcoxon rank-sum tests with false-discovery rate adjustment. Results: Extraction efficiency differed substantially by platform and specimen type. For CMV, QIAcube consistently produced the highest DNA recovery across all matrices, with particularly large differences in plasma and serum, where EZ1 and Maxwell RSC yielded significantly lower loads. The WNV results varied by matrix: EZ1 and QIAcube performed similarly in plasma, while Maxwell RSC achieved the highest RNA recovery in whole blood. While the QIAcube exhibited reduced WNV recovery in blood, it achieved the best performance in serum, as specified by the kit. No significant platform differences were observed for urine. Diluting whole blood reduced variability between platforms. Conclusions: Both sample matrix and extraction system strongly influence nucleic acid recovery. These results highlight the need for matrix-specific validation and standardized extraction approaches in molecular diagnostics. Full article

Cancer immunotherapy increasingly relies on nucleic acid-based vaccines, yet achieving efficient and safe delivery remains a critical limitation. Polyplexes—electrostatic complexes of cationic polymers and nucleic acids—have emerged as versatile carriers offering greater chemical tunability and multivalent targeting capacity compared to lipid nanoparticles, with lower immunogenicity than viral vectors. This review summarizes key design principles governing polyplex performance, including polymer chemistry, architecture, and assembly route—emphasizing microfluidic fabrication for improved size control and reproducibility. Mechanistically, effective systems support stepwise delivery: tumor targeting, cellular uptake, endosomal escape (via proton-sponge, membrane fusion, or photochemical disruption), and compartment-specific cargo release. We discuss therapeutic applications spanning plasmid DNA, siRNA, miRNA, mRNA, and CRISPR-based editing, highlighting preclinical data across multiple tumor types and early clinical evidence of on-target knockdown in human cancers. Particular attention is given to physiological barriers and engineering strategies—including size-switching systems, charge-reversal polymers, and tumor-penetrating peptides—that improve intratumoral distribution. However, significant challenges persist, including cationic toxicity, protein corona formation, manufacturing variability, and limited clinical responses to date. Current evidence supports polyplexes as a modular platform complementary to lipid nanoparticles in selected oncology indications, though realizing this potential requires continued optimization alongside rigorous translational development. Full article