Search Results (2,048)

Background: Hepatitis B virus (HBV) infection remains a major public health challenge in Latin America and the Caribbean (LAC). Mapping scientific production and viral genomic diversity is essential to identify consolidated research fields, as well as areas of opportunity to improve and expand research across the region. Methods: An integrated analysis combining bibliometrics, text-mining, and phylogenetics was performed on HBV literature indexed in PubMed, Scopus, and Web of Science (1970–2025), alongside 9528 GenBank sequences (including full-length genomes, individual genes, and partial diagnostic fragments). Results: A total of 4083 publications were identified, of which 72.1% (2942/4083) were from Brazil, Mexico, and Argentina. Most were original articles (75.8%; 2749/3628) involving human cohorts (95.8%; 2471/2580), where primary research fields centered on serological profiling, co-infections, vaccination, genotype characterization, and blood safety, whereas hepatocellular carcinoma, antiviral therapy, and metabolic comorbidities were the least frequently studied areas. In vitro (10.1%; 260/2580) and animal models (6.9%; 177/2580) accounted for a minor fraction of the literature. Eight circulating HBV genotypes (A–H) were detected, dominated by A (43.4%; 4138/9528), F (29.3%; 2787/9528), and D (19.8%; 1885/9528), while genotype H was largely confined to Mexico (3.2%; 306/9528). Marked geographic clustering was observed (p < 0.001), reflecting both autochthonous American and immigrant lineages. Conclusions: Epidemiological studies represent the most consolidated domain in LAC, yet research remains concentrated in a few countries with persistent experimental and clinical gaps. Fostering cross-border collaboration and investing in underexplored translational areas will be decisive in achieving regional hepatitis B elimination. Full article

Background: Drug-resistant tuberculosis (DR-TB) remains a major challenge in high-burden rural settings where biological, health-system, and social determinants interact. This study integrated whole-genome sequencing (WGS), mathematical modelling and Community-Based Participatory Research (CBPR)-informed principles to examine DR-TB within a conceptual biosocial framework. Methods: WGS data from 32 Mycobacterium tuberculosis isolates were analysed for resistance-associated mutations, phylogenetic lineages and genomic relatedness. A deterministic two-strain model explored drug-susceptible (DS) and DR-TB transmission. Hypothetical CBPR-informed scenarios modified transmission (β), treatment initiation (γ) and resistance amplification (α) parameters over 10 years. Results: Twenty-seven isolates (84.4%) showed resistance to at least one anti-TB drug, and 15 (46.9%) met MDR-TB criteria. Lineages 2 and 4 predominated. Under predefined assumptions, community-informed scenarios produced approximately 40–60% reductions in modelled DS-TB transmission and 20–35% reductions in DR-TB transmission relative to baseline. Conclusions: Integrating genomic evidence with transmission modelling and community-informed assumptions provides a useful hypothesis-generating framework for examining DR-TB. However, the modelled scenarios are exploratory and do not demonstrate the effectiveness of the CBPR intervention. Prospective studies using larger genomic datasets, longitudinal epidemiological data, and empirically measured community-level parameters are required. Full article

Emerging and novel ovine viruses pose increasing threats to animal health, livestock productivity, trade, food security, and public health preparedness. Their emergence is driven by complex interactions among animal movement, mixed-species production systems, wildlife–livestock interfaces, arthropod vectors, environmental changes, and viral evolution. This review critically compares current strategies for identifying major, emerging, re-emerging, zoonotic, and newly recognized ovine viruses, with emphasis on their analytical sensitivity, turnaround time, throughput, operational cost, accessibility, field applicability, validation status, and capacity for novel-virus detection. Conventional diagnostic approaches, including virus isolation, serology, antigen detection, histopathology, and immunohistochemistry, remain essential for confirmation and flock-level surveillance but may be limited by slow turnaround, dependence on specialized facilities, reduced sensitivity at low viral loads, and an inability to identify highly divergent or unknown viruses. Targeted molecular assays, including PCR, RT-PCR, qPCR, multiplex assays, digital PCR, isothermal amplification, and CRISPR-based diagnostics, have improved detection speed and sensitivity but generally require prior knowledge of viral genomic targets. Genomic and metagenomic approaches, including whole-genome sequencing, next-generation sequencing, nanopore sequencing, viral metagenomics, bioinformatics, and phylogenetic analysis, provide broader detection capabilities by enabling characterization of viral diversity, outbreak tracing, co-infection identification, and discovery of previously unrecognized viruses. However, their interpretation remains challenging due to low viral abundance, poor sample quality, host nucleic acid background, contamination, incomplete reference databases, limited computational capacity, and the inability of sequence detection alone to confirm disease causality. Therefore, future ovine virus surveillance requires integration of molecular diagnostics with active, passive, outbreak-based, risk-based, vector, wildlife, and animal-movement surveillance within a One Health framework. Linking genomic information with ecological, epidemiological, and environmental data will be essential for transforming ovine virus surveillance from reactive diagnosis toward proactive preparedness. Advances in standardized sampling, validated field diagnostics, affordable sequencing, curated databases, bioinformatics capacity, and cross-sector data sharing will strengthen early recognition, risk assessment, and preparedness against emerging viral threats in sheep. Full article

Epilepsy is a chronic neurological disorder with a high global prevalence. In Venezuela, the limited availability of epidemiological and pharmacogenetic data represents an important public health challenge. Antiseizure medications (ASMs) are frequently associated with adverse drug reactions (ADRs), which may be influenced by genetic variability in drug-metabolising enzymes. This study evaluated the association between the CYP2C9*2 and CYP2C9*3 variants and the occurrence of ADRs in patients receiving anticonvulsant treatment in the Venezuelan Andes. An observational, analytical, cross-sectional study was conducted in 72 patients. Genomic DNA was extracted from venous blood, and CYP2C9 genotypes were determined by real-time PCR using TaqMan^® probes. The frequencies of the CYP2C9*2 and CYP2C9*3 alleles were 0.15 and 0.06, respectively. The metaboliser phenotype was significantly associated with the presence of ADRs. The risk of ADRs was elevated in the intermediate/poor metaboliser group (IM/PM: OR = 17.45; 95%CI: 5.09–76.56; p < 0.001) and in patients on polypharmacy (OR = 15.03; 95%CI: 2.73–157.37; p = 0.001), although this latter estimate showed marked imprecision due to the width of its interval. Consistent with this, the ADR rate was higher in PM (100%; 3/3) and IM (84.2%; 16/19) than in normal group (20.9%; 9/43). In the monotherapy subgroup, the type of ASM showed no association with the occurrence of ADR (p = 0.741). Among normal metabolisers receiving polytherapy, regimens containing valproic acid were associated with the highest proportion of ADRs, with dual therapy including lamotrigine accounting for 28.57%. Although the overall analysis indicated differences in ADR occurrence according to polytherapy regimen (p = 0.043), the limited sample size restricts the strength of these findings. These results suggest that CYP2C9*2 and CYP2C9*3 variants may contribute to variability in the safety of anticonvulsant treatment among patients from the Venezuelan Andes by influencing CYP2C9 metaboliser phenotypes, and consequently, drug pharmacokinetics. Further studies in larger and more representative Venezuelan populations are warranted to validate these findings. Full article

Dengue virus (DENV) transmission in Brazil is characterized by recurrent epidemics involving the introduction, persistence, and replacement of viral lineages. However, temporal gaps in genomic surveillance limit our understanding of how these processes shape successive epidemics in Rio de Janeiro. Here, in a retrospective observational molecular epidemiology study, we combined archived genomic data with publicly available sequences and epidemiological surveillance data to investigate the temporal dynamics of DENV serotypes and lineages in Rio de Janeiro. Archived DENV-positive samples were curated and subjected to whole-genome amplicon sequencing, and the resulting consensus sequences were analyzed together with publicly available sequences using time-scaled phylogenetic reconstruction and epidemiological data. We recovered 35 DENV genomes from samples collected in 2013, 2018, 2020, and 2021, including DENV-1 genotype V, DENV-2 genotypes II and III, and DENV-4 genotype II. Analysis of the combined datasets identified multiple Rio de Janeiro-associated clades with distinct temporal patterns. Publicly available sequences supported the broader clade structure and long-term temporal patterns independently of most genomes generated here. The newly generated genomes made genotype-specific contributions: the five DENV-1 genotype V genomes placed archived 2020–2021 samples within previously represented Rio de Janeiro-associated groups, while the single DENV-2 genotype II genome provided phylogenetic placement of a travel-associated 2018 case. In contrast, the 20 DENV-2 genotype III genomes identified a Rio de Janeiro-associated cluster not represented among the public sequences, and the nine DENV-4 genotype II genomes increased representation of the 2013 epidemic. Thus, the principal contribution of retrospective sequencing was to fill specific temporal and geographic gaps rather than to redefine the broader historical phylogenetic structure of all genotypes. Full article

Human papillomavirus (HPV) remains the principal etiological agent of cervical cancer, accounting for more than 95% of cases worldwide. Although the carcinogenic role of high-risk genotypes such as HPV-16 and HPV-18 has been extensively established, growing evidence suggests that genetic variability within individual genotypes may contribute to differences in viral persistence, oncogenic potential, immune evasion, and clinical outcomes. This scoping review aimed to synthesize current evidence regarding intratype mutations, viral lineages, and sublineages of high-risk HPV genotypes and to examine their implications for cervical carcinogenesis, vaccine effectiveness, and molecular diagnosis. A literature search was conducted following the PRISMA-ScR framework using PubMed, Scopus, Web of Science, and supplementary searches and citation tracking. Fifty-four studies met the eligibility criteria and were included in the qualitative synthesis. The available evidence suggests considerable genomic heterogeneity among high-risk HPV genotypes, although the strength of the reported associations varies substantially across studies. Several observational studies have suggested that non-European HPV-16 lineages, particularly lineage D sublineages, may be associated with an increased risk of cervical cancer. Mutations affecting the E6, E7, and long control region (LCR) have been reported to be associated with altered viral transcriptional activity, persistence, and oncogenic potential. Genetic variability may influence molecular diagnostic performance and potentially affect vaccine-induced immune responses. However, most reported associations are supported by a limited number of observational studies and should therefore be interpreted with caution. Overall, the available evidence supports the integration of genomic surveillance into HPV prevention and control strategies while highlighting the need for additional high-quality studies to clarify the clinical significance of HPV intratype genomic diversity. Full article

Haemonchus contortus is a highly pathogenic hematophagous gastrointestinal nematode and one of the most important constraints to small-ruminant health and productivity worldwide, causing anemia, reduced weight gain, decreased milk production, and substantial economic losses. Understanding its genetic diversity and population structure is essential for improving parasite surveillance and informing sustainable control strategies. In this study, individual H. contortus larvae collected from Pakistani livestock were subjected to whole-genome sequencing, and complete mitochondrial (mt) genomes were assembled and analyzed using comparative mitogenomics, phylogenetic reconstruction, pairwise genetic distance estimation, and haplotype network analyses. Forty-one H. contortus larvae were successfully characterized for their mitochondrial genomes. The first complete mitochondrial genome of Pakistani H. contortus was 14,002 bp in length and comprised 12 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with a marked AT content of 78.37%. Mitochondrial genome organization and gene order were highly conserved relative to published H. contortus mitogenomes. Comparative analyses resolved the Pakistani isolates into two well-supported mitochondrial lineages, while maximum-likelihood phylogenetic analysis clustered all isolates within a robust H. contortus clade clearly distinct from H. placei (bootstrap support, 97–100%). Pairwise genetic distances among Pakistani isolates ranged from 0.00 to 0.05, indicating pronounced nucleotide divergence. Haplotype network analysis identified numerous unique haplotypes together with globally shared haplotypes, supporting substantial mitochondrial diversity. Collectively, these findings provide the first complete mitogenomic resource for H. contortus from Pakistan and advance our understanding of the genetic structure of this economically important veterinary parasite. The generated genomic resource will support molecular epidemiology, population genetic studies, veterinary parasite surveillance, and future investigations of parasite dissemination and anthelmintic resistance in ruminant production systems. Full article

Molecular technologies have transformed infectious disease surveillance, but their public health value depends on whether molecular signals can be converted into timely and effective action. Unlike molecular epidemiology, which primarily uses molecular variation to characterize distribution, relatedness, transmission, and evolution, molecular public health is defined here as an end-to-end operational framework that connects molecular evidence to population-level decisions, interventions, and evaluation. This narrative review integrates molecular detection, pathogen genomics, bioinformatics, metagenomics, wastewater and environmental surveillance, One Health monitoring, antimicrobial resistance genomics, multi-omics, and artificial intelligence. The framework progresses from detection and analytical interpretation to prediction, intervention, and feedback. Implementation maturity is heterogeneous: targeted PCR, short-read pathogen genomics, and bioinformatics-supported outbreak investigation are established in many defined use cases, whereas pathogen-agnostic metagenomics, multi-omics, and AI-enabled decision support remain more context dependent or emerging. Actionability is operationalized through analytical validity, epidemiological interpretability, sample-to-decision time relative to the intervention window, decision impact, and measurable post-intervention outcomes. Persistent barriers include sampling bias, uneven global capacity, incomplete metadata, insufficient standardization, governance concerns, and poorly defined trigger thresholds. The central criterion for the field should therefore be whether molecular information measurably improves prevention and control. Full article

Yersiniosis is a notifiable disease in Aotearoa|New Zealand, which includes Yersinia enterocolitica (YE) Biotype (BT) 1A, whose pathogenicity and clinical significance has been questioned. An analysis of yersiniosis cases with different YE biotypes (BTs) notified between 2018 and 2022 identified that YE BT 1A and YE BT 2/3 were more frequently observed among adults of European or Other ethnicity and young children of Asian ethnicity, respectively. A comparison of virulence-associated genes detected using whole-genome sequencing data from YE isolates confirmed that YE BT 1A lacked several recognized virulence genes. In vitro two-dimensional intestinal (Caco-2) cell assays showed that YE BT 1A (n = 4) from clinical cases attached and invaded at significantly lower levels than YE BT 2/3 and 4 (n = 3). Gut three-dimensional organ-on-a-chip infections performed using single isolates of YE BTs 2/3, 5, and 1A showed that the YE BT 1A isolate elicited a significantly larger interleukin-8 inflammatory response than the YE BT 2/3 or 5 isolates, which may suggest an acute inflammatory-mediated intestinal disease mechanism. While further work is required to elucidate the role of YE BT 1A in causing gastrointestinal illness, these findings highlight the need to distinguish cases infected with YE BT 1A from those infected with other YE BTs. Full article

Parkinson’s disease (PD) is influenced by genetic and environmental factors. Epidemiological evidence indicates that smoking is associated with reduced PD risk, potentially through oxidative stress-related pathways. PARK16 is a PD-susceptibility locus also implicated in oxidative stress regulation. This study examined gene–environment interaction involving smoking and a PARK16 single nucleotide polymorphism (SNP). A case–control study involving 999 Chinese subjects (497 cases, 502 controls) was conducted. PARK16 SNP rs6679073 (NC_000001.11:g.205787356C>A) was identified in a genome-wide association study in an Asian population. Logistic regression estimated adjusted odds ratios (ORs), controlling for age, sex, family history, and comorbidities. Gene–environment interactions were assessed using both additive (RERI, AP, and S) and multiplicative models. Smoking was not significantly associated with PD risk in the cohort (adjusted OR 0.78, 95% CI 0.54–1.12, and p = 0.179). rs6679073 was significantly associated with increased PD risk under the recessive model (AA vs. CC/CA: adjusted OR 1.47, 95% CI 1.11–1.93, and p = 0.007). An additive interaction between rs6679073 and smoking was observed (RERI 0.85, 95% CI 0.21–1.50; AP 0.51, 95% CI 0.12–0.89). These findings suggest a biologically plausible interaction between PARK16 rs6679073 and cigarette smoking in modulating PD risk and warrants further investigation. Understanding gene–environment interactions may inform the design of mechanistic studies and contribute to risk stratification in susceptible populations. Full article

Persistent high-risk human papillomavirus (HR-HPV) infection serves as the core prerequisite for cervical intraepithelial neoplasia (CIN) and invasive cervical cancer. Accumulated translational evidence confirms that vaginal microecological homeostasis dominated by protective Lactobacillus strains fundamentally governs the initiation, persistence, and spontaneous clearance of HR-HPV infection, while microbial dysbiosis featuring depleted lactobacilli and overgrown anaerobic pathogens creates a pro-inflammatory, immune-suppressive mucosal niche that accelerates viral retention and cervical malignant transformation. We conducted a narrative review of studies published primarily between January 2021 and April 2026. PubMed, Web of Science, CNKI, Wanfang Data, and VIP were searched using terms related to the vaginal microbiome, HR-HPV infection, CIN, cervical cancer, underlying mechanisms, microbial biomarkers, and microbiome-modulating interventions. Relevant peer-reviewed epidemiological, mechanistic, and clinical studies were prioritized, and the manuscript was prepared with reference to the Scale for the Assessment of Narrative Review Articles (SANRA). This review systematically delineates the bidirectional regulatory crosstalk between vaginal microbiota and HR-HPV across the cervical cancer continuum. Dysbiosis disrupts vaginal acidic barriers, reshapes local cytokine networks, impairs antiviral innate immunity, and modulates HPV E6/E7 oncogenic transcription; reciprocally, HR-HPV oncoproteins remodel microbial community structures to sustain a dysbiotic feedback loop. Three core carcinogenic cascades induced by dysbiotic flora are elaborated: epithelial barrier erosion, metabolic reprogramming, and epigenetic rewiring of host and viral genomes. Dynamic microbial characteristics corresponding to all stages of progressive cervical lesions, from transient HPV infection to high-grade CIN and carcinoma, are sorted out. The bench-to-bedside translational progress of microbiome-targeted interventions is summarized, including single/multi-strain probiotic supplementation, engineered lactic acid bacterial therapeutic vaccines, vaginal microbiota transplantation, and traditional Chinese medicine therapy that reconstructs vaginal eubiosis. The clinical application of microbial diversity, strain-level single-nucleotide variants, and taxonomic biomarkers for early screening, efficacy prediction, and postoperative recurrence risk stratification is illustrated. This comprehensive framework with the vaginal microbiome as the core clarifies the internal mechanism of HR-HPV progression along the entire pathway to cervical cancer and provides practical clinical means to block this cascade. Current bottlenecks, including inconsistent probiotic standards, preclinical model limitations, and unresolved gut–vagina microbiome interactions, require further investigation before widespread clinical translation. Full article

The global dissemination of coronaviruses continues to pose formidable threats to public health and socioeconomic development, making these viruses a major research priority. Porcine deltacoronavirus (PDCoV), an emerging porcine enteric virus identified over the past two decades, has resulted in substantial economic losses to the swine industry owing to its high mortality and persistent circulation across the globe. Beyond swine, PDCoV possesses a broad host spectrum and is capable of infecting avian species, mice, calves, and other animals. Most alarmingly, its zoonotic potential was highlighted in 2021 through the discovery of PDCoV genomic RNA in pediatric samples from Haiti, highlighting its potential to become the eighth coronavirus species known to infect humans. Despite these dual veterinary and public health threats, licensed vaccines and specific human therapeutics remain unavailable. These facts highlight an urgent demand for comprehensive and in-depth studies on PDCoV to mitigate its potential risks and forestall future outbreaks. This comprehensive review summarizes the latest research advances in PDCoV in four aspects: biological characteristics, epidemiology, pathogenic mechanisms, and antibody development. It is expected that this review can provide a robust theoretical basis for understanding PDCoV infection dynamics and accelerating the development of next-generation, broad-spectrum antiviral strategies to mitigate future interspecies spillover events. Full article

Since viral hemorrhagic septicemia virus (VHSV) was first identified in rainbow trout, it has evolved into four major genotypes in the process of infecting multiple hosts. The different levels of virulence among genotypes of VHSV are caused by genetic evolution. In this study, the complete genome sequences of global VHSV strains were obtained from the GenBank database and their genetic relationships were analyzed. The maximum likelihood (ML) phylogenetic tree based on the complete genomes of VHSV showed that globally, VHSV strains evolved into two region-specific clades, namely the European clade and the North American clade. North American VSHV strains are more conserved than European strains. Both European and North American strains are subjected to purifying selection. All VHSV proteins are gathered into their region-specific clusters in genetic distance space. Furthermore, North American and Asian strains have organized glycosylation sites in their G protein. An early Japanese strain, KRRV9822, which clusters into the North American clade, has undergone potential recombination. Together, the region-specific genetic relationship and mutation characteristics of global VHSV strains were revealed with a crucial perspective for epidemiological research on VHSV. Full article

Antimicrobial resistance (AMR) is an important One Health challenge, yet evidence on resistant Escherichia coli and Salmonella spp. in Romania is dispersed across animal species, food matrices, environmental compartments, and surveillance systems. This comprehensive narrative review synthesizes and critically evaluates evidence across animal–food–environment interfaces and places it in the context of broader European AMR patterns. Particular attention is given to isolate origin, resistance phenotypes, multidrug resistance, major resistance determinants, molecular epidemiology, and the strength of evidence supporting cross-sector connections. Studies most frequently addressed poultry and swine, where resistance to ampicillin, fluoroquinolones, sulfonamides, and tetracyclines was repeatedly reported, together with extended-spectrum cephalosporin resistance, particularly in E. coli. Evidence from cattle, foods of animal origin, companion animals, wildlife, wastewater, and aquatic environments shows that resistant bacteria and antimicrobial resistance genes occur across multiple compartments. Substantial heterogeneity in sampling design, susceptibility testing, and molecular characterization limits direct comparison between studies, while epidemiologically linked investigations and whole-genome sequencing across connected reservoirs remain uncommon. Priorities include more standardized cross-sector surveillance, stronger environmental monitoring, expanded genomic epidemiology, improved data interoperability, and continued antimicrobial stewardship. By integrating fragmented national evidence, this review identifies both well-characterized sectors and interfaces where important evidence gaps remain. Full article

This cross-sectional, culture-based study aimed to recover Klebsiella pneumoniae species complex (KpSC) isolates from fecal samples collected from clinically healthy chicken and turkey flocks in Diyarbakır, Türkiye, and to characterize the sequence-confirmed isolates. A total of 419 fecal samples from small-scale, family-operated farms were examined. Presumptive isolates were screened by MALDI-TOF MS and confirmed by 16S rRNA and rpoB gene sequencing. Antimicrobial susceptibility testing, phenotypic ESBL and carbapenemase assays, targeted PCR detection of resistance- and virulence-associated genes, multilocus sequence typing (MLST), and phylogenetic analyses were performed. Six KpSC isolates were confirmed from the 419 samples examined (6/419, 1.43%): K. pneumoniae (n = 4), K. quasipneumoniae (n = 1), and K. variicola (n = 1). All six were resistant to ampicillin, amoxicillin, and enrofloxacin; two were multidrug-resistant, and one showed an ESBL phenotype. No carbapenemase phenotype or targeted carbapenemase genes were detected. intI1 and bla_SHV were each detected in four isolates, while wabG and entB were present in all isolates. MLST identified six distinct sequence types, one of which, K. quasipneumoniae ST9812, was novel and associated with the novel rpoB allele 593, while one turkey-origin K. pneumoniae isolate belonged to ST15. These findings demonstrate phenotypic and molecular diversity among poultry-origin KpSC isolates and provide a basis for broader genomic investigation of their epidemiological significance. Full article