We have previously shown that the hepatitis C virus (HCV) E1E2 envelope glycoprotein can regulate HIV-1 long-terminal repeat (LTR) activity through disruption to NF-κB activation. This response is associated with upregulation of the endoplasmic reticulum (ER) stress response pathway. Here, we demonstrate that the SARS-CoV-2 S, M, and E but not the N structural protein can perform similar downmodulation of HIV-1 LTR activation, and in a dose-dependent manner, in both HEK293 and lung BEAS-2B cell lines. This effect is highest with the SARS-CoV-2 Wuhan S strain and decreases over time for the subsequent emerging variants of concern (VOC), with Omicron providing the weakest effect. We developed pseudo-typed viral particle (PVP) viral tools that allowed for the generation of cell lines constitutively expressing the four SARS-CoV-2 structural proteins and utilising the VSV-g envelope protein to deliver the integrated gene construct. Differential gene expression analysis (DGEA) was performed on cells expressing S, E, M, or N to determine cell activation status. Gene expression differences were found in a number of interferon-stimulated genes (ISGs), including IF16, IFIT1, IFIT2, and ISG15, as well as for a number of heat shock protein (HSP) genes, including HSPH1, HSPA6, and HSPBP1, with all four SARS-CoV-2 structural proteins. There were also differences observed in expression patterns of transcription factors, with both SP1 and MAVS upregulated in the presence of S, M, and E but not the N protein. Collectively, the results indicate that gene expression patterns associated with ER stress pathways can be activated by SARS-CoV-2 envelope glycoprotein expression. The results suggest the SARS-CoV-2 infection can modulate an array of cell pathways, resulting in disruption to NF-κB signalling, hence providing alterations to multiple physiological responses of SARS-CoV-2-infected cells.

The limitations of the current vaccination strategy for the Kyasanur Forest Disease virus (KFDV) underscore the critical need for effective antiviral treatments, highlighting the crucial importance of exploring novel therapeutic approaches through in silico drug design. Kyasanur Forest Disease, caused by KFDV, is a tick-borne disease with a mortality of 3–5% and an annual incidence of 400 to 500 cases. In the early stage of infection, the envelope protein plays a crucial role by facilitating host–virus interactions. The objective of this research is to develop effective antivirals targeting the envelope protein to disrupt the virus–host interaction. In line with this, the 3D structure of the envelope protein was modeled and refined through molecular modeling techniques, and subsequently, ligands were designed via de novo design and pharmacophore screening, yielding 12 potential hits followed by ADMET analysis. The top five candidates underwent geometry optimization and molecular docking. Notably, compounds L4 (SA28) and L3 (CNP0247967) are predicted to have significant binding affinities of −8.91 and −7.58 kcal/mol, respectively, toward the envelope protein, based on computational models. Both compounds demonstrated stability during 200 ns molecular dynamics simulations, and the MM-GBSA binding free-energy values were −85.26 ± 4.63 kcal/mol and −66.60 ± 2.92 kcal/mol for the envelope protein L3 and L4 complexes, respectively. Based on the computational prediction, it is suggested that both compounds have potential as drug candidates for controlling host–virus interactions by targeting the envelope protein. Further validation through in-vitro assays would complement the findings of the present in silico investigations.

Public pathogen-genomics repositories are increasingly used for antimicrobial resistance (AMR) surveillance, yet the reliability and interoperability of database-derived genotype–phenotype inference remain incompletely characterized. This study evaluated antibiotic-specific concordance between exported AMR genotype annotations and antimicrobial susceptibility testing (AST) phenotypes in the NCBI Pathogen Detection metadata for the Escherichia coli/Shigella organism group and used BV-BRC to assess complementary phenotype-related coverage and cross-resource linkage. Frozen NCBI Pathogen Detection and BV-BRC exports were analyzed retrospectively. NCBI records were filtered for assembly accessions, AMR genotype annotations, and interpretable resistant or susceptible AST results. Prespecified antibiotic-specific mapping rules were applied. Performance metrics, including sensitivity, specificity, accuracy, balanced accuracy, positive and negative predictive values and F1-score, were calculated, and their 95% confidence intervals were estimated using 10,000 isolate-level bootstrap replicates. BV-BRC was evaluated descriptively for phenotype-related coverage, evidence type, and accession overlap. Among 539,918 NCBI records, 10,201 met prespecified criteria for assembly accession, AMR genotype annotation, and interpretable resistant/susceptible AST data. These records generated 56,141 genotype–phenotype comparisons across eight priority antibiotics. Concordance was high for tetracycline (accuracy, 98.4%; F1-score, 98.1%) and ceftriaxone (accuracy, 97.9%; F1-score, 94.6%), but lower for amoxicillin–clavulanic acid (accuracy, 73.6%; F1-score, 44.5%), indicating antibiotic-specific limits of genotype-field inference. Discordance was explicitly separated into 2524 genotype-positive/phenotype-susceptible and 923 phenotype-resistant observations with no mapped genomic evidence of resistance. BV-BRC contributed 21,298 taxonomy-strict E. coli/Shigella genomes and 4745 phenotype-linked identifiers. Although 15,214 BioSample and 10,121 assembly accessions were shared across exports, no analysis-ready overlap remained between the final NCBI genotype–AST and BV-BRC phenotype-linked subsets after eligibility filtering. Public WGS-AMR databases can support large-scale surveillance-oriented concordance analyses, but performance is antibiotic specific and depends on mapping rules, phenotype definitions, evidence provenance, and accession linkage. These estimates do not constitute clinical diagnostic validation and should not replace phenotypic AST. Because the analysis was conducted at the combined organism-group level, these estimates may mask species-, pathotype-, or lineage-specific resistance dynamics.

Brucellosis remains an important zoonotic disease in southern Saudi Arabia; however, community-level knowledge, risk-related practices, and information pathways in Najran City are insufficiently characterized. This study assessed brucellosis-related knowledge, attitudes, practices, and information pathways among adults in Najran City to inform locally relevant One Health interventions. In this cross-sectional survey, adults were recruited using stratified time–location (venue-based) sampling across community and exposure-relevant sites in Najran City. A total of 608 adults completed a structured interviewer-administered questionnaire. Composite scores were calculated for knowledge (0–21), attitude (0–22), practice (0–64), and information-source breadth (0–6). Descriptive statistics, group comparisons, correlation analyses, and multivariable linear regressions were performed. The findings suggest that participants more commonly relied on interpersonal social networks, especially family and friends, for information related to brucellosis (53.9%), whereas formal sources were less commonly reported, including health professionals (7.9%), media (4.6%), internet sources (3.3%), educational institutions (2.0%), and agricultural or veterinary organizations (1.3%). Mean knowledge scores were moderate (10.7/21), attitudes were generally favorable (19.5/22), and practice scores were moderate (36.6/64). Exposure-related behaviors remained common, particularly the consumption of unpasteurized milk or dairy products (56.6%). The breadth of information sources showed a moderate positive correlation with knowledge (rho = 0.561), whereas attitude showed only small positive correlations with knowledge and practice. Finally, knowledge was weakly and inversely correlated with practice. Among adults recruited in this venue-based sample, favorable attitudes did not consistently correspond to safer practices. These findings support practical One Health interventions, including coordinated veterinary–public health messaging on animal abortion events, safe-dairy guidance at points of sale and community venues, workplace-based training for livestock-contact groups, and referral pathways linking suspected animal cases with veterinary services and human care-seeking. Because recruitment was venue-based and non-probability, the results should be interpreted as descriptive and hypothesis-generating rather than population-representative; however, they still identify practical communication and service-delivery priorities for future intervention studies in Najran.

Background: Monkeypox (MP) is an emerging disease with the capacity for worldwide dissemination, endangering all nations. Healthcare workers (HCWs) frequently act as the initial point of contact for MP patients; therefore, evaluating their understanding of the disease and their perspectives on MP immunisation is crucial for effective prevention and control. This study aimed to assess HCWs’ knowledge of and attitudes toward MP and associated vaccines. Methods: A cross-sectional study was performed, focusing on HCWs in Makkah, Saudi Arabia. Data were collected through a standardised, self-administered online questionnaire provided in both English and Arabic. The questionnaire gathered the participants’ sociodemographic information and assessed their knowledge, opinions, and attitudes concerning MP infection and vaccination. The questionnaire included multiple-choice items with response possibilities such as “Yes”, “No” and “Don’t know”. Results: In total, 428 HCWs participated in this study; 60.7% had adequate knowledge of MP, while 39.3% had inadequate knowledge. Some knowledge of specific aspects of the disease was reported to be variable, with 67.5% correctly identifying MP as a viral infection, 55.1% aware of the endemic nature of the disease in parts of Western and Central Africa, and 65.0% recognising skin rash as a common symptom. In terms of attitudes towards MP vaccination, 47.9% had a positive attitude, while 52.1% had a negative attitude. In total, 65.7% of the respondents indicated that vaccination is essential to controlling MP, while only 23.1% (95% CI: 19.1–27.1%) had received vaccination. Furthermore, 57.0% reported concerns about potential adverse effects. Educational level was significantly associated with knowledge of MP (p = 0.001), while job title (p = 0.008) and years of work experience (p = 0.018) were significantly associated with attitudes towards MP vaccination. Age group was significantly associated with MP vaccination status (p = 0.002), while gender, educational level, job title, and years of work experience were not significantly associated with vaccination status. Conclusions: HCWs demonstrated an adequate level of knowledge about MP; however, important knowledge gaps and negative attitudes towards MP vaccination remained. Despite recognising the importance of vaccination, vaccine uptake was low. Educational level was associated with knowledge about MP, while job title and years of work experience were associated with attitudes towards MP vaccination, and age group was associated with MP vaccination status. Targeted educational interventions and evidence-based awareness programmes may enhance knowledge, improve preparedness for future MP outbreaks, and decrease vaccine hesitancy among HCWs.

Whole-genome sequencing (WGS) has become a critical component of antimicrobial resistance (AMR) surveillance because it can characterize bacterial lineages, resistance determinants, and, when sequence resolution is sufficient, the mobile genetic elements that mediate dissemination. However, the practical value of WGS-based AMR inference remains constrained by fragmentation across AMR databases, inconsistent nomenclature, variable curation practices, and differences in analytical thresholds and reporting rules. Consequently, the same isolate may yield discordant resistome outputs across tools, limiting reproducibility, cross-study comparability, and surveillance integration. This review focuses on the interpretation of bacterial WGS data for AMR detection, with emphasis on AMR prediction tools, reference databases, read-mapping and assembly-based workflows, genotype–phenotype discordance, validation strategies, and harmonized reporting. General bioinformatics steps, including quality control, assembly, and polishing, are discussed only where they directly affect AMR inference, such as small-variant detection, plasmid reconstruction, and mobile genetic element context. The review further evaluates major AMR resources with respect to scope, curation depth, evidence models, updating practices, and interoperability across clinical and One Health applications. Rather than advocating a single universal database, we argue that the field would benefit more from federated harmonization based on shared ontologies, transparent provenance, versioned crosswalks, and benchmarked reporting standards. Within this context, AMR-GenoLink is introduced as a proposed reference framework for interoperable ingestion, standardized reporting, and provenance-aware integration of WGS-derived AMR evidence across human, animal, and environmental domains. The framework separates genomic feature detection from resistance interpretation, phenotype-linked validation, and evidence-proportionate reporting. Overall, this review argues that reliable WGS-based AMR interpretation is increasingly constrained not only by limitations in resistance-gene detection but also by insufficient harmonization across databases, analytical workflows, validation standards, and reporting frameworks.