Emerging Microbes & Infections

ObjectiveWest Nile virus lineage 2 (WNV-2) is a growing public health concern in Europe causing West Nile fever or West Nile neuroinvasive disease (WNND) with substantial morbidity and mortality; however, genomic data from Southern Italy are limited despite recent expansion of autochthonous transmission. The aim of the study was to characterise the phylogenetic and molecular features of the WNV-2 strain responsible for the first autochthonous human infection reported in Calabria (2023), and two more additional WNND cases detected in 2024. MethodsFull WNV-2 genomes were generated from the three cases. Phylogenetic analysis was performed using all publicly available WNV sequences up to September 2025. Amino-acid changes in the polyprotein were compared with known WNV-2 lineage and sub-lineage signatures. ResultsThe three sequences formed a monophyletic group within sub-lineage WNV-2a, clustering with strains circulating in Central-South-Eastern Europe and showing closest affinity to Hungarian sequences. Non-synonymous substitutions characteristic of the Hungary 578/10 ancestor (NS2B-119I, NS4B-14G, NS4B-49A and NS5-298A), were identified and absent from Central-Northern-Western European and previously reported Italian sequences. Additional substitutions (E-159T, E-399R and NS3-249P) corresponded to signatures from a fatal WNV-2 infection in a Great Grey owl in Slovakia. ConclusionsOur study provides the first report of Central-South-Eastern European WNV-2 circulation outside Eastern Europe supporting its likely spread through the Balkans into Italy by 2022. These findings underscore the rapid spread of WNV-2 in newly affected areas and highlight the critical need for sustained molecular surveillance.

Influenza A(H3N2) subclade K virus was detected in Canada early in the 2025/26 influenza season, bearing an antigenic transition in the hemagglutinin (HA) glycoprotein. Analysis of 396 HA sequences from Canada showed antigenic divergence from 2025/26 influenza vaccine strains, consistent with partial mismatch. Phylodynamic analysis revealed sustained pre-vaccine transmission without clear post-vaccine expansion. Phylogenetic and phylogeographic analyses indicated interprovincial mixing within a highly connected metapopulation, highlighting the value of genomic surveillance for real-time epidemiologic inference and public health decision-making.

In the past decade, dengue fever has emerged as a major public health on Reunion Island in the Southwest Indian Ocean. During the 2018-2022 outbreak, an unusual increase in ocular complications was reported in some patients. To investigate a potential viral cause, we analysed 447 blood samples from hospitalized patients with and without ophthalmic symptoms. Genetic sequencing revealed the co-circulation of two strains of dengue virus serotype 1, both genetically linked to strains previously identified in Asia. Notably, all patients with ophthalmic symptoms were infected with viruses from a single cluster within genotype I, which harbored several unique mutations. These findings suggest that the rare ocular complications observed during this outbreak may be associated with specific viral cluster. Further laboratory studies are required to confirm this potential link.

Mass drug administration (MDA) of praziquantel is an intervention used in the treatment and prevention of schistosomiasis. Its effectiveness and sustainability require identifying subpopulations that are at risk of infection. A longitudinal survey was conducted among 3,810 subjects aged 5-19 years old recruited at baseline across ten council wards in Katsina Ala, Benue, Nigeria, to determine the prevalence, intensity, and index of potential contamination of urogenital schistosomiasis for three successive phases: three months, six months, and nine months post-treatment periods. Urine samples were processed using microscopy and reagent strips (Medi Test Combi 9). Prevalence of infection was recorded in all the phases of the surveys, with the first having the highest prevalence (12.30%), followed by the third phase (9.12%) and the second phase (7.60%), the difference being significant (P < 0.05). The highest intensity of infection (16 ova/10 ml urine) was observed in the first phase, followed by the third phase (15.10 ova/10 ml urine) and the second phase (11 ova/10 ml urine). Peak prevalence, intensity, and relative index of potential contamination (Rel. IPC) occurred among pupils between the ages of 10 and 14 years old in both sexes. The result of the relative contribution of each age group in polluting the snail habitat with Schistosoma eggs, thus enabling transmission, showed to a greater extent that children aged 10-14 years old were responsible for contaminating the environment with a bulk of S. haematobium eggs and for the transmission and maintenance of the disease in the area.

In November 2025, a traveler from Cuba tested positive for chikungunya virus upon arrival to Mexico. The virus belonged to the East-Central-South-African lineage, clustering with a clade prevalent in Brazil. Ten years after the last chikungunya epidemic in Mexico, strengthened surveillance is required to anticipate transmission of this emergent lineage.

Household transmission of EV-D68 was identified in 35 of 1040 households (3.4%) in the Pacific Northwest between 2022-2024, with an estimated secondary attack rate of 15%. Sequences from within households clustered closely with 0 to 2 pairwise nucleotide differences (median 1) between cases 6-14 days apart (median 7).

The emergence of vaccine covered serotypes causing invasive pneumococcal disease (IPD) is a serious concern worldwide. We investigated the unexpected rise of serotype 4 causing IPD primarily in non-vaccinated young adults after the COVID-19 pandemic that further spread to adults [&ge;] 65 years in recent years. For this purpose, we conducted a retrospective study of serotype 4 IPD cases (n=827) reported in Spain between 2009 and 2024. Whole-genome sequencing was performed to assess clonal lineages and phylogenetic relationships. Clinical and epidemiological data were compared between serotype 4 and all other serotypes causing IPD. Epidemiological and genomic analysis confirmed that the rise started as an abrupt cluster of IPD cases in Seville (Andalusia) in the year 2022 due to the ST15063 within GPSC12 lineage. This outbreak initially caused pneumonia episodes that required hospitalization in young individuals associated with high rates of tobacco smoking, alcohol, and inhaled drugs such as cannabis and cocaine, followed by a general distribution pattern throughout the country in the following years, affecting the elderly population. Experimental studies to evaluate potential underlying mechanisms confirmed that ST15063 serotype 4 strains displayed enhanced infection rates of human lung cells that significantly increased in the presence of cigarette smoke exposure and by influenza H3N2 virus coinfection, but not with H1N1. These findings highlight the need for targeted vaccination strategies not only against pneumococcus but also against respiratory viruses such as influenza, RSV and COVID-19 and demonstrate the importance of molecular surveillance to establish effective interventions in high-risk populations.

Several African countries experienced a surge in acute hemorrhagic conjunctivitis (AHC) cases in 2024. Investigations in Kenya, Mayotte and Tanzania identified coxsackievirus A24 variant (CV-A24v) as the causative agent. To date, limited genomic data exist to elucidate the sources, epidemiology, and evolution of CV-A24v in Africa. We generated 245 CV-A24v genomes from samples collected between January and September 2024 in coastal Kenya. Phylogenetic analysis showed that these viruses belonged to genotype IV, with two major clusters identified that differed by 52 nucleotides and five amino acids, with recombination detected in the 3Dpol gene. The sequences clustered closely with contemporaneous Mayotte and Malawi sequences but were distinct from Asian sequences from 2023. Molecular clock dating revealed that the Kenyan sequences had a Most Recent Common Ancestor (MRCA) between June and October 2023. Our study provides the first detailed genomic analysis of CV-A24v from Africa to inform its future control strategies.

Human metapneumovirus (HMPV) is a significant cause of acute respiratory illness in both children and adults, yet its genomic epidemiology remains understudied compared to other respiratory viruses. Here, we report an expanded genomic surveillance of HMPV in the United States, utilizing 325 newly sequenced samples from two cohorts: the household-based HIVE study (2010-2022) in Michigan and the multicenter IVY network (2022-2025) of hospitalized adults. Our analyses revealed the continued predominance of the A2.2.2 clade and little geographic structure in the US. Genomic diversity is highest in the glycoprotein (G); we identified a shift from variants bearing the 180nt duplication to ones with a 111nt duplication. Phylogenetic analyses supported the duplication-deletion model for the origin of the duplications. The conserved fusion (F) protein shows limited antigenic variation and low rates of nonsynonymous substitutions, suggesting stability in epitopes targeted by vaccine candidates. These findings underscore the utility of enhanced genomic surveillance for understanding HMPV evolution and informing vaccine development. SummaryGenomic surveillance of HMPV in the United States over a 15 year period reveals extensive genetic diversity and more rapid evolution in the G protein compared to the F protein, which is targeted by vaccines under development.

The rapid diagnosis of Campylobacter infections is important for the management of infectious gastroenteritis. Although stool culture is considered the gold standard, its sensitivity is limited and it requires prolonged incubation times. We performed a prospective multicenter study at nine healthcare facilities in Japan to evaluate a Campylobacter rapid antigen test using stool specimens between March 2024 and August 2025. Patients with suspected infectious gastroenteritis were consecutively enrolled and tested using QuickNavi-Campylobacter and compared with the FilmArray Gastrointestinal Panel as the reference method. Discordant results were further evaluated by culturing and additional PCR assays. In total, 410 patients were included in the final analysis. The positive, negative, and total concordance rates between QuickNavi-Campylobacter and FilmArray Gastrointestinal Panel were 79%, 99%, and 93%, respectively. The positive concordance rate decreased in specimens collected [&ge;] 6 days after the onset of symptoms (50%). QuickNavi-Campylobacter demonstrated relatively good concordance with the FilmArray Gastrointestinal Panel in a real-world multicenter setting. These results suggest that this rapid antigen test may be particularly useful for the early diagnosis of suspected campylobacteriosis.

SARS-CoV-2 mutations play a key role in viral evolution, in immune escape, and potentially in disease severity. However, the clinical impact of most mutations remains poorly understood, particularly across different variants. A historical observational study was conducted using SARS-CoV-2 whole-genome sequencing data linked to clinical metadata from 175,503 COVID-19 cases in Israel. The dataset was stratified into four variant-specific periods: B.1.1.7, B.1.617.2, BA.1, and BA.2. Logistic regression models were applied separately within each period to assess the association between individual mutations and the need for hospitalization, adjusting for age, gender, and time since vaccination. False discovery rate correction was used to account for multiple testing. A total of 18 SARS-CoV-2 mutations were significantly associated with COVID-19 severity, of which eight remained statistically significant after false discovery rate correction. Among these, two were associated with increased risk and six with reduced risk. Most were non-synonymous mutations located in functionally relevant regions such as the spike protein and non-structural proteins. This study provides a variant-stratified assessment of SARS-CoV-2 mutations associated with clinical severity, revealing both known and novel associations. The findings highlight the importance of integrating genomic and clinical data in public health surveillance and may inform future outbreak preparedness by identifying mutations with potential clinical impact.

BackgroundThere is a need for synthetic peptide-based serologic assays that exploit avidity to replace whole antigens while enabling low-cost diagnostics in resource-limited settings. ObjectiveTo evaluate the diagnostic accuracy of a polymeric peptide-based ELISA leveraging avidity to enhance signal. MethodA 15-member SARS-CoV-2 peptide library corresponding to multiple epitope clusters and proteins was screened by indirect ELISA using pooled sera from RT-PCR-confirmed COVID-19 patients to identify peptides with possible diagnostic utility. The identified lead candidate, S559, possessed terminal cysteine-substitution to allow disulfide polymerization, and the resulting avidity gain was evaluated by comparing the apparent dissociation constant (KDapp) before and after depolymerization with N-acetylcysteine. The performance of an optimized ELISA using S559 was evaluated on 1,222 prospectively collected COVID-19 serum samples and 218 biobanked pre-COVID control serum samples. ResultsPolymeric S559 with a KDapp of 29.26 nM-1was demonstrated to have a 218% avidity gain relative to the completely depolymerized form. At pre-defined thresholds, the optimized S559 ELISA has a sensitivity and specificity of 83.39% (95%CI: 81.18% and 85.43%) and 96.79% (95%CI: 93.50% and 98.70%), respectively. At post hoc thresholds determined by Youden index, sensitivity and specificity reached 95.01 (95% CI: 93.63% - 96.16%) and 100.00% (95% CI: 98.32% - 100.00%), respectively. ConclusionHomomultivalent epitope presentation using polymeric S559 allows a highly specific immunoassay using human sera that may have important value in detecting antibodies, whether for diagnosing infection, confirming vaccination status or conducting surveillance.

Strengthening in-country sequencing capacity generated 28 Lassa virus genomes from human clinical cases, expanding our knowledge of Lassa fever in Guinea. Phylogeographic analysis revealed cross-border exchange between Liberia and the NZerekore region, and a Sierra Leone introduction into the Gueckedou area. Enhanced genomic surveillance is crucial to guide future public health actions.

ContextErogothioniene (EGT), a potent natural antioxidant, exerts hepatoprotection. However, human clinical evidence remains absent. Objectiveto observe the clinical efficacy and safety studies of GeneIII(R) L-Ergothioneine Capsules in the Hepatoprotective Efficacy. Materials and methodsThirty subjects with some abnormal liver function indicators were selected to take 2 capsules of 30mg GeneIII(R) L-Ergothioneine Capsules per day, for 30 consecutive days. The changes in serum liver function biomarkers, clinical efficacy self-rating scale, and Pittsburgh sleep quality index scale (PSQI) from baseline in different visit cycles were compared by self-control. All adverse events that occured after receiving the trial medication were also tracked and the incidence of adverse events during the trial period was calculated. ResultsAll subjects completed treatment and follow-up. After taking GeneIII(R) L-Ergothioneine Capsules, the subjects aspartate aminotransferase (AST) levels were significantly reduced compared to baseline (p=0.0082). Additionally, alanine aminotransferase (ALT) levels were also significantly reduced (p=0.0025), gamma-glutamyl transferase (GGT) levels were significantly reduced compared to baseline (p=0.0270). Physical function scores on the Clinical Efficacy Self-Assessment Scale improved significantly compared to baseline. Physical function scores decreased significantly by 39.04% compared to baseline (p<0.0001). Additionally, the level of daytime functional impairment on the Pittsburgh Sleep Quality Index was significantly reduced by 51.56% compared to baseline (p=0.0038). No adverse events occurred throughout the study. No side effects were observed clinically, confirming the reliable safety of GeneIII(R) L-Ergothioneine Capsules under the current study design. ConclusionGeneIII(R) L-Ergothioneine Capsules have a significant effect on improving liver function, physical function, and sleep quality in subjects, and the overall safety is good.

BackgroundUsing the FDA Adverse Event Reporting System (FAERS) database, this pharmacovigilance investigation systematically assessed the adverse events (AEs) associated with Fedratinib use in real-world clinical practice. MethodsUsing the FAERS database, we performed a disproportionality analysis incorporating four distinct signal detection methodologies: ROR, PRR, BCPNN, and MGPS. Subgroup analyses were conducted to evaluate the effects of age and gender on Fedratinib-associated AEs. Furthermore, a time-to-onset analysis was performed to characterize the temporal patterns of AEs. ResultsThe FAERS database comprised 10,011,422 individual case safety reports, of which 1,284 were classified as Fedratinib-related AEs, encompassing 38 significant preferred terms (PTs). The most frequently reported adverse reactions included diarrhoea, nausea, vomiting, constipation, abdominal discomfort, fatigue, anaemia, platelet count decreased, and Wernickes encephalopathy. New AEs emerged from the study, such as blood potassium increased, hyperkalaemia, gout, hypocalcaemia, renal failure, renal disorder, and gallbladder disorder. Higher rates were observed in males over 65 years of age. Most cases occurred within the first month of Fedratinib treatment, with the incidence of related AEs decreasing over time. ConclusionThis current study marks the debut investigation regarding Fedratinibs safety in actual clinical practice, which providing substantive evidence to inform future pharmacovigilance investigations of this drug.

Carbapenem-resistant (CR) bacteria have emerged and been spreading beyond healthcare-associated facilities into the environment. It is recognized that toilet bowl water in patient rooms of healthcare-associated facilities can be one of internal reservoirs of CR bacteria. In accordance with this idea, toilet bowl water samples were collected from patient rooms in a tertiary healthcare-associated facility in North Macedonia, and meropenem (MEM)-resistant bacterial isolates were obtained from the toilet bowl water. In this study, because a MEM-resistant C. braakii isolate, that was one of MEM-resistant opportunistic pathogens, was obtained from the toilet water, whole-genome sequencing (WGS) of this isolate was performed to obtain genetic characteristics of the blaNDM-1-positive C. braakii isolate. By the WGS, four contigs were constructed, the longest contig, contig 1 (5,189,681 bp), contained blaCTX-M with some additional antimicrobial-resistance genes (ARGs). Interestingly, blaNDM-1 was detected in contig 2 (177,260 bp) and contig 3 (64,168 bp). Plasmid replicon of contig 2 was IncA/C2 but plasmid replicon of contig 3 was IncN and different from one of contig 2. Genetic structures surrounding blaNDM-1 were different between these two blaNDM-1-positive plasmids implying transfer or insertion of blaNDM-1 had occurred by IS or other mechanism. Further molecular epidemiology will be needed to explain the mechanism that allowed the C. braakii isolate to possess two structurally different blaNDM-1 plasmids.

BackgroundNeutralising antibody titres are widely used as key immunogenicity endpoints in Ebola virus (EBOV) vaccine and monoclonal antibody clinical trials. However, direct comparison of results across studies remains challenging due to the use of heterogeneous neutralisation platforms, ranging from pseudotyped viruses to live EBOV assays. These limitations restrict assay standardisation, validation, scalability, and compliance with good clinical laboratory practice (GCLP), particularly in outbreak-prone and resource-limited settings. There is an unmet need for neutralisation assays that combine biological authenticity with clinical-trial compatibility. MethodsWe developed and optimised a fluorescence-based microneutralisation assay using a biologically contained EBOV lacking the essential VP30 gene (EBOV{Delta}VP30), enabling multi-cycle viral replication under containment level 2 conditions. Using a defined panel of serum samples from Ebola virus disease survivors and EBOV-negative controls, we benchmarked EBOV{Delta}VP30 neutralisation titres against previously generated data obtained with wild-type EBOV and pseudotyped virus platforms. Assay performance was evaluated in terms of sensitivity, reproducibility, discrimination between positive and negative samples, and correlation with live virus neutralisation. Calibration was performed using the WHO International Standard for anti-EBOV immunoglobulin. FindingsThe EBOV{Delta}VP30 microneutralisation assay robustly distinguished EBOV survivor sera from negative controls (p < 0{middle dot}0001) and demonstrated a strong correlation with live EBOV neutralisation titres (Spearman {rho} = 0{middle dot}8725). This correlation exceeded that observed for HIV-1-based pseudotyped assays and for the vesicular stomatitis virus-based platforms. The fluorescence-based read-out showed comparable sensitivity to conventional immunostaining, supporting its suitability for high-throughput and standardised implementation. Importantly, assay conditions were compatible with BSL-2 laboratories and GCLP-aligned workflows. InterpretationBiologically contained EBOV{Delta}VP30 provides a clinically relevant and scalable alternative to existing neutralisation platforms, bridging the gap between pseudotyped assays and wild-type virus testing. By improving biological relevance while maintaining accessibility and standardisation, this assay has the potential to enhance comparability of immunogenicity data across EBOV vaccine and therapeutic antibody (pre-)clinical trials, aligning with global outbreak preparedness and trial harmonisation objectives. FundingStated in acknowledgement section of manuscript. Research in contextO_ST_ABSEvidence before the studyC_ST_ABSBefore starting this study, we reviewed published work on how neutralising antibodies against Ebola virus are measured in vaccine and monoclonal antibody research. We searched PubMed, Web of Science, and reference lists of key review papers for studies published up to mid-2025, without restricting by language. Search terms included "Ebola virus", "neutralising antibodies", "neutralisation assay", "pseudovirus", "live virus", and "clinical trials". We focused on studies describing neutralisation tests using wild-type Ebola virus as well as commonly used pseudotyped virus systems. From this body of evidence, neutralisation assays using wild-type Ebola virus are considered the most biologically relevant but can only be performed in biosafety level 4 laboratories. This limits their availability, scalability, and use in clinical trials. Pseudotyped virus assays can be performed under lower biosafety conditions and are widely used, but multiple studies have reported variable performance and inconsistent agreement with live virus results. Although biologically contained Ebola viruses have been developed and used in laboratory research, their application as neutralisation assays and their direct comparison with both live virus and pseudotyped systems using the same human serum samples had not been systematically studied. As a result, it remained unclear whether such systems could support reliable immunogenicity assessment in clinical trials. Added value of this studyThis study shows that a biologically contained Ebola virus lacking the VP30 gene can be used to measure neutralising antibodies in a robust and scalable way under biosafety level 2 conditions. By directly comparing this system with wild-type Ebola virus and widely used pseudotyped assays using the same set of human serum samples, we demonstrate that neutralisation results obtained with the biologically contained virus closely align with those of the wild-type virus reference assay. The assay reliably distinguishes samples from Ebola survivors and uninfected individuals and can be read using different detection methods, making it compatible with GCLP-aligned workflows and suitable for further qualification and validation in support of clinical development. This work provides clear evidence that biologically contained Ebola virus can combine biological relevance with practical usability. Implications of all the available evidenceTogether with existing evidence, our findings indicate that biologically contained Ebola virus offers a valuable new option for measuring neutralising antibodies in vaccine and monoclonal antibody clinical trials. By reducing reliance on high-containment laboratories while preserving key features of authentic virus infection, this approach can improve the consistency and comparability of immunogenicity data across studies and sites. Broader use of such assays could support better decision-making during clinical development and strengthen outbreak preparedness. More generally, this work highlights how biologically contained viruses can help advance research licensure of medical countermeasures for high-consequence pathogens in ways that are directly relevant to human health.

A new H3N2 variant (named subclade K) possesses several key hemagglutinin substitutions and is circulating widely during the 2025-2026 influenza season. In this report, we completed experiments to determine if the 2025-2026 seasonal influenza vaccine elicits antibodies in humans that recognize this variant. We find that H3N2 subclade K viruses are antigenically advanced; however, the 2025-2026 seasonal influenza vaccine elicited antibodies in many individuals that efficiently recognized these viruses. Thus, the current seasonal influenza vaccine will likely be somewhat effective at preventing H3N2 subclade K virus infections.

RIG-I is a cytosolic immune receptor that provides the first line of defense by detecting viral RNA and triggering antiviral responses. Its physiological role in humans remains unclear, as no patients with complete RIG-I deficiency have yet been reported. We identified a critically ill COVID-19 patient with severe RIG-I deficiency caused by heterozygous RIG-I G731R, a novel dominant loss-of-function variant. The G731R mutation in helicase motif VI disrupts the arginine finger, impairing the ATPase activity of RIG-I, but not its RNA-binding ability. However, viral RNA binding fails to expose the signaling domains, thereby impairing the IFN-{beta} response of G731R. Instead, G731R competes with wild-type RIG-I, exerting a dominant negative effect. The loss-of-function is caused by bulky-charged substitutions at G731, as alanine or leucine substitution results in an unexpected gain-of-function phenotype. These findings highlight the importance of uncompromised RIG-I function for human antiviral immunity and the pleiotropic effects of single mutations.

Malaria remains a major public health concern in Cameroon, with Plasmodium falciparum responsible for most morbidity and mortality, particularly among children under five. In response to rising cases, Cameroon began implementing the RTS,S/AS01 malaria vaccine in early 2024. Given the vaccines strain-specific efficacy, understanding antigenic diversity and complexity of infection (COI) is critical for evaluating long-term impact. We analyzed 100 P. falciparum-positive dried blood spots collected in Mapoussere, Kaele Health District (2022-2023). Using the 4CAST amplicon sequencing assay, we targeted four genes: csp (circumsporozoite protein), ama (apical membrane antigen 1), sera2 (serine repeat antigen 2), and trap (thrombospondin-related anonymous protein). Haplotypes were identified using SeekDeep, and diversity metrics including heterozygosity (He), nucleotide diversity ({pi}), and selection statistics (Tajimas D, Fu and Lis D*, F*) were computed. We successfully genotyped csp in 35% of samples, identifying 22 haplotypes (He = 0.908; {pi} = 0.021). The vaccine-matched haplotype was present in 20% of genotyped infections. The T cell TH2 and TH3 epitopes of csp showed signs of balancing selection. Both ama and sera2 exhibited higher genotyping success and diversity, with ama showing significant Tajimas D values. COI was highest for ama (mean COI = 2.8), followed by sera2 (2.1), csp (1.3), and trap (1.2). This study provides a baseline of P. falciparum antigenic diversity and COI in a vaccine-targeted region. The presence of vaccine-matched strains and high diversity in TH2/TH3 epitopes in csp may influence vaccine efficacy. Continued molecular surveillance is essential to monitor antigenic shifts and guide future strategies.