Emerging Infectious Diseases

In summer 2025, several Eurasian Blackbird (Turdus merula) deaths were reported on the Isle of Arran in Scotland. Initial investigation included post-mortem examination, where no diagnosis was achieved. Following Orthoflavivirus and avian paramyxovirus testing, Usutu virus RNA was detected in two Blackbirds by reverse transcription-PCR. Phylogenetic analysis identified Usutu virus Africa 3.2 lineage which clustered closely with existing UK detections, indicating geographic expansion rather than a new incursion. Subsequent surveillance confirmed the presence of several potential mosquito vector species.

Highly pathogenic avian influenza virus (HPAIV) subtype H5N5 was detected in a one-year-old polar bear (Ursus maritimus) and an adjacent adult Atlantic walrus (Odobenus rosmarus rosmarus), both found deceased in Raudfjorden, Svalbard. This represents the first confirmed case of HPAI in a European polar bear and the second in an Atlantic walrus. Viral genomes were nearly identical and harbored PB2-E627V, a marker associated with mammalian adaptation. Several polar bears, including the deceased individual, had previously been observed feeding on the walrus carcass. Antibodies against H5 were detected in 75% of polar bears in 2023 (n=36) and 97% in 2024-2025 (n=65), suggesting extensive circulation of HPAIV in the population following the first detections in birds in Svalbard in 2022, whereas no antibodies were detected in samples from 2014-2022 (n=243).

A parvovirus recently associated with an outbreak in Dutch pigs was found in Denmark in symptomatic pigs and in fox (Vulpes vulpes) feces and spleens. Pig viruses were more closely related to each other than to viruses found in the respective local wildlife, suggesting a link between the farm outbreaks.

Dermatophilus congolensis is a zoonotic gram-positive bacterium causing dermatophilosis, a skin infection primarily affecting animals and uncommonly reported in humans. Although human infections have traditionally been associated with animal contact, recent reports suggest alternative transmission pathways. We investigated an outbreak among contact sport athletes in Trondheim, Norway, during July to September 2025, using structured interviews and whole-genome sequencing. Nine confirmed cases were identified. Symptoms were mild and consisted mainly of pustular lesions affecting the face, arms, back, and chest. None of the cases reported animal contact. Genomic analysis confirmed species identity and showed that outbreak isolates were highly related, differing by only 0-7 core-genome single nucleotide polymorphisms. The Trondheim isolates clustered with strains from recent outbreaks in Spain and France, suggesting international dissemination of a shared clone. These findings identify contact sports as a potential setting for transmission of human dermatophilosis and highlight the value of genomic surveillance for outbreak investigation.

Background. West Nile virus (WNV) genomic surveillance in the United States relies largely on mosquito and avian sequencing, while human-derived genomes remain scarce. Nucleic acid testing (NAT)-reactive blood donations provide a standardized source of acute human-phase virus, but low donor viremia complicates genome recovery. This study evaluated a sequencing strategy for WNV surveillance using these samples. Study Design and Methods. Amplicon sequencing, hybridization capture, and shotgun RNA-seq were evaluated for WNV lineage 1a recovery from donor plasma. Amplicon performance was characterized using a WHO International Standard dilution panel quantified by RT-dPCR, contemporary 2025 donations, archival 2010-2011 donations, and technical replicates. Two donations were processed by all three methods from matched plasma to compare performance metrics and consensus concordance. Results. Amplicon sequencing recovered near-complete genomes across the full dilution panel, including the lowest measured input, and across the viral-load range represented by the selected donor samples. Recovery from the two archival plasma samples was similar to that observed among contemporary donations. In the two matched donations, all three methods generated identical consensus sequences across shared callable positions. At lower input, amplicon and capture maintained near-complete recovery, whereas shotgun RNA-seq decreased to 87.2% coverage at 10X. For libraries achieving near-complete recovery, WNV-mapped-read requirements were similar, but amplicon sequencing required substantially fewer total reads. Discussion. NAT-reactive blood donations can support WNV genomic surveillance. Amplicon sequencing is an efficient first-pass approach for expected lineage 1a WNV, with capture and shotgun RNA-seq serving as escalation strategies for divergent lineages or unbiased pathogen detection.

Objectives: To estimate early growth rate, back-calculate transmission onset, and characterise the case-fatality trajectory of the 2026 Bundibugyo virus disease (BDBV) outbreak in the Democratic Republic of the Congo, the largest recorded BDBV outbreak to date. Design or methods: We analysed a corrected daily surveillance series (65 observations, 14 May to 27 July 2026) using non-linear least-squares regression and a Bayesian Poisson growth model fitted by Markov chain Monte Carlo, with five sensitivity analyses. Results: Early confirmed cases grew at 0.1261 per day (95% CI 0.0885-0.1636), a doubling time of 5.50 days (4.24-7.83), three-fold faster than previous BDBV outbreaks (15-18 days). Bayesian back-calculation placed transmission onset on 19 April 2026 (95% highest-density interval 9-27 April), 16 days before the WHO alert and 25 days before laboratory confirmation. Confirmed case-fatality ratio rose from 12.1% to 44.3%; a higher ratio among suspected than confirmed cases on 21 May (23.6% vs 10.8%; p=0.0080) supported progressive reclassification rather than increasing virulence. Conclusions: Rapid BDBV growth leaves little time for outbreak-triggered mobilisation. Sentinel alerts based on unexplained healthcare-worker death clusters, together with pre-positioned surveillance, diagnostic, and response capacity, could reduce avoidable amplification before confirmation.

Bangladesh reported a nationwide measles outbreak in April 2026 involving over 19,000 suspected cases, despite high reported first-dose vaccine coverage ([≥]95%). We assessed whether publicly available molecular data could support epidemiologic interpretation of this resurgence and evaluated broader sequence sharing practices across South Asia. We analyzed public outbreak reports, WHO/UNICEF Estimates of National Immunization Coverage (WUENIC), PubMed indexed literature, and NCBI GenBank records from nine regional countries. Public sequence visibility across the region was highly uneven. While India and Pakistan associated records dominated the public dataset, only 32 Bangladesh origin records were retrieved, and notably, none were collected after 2019. The sole 2026 Bangladesh linked molecular record was a travel associated genotype B3 genome isolated in Australia (PZ189094.1). Its closest public N450 relative was a contemporaneous Pakistan sequence (2-nucleotide difference). The historical Bangladesh sequences were more distant, precluding robust phylogenetic inference regarding local viral persistence, cross-border importation, or transmission direction. Immunization data revealed a high regional baseline but highlighted subnational vulnerability and a significant pandemic era coverage collapse in neighboring Myanmar. The absence of timely, publicly available genomic data during the critical early months of the outbreak highlights a severe genomic surveillance gap. Public molecular records were historically sparse and insufficient to reconstruct outbreak transmission dynamics. To support elimination goals, establishing targeted sequencing pipelines, enforcing minimum metadata standards, and ensuring rapid public data deposition are urgently needed. Keywords: measles; Bangladesh; South Asia; genomic surveillance; molecular epidemiology; immunization coverage

Trachoma programs are increasingly using serological tools to complement clinical indicators and to measure current and historical transmission of Chlamydia trachomatis (Ct). In January 2024, the Amhara Trachoma Program in Ethiopia implemented the Pgp3 lateral flow assay (LFA) for trachoma serosurveillance through the regional public health laboratory system. Three Amhara Public Health Institute Trachoma Molecular Laboratory scientists were trained and passed competency testing on the assay. The scientists then conducted LFA testing on dried blood spot (DBS) samples collected during a December 2023 trachoma impact survey in Tach Gaynt, Amhara. During testing, 2,542 DBS samples were processed over 12 days. Age-specific seroprevalence and seroconversion rates (SCRs) were estimated. Among children ages 1-5 years, seroprevalence was 20.8% (95% confidence interval [CI]): 17.4-24.7%), and the SCR was 7.9 per 100 child-years (95% CI: 4.6-13.5). Among children ages 1-9 years, seroprevalence was 26.0% (95% CI: 22.9-29.3%), and the SCR was 7.0 per 100 child-years (95% CI: 4.6-10.6). Seroprevalence among individuals ages 15 years and older was 85.8% (95% CI: 83.9-87.4%). Trachomatous inflammation-follicular prevalence among children ages 1-9 years (TF1-9) was 28.6% (95% CI: 22.1-35.4%), and Ct infection among children ages 1-5 years was 5.7%, suggesting ongoing transmission. The concordance between LFA results, TF1-9 prevalence, and Ct infection prevalence supports the utility of the LFA for trachoma surveillance in Ethiopia, with Pgp3 LFA testing performed in a regional public health laboratory. Integrating LFA-based serology into the Ethiopia national trachoma surveillance systems offers a scalable approach to guide programmatic decisions and support trachoma elimination as a public health problem.

Dengue (DENV) and chikungunya (CHIKV) are understudied in the Democratic Republic of the Congo (DRC) and across Africa despite evidence of transmission. We measured DENV and CHIKV IgG seroprevalences in Kinshasa Province, DRC, by antigen-capture ELISA, using dried blood spots from 2021. Force of infection (FOI) was estimated from age-stratified seroprevalences using Bayesian catalytic modeling. Among 1,250 participants, DENV IgG seroprevalence was 38.1% (95% CI: 34.5%-41.8%), increasing with age, and highest within peri-urban Kimpoko sites (54.9%). CHIKV IgG seroprevalence was 24.2% (95% CI: 21.1%-27.6%), increasing with age and comparable between peri-urban Kimpoko and rural Bu, with few seropositives in the city-center. DENV-CHIKV IgG co-occurrence was detected in 12.8% of participants. Time-varying FOI models provided best fit to age-stratified seroprevalences, with spatial variation detected. Sustained DENV and CHIKV circulation across Kinshasa highlights an under-appreciated transmission risk and underscores the need for strengthened arboviral surveillance in the DRC and surrounding region.

Rabies remains a significantly underreported fatal zoonosis in India, where the Arctic-like 1a (AL1a) lineage predominates in dog populations. While atypical clinical presentations in dogs can delay diagnosis and increase human exposure risk, genomic and clinical data on neonatal canine rabies remain limited. This study reports an exceptional case of rabies in a 54-day old unvaccinated German shepherd puppy which presented with severe pruritus and self-biting behaviour. The puppy was euthanized due to poor clinical response. Post-mortem testing revealed viral antigen (by Direct Fluorescent Antibody Test) and viral RNA (by real-time RTPCR) in the brain tissue. Whole-genome sequencing recovered a near-complete rabies virus genome (11,947 nucleotides; 99.5% genome coverage), classified within the AL1a_A1.1 sublineage. Phylogenetic analysis revealed close genetic relatedness to contemporary Indian rabies virus strains. Comparative genomic analysis identified 4, 3, 6, and 8 non-synonymous substitutions in the phosphoprotein, matrix, glycoprotein, and polymerase genes, respectively. This case is one of the youngest documented cases of canine rabies with atypical manifestations, caused by the AL1a viral clade. Our findings highlight the risks associated with neonatal canine rabies, the need for heightened clinical suspicion in atypical cases, and the importance of genomic surveillance to monitor evolving rabies virus lineages in endemic regions.

Coronaviruses of the genus Gammacoronavirus cause major poultry diseases, including infectious bronchitis in chickens and enteritis in turkeys and guinea fowl. Until now, no enteric coronavirus distinct from infectious bronchitis virus had been reported in chickens. Between late 2024 and 2025, severe enteritis outbreaks affected broiler farms in southwestern France, causing increased mortality, wet litter, cyanosis, lethargy, ruffled feathers, and high slaughter condemnation rates. Necropsy and histopathology revealed diffuse enteritis and dehydration. Metagenomic sequencing identified abundant coronavirus reads as the only pathogenic viral signal. Whole-genome phylogeny showed a novel gammacoronavirus lineage closely related to guinea fowl coronavirus but distinct from infectious bronchitis virus and turkey coronavirus. Viral RNA was detected in enterocytes by RNAscope in situ hybridization, and electron microscopy revealed coronavirus-like particles. These findings describe a novel enteritis-associated coronavirus in broiler chickens (ChECoV), although the drivers of its host-range expansion into chickens remain to be elucidated.

Background Sequencing of monkeypox virus (MPXV) from antigen rapid diagnostic tests (Ag-RDTs) could expand genomic surveillance during outbreaks in decentralized settings where sequencing equipment and cold chain transportation are unavailable. We aimed to evaluate the efficacy of MPXV sequencing from MPXV antigen Ag-RDTs. Methods We tested MPXV Ag-RDTs from three different brands using serial dilutions of cultured MPXV subclade Ib. Positive Ag-RDTs with different intensities of the test band were stored for 19 days, either at room temperature or at +4 degree C, after which viral DNA was extracted from the pads of the test cassettes. Metagenomic and tiled amplicon-based Oxford Nanopore technology sequencing methods were then performed. Results Viral DNA extraction from MPXV Ag-RDTs showed a consistent decrease in viral load of 3 logs compared to the initial viral load of the applied viral dilution. Both sequencing methods were able to reach high coverage but the tiled amplicon-based demonstrated more consistent results with a coverage always above 85%. Conclusion This proof-of-concept supports the development of this approach in the field, with the aim of combining genomic surveillance with decentralized testing, including in remote areas.

Early detection of mammalian adaptation in highly pathogenic avian influenza A(H5) depends on genomic surveillance, yet its distribution across high-burden regions is poorly characterized. We quantified open-access (GenBank/INSDC) H5 genomic coverage relative to reported outbreak burden across nine South Asian countries during 2015-2025, linking isolates to FAO EMPRES-i/WOAH events. Of 919 H5 isolates, 814 (89%) came from one country (Bangladesh); the other eight contributed 105. India, with the largest burden (322 events), yielded only 42 isolates (13 per 100); Nepal, 2 of 78; Afghanistan, none of 5. Concentration was extreme (Gini 0.83) and unchanged by adding restricted GISAID records (1,297 combined isolates; Bangladesh 89%) or by normalizing to poultry or human population. Because reported outbreaks track reporting effort, these coverage ratios are directional, not rates. This single-country dependency, deepest where burden is highest, is a regional early-warning vulnerability.

Diarrhea remains a leading cause of child morbidity and mortality. Improved and ongoing estimates of the etiology of hospitalized pediatric diarrhea in low- and middle-income countries (LMICs) are needed to help prioritize and evaluate the use of existing and upcoming vaccines and interventions. The Global Pediatric Diarrhea Surveillance (GPDS) network is a World Health Organization (WHO)-coordinated public health surveillance network investigating the etiology of hospitalized diarrhea among children aged <5 years in LMICs. The GPDS network enrolls children hospitalized with diarrhea at 38 sentinel surveillance sites in 31 LMICs. Randomly selected stool specimens were tested by TaqMan Array Card quantitative reverse-transcription polymerase chain reaction (qPCR) for 16 pathogens associated with diarrhea. We estimated pathogen-specific attributable fractions (AFs) and incidence of diarrheal hospitalizations at the global, regional, and country levels during 3 time periods: 2017-2018, 2019-2020, and 2021-2022, with a focus on the most recent results. During 2017-2022, the GPDS network enrolled 70,750 children aged <5 years hospitalized with diarrhea, of which 16,458 (23.3%) were randomly selected for qPCR testing. The most prevalent pathogen detected, regardless of quantity or modeled etiologic attribution, was rotavirus (weighted prevalence 30.4%), followed by adenovirus 40/41 (19.1%), norovirus (17.9%), Shigella (14.1%), and Campylobacter jejuni/coli (8.6%). Overall, in 2017-2022, rotavirus was the leading etiology globally (AF 32.5%; 95% Confidence Interval (CI): 27.4, 37.6), followed by Shigella (9.8%; 8.4, 11.3), adenovirus 40/41 (8.6%; 6.3, 10.8) and norovirus (6.7%; 5.6, 7.7). Over time, rotavirus consistently declined from an AF of 36.7% (95% CI: 28.7, 46.7) in 2017-2018 to 26.7% (20.7, 34.1) in 2021-2022. Norovirus AF increased slightly from 6.2% (4.7, 7.7) in 2017-2018 to 7.3% (5.0, 9.2) in 2021-2022. Global Shigella burden remained stable, and adenovirus 40/41 demonstrated significant volatility, peaking globally in 2019-2020 (11.9%; 5.9, 17.5). In 2021-2022, rotavirus was the leading cause of hospitalized diarrhea in 6 of 9 geographic groupings, norovirus predominated in Central and South America, and Shigella was the leading etiology in South Asia. In the subset of countries that had introduced rotavirus vaccine, the leading etiologies in 2021-2022 were rotavirus (18.4%; 15.8, 21.5) and Shigella (16.4%; 11.8, 21.1). In 2021-2022, rotavirus had the highest attributable incidence of hospitalized diarrhea in children (2.3 per 1,000 child-years; 1.8, 3.0), followed by Shigella (0.9; 0.7, 1.1), norovirus (0.6; 0.4, 0.8) and adenovirus 40/41 (0.6; 0.4, 0.8). Despite the widespread use of rotavirus vaccines, rotavirus remained the leading cause of severe diarrhea among children aged <5 years in LMICs globally. However, the proportion of pediatric diarrhea attributable to rotavirus consistently declined from 2017-2018 to 2021-2022, and there were notable differences in the distribution of diarrheal etiologies between regions and across time periods. Shigella, norovirus, and enteric adenoviruses were also associated with a substantial burden of disease. Improving the efficacy and coverage of rotavirus vaccination and prioritizing interventions against other enteric pathogens could further reduce diarrhea morbidity and mortality.

Antimicrobial resistance constitutes a major threat to global public health. Among emerging extensively drug-resistant bacteria (eXDR), carbapenemase-producing Enterobacteriaceae (CPE) expose hospitals to outbreaks through rapid dissemination, and to therapeutic limitations. Through a mixed epidemiological-qualitative methods study, we report the most extensive CPE carriage outbreak known to date in France, which occurred at Hopital Europeen Marseille (HEM) between January and June 2025. By the end of November 2024, the admission of an index patient returning from Senegal carrying an NDM-producing Escherichia coli led to an extensive transmission, despite adherence to national screen and isolate guidelines. More than 7,500 rectal screening tests evidenced 481 CPE carriers (including 343 NDM, 129 OXA-48-like and 9 other CPE), and 14 vancomycin-resistant Enterococcus faecium carriers. This major outbreak conducted to a phenomenal involvement of clinical, technical and administrative teams within the institution. It highlighted operational limitations in current screening, cohorting and biocleaning strategies in the context of hospital-wide outbreak. We describe the outbreak trajectory, the control measures implemented and provide a structured synthesis of lessons learned across organisational, scientific and policy domains.

Canine distemper--a measles-like disease with high mortality and presently without a cure--poses a major threat to wild and domestic carnivores globally. Domestic dogs are generally considered to be the main reservoir and long-range transmitter of the disease, but the role of wildlife is likely underestimated and the long-term persistence of CDV in wildlife has never been assessed. We sequenced canine distemper virus (CDV) full and partial genomes that were sampled over a decade (2012-2021) from Arctic foxes and other canids in Alaska and Yellowstone, and compiled a dataset of all published CDV genomes sampled across 32 species globally. We show the first ever evidence of persistence of CDV in wildlife (for almost a decade) with explosive transmission dynamics crossing host species barriers. Strains sampled from the Arctic for the first time connect North America to Eurasia, and are distinct from the Yellowstone strain and other known North American lineages. This suggests that separate wildlife outbreaks occur concurrently in North America, with possible introductions from Eurasia. The long-term persistence, long-range movement and explosive spread of this devastating panzootic virus that we document within wildlife is alarming and highlights the need for increased monitoring efforts to better protect wildlife populations globally.

We report the detection of a novel hantavirus in the lung tissue of two diseased Australian dolphins with histopathological changes. Phylogenetic analysis placed this virus within the genus Mobatvirus. This highlights the ability of hantaviruses to infect non-terrestrial mammals and the potential role of marine mammals as one health sentinels.

Background Nipah virus (NiV) is a priority zoonotic pathogen causing high-fatality outbreaks. Early NiV outbreaks in Malaysia and Singapore had limited transmission beyond spillover events. However, since 2001, NiV outbreaks with person-to-person transmission have occurred in Bangladesh and India, driven by the NiV-Bangladesh genotype and NiV-India genotype. Our study aims to estimate the reproduction number, offspring dispersion, and serial interval governing NiV transmission in Bangladesh and India during 2001-2026. Methods We conducted a systematic review of NiV outbreak investigations in Bangladesh and India, searching PubMed, Embase, Web of Science, and grey literature through 28 February 2026. Case-level offspring counts from 27 eligible sources (323 cases across 67 outbreaks) were used as input to a hierarchical Bayesian negative binomial offspring distribution model. The serial interval was estimated by parametric distribution fitting to 137 transmission pairs. Country-stratified and sensitivity analyses were performed to evaluate the robustness of estimates. Results Pooling across 67 outbreaks, we estimated a median reproduction number of 0.46 (95% CrI: 0.28-0.73), an offspring dispersion parameter of 0.07 (0.05-0.10), and a serial interval of 13.3 days (95% CI: 12.8-13.8). Country-stratified median reproduction numbers were 0.48 (0.23-0.97) for India and 0.35 (0.19-0.59) for Bangladesh, and dispersion parameters were 0.04 (0.02-0.07) and 0.11 (0.06-0.18), respectively, indicating marked overdispersion in both settings. Conclusion NiV transmission is self-limiting on average and highly overdispersed, suggesting that a disproportionate share of onward transmission arises from a small number of cases. This epidemiological profile supports targeted containment measures, including contact tracing and quarantine, for effective NiV outbreak control.

Background: Faecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridioides difficile infections, yet the diversity of FMT formulations and delivery routes hampers comparisons across studies. Oral frozen capsules are widely used and current guidelines recommend storage at -80C for up to two years. Despite extensive use of FMT, data on the long-term persistence and maintenance of their microbial composition remains limited. Method: In this prospective study, we assessed the temporal stability of bacterial profiles in frozen FMT capsules derived from 48 donations of 10 healthy donors. Using metabarcoding, we longitudinally profiled one capsule per donation thawed within a month of production and after 3, 6, 12, and 24 months of storage. We used linear mixed effect models to evaluate changes in alpha diversity and community composition over time. Results: Species richness remained stable across all timepoints, whilst species evenness decreased slightly. Although changes in community composition were detectable, they were small and mostly affected low-abundance genera. Clinical efficacy, assessed in a subset of recipients, was not associated with storage duration. Conclusion: Our findings demonstrate that frozen FMT capsules preserve their bacterial community structure for at least two years of storage at -80C, supporting their suitability for long-term biobanking and standardised clinical or research use.

Human metapneumovirus (HMPV) and human parainfluenza viruses (HPIV 1-4) are common causes of seasonal respiratory illness, but their household transmission dynamics remain poorly defined. We analyzed weekly symptom data and nasal swabs from a prospective household surveillance study in Washington and Oregon from June 2022 to March 2024. Swabs were tested for HMPV and HPIV, and a subset underwent whole-genome sequencing. Distinct index cases occurred in 236 (23%) and 341 (36%) of 1,040 households for HMPV and HPIV, respectively. Household secondary attack rates (SAR) and median generation times were similar for HMPV (8.7%, 7 days) and HPIV (7.3%, 7 days). Sequenced samples reflected contemporaneous circulating strains during the same period, with household sequences clustering closely together. High-quality viral whole genome sequences were recovered for two or more individuals within a household in a total of 26 households for HMPV and 45 households for HPIV. Intra-household pairwise nucleotide (nt) distance ranged from 0 to 14 nt (median 0) for HMPV and 0-8 nt (median 1) for HPIV when cases occurred 0-15 days apart. Transmission occurred primarily from children to adults, emphasizing the importance of childcare- and school-associated spread and supporting child-focused prevention strategies to reduce household transmission.