Emerging Infectious Diseases

Many studies have identified antibiotic resistant (ABR) Escherichia coli on meat. Appropriate hand hygiene and cooking practices should minimise the risk of gastrointestinal colonisation with ABR E. coli found on meat, and the subsequent chance of causing resistant opportunistic extraintestinal infection. There are large gaps in our understanding of the prevalence, origins and zoonotic potential of ABR E. coli found on meat, however, and particularly for meat reared in extensive farming systems. Wales is a devolved nation within the United Kingdom having large populations of extensively-reared sheep and beef cattle. To help address knowledge gaps around ABR E. coli on extensively reared meat, therefore, beef mince and lamb loin/leg steaks/chops were purchased from 50 (beef) and 46 (lamb) independent butchers across Wales. Following enrichment culture, 200 g meat samples were found to be positive for E. coli resistant to amoxicillin (31% positivity), streptomycin (28%), spectinomycin (29%), amoxicillin-clavulanate (11%), 3rd generation cephalosporins (2%) and fluoroquinolones (5%). Phylogenetic analysis confirmed that Welsh lamb meat ABR E. coli isolates (n=79) are more closely related to those found in faecal samples collected around sheep (n=352) than around beef cattle (n=361) on Welsh farms. This suggests that faecal contamination at or around slaughter is their primary origin. We found no closely related meat/infection clones (<20 SNPs distant and the same antibiotic resistance genes) when comparing ABR E. coli from Welsh meat (n=92) and those causing extraintestinal infections in people (n=2387) in an English region bordering Wales. We conclude, therefore, that the wider zoonotic implications of finding ABR E coli on beef and lamb meat sold at independent butchers in Wales are small.

This report describes lethal Nannizziopsis-associated dermatomycosis in a breeding colony of the family Diplodactylidae (Correlophus ciliatus and Rhacodactylus auriculatus). After introducing one gecko from overseas, three with indirect contact history died due to severe skin lesions. Extensive lesions were observed on the toe pads and ventral surface, along with necrotic dermatitis and cellulitis associated with fungi forming hyphae. Subsequently, four geckos developed diarrhea, melena, emaciation, and fungal dermatitis of the toe pads and died. Histopathologically, the fungal morphologies observed in the skin lesions of the seven geckos were consistent, and Nannizziopsis arthrosporioides was isolated and identified in two of them. To our knowledge, this is the first report of a fatal outbreak of N. arthrosporioides in geckos.

Dromedary camels are the main reservoir for Middle East respiratory syndrome coronavirus (MERS-CoV), a re-emerging infectious disease with pandemic potential. Somalia harbours approximately 32% of dromedary camels globally. We investigated current and past MERS-CoV infections among occupationally-exposed workers in slaughterhouses, dairy farms, livestock markets and a quarantine station. Sera and nasopharyngeal/oropharyngeal swabs from 770 workers were analysed for MERS-CoV antibodies by Enzyme-Linked Immunosorbent Assay (ELISA) and virus neutralization and for viral RNA by Real Star(R) MERS-CoV Reverse Transcription Polymerase Chain Reaction (RT-PCR). One farm worker with no travel history in the Qardo district, Karkar region, Puntland was sero-positive by ELISA and virus neutralization, providing the first-ever evidence of zoonotic spillover of MERS-CoV to humans in Somalia. This finding highlights the need to strengthen MERS-CoV surveillance across Somalia, along with an urgent need to strengthen national laboratory capacity and integrate MERS into diagnostic algorithms to generate accurate and reliable infection data and studies to understand the socio-cultural and potential risk factors for MERS-CoV.

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).

Hantavirids, specifically the members within the genus Orthohantavirus, represent a significant global public health threat, with bat-associated lineages challenging traditional reservoir paradigms. To investigate the genetic diversity of hantavirids in Southeast Asia, we conducted an expanded surveillance program in Lao PDR from May 2023 to October 2025 in bat populations and wild animals from local wet markets. Using molecular screening and deep sequencing to characterize hantavirids from bat populations and wild animals from local wet markets, we identified 20 positive samples across four bat species, recovering coding-complete genomes for multiple novel variants. Phylogenetic analysis confirmed that these viruses form a monophyletic group within Mobatvirus, resolving into two major subclades. The first subclade clustered with Quezon and Robina viruses found in fruit-eating bats. The second subclade further split into two lineages corresponding to Thakrong and Xuan Son viruses, which are associated with trident and leaf-nosed bats, respectively. Despite the strong host specificity observed, the detection of these viruses in a wet market, a critical interface for human-wildlife contact, indicates a potential zoonotic risk. These findings significantly expand the known diversity of mobatviruses in Laos and highlight the urgent need for serological surveillance in at-risk human populations to assess the potential for spillover.

BackgroundMpox virus (MPXV) has caused recurrent outbreaks in West Africa. However, Guinea had not previously reported laboratory-confirmed cases or MPXV genomic data. MethodsSuspected cases were identified in the NZerekore region as well as in the Conakry (Sept 2024- Dec 2025) and confirmed by real-time PCR in regional and central laboratories, respectively. Whole-genome sequencing using nanopore technology was performed in-country, followed by phylogenetic and time-scaled evolutionary analyses. FindingsThe first mpox case was clinically diagnosed in September 2024 in the NZerekore region and laboratory-confirmed by the prefectural laboratory in Gueckedou. In total, seven cases were confirmed in Forest Guinea, of which five complete or almost complete MPXV genomes were recovered. All belonged to MPXV clade IIa. Genomic divergence, ancestral dating, and low APOBEC3-associated mutation frequencies were consistent with multiple independent zoonotic spillover events. In June 2025, one of the first mpox cases of an unfolding outbreak was confirmed in Conakry. Whole genome sequencing revealed MPXV clade IIb lineage G.1. By December 2025, the number of laboratory-confirmed mpox cases nationwide increased to 2,151. A total of nine outbreak strains were sequenced, all belonging to Clade IIb. The genomes clustered with contemporaneous genomes from Sierra Leone and showed high APOBEC3-associated mutation frequencies, suggesting sustained human-to-human transmission in the region. InterpretationThese data demonstrate simultaneous circulation of MPXV clade IIa and IIb strains in Guinea, likely resulting from zoonotic spillover and human-to-human transmission, respectively. Decentralised diagnostics and in-country sequencing facilitated rapid case confirmation and genomic surveillance, highlighting the importance of these critical capacities for outbreak preparedness and response. FundingGerman Federal Ministry of Health and the German Center for Infection Research (DZIF).

Filoviruses, particularly Ebola virus (EBOV), remain a major public health concern in Central Africa. However, their circulation in wildlife during inter-epidemic periods remains poorly documented. Non-human primates (NHPs) may serve as ecological sentinels of viral dynamics at human-forest interfaces, yet surveillance is constrained by the limitations of invasive sampling. We conducted a non-invasive investigation of EBOV exposure in free-ranging NHPs from the Mabali Forest Reserve (Equateur Province, Democratic Republic of Congo) for Ebola virus disease. A total of 630 fecal samples were collected and screened for active infection by PCR targeting the EBOV nucleoprotein gene; all samples tested negative. Molecular identification of host species was achieved in 569 samples (90.3%). Fecal serology using an automated capillary western blot platform (JESS), targeting EBOV nucleoprotein, glycoprotein and viral protein 40 antigens, identified four seropositive individuals (0.70%), including two Cercopithecus ascanius and two C. wolfi. The detection of discrete immunoreactive bands consistent with EBOV-specific antibodies suggests prior exposure despite the absence of active outbreaks. These findings provide the first serological evidence compatible with EBOV exposure in these two Cercopithecus species and support the hypothesis of low-level or cryptic viral circulation in forest ecosystems. The study highlights the feasibility and value of fecal serology as a non-invasive One Health surveillance tool for monitoring zoonotic pathogens at wildlife-human interfaces.

BackgroundHeartland virus (HRTV) is an emerging tick-borne virus capable of causing severe illness and death. The burden of disease is likely underestimated due to limited seroprevalence studies, lack of commercially available diagnostic tests, and an overlapping clinical syndrome with more commonly diagnosed bacterial diseases such as spotted fever group rickettsiosis or ehrlichiosis. MethodsActive surveillance for Heartland virus disease was conducted at a large academic center from March to September 2024. Enrolled subjects included those who had testing sent for Ehrlichia polymerase chain reaction (PCR) along with fever and 2 of the 3 criteria: leukopenia, thrombocytopenia, and/or elevated liver function tests. Specimens with detectable RNA underwent whole genome sequencing and analysis. FindingsOver 800 specimens were received with 53 individuals meeting enrollment criteria. Among these 53, two (3.8%) had detectable HRTV RNA in whole blood during the time of Ehrlichia PCR testing. The two cases had disparate clinical manifestations: one with mild disease which was identified in an outpatient setting, while a second case required intensive care unit-level support. Heartland virus genome sequences from the two cases were more similar to viruses from other states than they were to one another. InterpretationDespite only two prior reported cases of Heartland virus disease in North Carolina, we identified two individuals with acute HRTV viremia. Further surveillance for HRTV disease is necessary to understand the burden of disease and to facilitate further studies of virus pathogenesis and host responses. FundingFunding for the study was provided by a Creativity Hub Award to Dr. Boyce from the UNC Office of the Vice Chancellor for Research. Dr. Zychowskis effort was supported by the T32 NIAD grant AI070114.

People who inject drugs (PWID) and people who use drugs (PWUD) bear a disproportionate burden of hepatitis C virus (HCV) infection globally. In South Africa, HCV testing and treatment remain limited outside externally funded projects. This study investigated the implementation feasibility of assisted HCV self-testing (HCVST) among PWID and PWUD in Johannesburg. Between 12th May 2023 and 28th March 2024, participants were recruited to an implementation study across mobile harm reduction sites and a central clinic. Participants performed self-tests using either oral-fluid or blood-based HCV antibody rapid tests. Reactive results were followed by on-site venous sampling for confirmatory RNA testing and referral for direct-acting antiviral (DAA) therapy at a centralized facility. We describe HCV case-detection, care cascade progression, and behavioral risk factors associated with HCV reactivity using logistic regression. Of 1,566 participants tested, 998 (63.7%) were HCV reactive. The median age was 31 years (IQR 28-35); 82.2% were male and 77.1% identified as PWID. Ever injecting drugs (OR 35.6, 95% CI 23.6-56.0), frequent injecting ([&ge;] daily: OR 36.7, 95% CI 25.1-55.3), and recent needle sharing (OR 7.3, 95% CI 5.8-9.3) were the strongest predictors of HCV reactivity. Histories of incarceration were also independently associated with HCV reactivity (OR 3.2, 95% CI 2.6-4.0). Despite high self-testing acceptability, progression through the care cascade was limited: among 854 RNA-confirmed infections, only 147 (17.2%) were prioritized for treatment, with three participants achieiving sustained virologic response. Thematic analysis identified fear of needles, poor venous access, and structural barriers, notably centralized treatment delivery, as key impediments to linkage. This study showed a high burden of HCV among PWID and PWUD in Johannesburg and demonstrates that assisted HCVST is acceptable. Centralized treatment models severely constrained linkage to care. Simplified delivery of treatment is critical in transforming diagnosis into cure.

BackgroundViral hemorrhagic fevers (VHFs) remain a major public health threat in resource-limited settings. The 2014-2016 Ebola virus disease epidemic exposed critical gaps in laboratory preparedness and diagnostic capacity in most-at-risk countries, including Guinea. Sustainable in-country laboratory capacity is essential for early detection and rapid response to VHF outbreaks, including Lassa fever. MethodsA long-term laboratory capacity-strengthening programme was implemented in Guinea, combining training of local personnel, provision of molecular diagnostic tools, and ongoing technical and financial support. In 2017, a permanent VHF diagnostic laboratory was established in Gueckedou. In 2021, a second laboratory in NZerekore was strengthened, expanding coverage in Forest Guinea. Both laboratories provided free access to VHF diagnostic services for suspected cases and contributed to routine surveillance. Testing activity and confirmed cases from 2017 to 2024 were analyzed. FindingsBetween 2017 and 2024, 4683 samples from suspected VHF cases were tested across the two laboratories. The laboratories supported rapid outbreak detection and case management, notably during the 2021 resurgence of Ebola virus disease and the Marburg virus disease outbreak in Guinea. Prior to this programme, local laboratory capacity for routine Lassa fever detection and reporting was absent in endemic areas of Forest Guinea. Between 2020 and 2024, 30 laboratory-confirmed Lassa fever cases were identified, with a case fatality rate of 67{middle dot}9%. InterpretationThe establishment of locally embedded laboratory infrastructure and a trained workforce improved VHF preparedness, surveillance, and response in Guinea. Beyond providing new insights into Lassa fever epidemiology, this programme shows how sustained investment in laboratory capacity can strengthen early detection, prevention strategies and health system resilience in VHF-endemic settings. FundingGerman Federal Ministry of Health, German Center for Infection Research

Background Rifampicin-resistant tuberculosis (RR-TB) is a major threat to public health in Viet Nam, with nearly 10,000 incident cases estimated annually. It is uncertain whether these cases are driven by transmission of resistant strains or de novo resistance acquisition during treatment. Methods We undertook dense, city-wide sampling of adults newly diagnosed with pulmonary RR-TB in Ho Chi Minh City, Viet Nam's largest city, between March 2020 and April 2024. Participants provided sputum for culture and whole-genome sequencing (WGS), and demographic and clinical data were collected at enrolment. Phylogenetic analyses were combined with clinical histories to infer transmitted versus acquired rifampicin resistance. Estimates were corrected for sampling coverage using simulation-extrapolation (SIMEX). Temporal emergence of rifampicin resistance was reconstructed by lineage using Bayesian phylogenetic dating, and the geographic and demographic structure of transmission networks was assessed using geocoded residential data and commute time-based analyses. Findings Among 2,319 RR-TB cases diagnosed during the study period, 1,491 (64%) isolates were successfully sequenced. After accounting for sampling and phylogenetic uncertainty, we estimated that between 72% and 87% of all RR-TB arose through transmission of already-resistant strains with the remainder due to de novo acquired resistance. Bayesian dating analyses revealed that resistance emergence events occurred repeatedly from the 1980s to the present, with early events seeding long-lived, city-wide transmission networks. Transmission networks were geographically dispersed across the city, with limited household clustering, and only weakly structured by host demographics, consistent with diffuse, city-wide transmission rather than localised or assortative spread. Interpretation RR-TB in Ho Chi Minh City is driven predominantly by ongoing transmission, but a substantial minority of cases arise from newly acquired resistance. Alongside promoting early diagnosis and treatment to interrupt transmission, the main drivers of acquired resistance need to be identified to control RR-TB.

The measles outbreak in Jalisco, Mexico (January-February 2026) experienced vigorous sustained transmission with an exponential growth rate = 0.10 (95% CI: 0.10-0.11) per day, doubling time = 6.3 days (95% CI: 6.3-6.9), yielding the effective reproduction number at 3.34 (95% CI: 3.16-3.54), with elevated incidence among infants and young adults.

Objectives: A pooled testing algorithm for tuberculosis (TB), in which sputum specimens from multiple individuals are tested in pools with individual testing of positive pools, can optimise diagnostic resources. This study evaluated the diagnostic accuracy and cartridge savings of pooled testing with the Xpert MTB/RIF Ultra assay (Xpert Ultra) relative to individual Xpert Ultra testing. Methods: We conducted a cross sectional study among 2,396 adults (aged above 15 years) with presumptive TB enrolled between July 2024 and February 2025, through facility based case finding (FBCF) and community based case finding (CBCF). Participants submitted two sputum specimens. The first underwent individual Xpert Ultra testing; remnant specimens were combined into four specimen pools and tested again with Xpert-Ultra. The second specimen was used to inoculate liquid culture (BACTEC MGIT). Data were used to simulate an up-front pooled testing strategy; sensitivity and specificity of this approach was estimated against culture, and cartridge use was compared with individual Xpert-Ultra testing. Results: Of 2,396 participants, 395 (16.5%) had a positive Xpert Ultra and/or culture, including 360/912 (39.5%) in FBCF and 35/1484 (2.4%) in CBCF. The pooled testing approach had sensitivity of 82.4% (95% confidence interval [CI], 77.9; 86.3) and specificity of 98.5% (97.8; 99.0) compared to culture, with lower sensitivity than individual Xpert-Ultra testing (86.5%, 82.4; 89.9) but high specificity (98.1%, 97.4; 98.7). Sensitivity of pooled testing was lower in CBCF (59.1%, 36.4; 79.3) than in FBCF (84.0%, 79.5;87%), whereas cartridge savings were greater in CBCF (69.1% vs 9.6%). The pooling strategy reduced Xpert-Ultra cartridge use by 46.5%, saving USD 14,447. Conclusions: Pooled Xpert-Ultra testing among adults appears resource-efficient for TB screening in Vietnam. As sensitivity is lower compared to individual Xpert Ultra testing, particularly for paucibacillary disease, these losses should be carefully weighed against gains in affordability and expand access to molecular testing. Careful, context-specific implementation is essential to maximise programmatic benefit while minimising missed persons with TB.

Acinetobacter baumannii is a major cause of severe hospital-acquired infections, with a steadily increasing global prevalence driven by a few clinically adapted lineages. Animals and natural environments also harbor A. baumannii populations, but assessing their connections to clinical lineages is limited by sparse genomic data and a lack of integrated sampling. We conducted a local One Health genomic epidemiology study, sampling, isolating, sequencing, and characterizing several hundred A. baumannii isolates from clinical, animal, and environmental contexts. Within a geographically restricted area, we recovered several globally distributed clinical lineages (international clones, ICs), as well as livestock- and environment-associated lineages shared across Europe, highlighting widespread dissemination beyond clinical settings. Isolates closely related to the emerging clinical lineage IC11 were found in livestock, but no other clinically associated lineages were detected outside clinical contexts. Among these, the epidemic superlineage IC2 was identified in both human and veterinary clinical settings, indicating that similar practices in human and animal medicine select for closely related opportunistic pathogens. We found that hospitals host distinct, antibiotic-sensitive endemic populations capable of causing infection. These populations belong to a diversifying clade spanning clinical and environmental contexts and carry a high load of insertion sequences. Strong plasmid conservation further suggests frequent horizontal gene transfer across ecological compartments. Overall, A. baumannii comprises diverse, context-adapted lineages with a high potential for global spread. Although intercontext transmission appears limited, plasmids may overcome these ecological barriers. Our findings underscore the need for integrated One Health surveillance to better understand transmission pathways and limit the emergence of clinically adapted strains.

Introduction: Herpes simplex virus type 1 (HSV-1) is highly prevalent worldwide, making accurate serological testing essential for both clinical diagnosis and epidemiological surveillance. Automated chemiluminescent immunoassays (CLIAs) offer operational advantages over enzyme-linked immunosorbent assays (ELISAs); however, their diagnostic performance relative to Western blot (WB) confirmation in high-prevalence settings remains insufficiently characterized. Hypothesis/Gap Statement: The comparative diagnostic accuracy of CLIA- and ELISA-based assays for HSV-1 IgG detection, when benchmarked against a WB reference standard in endemic populations, remains unclear. Aim: This study aimed to evaluate HSV-1 IgG seroprevalence and diagnostic performance of one CLIA and two ELISA platforms using Western blot as the reference method. Methodology: Four hundred archived serum samples from adult male craft and manual workers in Qatar were tested using the Mindray CL-900i CLIA, HerpeSelect ELISA, NovaLisa ELISA, and Euroimmun Western blot. Seroprevalence, diagnostic accuracy, and interassay agreement were assessed using WB as the reference standard, with equivocal and indeterminate results excluded from analysis. Results: HSV-1 IgG seroprevalence estimates were comparable across assays: HerpeSelect 72.5%, Mindray 70.5%, NovaLisa 66.3%, and Western blot 66.5%, with no statistically significant differences (all p > 0.05). The Mindray CLIA demonstrated the highest diagnostic performance (sensitivity 95.7%, specificity 88.9%, accuracy 93.4%) and strong agreement with Western blot ({kappa} = 0.85). HerpeSelect showed substantial agreement ({kappa} = 0.81), while NovaLisa exhibited lower specificity. Conclusion: CLIA- and ELISA-based assays produced comparable HSV-1 seroprevalence estimates in this high-prevalence population; however, diagnostic accuracy varied across platforms. The CLIA platform demonstrated the strongest agreement with Western blot, supporting its use in high-throughput settings, while confirmatory testing remains important to minimize misclassification.

Introduction Improved diagnostics are needed for people at risk of tuberculosis, especially adolescents. Tongue swab (TS) molecular testing has emerged as a promising strategy for tuberculosis diagnosis. We evaluated diagnostic accuracy and acceptability of Xpert MTB/RIF Ultra (Xpert) using TS samples for tuberculosis detection among adolescents. Methods We conducted a cross-sectional diagnostic accuracy study with consecutive recruitment in Vietnam. Adolescents aged 10-19 who were recommended to undergo investigation for tuberculosis and had not received tuberculosis treatment in the past years were eligible. Participants provided TS and sputum samples and completed a structured survey regarding sampling experiences. TS was tested on Xpert, with sputum tested on Xpert and liquid culture. We utilised a composite reference standard of a positive result on sputum Xpert or sputum culture to define disease status. Sensitivity, specificity, and diagnostic yield were calculated for TS Xpert. Results From July to December 2025, we enrolled 225 adolescents from Can Tho and An Giang provinces in southern Vietnam. Fewer than half (96/225, 43%) the participants exhibited a tuberculosis -like symptom, and the majority (157/225, 70%) were close contacts of a person recently diagnosed with tuberculosis. TS were collected from all adolescents, while 116 (52%) could provide mucopurulent sputum. Tuberculosis prevalence was relatively low (12/225, 5.3%). TS Xpert sensitivity (90% CI) and specificity (90% CI) were 58.3% (35.6, 78.0) and 99.5% (97.9, 99.9), respectively. Diagnostic yield among all diagnosed was 58.3% (7/12). TS sampling was highly acceptable to adolescents; the short time and simplicity of collecting TS were considered favourably. Conclusions The sensitivity and diagnostic yield of TS Xpert was relatively low among adolescents recommended for tuberculosis investigation, which includes asymptomatic individuals who may not provide high quality sputum. Specificity was excellent, and everyone could provide a TS. TS high acceptability indicates it remains a promising sample for diagnostic algorithms.

Background: Binary interpretation of Mycobacterium tuberculosis (Mtb) interferon gamma release assay (IGRA) results discards information about recency of exposure and disease risk. We analysed quantitative IGRA responses to Mtb in a community--based survey to investigate associations with response magnitude and inform understanding of transmission dynamics. Methods: We included QuantiFERON--TB Gold Plus (QFT--Plus) results from 2,895 participants (10--40 years old) in Blantyre, Malawi. Bayesian regression models assessed the probability of a positive response ([&ge;]0.35 IU/mL), response magnitude, and associated factors. We also investigated associations with a TB2-TB1 differential >0.6 IU/mL (proposed to reflect recent transmission), and how hypothetical alternative IGRA positivity thresholds affected inference about age-- and sex--specific transmission. Results: 17.4% (503/2,895) of participants had positive TB1 or TB2 responses at the QFT--Plus positivity threshold (0.35 IU/mL). The distributions of TB1 and TB2 responses, among participants with positive QFT--Plus, were similar across age and sex. A TB2-TB1 differential >0.6 IU/mL occurred in 3.8% (109/2,895) of participants and was not associated with age or sex. However, participants with HIV had reduced odds of TB2-TB1>0.6 IU/mL (adjusted odds ratio 0.37 [0.14--0.93]). At higher hypothetical positivity thresholds, the mean predicted Mtb immunoreactivity prevalence among males exceeded that in females at an earlier age: at 19 years, predicted immunoreactivity prevalence ratios were 0.90 (0.83--0.99) and 1.02 (0.89--1.15) at 0.1 IU/mL and 0.5 IU/mL thresholds, respectively. Conclusions: Quantitative IGRA responses offer information about age-- and sex--specific immunoreactivity and transmission risks that dichotomisation obscures. In high-burden settings, quantitative IGRA responses may clarify Mtb transmission patterns and guide targeted public health strategies.

Bovine coronavirus (BCoV) is an important contributor to the respiratory disease complex in cattle; however, integrated genomic and epidemiological data describing currently circulating respiratory BCoV strains in the United States remain limited. The objective of this study was to monitor respiratory BCoV at the genomic level and analyze its epidemiological patterns over a five-year period. A total of 4,505 respiratory samples submitted to a diagnostic laboratory between January 2020 and November 2025 were analyzed, of which 693 (15.38%) tested positive for BCoV. Positivity was highest in young calves (0-40 days; 20.0%) and declined significantly with increasing age based on logistic regression analysis. Temporal trend analysis using LOESS smoothing and the Mann-Kendall test showed no significant monotonic change in BCoV detection during the study period. Co-infection analysis indicated that BCoV was commonly detected with other viral respiratory pathogens, while bacterial pathogens predominated in many samples. Lung tissues from infected cattle were screened by RT-PCR, and selected samples with high viral loads were subjected to next-generation sequencing. Complete genome sequencing identified four respiratory BCoV isolates ([~]31 kb), all clustering within genotype GIIb with recent U.S. strains. Comparative genomic analysis revealed several amino acid substitutions in structural and non-structural proteins that may influence viral attachment, replication, and tissue tropism. These findings provide updated epidemiological and genomic insights into respiratory BCoV circulating in U.S. cattle.

Serological data provide important insights into SARS-CoV-2 transmission and immunity, particularly in regions with limited routine surveillance such as sub-Saharan Africa. However, antibody waning and boosting following reinfection or vaccination remain poorly characterised, complicating interpretation of serological measurements. Improved understanding of these dynamics is critical for accurate epidemiological inference. Modelling longitudinal serological data provides a means to quantify antibody kinetics and reconstruct infection histories. We analysed 15,679 neutralising antibody (nAb) titres from 1,675 unvaccinated, HIV-uninfected participants in urban (Lilongwe) and rural (Karonga) Malawi (February 2021 - April 2022). NAb titres against ancestral B.1, Beta, Delta, and Omicron (BA.1/BA.2) viruses were measured using an HIV-based SARS-CoV-2 pseudotyped virus neutralisation assay. A multi-level Bayesian model was used to reconstruct infection histories and antibody kinetics. The model identified 429 infections (95% credible interval 417-441), including 39 (9.1%) that had not been identified by traditional seroconversion-based thresholds. Antibody levels waned rapidly, with 48% (0.403-0.560) of the acute boost remaining after three months and only 5% (0.027-0.098) after one year. Pre-Omicron infections generated stronger antibody boosts than Omicron infections. Responses varied, with individuals clustering into low and high responders. Cross-reactive responses extended across substantial antigenic distances - Omicron infections induced broader immunity. Seroincidence was higher in Lilongwe than in Karonga (0.41 vs. 0.27 infections per person per three months), driven by the early 2022 Omicron wave. Reinfections were common, particularly among adults and urban residents. SARS-CoV-2 nAb responses following infection were heterogeneous and declined rapidly. This rapid waning underscores the importance of vaccination for sustained protection, while cross-reactivity suggests only partial immunity from prior variants. Identifying reinfections is essential for understanding transmission and finding populations at higher repeat infection risk, particularly where routine surveillance is limited.

Highly pathogenic avian influenza (HPAI) viruses of H5N1 clade 2.3.4.4b, are spreading worldwide, posing a threat to wildlife, domestic animals, and humans. In 2025, a multidisciplinary collaboration for HPAI H5N1 surveillance among birds within Galveston County, Texas, was initiated. Between November and December 2025, oropharyngeal and cloacal swabs were collected from wild and domestic birds reported as dead or dying by Galveston County residents. Specimens were studied with molecular assays, Sanger sequencing, virus isolation, and next-generation sequencing. Molecular evidence of HPAI H5N1 was detected in 7 of 10 (70%) birds, and the virus was successfully cultured in MDCK cells. Next-generation sequencing analysis of eight influenza A genome segments demonstrated a 4:4 gene segment reassortant constellation within clade 2.3.4.4b, consistent with genotype D1.1. Community members exposed to HPAI were offered antiviral prophylaxis. No human infections were identified. This surveillance demonstrates that community involvement combined with cross-sectoral collaboration can ensure rapid detection and characterization of circulating avian influenza viruses. Sustained local surveillance is essential for early warning, risk assessment, and prevention of virus spread to poultry, mammals, and humans.