Sensitive and high-throughput testing for Neisseria gonorrhoeae (NG) is widely underpinned by automated commercial solutions using nucleic acid amplification tests. We outline our experience of using Roche Cobas 8800 CT/NG (Cobas NG) for primary testing of NG at scale. Over 360000 specimens were tested over a three-year period. A disproportionate number of ‘indeterminate’ oropharyngeal swabs (25%) tested positive by Cobas NG but failed to confirm by Xpert CT/NG, significantly higher than genital samples (4%) (chi-square p-value <0.05). Such samples are highly problematic, as they fail to provide a definitive result for the patient. To investigate this non-specificity, publicly available sequences for Cobas NG DR-9 targets were aligned with Neisseria genome databases. We found a strain of Neisseria lactamica (PubMLST 49718), isolated from a throat swab, which was predicted to cross-react with Cobas NG. We subsequently confirmed a Cobas NG false-positive result with this isolate. BLAST analysis showed the target gene NG DR-9 was rare among available non-NG Neisseria whole genome sequences. This may suggest the existence of an as-yet unknown and difficult to cultivate oral commensal that contains NG DR-9. Our findings further highlight the need for NG confirmatory testing of oropharyngeal samples screened with Cobas NG.

We analysed 15,982 quality-controlled SARS-CoV-2 genome sequences from Hong Kong, obtained from NCBI and GISAID between 2020 and 2023, to characterize lineage dynamics, mutational profiles, demographic distributions, and variant-specific viral entry. Genomic surveillance identified 543 lineages and 5,982 unique mutations. Lineages A, B, and B.4 dominated the initial epidemic waves, whereas Delta and Omicron emerged and predominated in later waves. Omicron BA.1 and BA.2 exhibited distinct distributions across gender and age groups, while JN.1 harboured several novel mutations. Molecular simulations comparing spike receptor-binding domain (SRBD)–ACE2 interactions revealed significant differences in binding affinity among variants (F = 4.404, p = 9.12 × 10⁻⁷). JN.1 demonstrated enhanced ACE2-binding affinity, suggesting increased viral entry and potential transmissibility. By integrating genomic, demographic, and molecular evidence, this study provides a comprehensive account of SARS-CoV-2 evolution in Hong Kong and highlights the public health relevance of emerging variants. These findings support sustained genomic surveillance and demographic monitoring to strengthen pandemic preparedness. Future research should evaluate public health strategies and adopt holistic frameworks integrating population characteristics with genomic evidence to mitigate the effects of future variants.

Performance of a prototype measles IgM rapid diagnostic test (RDT) was evaluated during suspected measles outbreaks in Uganda.

Oral fluid (OF), capillary blood (CAP) and serum samples were collected from participants. OF and CAP were tested using the RDT at patient contact, while usability was assessed through questionnaires administered to health workers, patients, and guardians. Residual OF and IgM-positive RDTs from OF testing underwent measles qRT-PCR at Uganda Virus Research Institute. RDT performance was compared with Siemens anti-measles IgM ELISA performed on sera and with true measles cases, defined as measles ELISA IgM-positive and/or OF RT-PCR positive.

Compared to ELISA, RDT sensitivity and specificity were 97.9% (95% CI: 93.7%–99.3%) and 91.7% (95% CI: 84.7%–95.7%) for CAP, and 96.7% (95% CI: 92.2%–98.6%) and 88.0% (95% CI: 80.7%–92.8%) for OF, respectively. Compared with true measles cases, sensitivity and specificity were 90.4% (95% CI: 84.9%–94.1%) and 89.2% (95% CI: 81.5%–94.0%) for CAP, and 88.5% (95% CI: 82.8%–92.5%) and 86.1% (95% CI: 78.1%–91.5%) for OF, respectively.

OF and CAP sampling, and RDT use were highly acceptable, and health workers reported the RDT could improve measles management. The RDT demonstrated good accuracy and usability for outbreak settings.

This observational descriptive study analyses the hospital burden of respiratory syncytial virus (RSV) among adults in Spain using the Minimum Basic Data Set (MBDS) from the Spanish National Hospital Data Surveillance System. Hospital admissions of adults diagnosed with non-bronchiolitis RSV infection between 2016 and 2023 were identified using ICD-10-CM codes. A total of 288,297 RSV-related hospitalizations were recorded, with a mean patient age of 76.18 years. The overall hospitalization rate was 92.43 per 100,000 inhabitants, and the mortality rate was 5.32 per 100,000. The most common severe comorbidities at admission were congestive heart failure, diabetes, and chronic obstructive pulmonary disease. Patients aged over 65 years had a significantly higher risk of in-hospital mortality (OR 1.78; 95% CI: 1.64–1.93) compared to those aged 40–64 years, increasing to 2.22 (95% CI: 2.05–2.40) in the presence of at least one severe comorbidity. Male sex was also associated with increased mortality risk (OR 1.24; 95% CI: 1.20–1.28). In conclusion, RSV represents a substantial cause of hospitalization and mortality among adults in Spain, particularly in patients over 60 years, males, and those with underlying comorbidities.

Viral interference between SARS-CoV-2 and other respiratory virus infections has been implicated, but symptom-based testing in observational studies may bias estimations. We used individual participant data from ten cohort studies conducted during pandemic years 2020–2024 to study virus interference. Respiratory samples were PCR-tested for viruses including SARS-CoV-2. The primary analysis was based on samples collected from cohort participants regardless of respiratory symptoms. A secondary analysis included only symptom-based testing data. We estimated odds ratios for co-occurrence of SARS-CoV-2 with other respiratory viruses. The primary analysis included data from six cohorts (n = 1 023). In total 205 of 2 465 samples were SARS-CoV-2 positive (8.3%). Co-detections with SARS-CoV-2 occurred less frequently than expected under the assumption of zero interference (OR: 0.72; 95% CI: 0.40–1.25) for samples positive for another virus. The secondary analysis (five cohorts, n = 1 715) included 2 088 samples from symptomatic subjects, with 506 SARS-CoV-2 infections (24.2%). The OR of SARS-CoV-2 detection was 0.16 (95% CI: 0.10–0.25) for samples positive for another virus. Minimizing selection bias, our results still point towards negative viral interference with SARS-CoV-2, but effect-estimates are weaker and non-significant. Apart from selection bias, the stronger effects found in symptomatic individuals could also indicate that symptomatic infection enhances virus interference.

Yersinia pseudotuberculosis and Yersinia enterocolitica are globally found zoonotic gastrointestinal bacteria known to cause human infections, transmitted by consumption of contaminated food or environmental contact. Y. enterocolitica is the dominant species in causing yersiniosis, and is under ascertained in England. Diagnostic laboratories across England undertake detection of Yersinia in stool and other sterile sites using UK Standards for Microbiology Investigations. In 2022, there was an exceedance of invasive and gastrointestinal Yersinia notifications across England. Recommendations were made that all Yersinia detected in diagnostic laboratories be cultured and sent to England’s national reference laboratory, Gastrointestinal Bacteria Reference Unit, UK Health Security Agency for whole genome sequencing, speciation, genomic profiling, and clustering. Here we describe the epidemiology of all Yersinia spp. reported in England to the UKHSA from the regional laboratories and the reference laboratory leading up to and following the exceedance in 2022. We aim to capture and describe the changes and developments in surveillance of Yersinia spp. between 2017 and 2024.

The Moving Epidemic Method (MEM) is the ECDC/WHO-Europe-endorsed approach for establishing influenza epidemic thresholds and intensity levels, yet no positivity-based MEM analysis exists for Türkiye or any country in the WHO Western Asia transmission zone. Weekly influenza positivity rates from FluNet sentinel surveillance were analysed for ten of twelve seasons (2013/2014–2024/2025, excluding two COVID-19 pandemic seasons) using the mem R package with cross-validated optimized slope parameter, and Türkiye’s average epidemic curve and thresholds were compared with the Western Asia (excluding Türkiye) and South West Europe zones using Lin’s concordance correlation coefficient (CCC), root mean square deviation (RMSD) and complementary correlation metrics. The epidemic threshold was 10.59% positivity, with intensity thresholds at 42.56% (medium), 60.92% (high), and 71.38% (very high); cross-validated sensitivity was 0.77, specificity 0.88, and Matthews correlation coefficient 0.65. Türkiye’s average curve showed higher concordance with Western Asia (CCC=0.890; RMSD=4.22 percentage points) than South West Europe (CCC=0.672; RMSD=12.48) despite similar Pearson correlations (0.922 vs. 0.939), and the Western Asia epidemic threshold (11.50%) closely matched Türkiye’s. These first operational MEM thresholds for Türkiye and the first positivity-based thresholds for the Western Asia zone confirm alignment with the current WHO transmission zone classification and support integration into routine surveillance.

COVID-19 was the most recent pandemic to highlight profound ethnic inequities. However, most mathematical epidemiological models do not adequately represent these inequities, limiting the potential for such models to inform equitable public health responses and interventions. This systematic review identifies mathematical models of infectious respiratory disease transmission that report results by ethnic group and surveys the different mathematical modelling approaches used to attempt to capture ethnicity-related outcomes. Only 28 studies met the inclusion criteria, which is rare relative to the volume of infectious disease modelling literature. The most common model frameworks were compartmental models (11 studies), individual-based models (12 studies), and metapopulation models (5 studies). Across these studies, ethnic heterogeneities were represented directly by incorporating some combination of ethnic group population demographics, ethnicity-specific interaction patterns, and ethnicity-specific disease parameters, or indirectly through spatial differences in interaction patterns or disease transmission. Consideration of ethnicity in mathematical models of disease transmission is in its infancy, with only three of the studies published before 2020, but it has the potential to provide improved evidence for public health action that reduces the epidemic burden and inequities across ethnic groups.

Social contact surveys, measuring who contacts whom, are widely used for epidemic intelligence and public health decision-making. Despite their widespread use, sample size calculations are not performed. We conducted a review of social contact surveys (2008–2025) to characterize current practice. We characterized the impact of survey size on epidemic metrics using two social contact surveys, the UK Social Contact Survey and POLYMOD (Europe), and two methods. For each dataset and approach, we generated repeated subsamples and calculated the resulting reproduction numbers, characterized their distributions, and measured uncertainty. We identified 107 unique social contact surveys from 57 studies. Sample sizes ranged from 30 to more than 10 000 participants, with a median of 1 438. One quarter of surveys contained fewer than 1 000 participants. Our analysis supports recruiting at least 1 000 participants for general-population social contact surveys used for epidemic modelling. Increasing sample size to 2 000 participants provides worthwhile gains in the precision of epidemic estimates, particularly for analyses using finer age stratification or individual-level approaches. Beyond approximately 3 000 participants, additional improvements in precision were small for the epidemic metrics analysed. This provides a practical balance between precision and participant burden.

Salmonella is a leading cause of foodborne illness in the United States, yet rural–urban differences in incidence and their underlying drivers remain poorly characterized. We conducted an ecological analysis of deidentified probable and confirmed Salmonella cases from the National Notifiable Diseases Surveillance System (NNDSS), 2011–2023, to evaluate temporal, regional, and population-level determinants of Salmonella incidence. Multivariable negative binomial models assessed rural–urban differences nationally and by U.S. Census region, and Blinder–Oaxaca decomposition quantified contributions of demographic, socioeconomic, healthcare access, and health-related factors. Age-adjusted incidence was consistently higher in rural than in urban counties. After adjustment, rural counties had higher incidence nationally and separately in all four regions (Northeast, Midwest, West, and South). County-level factors explained 66% of the national rural–urban gap, driven primarily by age structure, income, education, and food environment. Adults aged ≥65 years accounted for approximately 60% of the explained difference and were the dominant contributor in some regions. Regional variation was evident, with age predominating in the Midwest and West and education contributing more in the Northeast and South. A substantial unexplained component remained. These findings highlight persistent, regionally heterogeneous disparities and underscore the need for targeted, region-specific surveillance and prevention strategies.

The Histoplasma capsulatum complex clusters cryptic species with genetic diversities linked to their geographic distribution and virulence. The American continent harbours its highest diversity, making this region the main axis for H. capsulatum spread. Species of this complex cause respiratory-systemic mycosis known as histoplasmosis. Infection occurs through the inhalation of fungal propagules that grow in sites such as caves, mines, and abandoned buildings, where environments rich in organic matter containing micronutrients present in bat and bird guano favour the development of these fungal pathogens. This research was conducted in the state of Nayarit, Mexico, where the combination of environmental factors and the constant occurrence of bats in urban and rural areas contributes to the proliferation of H. capsulatum. The presence of the fungus was detected by nested-PCR using a specific marker (Hcp100) for H. capsulatum, either in guano or in bat organ samples collected in the municipalities of Tepic, Santa María del Oro (SAMAO), and La Yesca, Nayarit. Out of 27 guano samples analysed by nested-PCR, 21 were positive for H. capsulatum, while of the 12 bats studied, only five revealed infections. The fungus was isolated from a lung sample of a nectarivorous bat (Glossophaga mutica) by culture. The results suggest a potential risk to exposed populations, including different specialized workers and tourists who explored bat roosts. Avoiding guano accumulation, restricting access to bat roosts, and implementing bat-exclusion strategies in homes are general recommendations to prevent fungal infections.

Seroprevalence surveys reveal the extent of humoral immunity against pathogens such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and under some circumstances represent cumulative incidence of prior infection. However, antibody waning – or seroreversion – biases these estimates by reducing assay sensitivity in a time-varying manner. Because assay sensitivity decays over time, naively using serosurveys can substantially bias estimates of SARS-CoV-2 cumulative incidence and fatality rates. The Bayesian assay-specific, time-varying sensitivity adjustment developed in this paper can reliably correct for this bias and account for the delay between infection and serosurvey. In seroprevalence studies conducted in the United States in 2020, adjusting for time-varying sensitivity increased cumulative incidence by up to 1.4-fold, with an adjustment of 1.08 for a national study. Our estimates contrast with a previously published 2-fold adjustment that did not account for assay design. This suggests that previous analyses overestimated cumulative incidence by applying seroreversion corrections that did not account for assay-specific effects, or underestimated cumulative incidence by not applying seroreversion corrections. These biases imply fatality rate underestimation and overestimation, respectively. Our model provides a framework for design-specific time-varying sensitivity corrections in seroprevalence surveys for other pathogens.

Lassa fever is endemic across West Africa, yet the completeness of national surveillance remains poorly quantified. We developed and applied a Reporting Completeness Index (RCI) to quantify surveillance performance in Nigeria from 2012 to 2025. Annual confirmed cases and deaths reported by the Nigeria Centre for Disease Control and Prevention were analysed. RCI was defined as the ratio of reported confirmed cases to expected cases estimated from reported deaths using a reference case fatality rate of 16.5%. Uncertainty was assessed using Monte Carlo simulation, while Mann–Kendall and Spearman tests, Sen’s slope, change-point detection, and sensitivity analyses across five CFR assumptions (10–25%) assessed temporal patterns and robustness. National RCI increased from 26.1% in 2012 to a mean of 103.6% after 2019, representing an approximately four-fold improvement. The upward trend was significant (Mann–Kendall τ = 0.51, p = 0.015; Sen’s slope = 5.84% per year), with a structural break identified in 2019 (p < 0.001). The improvement coincided with expanded laboratory capacity and deployment of SORMAS. RCI provides a transparent, reproducible approach for monitoring surveillance completeness in resource-limited settings.

Health system decision-makers need evidence on how modifiable factors contribute to inequalities to inform effective interventions. We examined ethnic group and deprivation inequalities in influenza and COVID-19 hospitalizations in England (2023–2024) among vaccine-eligible individuals, using causal mediation analysis to assess the roles of deprivation, vaccination uptake and comorbidities. For influenza, hospitalization odds were highest among Pakistani and Bangladeshi groups, compared with White British individuals. Deprivation mediated 26% of the total ethnic group effect for the Pakistani group and 41% for the Bangladeshi group, whilst comorbidities contributed little. Ethnic group differences in COVID-19 hospitalizations were minimal in this post-pandemic period. For both infections, the most deprived group had disproportionately high hospitalization compared to the least deprived. For influenza, vaccination uptake mediated 17%–26% of deprivation effects, whilst for COVID-19, there were no meaningful residual deprivation inequalities after including vaccination uptake and comorbidities. Vaccination uptake and deprivation mediate a substantial proportion of inequalities in hospitalization for influenza and COVID-19 in the vaccine-eligible cohort. Improving vaccination coverage in under-vaccinated groups should remain a public health priority.

The effectiveness of the 13-valent pneumococcal conjugate vaccine (PCV13) to prevent vaccine-serotype (VT) invasive pneumococcal disease (IPD) in children aged 2–59 months was assessed using data from 4 geographically defined areas in Canada with IPD surveillance, including immunization status. VT IPD cases and IPD controls with non-PCV13 types or PCV13-related serotypes (NVT/NR) during the years 2010–2019 were eligible. Vaccine effectiveness (VE) was estimated by the indirect cohort method, using multivariate logistic regression models. In total, 367 VT IPD cases and 564 NVT/NR IPD controls were included. VE of ≥1 dose of PCV13 against VT IPD was 70% [95% confidence interval: 49%–83%], lower against serotype 19A IPD (VE = 58%; 95%CI, 14%–80%) and against serotype 3 IPD (VE = 46%; 95%CI, −36% to 79%), but higher against all other PCV13 serotypes (VE = 90%; 95%CI, 78%–96%). Waning of protection was seen against all VT IPD, particularly for serotype 3, with a VE of 89% [54%–97%] during the first 5 months after the third dose but no protection remaining after 18 months. As serotype 3 and serotype 19A are still frequent causes of IPD in children, more effective vaccines are needed.

State of emergency and other mobility-restricting public health and social measures were used during the COVID-19 pandemic in Japan. This study aimed to epidemiologically estimate their impact on the pandemic by comparing observed and counterfactual situations in Osaka and Tokyo during 2020–2021. Weekly nighttime population data were used to predict the effective reproduction number. The first three epidemic waves in 2020–2021 were modelled using the age-dependent transmission model. We used the nighttime population data in 2019 as the counterfactual, and simulated the COVID-19 epidemic in the absence of public health and social measures. In Osaka, predicted counterfactual mortality was 71525 deaths in the first wave, 13589 in the second, and 18814 in the third. These estimates were approximately 832, 100, and 21 times the observed values, respectively. In Tokyo, the predicted counterfactual mortality was 57018, 4361, and 17100 deaths for the three waves, respectively. These estimates were approximately 416, 42, and 14 times the observed numbers, respectively. If the nighttime population remained comparable to that in 2019 and if it continued to predict the epidemic in the absence of public health and social measures, we could have seen far more COVID-19 deaths in Osaka and Tokyo.

With the recent resurgence of global measles outbreaks, it is crucial to understand measles transmission dynamics to guide timely and effective public health responses and parameterize infectious disease models for accurate outbreak projections. This systematic review aims to provide a comprehensive resource of measles transmission-related epidemiological parameters. A search was conducted from inception to 14 May 2024. English and French primary studies of transmission-related epidemiological parameters were included, and standard systematic review methodology was followed. Evidence was synthesized using random-effects meta-analyses and descriptive plots. Subgroup analyses by World Health Organization (WHO) region, population, decade, and quality of reporting were conducted to explore heterogeneity. Between 1910 and 2024, 1 209 estimates across 32 transmission-related epidemiological parameters from 612 studies were reported. Measles was characterized by a pooled incubation period (13.5 days, 95%CI 12.6–14.4; I2 = 95.9%), serial interval (12.4 days, 95%CI 11.5–13.4; I2 = 97.6%), symptom onset to hospitalization (4.8 days, 95%CI 3.7–5.8, I2 = 99.7%), and basic reproduction number median 11.5 (range of 0–57). This work is part of a global epidemic preparedness and response project to establish an accessible living Global Repository of Epidemiological Parameters aimed at reducing duplicative efforts in identifying and summarizing epidemiological parameters.

Universal RSV immunization strategies for infants, including monoclonal antibody administration and maternal vaccination during pregnancy, were implemented in Greece for the first time during the 2025–2026 season. We conducted a prospective observational study of infants aged <12 months hospitalized with bronchiolitis at a quaternary paediatric hospital in Greece between November 2025 and April 2026. Bronchiolitis incidence was compared with that of the 2023–2024 and 2024–2025 seasons. Severity of bronchiolitis was assessed using the modified Tal score. Across the three seasons, 854 of 15246 admissions were due to bronchiolitis. The incidence decreased significantly in 2025–2026 to 42 per 1000 admissions, compared to 64 and 59 in 2024–2025 and 2023–2024, respectively. The 2025–2026 epidemic curve of bronchiolitis was flatter and more prolonged, with a delayed peak in March. Of 186 infants with bronchiolitis, 19.9% had received RSV immunization. Disease severity and oxygen requirements did not differ significantly between immunized and unimmunized infants, although unimmunized infants were older and had a trend towards higher complication rates. In conclusion, national RSV immunization was associated with reduced bronchiolitis hospitalizations and complications. However, the smaller-than-expected reduction in disease rates underscores the need to improve awareness, coverage, and timely immunization.