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Journal articlede Lima STS, Claro IM, Hua X, et al., 2025,
Active West Nile virus transmission in Brazil: an epidemiological study
, The Lancet Regional Health. Americas, Vol: 51, ISSN: 2667-193XBackgroundWest Nile virus (WNV) is a mosquito-borne flavivirus that can cause neurological and fatal disease in animals and humans. Since its introduction into the USA in 1999, WNV has become the leading arbovirus in North America. In contrast, no major WNV outbreak has been reported in South America. Our study investigated active WNV circulation in Brazil.MethodsWe examined WNV epidemiological, molecular, genomic, and serological data from Brazil from January 2014 to December 2024. We also conducted WNV testing in 561 patients with febrile illness, neuroinvasive disease, or death between January 2019 and January 2024 in Ceará State, Brazil. Next, we conducted time series, mapping, ecological niche modeling, age-sex distribution, phylogenetic analyses, and statistical hypothesis tests.FindingsBetween January 2014 and December 2024, 110 West Nile cases were reported from 13 of 27 Brazilian states. In addition, our retrospective study in Ceará State revealed 12.1% (68 of 561 patients) were WNV cases, peaking in 2023, when 42.6% (29 of 68) of cases occurred. Among WNV cases, 7 (10.3%) had detected WNV RNA in serum, cerebrospinal fluid, or both, whereas 62 (89.7%) were IgM-positive, with 29 presenting with neurological complications, 35 with febrile illness, and four fatalities. WNV cases were reported in all months, with the highest numbers between May and August. Most cases were female (female-to-male ratio, 1.1:1), and the median age of patients was 40 years (interquartile range, 20–57). Our phylogenetic analysis showed that WNV lineage 1a circulated in Ceará State and caused a fatal horse case. Our ecological niche models identified several areas, mainly situated in the Northeast region, linked to a potentially higher risk of human exposure to local WNV circulation.InterpretationThese findings comprehensively described consistent WNV circulation in Brazil and may contribute to informing public health policy, focusing on the strategies to d
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Journal articleDankwa EA, Cavalli L, Balasubramanian R, et al., 2025,
Calibration of transmission-dynamic infectious disease models: a scoping review and reporting framework
, PLoS Computational Biology, Vol: 21, ISSN: 1553-734XObjective/BackgroundTransmission-dynamic models are commonly used to study infectious disease epidemiology. Calibration involves identifying model parameter values that align model outputs with observed data or other evidence. Inaccurate calibration and inconsistent reporting produce inference errors and limit reproducibility, compromising confidence in the validity of modeled results. No standardized framework exists for reporting on calibration of infectious disease models, and an understanding of current calibration approaches is lacking.MethodsWe developed the Purpose-Inputs-Process-Outputs (PIPO) framework for reporting calibration practices and applied it in a scoping review to assess calibration approaches and evaluate reporting comprehensiveness in transmission-dynamic models of tuberculosis, HIV and malaria published between January 1, 2018, and January 16, 2024. We searched relevant databases and websites to identify eligible publications, including peer-reviewed studies where these models were calibrated to empirical data or published estimates.ResultsWe identified 411 eligible studies encompassing 419 models, with 74% (n = 309) being compartmental models and 20% (n = 81) individual-based models (IBMs). The predominant analytical purpose was to evaluate interventions (71% of models, n = 298). Parameters were calibrated mainly because they were unknown or ambiguous (40%, n = 168), or because determining their value was relevant to the scientific question beyond being necessary to run the model (20%, n = 85). The choice of calibration method was significantly associated with model structure (p-value<0.001) and stochasticity (p-value = 0.006), with approximate Bayesian computation more frequently used with IBMs and Markov-Chain Monte Carlo with compartmental models. Regarding reporting comprehensiveness, all PIPO framework items were reported in 4% (n = 18) o
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Journal articleStannah J, Knight J, Sandfort T, et al., 2025,
The effect of sexual and gender minority violence on depression, hazardous drinking, condom use, and HIV acquisition: an individual participant data meta-analysis of the CohMSM, HPTN 075, and Anza Mapema cohort studies in Africa
, AIDS and Behavior, Vol: 29, Pages: 3557-3572, ISSN: 1090-7165Some sexual and gender minorities (SGM), including men who have sex with men and transgender women, are disproportionately vulnerable to HIV. Many SGM in Africa report experiencing verbal or physical violence due to their sexual and/or gender identities or behaviours. The pathways linking such SGM violence to HIV acquisition are complex. We described experiences of verbal and physical SGM violence and explored pathways to HIV acquisition among SGM assigned male sex at birth using a two-stage individual participant data meta-analysis of three African cohort studies: CohMSM (Burkina Faso, Côte d’Ivoire, Mali, Togo), HPTN 075 (Kenya, Malawi, South Africa), and Anza Mapema (Kenya). SGM violence was assessed at baseline and follow-up visits. We fit log-linear sequential conditional mean models using generalised estimating equations to estimate risk ratios linking SGM violence, moderate-to-severe depressive symptoms, hazardous drinking, condom use, and HIV acquisition, adjusted for baseline confounders and previous exposure and outcome. We pooled study estimates using random effects meta-analysis. SGM violence, mostly verbal, was reported by 36% (570/1590) participants at baseline (past 6–12 months), and 20% (321/1590) during the first year of follow-up (past 3–6 months). Baseline SGM violence was not associated with HIV acquisition (pooled adjusted risk ratio [aRR] = 1.0, 95% CI 0.5–1.9). During follow-up, SGM violence also showed no clear relationship with HIV, but was linked to depressive symptoms at the same visit (pooled aRR = 1.7, 1.3–2.1), in turn associated with hazardous drinking (pooled aRR = 1.4, 1.1–1.7). Impacts on condom use were inconclusive. SGM in Africa face high rates of violence, which are associated with depressive symptoms and hazardous drinking–potential routes to HIV vulnerability. While our study did not conclusively demonstrate higher HIV incidence among SGM
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Journal articleSteyn N, Parag KV, 2025,
Robust uncertainty quantification in popular estimators of the instantaneous reproduction number
, American Journal of Epidemiology, Vol: 194, Pages: 3355-3363, ISSN: 0002-9262The instantaneous reproduction number () is a key measure of the rate of spread of an infectious disease. Correctly quantifying uncertainty in estimates is crucial for making well-informed decisions. Popular estimators leverage smoothing techniques to distinguish signal from noise. Examples include EpiEstim and EpiFilter, which are both controlled by a “smoothing parameter” that is traditionally selected by users. We demonstrate that the values of these smoothing parameters are unknown, vary markedly with epidemic dynamics, and show that data-driven smoothing is crucial for accurate uncertainty quantification of real-time estimates. We derive novel model likelihoods for the smoothing parameters in both EpiEstim and EpiFilter and develop a Bayesian framework to automatically marginalise these parameters when fitting to epidemiological time-series data. This yields marginal posterior predictive distributions which prove integral to rigorous model evaluation. Applying our methods, we find that default parameterisations of these widely-used estimators can negatively impact inference, delaying detection of epidemic growth, and misrepresenting uncertainty (typically producing overconfident estimates), with implications for public health decision-making. Our extensions mitigate these issues, provide a principled approach to uncertainty quantification, improve the robustness of real-time inference, and facilitate model comparison using observable quantities.
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Journal articleGrimm SL, Kaufman JT, Rice DP, et al., 2025,
Inferring the sensitivity of wastewater metagenomic sequencing for early detection of viruses: a statistical modelling study
, Lancet Microbe, Vol: 6Background Metagenomic sequencing of wastewater (W-MGS) can in principle detect any known or novel pathogen in a population. We aimed to quantify the sensitivity and cost of W-MGS for viral pathogen detection by jointly analysing W-MGS and epidemiological data for a range of human-infecting viruses. Methods In this statistical modelling study, we analysed sequencing data from four studies of untargeted W-MGS to estimate the relative abundance of 11 human-infecting viruses. Corresponding prevalence and incidence estimates were obtained or calculated from academic and public health reports. We combined these estimates using a hierarchical Bayesian model to predict relative abundance at set prevalence or incidence values, allowing comparison across studies and viruses. These predictions were then used to estimate the sequencing depth and concomitant cost required for pathogen detection using W-MGS with or without use of a hybridisation capture enrichment panel. Findings After controlling for variation in local infection rates, relative abundance varied by orders of magnitude across studies for a given virus. For instance, a local SARS-CoV-2 weekly incidence of 1% corresponded to a predicted SARS-CoV-2 relative abundance ranging from 3·8 × 10<sup>−10</sup> to 2·4 × 10<sup>−7</sup> across studies, translating to orders-of-magnitude variation in the cost of operating a system able to detect a SARS-CoV-2-like pathogen at a given sensitivity. Use of a respiratory virus enrichment panel in two studies greatly increased predicted relative abundance of SARS-CoV-2, lowering yearly costs by 27-fold (from US$7·87 million to $287 000) and 29-fold (from $1·98 million to $69 100) for a system able to detect a SARS-CoV-2-like pathogen before reaching 0·01% cumulative incidence. Interpretation The large variation in viral relative abundance after controlling for epidemiological factors indicates that ot
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Journal articleKwun MJ, Ion A, Apagyi KJ, et al., 2025,
Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage
, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 42, ISSN: 0737-4038 -
Journal articleWill I, Stevens EJ, King KC, et al., 2025,
Host Transcriptomics Reveal Reduction in Defence-Reproduction Trade-Offs During Coinfection
, MOLECULAR ECOLOGY, Vol: 34, ISSN: 0962-1083 -
Journal articleGasasira M-F, Garcia L, Donnadieu F, et al., 2025,
A Multiplex Serological Assay for the Detection of Antibody Responses to Arboviruses
, JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, ISSN: 1940-087X -
Journal articleMills C, Alrefae T, Hart WS, et al., 2025,
Renewal equations for mosquito-borne diseases
, METHODS IN ECOLOGY AND EVOLUTION, Vol: 16, Pages: 2653-2666, ISSN: 2041-210X -
Journal articleMacAlasdair N, Pontinen AK, Ling C, et al., 2025,
Genetic population structure of <i>Haemophilus influenzae</i> at local and global scales
, NATURE MICROBIOLOGY, ISSN: 2058-5276
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