Epidemics最新文献

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Modeling the transmission dynamics of African swine fever virus within commercial swine barns: Quantifying the contribution of multiple transmission pathways 模拟非洲猪瘟病毒在商业猪舍内的传播动态:量化多种传播途径的贡献
IF 3 3区 医学
Epidemics Pub Date : 2025-04-24 DOI: 10.1016/j.epidem.2025.100828
Aniruddha Deka , Jason A. Galvis , Christian Fleming , Maryam Safari , Chi-An Yeh , Gustavo Machado
{"title":"Modeling the transmission dynamics of African swine fever virus within commercial swine barns: Quantifying the contribution of multiple transmission pathways","authors":"Aniruddha Deka ,&nbsp;Jason A. Galvis ,&nbsp;Christian Fleming ,&nbsp;Maryam Safari ,&nbsp;Chi-An Yeh ,&nbsp;Gustavo Machado","doi":"10.1016/j.epidem.2025.100828","DOIUrl":"10.1016/j.epidem.2025.100828","url":null,"abstract":"<div><div>The transmission of African swine fever virus (ASFV) within swine barns occurs through direct and indirect pathways. Identifying and quantifying the roles of ASFV dissemination within barns is crucial for developing disease control strategies. We created a stochastic transmission model to examine the ASFV dissemination dynamics through transmission routes within commercial swine barns. We consider seven transmission routes at three disease dynamics levels: within-pens, between-pens, and within-room transmission, along with the transfer of pigs between pens within rooms. We simulated ASFV spread within barns of various sizes and layouts from rooms with a median of 32 pens (IQR: 28-40), where each pen housed a median of 34 pigs (IQR: 29-36). Our model enables tracking the viral load in each pen and monitoring the disease status at the pen level. Results show that between-pen transmission pathways exhibited the highest contribution in spread, accounting for 66.76%, whereas within-pen and within-room pathways account for 26.12% and 7.12%, respectively. Nose-to-nose contact between pens was the primary dissemination route, comprising an average of 46.04%. On the other hand, aerosol transmission within pens had the lowest contribution, accounting for less than 1%. Furthermore, we show that the daily transfer of pigs between pens did not impact the spread of ASFV. On average, at the room level, the combined approach of passive daily surveillance and mortality-focused surveillance enabled ASFV detection within 18 (IQR: 16-19) days. The model allows us to monitor the viral load variation across the room over time, revealing that most of the viral load accumulates in pens closer to the exhaust fans after a month. This work significantly deepens our understanding of ASFV spread within commercial swine production farms in the U.S. and highlights the main transmission pathways that should be prioritized when implementing ASFV countermeasure actions at the room level.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"51 ","pages":"Article 100828"},"PeriodicalIF":3.0,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143878659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Estimating social contact rates for the COVID-19 pandemic using Google mobility and pre-pandemic contact surveys 利用谷歌流动性和大流行前接触调查估计COVID-19大流行的社会接触率
IF 3 3区 医学
Epidemics Pub Date : 2025-04-23 DOI: 10.1016/j.epidem.2025.100830
Em Prestige , Pietro Coletti , Jantien Backer , Nicholas G. Davies , W. John Edmunds , Christopher I. Jarvis
{"title":"Estimating social contact rates for the COVID-19 pandemic using Google mobility and pre-pandemic contact surveys","authors":"Em Prestige ,&nbsp;Pietro Coletti ,&nbsp;Jantien Backer ,&nbsp;Nicholas G. Davies ,&nbsp;W. John Edmunds ,&nbsp;Christopher I. Jarvis","doi":"10.1016/j.epidem.2025.100830","DOIUrl":"10.1016/j.epidem.2025.100830","url":null,"abstract":"<div><div>During the COVID-19 pandemic, aggregated mobility data was frequently used to estimate changing social contact rates. By taking pre-pandemic contact matrices, and transforming these using pandemic-era mobility data, infectious disease modellers attempted to predict the effect of large-scale behavioural changes on contact rates. This study explores the most accurate method for this transformation, using pandemic-era contact surveys as ground truth. We compared four methods for scaling synthetic contact matrices: two using fitted regression models and two using “naïve” mobility or mobility squared models. The regression models were fitted using the CoMix contact survey and Google mobility data from the UK over March 2020 – March 2021. The four models were then used to scale synthetic contact matrices—a representation of pre-pandemic behaviour—using mobility data from the UK, Belgium and the Netherlands to predict the number of contacts expected in “work” and “other” settings for a given mobility level. We then compared partial reproduction numbers estimated from the four models with those calculated directly from CoMix contact matrices across the three countries. The accuracy of each model was assessed using root mean squared error. The fitted regression models had substantially more accurate predictions than the naïve models, even when models were applied to out-of-sample data from the UK, Belgium and the Netherlands. Across all countries investigated, the linear fitted regression model was the most accurate and the naïve model using mobility alone was the least accurate. When attempting to estimate social contact rates during a pandemic without the resources available to conduct contact surveys, using a model fitted to data from another pandemic context is likely to be an improvement over using a “naïve” model based on mobility data alone. If a naïve model is to be used, mobility squared may be a better predictor of contact rates than mobility per se.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"51 ","pages":"Article 100830"},"PeriodicalIF":3.0,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Detection of surges of SARS-Cov-2 using nonparametric Hawkes models 利用非参数霍克斯模型检测 SARS-Cov-2 的激增
IF 3 3区 医学
Epidemics Pub Date : 2025-04-12 DOI: 10.1016/j.epidem.2025.100824
Sophie Phillips , George Mohler , Frederic Schoenberg
{"title":"Detection of surges of SARS-Cov-2 using nonparametric Hawkes models","authors":"Sophie Phillips ,&nbsp;George Mohler ,&nbsp;Frederic Schoenberg","doi":"10.1016/j.epidem.2025.100824","DOIUrl":"10.1016/j.epidem.2025.100824","url":null,"abstract":"<div><div>Hawkes point process models have been shown to forecast the number of daily new cases of epidemic diseases, including SARS-CoV-2 (Covid-19), with high accuracy. Here, we explore how accurately Hawkes models forecast surges of Covid-19 in the United States. We use Hawkes models to estimate the effective reproduction rate <span><math><msub><mrow><mi>R</mi></mrow><mrow><mi>t</mi></mrow></msub></math></span> and transmission density parameters for Covid-19 case counts in each of the 50 United States, then forecast <span><math><msub><mrow><mi>R</mi></mrow><mrow><mi>t</mi></mrow></msub></math></span> in future weeks with simple exponential smoothing. A classifier based on <span><math><mrow><msub><mrow><mi>R</mi></mrow><mrow><mi>t</mi></mrow></msub><mo>&gt;</mo><mi>x</mi></mrow></math></span> is applied to predict upcoming surges in cases each week from August 2020 to December 2021, using only data available up to that week. At false alarm rates below 5%, the forecasts based on <span><math><msub><mrow><mi>R</mi></mrow><mrow><mi>t</mi></mrow></msub></math></span> are correct more often than forecasts based on smoothing the raw case count data, achieving a maximum accuracy of 90% with <span><math><mrow><msub><mrow><mi>R</mi></mrow><mrow><mi>t</mi></mrow></msub><mo>&gt;</mo><mn>1</mn><mo>.</mo><mn>39</mn></mrow></math></span>. The optimal decision boundary uses a combination of <span><math><msub><mrow><mi>R</mi></mrow><mrow><mi>t</mi></mrow></msub></math></span> and observed data.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"51 ","pages":"Article 100824"},"PeriodicalIF":3.0,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143830099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The effect of COVID-19 vaccination on change in contact and implications for transmission COVID-19疫苗接种对接触改变的影响及其对传播的影响
IF 3 3区 医学
Epidemics Pub Date : 2025-04-09 DOI: 10.1016/j.epidem.2025.100827
Carol Y. Liu , Aaron Siegler , Patrick Sullivan , Samuel M. Jenness , Stefan Flasche , Benjamin Lopman , Kristin Nelson
{"title":"The effect of COVID-19 vaccination on change in contact and implications for transmission","authors":"Carol Y. Liu ,&nbsp;Aaron Siegler ,&nbsp;Patrick Sullivan ,&nbsp;Samuel M. Jenness ,&nbsp;Stefan Flasche ,&nbsp;Benjamin Lopman ,&nbsp;Kristin Nelson","doi":"10.1016/j.epidem.2025.100827","DOIUrl":"10.1016/j.epidem.2025.100827","url":null,"abstract":"<div><h3>Background</h3><div>Monitoring human behavior as epidemic intelligence can critically complement traditional surveillance systems during epidemics. Retrospective analysis of novel behavioral data streams initiated during the COVID-19 pandemic help illustrate their utility. During the pandemic, behavior changed rapidly and was increasingly influenced by individual choice in response to changes such as newly available vaccines. Vaccines provided substantial protection against severe disease and deaths; however, their effect on behavior is understudied and it is unclear if vaccine effects against infection fully offset relaxation of social distancing behaviors.</div></div><div><h3>Methods &amp; results</h3><div>We analyzed data from a longitudinal cohort sampled from U.S. households that measured contact rates, risk mitigation and COVID-19 vaccination status between August 2020-April 2022. Contact rates universally increased across survey rounds among all sociodemographic groups, but unvaccinated individuals had persistently higher contact rates. Using a multilevel generalized linear mixed effects model, we found that individuals who newly completed a primary vaccine series had an additional increase of 1.93 (95 % CI: 0.27–3.59) contacts compared to individuals who remained unvaccinated. Using observed contact rates to estimate transmission, we found that observed increases in contact rates were not fully offset by vaccine protection against infection, but transmission was still maintained below levels without distancing and vaccination despite clusters of individuals with high contact and no vaccination.</div></div><div><h3>Conclusion</h3><div>We estimated changes in contact rates following vaccination and inferred the joint effect of changes in vaccination and contacts on population-level transmission, finding that observed increases in contact rates were not fully offset by vaccine effects. Our work highlights the potential utility of ongoing longitudinal monitoring of contact patterns during epidemics.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"51 ","pages":"Article 100827"},"PeriodicalIF":3.0,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143880911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimizing influenza vaccine allocation by age using cost-effectiveness analysis: A comparison of 6720 vaccination program scenarios in children and adults in Belgium 使用成本-效果分析优化按年龄分配流感疫苗:比利时6720例儿童和成人疫苗接种方案的比较
IF 3 3区 医学
Epidemics Pub Date : 2025-04-05 DOI: 10.1016/j.epidem.2025.100826
Regina Manansala , Joke Bilcke , Lander Willem , Niel Hens , Philippe Beutels
{"title":"Optimizing influenza vaccine allocation by age using cost-effectiveness analysis: A comparison of 6720 vaccination program scenarios in children and adults in Belgium","authors":"Regina Manansala ,&nbsp;Joke Bilcke ,&nbsp;Lander Willem ,&nbsp;Niel Hens ,&nbsp;Philippe Beutels","doi":"10.1016/j.epidem.2025.100826","DOIUrl":"10.1016/j.epidem.2025.100826","url":null,"abstract":"<div><h3>Background</h3><div>Many European countries prioritize groups for annual influenza vaccination based on risk of severe disease and death. This has resulted in relatively high influenza vaccination coverage in older adults in Belgium. However, coverage is much lower in younger adults and negligible in children. Children and young adults are known to play a major role in the transmission dynamics of influenza. Thus, an important policy question is how influenza vaccines can be optimally allocated across age groups, taking indirect effects into account.</div></div><div><h3>Methods</h3><div>We adapted a dynamic transmission model to reproduce influenza seasonality in Belgium comparing 6720 mutually exclusive vaccination options, including current practice. Vaccination options were defined by different combinations of coverage level changes in nine age groups. We performed an economic evaluation comparing all options from a healthcare payer perspective. Quality-adjusted life-years (QALYs) were the primary health outcome. We expressed parametric uncertainty using the Incremental Net Monetary Benefits (INMB) approach.</div></div><div><h3>Results</h3><div>Of all the vaccination options considered, over 90 % dominated the current Belgian vaccination strategy in terms of cost-effectiveness. Children were estimated to contribute a substantial indirect protective effect to the overall population. The most cost-effective program increases vaccination coverage rates for children to 90 %, 50–64 years old to 48 %, and 65–74 years old to 75 %.</div></div><div><h3>Discussion</h3><div>Overall QALY gains can be maximized in seasonal influenza vaccination programs at acceptable costs by achieving high vaccination coverage in childhood age groups. Programmatic and ethical concerns towards such an implementation in the Belgian context need to be separately considered.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"51 ","pages":"Article 100826"},"PeriodicalIF":3.0,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143833472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Machine learning approaches for real-time ZIP code and county-level estimation of state-wide infectious disease hospitalizations using local health system data 机器学习方法实时邮政编码和县级估计全州传染病住院使用当地卫生系统数据
IF 3 3区 医学
Epidemics Pub Date : 2025-04-03 DOI: 10.1016/j.epidem.2025.100823
Tanvir Ahammed , Md Sakhawat Hossain , Christopher McMahan , Lior Rennert
{"title":"Machine learning approaches for real-time ZIP code and county-level estimation of state-wide infectious disease hospitalizations using local health system data","authors":"Tanvir Ahammed ,&nbsp;Md Sakhawat Hossain ,&nbsp;Christopher McMahan ,&nbsp;Lior Rennert","doi":"10.1016/j.epidem.2025.100823","DOIUrl":"10.1016/j.epidem.2025.100823","url":null,"abstract":"<div><div>The lack of conventional methods of estimating real-time infectious disease burden in granular regions inhibits timely and efficient public health response. Comprehensive data sources (e.g., state health department data) typically needed for such estimation are often limited due to 1) substantial delays in data reporting and 2) lack of geographic granularity in data provided to researchers. Leveraging real-time local health system data presents an opportunity to overcome these challenges. This study evaluates the effectiveness of machine learning and statistical approaches using local health system data to estimate current and previous COVID-19 hospitalizations in South Carolina. Random Forest models demonstrated consistently higher average median percent agreement accuracy compared to generalized linear mixed models for current weekly hospitalizations across 123 ZIP codes (72.29 %, IQR: 63.20–75.62 %) and 28 counties (76.43 %, IQR: 70.33–81.16 %) with sufficient health system coverage. To account for underrepresented populations in health systems, we combined Random Forest models with Classification and Regression Trees (CART) for imputation. The average median percent agreement was 61.02 % (IQR: 51.17–72.29 %) for all ZIP codes and 72.64 % (IQR: 66.13–77.69 %) for all counties. Median percent agreement for cumulative hospitalizations over the previous 6 months was 80.98 % (IQR: 68.99–89.66 %) for all ZIP codes and 81.17 % (IQR: 68.55–91.33 %) for all counties. These findings emphasize the effectiveness of utilizing real-time health system data to estimate infectious disease burden. Moreover, the methodologies developed in this study can be adapted to estimate hospitalizations for other diseases, offering a valuable tool for public health officials to respond swiftly and effectively to various health crises.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"51 ","pages":"Article 100823"},"PeriodicalIF":3.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143815115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Analysis insights to support the use of wastewater and environmental surveillance data for infectious diseases and pandemic preparedness 分析见解,支持将废水和环境监测数据用于传染病和大流行防范
IF 3 3区 医学
Epidemics Pub Date : 2025-03-28 DOI: 10.1016/j.epidem.2025.100825
KM O’Reilly , MJ Wade , K. Farkas , F. Amman , A. Lison , JD Munday , J. Bingham , ZE Mthombothi , Z. Fang , CS Brown , RR Kao , L. Danon
{"title":"Analysis insights to support the use of wastewater and environmental surveillance data for infectious diseases and pandemic preparedness","authors":"KM O’Reilly ,&nbsp;MJ Wade ,&nbsp;K. Farkas ,&nbsp;F. Amman ,&nbsp;A. Lison ,&nbsp;JD Munday ,&nbsp;J. Bingham ,&nbsp;ZE Mthombothi ,&nbsp;Z. Fang ,&nbsp;CS Brown ,&nbsp;RR Kao ,&nbsp;L. Danon","doi":"10.1016/j.epidem.2025.100825","DOIUrl":"10.1016/j.epidem.2025.100825","url":null,"abstract":"<div><div>Wastewater-based epidemiology is the detection of pathogens from sewage systems and the interpretation of these data to improve public health. Its use has increased in scope since 2020, when it was demonstrated that SARS-CoV-2 RNA could be successfully extracted from the wastewater of affected populations. In this <em>Perspective</em> we provide an overview of recent advances in pathogen detection within wastewater, propose a framework for identifying the utility of wastewater sampling for pathogen detection and suggest areas where analytics require development. Ensuring that both data collection and analysis are tailored towards key questions at different stages of an epidemic will improve the inference made. For analyses to be useful we require methods to determine the absence of infection, early detection of infection, reliably estimate epidemic trajectories and prevalence, and detect novel variants without reliance on consensus sequences. This research area has included many innovations that have improved the interpretation of collected data and we are optimistic that innovation will continue in the future.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"51 ","pages":"Article 100825"},"PeriodicalIF":3.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143737878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Does spatial information improve forecasting of influenza-like illness? 空间信息能改善流感样疾病的预测吗?
IF 3 3区 医学
Epidemics Pub Date : 2025-03-18 DOI: 10.1016/j.epidem.2025.100820
Gabrielle Thivierge , Aaron Rumack , F. William Townes
{"title":"Does spatial information improve forecasting of influenza-like illness?","authors":"Gabrielle Thivierge ,&nbsp;Aaron Rumack ,&nbsp;F. William Townes","doi":"10.1016/j.epidem.2025.100820","DOIUrl":"10.1016/j.epidem.2025.100820","url":null,"abstract":"<div><div>Seasonal influenza forecasting is critical for public health and individual decision making. We investigate whether the inclusion of data about influenza activity in neighboring states can improve point predictions and distribution forecasting of influenza-like illness (ILI) in each US state using statistical regression models. Using CDC FluView ILI data from 2010–2019, we forecast weekly ILI in each US state with quantile, linear, and Poisson autoregressive models fit using different combinations of ILI data from the target state, neighboring states, and the US population-weighted average. Scoring with root mean squared error and weighted interval score indicated that the covariate sets including neighbors and/or the US weighted average ILI showed slightly higher accuracy than models fit only using lagged ILI in the target state, on average. Additionally, the improvement in performance when including neighbors was similar to the improvement when including the US average instead, suggesting the proximity of the neighboring states is not the driver of the slight increase in accuracy. There is also clear within-season and between-season variability in the effect of spatial information on prediction accuracy.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"51 ","pages":"Article 100820"},"PeriodicalIF":3.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143714961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages 传染性的发作解释了结核分枝杆菌谱系间传播性的差异。
IF 3 3区 医学
Epidemics Pub Date : 2025-03-11 DOI: 10.1016/j.epidem.2025.100821
Etthel M. Windels , Cecilia Valenzuela Agüí , Bouke C. de Jong , Conor J. Meehan , Chloé Loiseau , Galo A. Goig , Michaela Zwyer , Sonia Borrell , Daniela Brites , Sebastien Gagneux , Tanja Stadler
{"title":"Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages","authors":"Etthel M. Windels ,&nbsp;Cecilia Valenzuela Agüí ,&nbsp;Bouke C. de Jong ,&nbsp;Conor J. Meehan ,&nbsp;Chloé Loiseau ,&nbsp;Galo A. Goig ,&nbsp;Michaela Zwyer ,&nbsp;Sonia Borrell ,&nbsp;Daniela Brites ,&nbsp;Sebastien Gagneux ,&nbsp;Tanja Stadler","doi":"10.1016/j.epidem.2025.100821","DOIUrl":"10.1016/j.epidem.2025.100821","url":null,"abstract":"<div><div><em>Mycobacterium tuberculosis</em> complex (MTBC) lineages show substantial variability in virulence, but the epidemiological consequences of this variability have not been studied in detail. Here, we aimed for a lineage-specific epidemiological characterization by applying phylodynamic models to genomic data from different countries, representing the most abundant MTBC lineages. Our results suggest that all lineages are associated with similar durations and levels of infectiousness, resulting in similar reproductive numbers. However, L1 and L6 are associated with a delayed onset of infectiousness, leading to longer periods between subsequent transmission events. Together, our findings highlight the role of MTBC genetic diversity in tuberculosis disease progression and transmission.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"51 ","pages":"Article 100821"},"PeriodicalIF":3.0,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Collaborative forecasting of influenza-like illness in Italy: The Influcast experience 意大利流感样疾病的协同预测:influucast的经验
IF 3 3区 医学
Epidemics Pub Date : 2025-02-14 DOI: 10.1016/j.epidem.2025.100819
Stefania Fiandrino , Andrea Bizzotto , Giorgio Guzzetta , Stefano Merler , Federico Baldo , Eugenio Valdano , Alberto Mateo Urdiales , Antonino Bella , Francesco Celino , Lorenzo Zino , Alessandro Rizzo , Yuhan Li , Nicola Perra , Corrado Gioannini , Paolo Milano , Daniela Paolotti , Marco Quaggiotto , Luca Rossi , Ivan Vismara , Alessandro Vespignani , Nicolò Gozzi
{"title":"Collaborative forecasting of influenza-like illness in Italy: The Influcast experience","authors":"Stefania Fiandrino ,&nbsp;Andrea Bizzotto ,&nbsp;Giorgio Guzzetta ,&nbsp;Stefano Merler ,&nbsp;Federico Baldo ,&nbsp;Eugenio Valdano ,&nbsp;Alberto Mateo Urdiales ,&nbsp;Antonino Bella ,&nbsp;Francesco Celino ,&nbsp;Lorenzo Zino ,&nbsp;Alessandro Rizzo ,&nbsp;Yuhan Li ,&nbsp;Nicola Perra ,&nbsp;Corrado Gioannini ,&nbsp;Paolo Milano ,&nbsp;Daniela Paolotti ,&nbsp;Marco Quaggiotto ,&nbsp;Luca Rossi ,&nbsp;Ivan Vismara ,&nbsp;Alessandro Vespignani ,&nbsp;Nicolò Gozzi","doi":"10.1016/j.epidem.2025.100819","DOIUrl":"10.1016/j.epidem.2025.100819","url":null,"abstract":"<div><div>Collaborative hubs that integrate multiple teams to generate ensemble projections and forecasts for shared targets are now regarded as state-of-the-art in epidemic predictive modeling. In this paper, we introduce Influcast, Italy’s first epidemic forecasting hub for influenza-like illness. During the 2023/2024 winter season, Influcast provided 20 rounds of forecasts, involving five teams and eight models to predict influenza-like illness incidence up to four weeks in advance at the national and regional administrative level. The individual forecasts were synthesized into an ensemble and benchmarked against a baseline model. Across all models, the ensemble most frequently ranks among the top performers at the national level considering different metrics and forecasting rounds. Additionally, the ensemble outperforms the baseline and most individual models across all regions. Despite a decline in absolute performance over longer horizons, the ensemble model outperformed the baseline in all considered horizons. These findings show the importance of multimodel forecasting hubs in producing reliable short-term influenza-like illnesses forecasts that can inform public health preparedness and mitigation strategies.</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"50 ","pages":"Article 100819"},"PeriodicalIF":3.0,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143429019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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