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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 Q2 INFECTIOUS DISEASES Pub Date : 2025-04-03 DOI: 10.1016/j.epidem.2025.100823
Tanvir Ahammed , Md Sakhawat Hossain , Christopher McMahan , Lior Rennert
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.
由于缺乏估算细粒度地区实时传染病负担的常规方法,无法及时有效地采取公共卫生应对措施。由于 1) 数据报告严重滞后,2) 提供给研究人员的数据缺乏地理粒度,此类估算通常所需的综合数据源(如州卫生部门数据)往往受到限制。利用当地卫生系统的实时数据为克服这些挑战提供了机会。本研究评估了机器学习和统计方法的有效性,这些方法使用当地卫生系统数据来估算南卡罗来纳州当前和以往的 COVID-19 住院情况。在 123 个邮政编码(72.29%,IQR:63.20-75.62%)和 28 个有足够医疗系统覆盖范围的县(76.43%,IQR:70.33-81.16%)中,随机森林模型与广义线性混合模型相比,在当前每周住院情况方面显示出更高的平均中位数百分比一致性准确率。为了考虑到医疗系统中代表性不足的人群,我们将随机森林模型与分类和回归树 (CART) 结合起来进行估算。所有邮政编码和所有县的平均一致率中位数分别为 61.02 %(IQR:51.17-72.29 %)和 72.64 %(IQR:66.13-77.69 %)。在所有邮政编码中,前 6 个月累计住院治疗的中位同意率为 80.98 %(IQR:68.99-89.66 %),在所有县中为 81.17 %(IQR:68.55-91.33 %)。这些发现强调了利用实时卫生系统数据估算传染病负担的有效性。此外,本研究开发的方法还可用于估算其他疾病的住院人数,为公共卫生官员迅速有效地应对各种卫生危机提供了宝贵的工具。
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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 Q2 INFECTIOUS DISEASES 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
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 Perspective 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.
基于废水的流行病学是从污水系统中检测病原体并对这些数据进行解释以改善公共卫生。自2020年以来,其使用范围有所扩大,当时证明可以从受影响人群的废水中成功提取SARS-CoV-2 RNA。在这一观点中,我们概述了废水中病原体检测的最新进展,提出了一个确定废水采样用于病原体检测的框架,并提出了分析需要发展的领域。确保数据收集和分析都针对流行病不同阶段的关键问题进行调整,将改进所作的推断。为了使分析有用,我们需要确定是否存在感染、早期发现感染、可靠地估计流行轨迹和流行程度,以及在不依赖于共识序列的情况下发现新的变异的方法。这一研究领域包含了许多改进了对收集数据的解释的创新,我们乐观地认为创新将在未来继续。
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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 Q2 INFECTIOUS DISEASES Pub Date : 2025-03-18 DOI: 10.1016/j.epidem.2025.100820
Gabrielle Thivierge , Aaron Rumack , F. William Townes
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.
季节性流感预测对公共卫生和个人决策至关重要。我们使用统计回归模型研究是否将邻近州流感活动数据纳入可以改善美国每个州流感样疾病(ILI)的点预测和分布预测。利用CDC FluView 2010-2019年的ILI数据,我们使用分位数、线性和泊松自回归模型对美国每个州的每周ILI进行预测,这些模型使用来自目标州、邻近州和美国人口加权平均值的ILI数据的不同组合进行拟合。用均方根误差和加权区间得分进行评分表明,包含邻居和/或美国加权平均ILI的协变量集平均比仅使用滞后ILI拟合的模型在目标状态下的准确率略高。此外,包括邻居时的性能改进与包括美国平均水平时的改进相似,这表明邻近州的接近程度并不是准确性略有提高的驱动因素。空间信息对预测精度的影响也存在明显的季节内和季节间变异性。
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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 Q2 INFECTIOUS DISEASES 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
Mycobacterium tuberculosis 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.
结核分枝杆菌复合体(MTBC)菌系在毒力方面表现出很大的变异性,但这种变异性对流行病学的影响尚未得到详细研究。在此,我们将系统动力学模型应用于来自不同国家的基因组数据,以代表最丰富的 MTBC 品系,从而对该品系的特定流行病学特征进行分析。我们的结果表明,所有品系都具有相似的感染持续时间和水平,从而导致相似的繁殖数量。然而,L1 和 L6 的传染性起始时间较晚,导致后续传播事件之间的间隔时间较长。总之,我们的研究结果凸显了 MTBC 遗传多样性在结核病进展和传播中的作用。
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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 Q2 INFECTIOUS DISEASES 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
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.
整合多个团队为共享目标生成整体预测和预测的协作中心现在被视为流行病预测建模领域的最先进技术。在本文中,我们介绍influucast,意大利第一个流感样疾病的流行预测中心。在2023/2024年冬季,influucast提供了20轮预测,涉及5个团队和8个模型,在国家和区域行政层面提前最多四周预测流感样疾病的发病率。单个预测被合成为一个整体,并根据基线模型进行基准测试。在所有模型中,考虑到不同的指标和预测轮,整体最经常在国家层面上名列前茅。此外,在所有地区,集成模型的性能都优于基线模型和大多数单个模型。尽管在较长的视界内,整体模型的绝对性能有所下降,但在所有考虑的视界内,整体模型的性能都优于基线。这些发现表明,多模式预测中心在提供可靠的短期流感样疾病预测方面的重要性,这些预测可以为公共卫生防范和缓解战略提供信息。
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引用次数: 0
A prospective real-time transfer learning approach to estimate influenza hospitalizations with limited data 基于有限数据估计流感住院的前瞻性实时迁移学习方法
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2025-02-07 DOI: 10.1016/j.epidem.2025.100816
Austin G. Meyer , Fred Lu , Leonardo Clemente , Mauricio Santillana
Accurate, real-time forecasts of influenza hospitalizations would facilitate prospective resource allocation and public health preparedness. State-of-the-art machine learning methods are a promising approach to produce such forecasts, but they require extensive historical data to be properly trained. Unfortunately, data on influenza hospitalizations, for the 50 states in the United States, are only available since the beginning of 2020. In addition, the data are far from perfect as they were under-reported for several months before health systems began consistently submitting their data. To address these issues, we propose a transfer learning approach. We extend the currently available two-season dataset for state-level influenza hospitalizations by an additional ten seasons. Our method leverages influenza-like illness (ILI) data to infer historical estimates of influenza hospitalizations. This data augmentation enables the implementation of advanced machine learning techniques, multi-horizon training, and an ensemble of models to improve hospitalization forecasts. We evaluated the performance of our machine learning approaches by prospectively producing forecasts for future weeks and submitting them in real time to the Centers for Disease Control and Prevention FluSight challenges during two seasons: 2022–2023 and 2023–2024. Our methodology demonstrated good accuracy and reliability, achieving a fourth place finish (among 20 participating teams) in the 2022–23 and a second place finish (among 20 participating teams) in the 2023–24 CDC FluSight challenges. Our findings highlight the utility of data augmentation and knowledge transfer in the application of machine learning models to public health surveillance where only limited historical data is available.
准确、实时的流感住院预测将有助于未来的资源分配和公共卫生准备。最先进的机器学习方法是产生这种预测的一种很有前途的方法,但它们需要大量的历史数据来进行适当的训练。不幸的是,美国50个州的流感住院数据只能从2020年初开始获得。此外,这些数据远非完美,因为在卫生系统开始持续提交数据之前的几个月里,这些数据都没有得到充分报告。为了解决这些问题,我们提出了一种迁移学习方法。我们将目前可用的州级流感住院两季数据集额外扩展了十个季节。我们的方法利用流感样疾病(ILI)数据来推断流感住院的历史估计。这种数据增强使先进的机器学习技术、多视界训练和模型集成得以实现,从而改善住院预测。我们对机器学习方法的性能进行了评估,方法是对未来几周进行前瞻性预测,并在2022-2023和2023-2024两个季节向疾病控制与预防中心提交实时预测。我们的方法证明了良好的准确性和可靠性,在2022-23赛季获得了第四名(在20支参赛队伍中),在2023-24赛季获得了第二名(在20支参赛队伍中)。我们的研究结果强调了数据增强和知识转移在将机器学习模型应用于只有有限历史数据可用的公共卫生监测中的效用。
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引用次数: 0
Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter 基于超人口网络和卡尔曼滤波的北美地区COVID-19模型
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2025-01-26 DOI: 10.1016/j.epidem.2025.100818
Matteo Perini , Teresa K. Yamana , Marta Galanti , Jiyeon Suh , Roselyn Kaondera-Shava , Jeffrey Shaman

Background

Understanding the dynamics of infectious disease spread and predicting clinical outcomes are critical for managing large-scale epidemics and pandemics, such as COVID-19. Effective modeling of disease transmission in interconnected populations helps inform public health responses and interventions across regions.

Methods

We developed a novel metapopulation model for simulating respiratory virus transmission in the North America region, specifically for the 96 states, provinces, and territories of Canada, Mexico, and the United States. The model is informed by COVID-19 case data, which are assimilated using the Ensemble Adjustment Kalman filter (EAKF), a Bayesian inference algorithm. Additionally, commuting and mobility data are used to build and adjust the network and movement across locations on a daily basis.

Results

This model-inference system provides estimates of transmission dynamics, infection rates, and ascertainment rates for each of the 96 locations from January 2020 to March 2021. The results highlight differences in disease dynamics and ascertainment among the three countries.

Conclusions

The metapopulation structure enables rapid simulation at a large scale, and the data assimilation method makes the system responsive to changes in system dynamics. This model can serve as a versatile platform for modeling other infectious diseases across the North American region.
背景:了解传染病传播动态并预测临床结果对于管理大规模流行病和流行病(如COVID-19)至关重要。相互联系人群中疾病传播的有效建模有助于为跨区域的公共卫生反应和干预提供信息。方法:我们开发了一种新的元种群模型来模拟北美地区呼吸道病毒的传播,特别是加拿大、墨西哥和美国的96个州、省和地区。该模型由COVID-19病例数据提供信息,这些数据使用贝叶斯推理算法集成调整卡尔曼滤波(EAKF)同化。此外,通勤和移动数据用于建立和调整每天在不同地点之间的网络和移动。该模型推理系统提供了2020年1月至2021年3月期间96个地点的传播动态、感染率和确定率的估计值。结果突出了这三个国家在疾病动态和确定方面的差异。结论:超种群结构可以实现大尺度的快速模拟,数据同化方法可以使系统对系统动力学变化做出响应。该模型可作为北美地区其他传染病建模的通用平台。
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引用次数: 0
Estimating nosocomial transmission of micro-organisms in hospital settings using patient records and culture data 利用病人记录和培养数据估计医院环境中微生物的院内传播
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2025-01-25 DOI: 10.1016/j.epidem.2025.100817
Jaime Cascante Vega , Rami Yaari , Tal Robin , Lingsheng Wen , Jason Zucker , Anne-Catrin Uhlemann , Sen Pei , Jeffrey Shaman
Pathogenic bacteria are a major threat to patient health in hospitals. Here we leverage electronic health records from a major New York City hospital system collected during 2020–2021 to support simulation inference of nosocomial transmission and pathogenic bacteria detection using an agent-based model (ABM). The ABM uses these data to inform simulation of importation from the community, nosocomial transmission, and patient spontaneous decolonization of bacteria. We additionally use patient clinical culture results to inform an observational model of detection of the pathogenic bacteria. The model is coupled with a Bayesian inference algorithm, an iterated ensemble adjustment Kalman filter, to estimate the likelihood of detection upon testing and nosocomial transmission rates. We evaluate parameter identifiability for this model-inference system and find that the system is able to estimate modelled nosocomial transmission and effective sensitivity upon clinical culture testing. We apply the framework to estimate both quantities for seven prevalent bacterial pathogens: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus (both sensitive, MSSA, and resistant, MRSA, phenotypes), Enterococcus faecium and Enterococcus faecalis. We estimate that nosocomial transmission for E. coli is negligible. While bacterial pathogens have different importation rates, nosocomial transmission rates were similar among organisms, except E. coli. We also find that estimated likelihoods of detection are similar for all pathogens. This work highlights how fine-scale patient data can support inference of the epidemiological properties of micro-organisms and how hospital traffic and patient contact determine epidemiological features. Evaluation of the transmission potential for different pathogens could ultimately support the development of hospital control measures, as well as the design of surveillance strategies.
致病菌是医院病人健康的主要威胁。在这里,我们利用2020-2021年期间从纽约市主要医院系统收集的电子健康记录,使用基于代理的模型(ABM)支持医院传播和致病菌检测的模拟推断。ABM使用这些数据来模拟从社区输入、医院传播和患者自发的细菌去菌落。此外,我们使用患者临床培养结果来告知病原菌检测的观察模型。该模型与贝叶斯推理算法、迭代集合调整卡尔曼滤波相结合,以估计检测检测的可能性和医院传播率。我们评估了该模型推理系统的参数可辨识性,并发现该系统能够估计模拟的医院传播和临床培养测试的有效敏感性。我们应用该框架来估计7种流行的细菌病原体的数量:大肠杆菌、肺炎克雷伯菌、铜绿假单胞菌、金黄色葡萄球菌(敏感型,MSSA,耐药型,MRSA,表型)、屎肠球菌和粪肠球菌。我们估计大肠杆菌的医院传播是可以忽略不计的。虽然细菌病原体有不同的输入率,但除大肠杆菌外,微生物之间的医院传播率相似。我们还发现,所有病原体的检测估计可能性是相似的。这项工作强调了精细尺度的患者数据如何支持微生物流行病学特性的推断,以及医院交通和患者接触如何决定流行病学特征。对不同病原体传播潜力的评估最终可支持医院控制措施的制定以及监测战略的设计。
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引用次数: 0
Estimating the generation time for influenza transmission using household data in the United States 利用美国家庭数据估计流感传播的产生时间。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2025-01-18 DOI: 10.1016/j.epidem.2025.100815
Louis Yat Hin Chan , Sinead E. Morris , Melissa S. Stockwell , Natalie M. Bowman , Edwin Asturias , Suchitra Rao , Karen Lutrick , Katherine D. Ellingson , Huong Q. Nguyen , Yvonne Maldonado , Son H. McLaren , Ellen Sano , Jessica E. Biddle , Sarah E. Smith-Jeffcoat , Matthew Biggerstaff , Melissa A. Rolfes , H. Keipp Talbot , Carlos G. Grijalva , Rebecca K. Borchering , Alexandra M. Mellis
The generation time, representing the interval between infections in primary and secondary cases, is essential for understanding and predicting the transmission dynamics of seasonal influenza, including the real-time effective reproduction number (Rt). However, comprehensive generation time estimates for seasonal influenza, especially since the 2009 influenza pandemic, are lacking. We estimated the generation time utilizing data from a 7-site case-ascertained household study in the United States over two influenza seasons, 2021/2022 and 2022/2023. More than 200 individuals who tested positive for influenza and their household contacts were enrolled within 7 days of the first illness in the household. All participants were prospectively followed for 10 days, completing daily symptom diaries and collecting nasal swabs, which were then tested for influenza via RT-PCR. We analyzed these data by modifying a previously published Bayesian data augmentation approach that imputes infection times of cases to obtain both intrinsic (assuming no susceptible depletion) and realized (observed within household) generation times. We assessed the robustness of the generation time estimate by varying the incubation period, and generated estimates of the proportion of transmission occurring before symptomatic onset, the infectious period, and the latent period. We estimated a mean intrinsic generation time of 3.2 (95 % credible interval, CrI: 2.9–3.6) days, with a realized household generation time of 2.8 (95 % CrI: 2.7–3.0) days. The generation time exhibited limited sensitivity to incubation period variation. Estimates of the proportion of transmission that occurred before symptom onset, the infectious period, and the latent period were sensitive to variations in the incubation period. Our study contributes to the ongoing efforts to refine estimates of the generation time for influenza. Our estimates, derived from recent data following the COVID-19 pandemic, are consistent with previous pre-pandemic estimates, and will be incorporated into real-time Rt estimation efforts.
代时间代表了原发性和继发性病例感染之间的间隔,对于了解和预测季节性流感的传播动态至关重要,包括实时有效繁殖数(Rt)。然而,缺乏对季节性流感产生时间的全面估计,特别是自2009年流感大流行以来。我们利用美国在2021/2022和2022/2023两个流感季节进行的7个地点病例确定家庭研究的数据估计了产生时间。200多名流感检测呈阳性的个人及其家庭接触者在家庭中首次发病后7天内进行了登记。所有参与者都被前瞻性随访10天,完成每日症状日记并收集鼻拭子,然后通过RT-PCR检测流感。我们通过修改先前发表的贝叶斯数据增强方法来分析这些数据,该方法计算病例的感染次数,以获得内在(假设没有易感耗尽)和实际(在家庭中观察到的)世代时间。我们通过改变潜伏期来评估生成时间估计的稳健性,并生成在症状出现之前、传染期和潜伏期发生的传播比例的估计。我们估计平均内在发电时间为3.2(95 %可信区间,CrI: 2.9-3.6)天,实现的家庭发电时间为2.8(95 % CrI: 2.7-3.0)天。产生时间对潜伏期变化的敏感性有限。在症状出现之前、传染期和潜伏期发生的传播比例的估计对潜伏期的变化很敏感。我们的研究有助于改进流感产生时间的持续努力。我们的估计是根据COVID-19大流行后的最新数据得出的,与之前的大流行前估计一致,并将纳入实时Rt估计工作。
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引用次数: 0
Reconstructing the first COVID-19 pandemic wave with minimal data in England 用最少的数据重建英格兰的第一次COVID-19大流行浪潮。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2025-01-14 DOI: 10.1016/j.epidem.2025.100814
Siyu Chen , Jennifer A. Flegg , Katrina A. Lythgoe , Lisa J. White
Accurate measurement of exposure to SARS-CoV-2 in the population is crucial for understanding the dynamics of disease transmission and evaluating the impacts of interventions. However, it was particularly challenging to achieve this in the early phase of a pandemic because of the sparsity of epidemiological data. We previously developed an early pandemic diagnostic tool that linked minimum datasets: seroprevalence, mortality and infection testing data to estimate the true exposure in different regions of England and found levels of SARS-CoV-2 population exposure to be considerably higher than suggested by seroprevalence surveys. Here, we re-examine and evaluate the model in the context of reconstructing the first COVID-19 epidemic wave in England from three perspectives: validation against the Office for National Statistics (ONS) Coronavirus Infection Survey, relationship among model performance and data abundance and time-varying case detection ratios. We find that our model can recover the first, unobserved, epidemic wave of COVID-19 in England from March 2020 to June 2020 if two or three serological measurements are given as additional model inputs, while the second wave during winter of 2020 is validated by estimates from the ONS Coronavirus Infection Survey. Moreover, the model estimates that by the end of October in 2020 the UK government’s official COVID-9 online dashboard reported COVID-19 cases only accounted for 9.1 % of cumulative exposure, dramatically varying across the two epidemic waves in England in 2020, 4.3 % vs 43.7 %.
准确测量人群中SARS-CoV-2暴露情况对于了解疾病传播动态和评估干预措施的影响至关重要。然而,由于流行病学数据稀少,在大流行的早期阶段实现这一目标尤其具有挑战性。我们之前开发了一种早期大流行诊断工具,该工具将最低数据集:血清阳性率、死亡率和感染检测数据联系起来,以估计英格兰不同地区的真实暴露情况,并发现SARS-CoV-2人群暴露水平远高于血清阳性率调查所显示的水平。本文从英国国家统计局(ONS)冠状病毒感染调查的验证、模型性能与数据丰度的关系以及时变病例检出率三个方面,在重构英国第一次COVID-19流行波的背景下对模型进行重新检验和评估。我们发现,如果将两到三个血清学测量值作为额外的模型输入,我们的模型可以恢复2020年3月至2020年6月英格兰第一次未观察到的COVID-19流行波,而2020年冬季的第二波流行波通过英国国家统计局冠状病毒感染调查的估计得到验证。此外,该模型估计,到2020年10月底,英国政府官方COVID-9在线仪表板报告的COVID-19病例仅占累积暴露量的9.1% %,在2020年英格兰的两波疫情中差异很大,分别为4.3% %和43.7% %。
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Epidemics
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