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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 : 2025-03-01 Epub 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
Infectious diseases: Household modeling with missing data 传染病:缺少数据的家庭建模。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2025-03-01 Epub Date: 2024-12-16 DOI: 10.1016/j.epidem.2024.100811
Oron Madmon, Yair Goldberg
Over three years since the first identified SARS-CoV-2 case was discovered, the role of adolescents and children in spreading the virus remains unclear. Specifically, estimating the relative susceptibility of a child with respect to an adult is still an open question. In our work, we generalize a well-known household model for modeling infectious diseases, to include missing tests. Due to missingness, the likelihood of the generalized model cannot be maximized directly. Thus, we propose an estimation methodology, using a novel EM algorithm, for estimating the MLE in the presence of missing data. We implement the proposed mechanism using R software. Using a simulation study, we illustrate the performance of the proposed estimation methodology compared with the estimation procedure in the complete case. Finally, using the proposed estimation methodology we analyzed a dataset containing SARS-CoV-2 testing results, collected from the city of Bnei Brak, Israel, during the beginning of the pandemic. Using this dataset, we show that adolescents are less susceptible than adults, and children are less susceptible than adolescents.
自第一例确诊的SARS-CoV-2病例被发现以来的三年多时间里,青少年和儿童在病毒传播中的作用仍不清楚。具体来说,估计儿童相对于成人的相对易感性仍然是一个悬而未决的问题。在我们的工作中,我们推广了一个众所周知的传染病建模家庭模型,包括缺失测试。由于缺失,广义模型的似然不能直接最大化。因此,我们提出了一种估计方法,使用一种新的EM算法来估计存在缺失数据的最大似然。我们使用R软件实现了所提出的机制。通过仿真研究,我们将所提出的估计方法与完整情况下的估计过程进行了比较。最后,使用提出的估计方法,我们分析了一个包含SARS-CoV-2检测结果的数据集,该数据集是在大流行开始时从以色列Bnei Brak市收集的。使用这个数据集,我们表明青少年比成年人更不容易受到影响,儿童比青少年更不容易受到影响。
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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 : 2025-03-01 Epub 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 : 2025-03-01 Epub 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 effective reproduction numbers using wastewater data from multiple sewersheds for SARS-CoV-2 in California counties 利用加州各县多个下水道的污水数据估计SARS-CoV-2的有效繁殖数量。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2025-03-01 Epub Date: 2024-12-06 DOI: 10.1016/j.epidem.2024.100803
Sindhu Ravuri , Elisabeth Burnor , Isobel Routledge , Natalie M. Linton , Mugdha Thakur , Alexandria Boehm , Marlene Wolfe , Heather N. Bischel , Colleen C. Naughton , Alexander T. Yu , Lauren A. White , Tomás M. León
The effective reproduction number serves as a metric of population-wide, time-varying disease spread. During the early years of the COVID-19 pandemic, this metric was primarily derived from case data, which has varied in quality and representativeness due to changes in testing volume, test-seeking behavior, and resource constraints. Deriving nowcasting estimates from alternative data sources such as wastewater provides complementary information that could inform future public health responses. We estimated county-aggregated, sewershed-restricted wastewater-based SARS-CoV-2 effective reproduction numbers from May 1, 2022 to April 30, 2023 for five counties in California with heterogeneous population sizes, clinical testing rates, demographics, wastewater coverage, and sampling frequencies. We used two methods to produce sewershed-restricted effective reproduction numbers, both based on smoothed and deconvolved wastewater concentrations. We then population-weighted and aggregated these sewershed-level estimates to arrive at county-level effective reproduction numbers. Using mean absolute error (MAE), Spearman’s rank correlation (ρ), confusion matrix classification, and cross-correlation analyses, we compared the timing and trajectory of our two wastewater-based models to: (1) a publicly available, county-level ensemble of case-based estimates, and (2) county-aggregated, sewershed-restricted case-based estimates. Both wastewater models demonstrated high concordance with the traditional case-based estimates, as indicated by low mean absolute errors (MAE ≤ 0.09), significant positive Spearman correlation (ρ ≥ 0.66), and high confusion matrix classification accuracy (≥ 0.81). The relative timings of wastewater- and case-based estimates were less clear, with cross-correlation analyses suggesting strong associations for a wide range of temporal lags that varied by county and wastewater model type. This methodology provides a generalizable, robust, and operationalizable framework for estimating county-level wastewater-based effective reproduction numbers. Our retrospective evaluation supports the potential usage of real-time wastewater-based nowcasting as a complementary epidemiological tool for surveillance by public health agencies at the state and local levels. Based on this research, we produced publicly available wastewater-based nowcasts for the California Communicable diseases Assessment Tool (calcat.cdph.ca.gov).
有效繁殖数可作为种群范围内随时间变化的疾病传播的度量。在COVID-19大流行的最初几年,这一指标主要来自病例数据,由于检测量、寻求检测行为和资源限制的变化,这些数据的质量和代表性各不相同。从废水等替代数据来源得出临近预报估计数,可提供补充信息,为今后的公共卫生对策提供信息。我们估计了2022年5月1日至2023年4月30日期间加州5个县的县聚集性、下水道限制废水的SARS-CoV-2有效繁殖数,这些县的人口规模、临床检测率、人口统计学、废水覆盖率和采样频率各不相同。我们使用了两种方法来产生下水道限制的有效繁殖数,这两种方法都是基于平滑和反卷积的废水浓度。然后,我们对这些下水道水平的估计进行人口加权和汇总,以得出县级的有效再生产数字。利用平均绝对误差(MAE)、斯皮尔曼秩相关(ρ)、混淆矩阵分类和交叉相关分析,我们将两个基于废水的模型的时间和轨迹进行了比较:(1)公开可用的、县级的基于病例的估计集合,以及(2)县级汇总的、受下水道限制的基于病例的估计。这两种废水模型都与传统的基于案例的估计具有很高的一致性,这表明平均绝对误差低(MAE≤0.09),Spearman正相关显著(ρ≥0.66),混淆矩阵分类精度高(≥0.81)。基于废水和基于案例的估算的相对时间不太清楚,相互关联分析表明,随着国家和废水模型类型的不同,时间滞后的范围也有所不同。该方法为估计县级废水有效再生产数提供了一个可推广、可靠和可操作的框架。我们的回顾性评估支持将基于废水的实时临近预报作为州和地方各级公共卫生机构监测的补充流行病学工具的潜力。基于这项研究,我们为加州传染病评估工具(calcat.cdph.ca.gov)制作了公开可用的基于废水的临近预报。
{"title":"Estimating effective reproduction numbers using wastewater data from multiple sewersheds for SARS-CoV-2 in California counties","authors":"Sindhu Ravuri ,&nbsp;Elisabeth Burnor ,&nbsp;Isobel Routledge ,&nbsp;Natalie M. Linton ,&nbsp;Mugdha Thakur ,&nbsp;Alexandria Boehm ,&nbsp;Marlene Wolfe ,&nbsp;Heather N. Bischel ,&nbsp;Colleen C. Naughton ,&nbsp;Alexander T. Yu ,&nbsp;Lauren A. White ,&nbsp;Tomás M. León","doi":"10.1016/j.epidem.2024.100803","DOIUrl":"10.1016/j.epidem.2024.100803","url":null,"abstract":"<div><div>The effective reproduction number serves as a metric of population-wide, time-varying disease spread. During the early years of the COVID-19 pandemic, this metric was primarily derived from case data, which has varied in quality and representativeness due to changes in testing volume, test-seeking behavior, and resource constraints. Deriving nowcasting estimates from alternative data sources such as wastewater provides complementary information that could inform future public health responses. We estimated county-aggregated, sewershed-restricted wastewater-based SARS-CoV-2 effective reproduction numbers from May 1, 2022 to April 30, 2023 for five counties in California with heterogeneous population sizes, clinical testing rates, demographics, wastewater coverage, and sampling frequencies. We used two methods to produce sewershed-restricted effective reproduction numbers, both based on smoothed and deconvolved wastewater concentrations. We then population-weighted and aggregated these sewershed-level estimates to arrive at county-level effective reproduction numbers. Using mean absolute error (MAE), Spearman’s rank correlation (ρ), confusion matrix classification, and cross-correlation analyses, we compared the timing and trajectory of our two wastewater-based models to: (1) a publicly available, county-level ensemble of case-based estimates, and (2) county-aggregated, sewershed-restricted case-based estimates. Both wastewater models demonstrated high concordance with the traditional case-based estimates, as indicated by low mean absolute errors (MAE ≤ 0.09), significant positive Spearman correlation (ρ ≥ 0.66), and high confusion matrix classification accuracy (≥ 0.81). The relative timings of wastewater- and case-based estimates were less clear, with cross-correlation analyses suggesting strong associations for a wide range of temporal lags that varied by county and wastewater model type. This methodology provides a generalizable, robust, and operationalizable framework for estimating county-level wastewater-based effective reproduction numbers. Our retrospective evaluation supports the potential usage of real-time wastewater-based nowcasting as a complementary epidemiological tool for surveillance by public health agencies at the state and local levels. Based on this research, we produced publicly available wastewater-based nowcasts for the California Communicable diseases Assessment Tool (<span><span>calcat.cdph.ca.gov</span><svg><path></path></svg></span>).</div></div>","PeriodicalId":49206,"journal":{"name":"Epidemics","volume":"50 ","pages":"Article 100803"},"PeriodicalIF":3.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142899655","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
Retrospective modelling of the disease and mortality burden of the 1918–1920 influenza pandemic in Zurich, Switzerland 1918-1920年瑞士苏黎世流感大流行的疾病和死亡率负担回顾性建模
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2025-03-01 Epub Date: 2025-01-11 DOI: 10.1016/j.epidem.2025.100813
Ella Ziegler , Katarina L. Matthes , Peter W. Middelkamp , Verena J. Schuenemann , Christian L. Althaus , Frank Rühli , Kaspar Staub

Background

Our study aims to enhance future pandemic preparedness by integrating lessons from historical pandemics, focusing on the multidimensional analysis of past outbreaks. It addresses the gap in existing modelling studies by combining various pandemic parameters in a comprehensive setting. Using Zurich as a case study, we seek a deeper understanding of pandemic dynamics to inform future scenarios.

Data and methods

We use newly digitized weekly aggregated epidemic/pandemic time series (incidence, hospitalisations, mortality and sickness absences from work) to retrospectively model the 1918–1920 pandemic in Zurich and investigate how different parameters correspond, how transmissibility changed during the different waves, and how public health interventions were associated with changes in these pandemic parameters.

Results

In general, the various time series show a good temporal correspondence, but differences in their expression can also be observed. The first wave in the summer of 1918 did lead to illness, absence from work and hospitalisations, but to a lesser extent to increased mortality. In contrast, the second, longest and strongest wave in the autumn/winter of 1918 also led to greatly increased (excess) mortality in addition to the burden of illness. The later wave in the first months of 1920 was again associated with an increase in all pandemic parameters. Furthermore, we can see that public health measures such as bans on gatherings and school closures were associated with a decrease in the course of the pandemic, while the lifting or non-compliance with these measures was associated with an increase of reported cases.

Discussion

Our study emphasizes the need to analyse a pandemic's disease burden comprehensively, beyond mortality. It highlights the importance of considering incidence, hospitalizations, and work absences as distinct but related aspects of disease impact. This approach reveals the nuanced dynamics of a pandemic, especially crucial during multi-wave outbreaks.
背景:我们的研究旨在通过整合历史大流行的经验教训,重点是对过去疫情的多维分析,加强未来的大流行防范。它将各种流行病参数综合起来,填补了现有模型研究中的空白。我们以苏黎世为案例研究,力求更深入地了解大流行动态,为未来情景提供信息。数据和方法:我们使用最新数字化的每周汇总流行病/大流行时间序列(发病率、住院率、死亡率和疾病缺勤率)对1918-1920年苏黎世大流行进行回顾性建模,并调查不同参数如何对应,在不同浪潮中传播率如何变化,以及公共卫生干预措施如何与这些大流行参数的变化相关联。结果:总体而言,各时间序列表现出较好的时间对应性,但在表达上也存在差异。1918年夏天的第一波浪潮确实导致了疾病、缺勤和住院,但在较小程度上增加了死亡率。相比之下,1918年秋冬的第二波,最长和最强的一波,除了疾病负担之外,也导致了死亡率的大幅增加。1920年头几个月的后一波疫情再次与所有大流行参数的增加有关。此外,我们可以看到,禁止集会和关闭学校等公共卫生措施与大流行期间的减少有关,而取消或不遵守这些措施与报告病例的增加有关。讨论:我们的研究强调需要全面分析大流行的疾病负担,而不仅仅是死亡率。它强调了将发病率、住院和缺勤视为疾病影响的不同但相关方面的重要性。这种方法揭示了大流行的微妙动态,在多波暴发期间尤其重要。
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引用次数: 0
Predicting the impact of non-pharmaceutical interventions against COVID-19 on Mycoplasma pneumoniae in the United States 预测美国针对COVID-19的非药物干预措施对肺炎支原体的影响
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-12-01 Epub Date: 2024-11-30 DOI: 10.1016/j.epidem.2024.100808
Sang Woo Park , Brooklyn Noble , Emily Howerton , Bjarke F. Nielsen , Sarah Lentz , Lilliam Ambroggio , Samuel Dominguez , Kevin Messacar , Bryan T. Grenfell
The introduction of non-pharmaceutical interventions (NPIs) against COVID-19 disrupted circulation of many respiratory pathogens and eventually caused large, delayed outbreaks, owing to the build up of the susceptible pool during the intervention period. In contrast to other common respiratory pathogens that re-emerged soon after the NPIs were lifted, longer delays (> 3 years) in the outbreaks of Mycoplasma pneumoniae (Mp), a bacterium commonly responsible for respiratory infections and pneumonia, have been reported in Europe and Asia. As Mp cases are continuing to increase in the US, predicting the size of an imminent outbreak is timely for public health agencies and decision makers. Here, we use simple mathematical models to provide robust predictions about a large Mp outbreak ongoing in the US. Our model further illustrates that NPIs and waning immunity are important factors in driving long delays in epidemic resurgence.
针对COVID-19的非药物干预措施(npi)的引入扰乱了许多呼吸道病原体的循环,并最终由于干预期间易感人群的积累而导致大规模延迟暴发。与其他常见呼吸道病原体在国家行动计划解除后不久重新出现的情况相反,据报道,在欧洲和亚洲,肺炎支原体(一种通常导致呼吸道感染和肺炎的细菌)暴发的时间延迟较长(50至30年)。随着美国的新冠肺炎病例持续增加,对公共卫生机构和决策者来说,预测即将爆发的疫情规模是及时的。在这里,我们使用简单的数学模型来提供关于美国正在发生的大规模Mp爆发的可靠预测。我们的模型进一步表明,npi和免疫力下降是导致流行病长期延迟复发的重要因素。
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引用次数: 0
Quantifying the impact of prevalence-dependent adaptive behavior on COVID-19 transmission: A modeling case study in Maryland 量化流行依赖性适应行为对 COVID-19 传播的影响:马里兰州的模型案例研究
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-12-01 Epub Date: 2024-10-11 DOI: 10.1016/j.epidem.2024.100799
Alexander Tulchinsky , Gary Lin , Alisa Hamilton , Nodar Kipshidze , Eili Klein
The COVID-19 pandemic highlighted the need for robust epidemic forecasts, projecting health burden over short- and medium-term time horizons. Many COVID-19 forecasting models incorporate information on infection transmission, disease progression, and the effects of interventions, but few combine information on how individuals change their behavior based on altruism, fear, risk perception, or personal economic circumstances. Moreover, early models of COVID-19 produced under- and over-estimates, failing to consider the complexity of human responses to disease threat and prevention measures. In this study, we modeled adaptive behavior during the first year of the COVID-19 pandemic in Maryland, USA. The adapted compartmental model incorporates time-varying transmissibility informed on data of environmental factors (e.g., absolute humidity) and behavioral factors (aggregate mobility and perceived risk). We show that humidity and mobility alone did little to explain transmissibility after the first 100 days. Including adaptive behavior in the form of perceived risk as a function of hospitalizations more effectively explained inferred transmissibility and improved out-of-sample fit, demonstrating the model’s potential in real-time forecasting. These results demonstrate the importance of incorporating endogenous behavior in models, particularly during a pandemic, to produce more accurate projections, which could lead to more impactful and efficient decision making and resource allocation.
COVID-19 大流行突显了对强有力的流行病预测的需求,预测中短期的健康负担。许多 COVID-19 预测模型都包含了有关感染传播、疾病进展和干预效果的信息,但很少有模型结合了有关个人如何因利他主义、恐惧、风险意识或个人经济状况而改变其行为的信息。此外,早期的 COVID-19 模型产生了过低或过高的估计值,没有考虑到人类对疾病威胁和预防措施反应的复杂性。在本研究中,我们对美国马里兰州 COVID-19 大流行第一年的适应行为进行了建模。经过改编的分区模型结合了环境因素(如绝对湿度)和行为因素(总流动性和感知风险)的时变传播性数据。我们的研究表明,在最初的 100 天之后,仅凭湿度和流动性几乎无法解释传播性。将作为住院函数的感知风险形式的适应性行为纳入其中,可以更有效地解释推断的传播性,并提高样本外拟合度,证明了该模型在实时预测方面的潜力。这些结果表明了在模型中加入内生行为的重要性,尤其是在大流行期间,这样可以产生更准确的预测,从而做出更有影响力和更有效的决策并分配资源。
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引用次数: 0
Modelling plausible scenarios for the Omicron SARS-CoV-2 variant from early-stage surveillance 根据早期监测结果,为 Omicron SARS-CoV-2 变体建立模型。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-12-01 Epub Date: 2024-11-04 DOI: 10.1016/j.epidem.2024.100800
Christopher J. Banks , Ewan Colman , Anthony J. Wood , Thomas Doherty , Rowland R. Kao
We used a spatially explicit agent-based model of SARS-CoV-2 transmission combined with spatially fine-grained COVID-19 observation data from Public Health Scotland to investigate the initial rise of the Omicron (BA.1) variant of concern. We evaluated plausible scenarios for transmission rate advantage and vaccine immune escape relative to the Delta variant based on the data that would have been available at that time. We also explored possible outcomes of different levels of imposed non-pharmaceutical intervention. The initial results of these scenarios were used to inform the Scottish Government in the early outbreak stages of the Omicron variant.
Using the model with parameters fit over the Delta variant epidemic, some initial assumptions about Omicron transmission rate advantage and vaccine escape, and a simple growth rate fitting procedure, we were able to capture the initial outbreak dynamics for Omicron. We found that the modelled dynamics hold up to retrospective scrutiny. The modelled imposition of extra non-pharmaceutical interventions planned by the Scottish Government at the time would likely have little effect in light of the transmission rate advantage held by the Omicron variant and the fact that the planned interventions would have occurred too late in the outbreak’s trajectory. Finally, we found that any assumptions made about the projected distribution of vaccines in the model population had little bearing on the outcome, in terms of outbreak size and timing. Instead, it was the landscape of prior immunity that was most important.
我们使用了基于空间明确代理的 SARS-CoV-2 传播模型,并结合苏格兰公共卫生部门提供的空间精细 COVID-19 观察数据,研究了令人担忧的 Omicron (BA.1) 变种的最初兴起。我们根据当时可获得的数据,评估了相对于德尔塔变异体的传播率优势和疫苗免疫逃逸的可能情况。我们还探讨了不同程度的强制非药物干预可能产生的结果。在奥米克隆变种疫情爆发的早期阶段,苏格兰政府参考了这些方案的初步结果。利用模型参数拟合三角洲变种疫情、一些关于奥米克隆传播率优势和疫苗逃逸的初始假设以及一个简单的增长率拟合程序,我们能够捕捉到奥米克隆的初始疫情动态。我们发现,模拟的疫情动态经得起回顾性检验。鉴于奥米克隆变体所具有的传播率优势,以及计划中的干预措施在疫情发展过程中出现得太晚,苏格兰政府当时计划采取的额外非药物干预措施可能效果甚微。最后,我们发现,就疫情规模和爆发时间而言,对模型人群中疫苗的预期分布所做的任何假设对结果的影响都很小。相反,最重要的是先前的免疫状况。
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引用次数: 0
Optimizing spatial distribution of wastewater-based epidemiology to advance health equity 优化基于废水的流行病学空间分布,促进健康公平。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-12-01 Epub Date: 2024-11-10 DOI: 10.1016/j.epidem.2024.100804
Maria L. Daza-Torres , J. Cricelio Montesinos-López , César Herrera , Yury E. García , Colleen C. Naughton , Heather N. Bischel , Miriam Nuño
In 2022, the US Centers for Disease Control and Prevention commissioned the National Academies of Sciences, Engineering, and Medicine to assess the role of community-level wastewater-based epidemiology (WBE) beyond COVID-19. WBE is recognized as a promising mechanism for promptly identifying infectious diseases, including COVID-19 and other novel pathogens. An important conclusion from this initiative is the critical importance of maintaining equity and expanding access to fully realize the benefits of wastewater surveillance for marginalized communities. To address this need, we propose an optimization framework that strategically allocates wastewater monitoring resources at the wastewater treatment plant (WWTP) level, ensuring more effective and equitable distribution of surveillance efforts to serve underserved populations.
The purpose of the framework is to obtain a balanced spatial distribution, inclusive population coverage, and efficient representation of disadvantaged groups in the allocation of resources for WBE. Furthermore, the framework concentrates on areas with high population density and gives priority to vulnerable regions, as well as identifying signals that display significant variations from other monitored sources. The optimization objective is to maximize a weighted combination of these critical factors. This problem is formulated as an integer optimization problem and solved using simulated annealing. We evaluate various scenarios, considering different weighting factors, to optimize the allocation of WWTPs with monitoring systems. This optimization framework provides an opportunity to enhance WBE by providing customized monitoring strategies created to address specific priorities and situations, thus enhancing the decision-making processes in public health responses.
2022 年,美国疾病控制和预防中心委托美国国家科学、工程和医学院评估社区级废水流行病学 (WBE) 在 COVID-19 之后的作用。WBE 被认为是及时发现传染病(包括 COVID-19 和其他新型病原体)的一种有前途的机制。这项计划得出的一个重要结论是,要充分实现废水监测为边缘化社区带来的益处,保持公平和扩大普及至关重要。为了满足这一需求,我们提出了一个优化框架,在污水处理厂 (WWTP) 层面战略性地分配污水监测资源,确保更有效、更公平地分配监测工作,为得不到充分服务的人群提供服务。该框架的目的是在分配 WBE 资源时实现均衡的空间分布、全面的人口覆盖和弱势群体的有效代表。此外,该框架集中于人口密度高的地区,优先考虑易受影响的地区,并识别与其他监测来源有显著差异的信号。优化目标是最大化这些关键因素的加权组合。这个问题被表述为一个整数优化问题,并使用模拟退火法加以解决。考虑到不同的加权因素,我们对各种方案进行了评估,以优化配备监控系统的污水处理厂的分配。这一优化框架提供了一个机会,通过提供针对特定优先事项和情况的定制监测策略来提高水环境经济效益,从而加强公共卫生应对措施的决策过程。
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引用次数: 0
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Epidemics
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