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Forecasting SARS-CoV-2 epidemic dynamic in Poland with the pDyn agent-based model 利用基于 pDyn 的代理模型预测波兰的 SARS-CoV-2 流行动态。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-11-12 DOI: 10.1016/j.epidem.2024.100801
Karol Niedzielewski , Rafał P. Bartczuk , Natalia Bielczyk , Dominik Bogucki , Filip Dreger , Grzegorz Dudziuk , Łukasz Górski , Magdalena Gruziel-Słomka , Jędrzej Haman , Artur Kaczorek , Jan Kisielewski , Bartosz Krupa , Antoni Moszyński , Jędrzej M. Nowosielski , Maciej Radwan , Marcin Semeniuk , Urszula Tymoszuk , Jakub Zieliński , Franciszek Rakowski
We employ pDyn (derived from “pandemics dynamics”), an agent-based epidemiological model, to forecast the fourth wave of the SARS-CoV-2 epidemic, primarily driven by the Delta variant, in Polish society. The model captures spatiotemporal dynamics of the epidemic spread, predicting disease-related states based on pathogen properties and behavioral factors. We assess pDyn’s validity, encompassing pathogen variant succession, immunization level, and the proportion of vaccinated among confirmed cases. We evaluate its predictive capacity for pandemic dynamics, including wave peak timing, magnitude, and duration for confirmed cases, hospitalizations, ICU admissions, and deaths, nationally and regionally in Poland. Validation involves comparing pDyn’s estimates with real-world data (excluding data used for calibration) to evaluate whether pDyn accurately reproduced the epidemic dynamics up to the simulation time. To assess the accuracy of pDyn’s predictions, we compared simulation results with real-world data acquired after the simulation date. The findings affirm pDyn’s accuracy in forecasting and enhancing our understanding of epidemic mechanisms.
我们采用基于代理的流行病学模型 pDyn(源于 "大流行病动力学")来预测 SARS-CoV-2 在波兰社会的第四波流行(主要由 Delta 变种驱动)。该模型捕捉了疫情传播的时空动态,根据病原体特性和行为因素预测疾病相关状态。我们评估了 pDyn 的有效性,包括病原体变异的继承、免疫水平以及确诊病例中接种疫苗的比例。我们评估了 pDyn 对大流行动态的预测能力,包括波峰时间、波峰规模以及确诊病例、住院人数、重症监护室入院人数和死亡人数在波兰全国和各地区的持续时间。验证包括将 pDyn 的估计值与真实世界的数据(不包括用于校准的数据)进行比较,以评估 pDyn 是否准确再现了模拟时间内的疫情动态。为了评估 pDyn 预测的准确性,我们将模拟结果与模拟日期之后获得的真实世界数据进行了比较。研究结果肯定了 pDyn 预测的准确性,并加深了我们对流行病机制的理解。
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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 : 2024-11-10 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
Building in-house capabilities in health agencies and outsourcing to academia or industry: Considerations for effective infectious disease modelling. 卫生机构内部能力建设和外包给学术界或产业界:建立有效传染病模型的考虑因素。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-11-09 DOI: 10.1016/j.epidem.2024.100802
Rachael Pung, Adam J Kucharski

Infectious disease models provide a systematic way to estimate crucial features of epidemic dynamics and explore different transmission and control scenarios. Given the importance of model-based analysis in managing public health crises, there has been an increase in post-pandemic creation of both academia-driven modelling centres, hubs and consortiums and government-driven public health agencies with in-house modelling units or teams. However, in the past, the delineation of roles and responsibilities between government- and academia-led modelling groups has often been unclear. Who should perform which tasks and when? This ambiguity can increase the risk of duplicated work or unaddressed gaps in analysis. It also raises questions about the sustainability of modelling capacity for addressing routine operational analytical needs while also developing new approaches that can be tailored for emergencies. In the sections below, we discuss factors that could inform decisions about where to locate infectious disease modelling activity. Rather than giving a fixed set of rules, we outlined key considerations and trade-offs that could be taken into account to enable academic and government modelling activities to complement each other effectively, which can in turn be refined as new public health crises emerge in future.

传染病模型为估算流行病动态的关键特征以及探索不同的传播和控制方案提供了一种系统的方法。鉴于基于模型的分析在管理公共卫生危机中的重要性,疫情过后,学术界驱动的建模中心、中心和联盟,以及政府驱动的公共卫生机构内部建模单位或团队都在增加。然而,在过去,政府和学术界主导的建模小组之间的角色和责任划分往往并不明确。谁应该在何时执行哪些任务?这种不明确性可能会增加重复工作的风险,或在分析中出现无法解决的漏洞。它还会引发建模能力的可持续性问题,既要满足日常业务分析需求,又要开发适合紧急情况的新方法。在下面的章节中,我们将讨论一些因素,这些因素可以为我们决定在哪里开展传染病建模活动提供参考。我们并没有给出一套固定的规则,而是概述了可以考虑的关键因素和权衡,以使学术界和政府的建模活动能够有效互补,并随着未来新的公共卫生危机的出现而不断完善。
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引用次数: 0
Direct and indirect effects of hepatitis B vaccination in four low- and middle-income countries 四个中低收入国家乙肝疫苗接种的直接和间接影响。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-11-06 DOI: 10.1016/j.epidem.2024.100798
Margaret J. de Villiers , Edward de Villiers , Shevanthi Nayagam , Timothy B. Hallett
Population-level vaccination effects of the hepatitis B vaccine were investigated in four low- and middle-income countries with different levels of vertical and horizontal transmission. Indirect vaccination effects constitute a large proportion of overall vaccination effects of the vaccination programmes in all four countries (over 70% by 2030 in all four countries). However, countries with higher levels of vertical transmission benefit less from indirect vaccination effects from the infant hepatitis B vaccine series during the first decades of the vaccination programme, making the birth dose vaccine more important in these countries. Vaccination, even at levels that do not fully control transmission, has a great effect on the development of disease as it also increases the average age of infection, thereby causing a decrease in the number of chronic infections relative to the number of acute infections.
在纵向和横向传播程度不同的四个中低收入国家调查了乙肝疫苗在人口层面的接种效果。间接接种效果在所有四个国家的疫苗接种计划的总体接种效果中占很大比例(到 2030 年,所有四个国家的间接接种效果均超过 70%)。然而,纵向传播水平较高的国家在疫苗接种计划的前几十年从婴儿乙肝疫苗系列的间接接种效果中获益较少,因此出生剂量疫苗在这些国家更为重要。接种疫苗,即使不能完全控制传播,也会对疾病的发展产生巨大影响,因为它还会提高平均感染年龄,从而使慢性感染人数相对于急性感染人数有所减少。
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引用次数: 0
Estimating pathogen spread using structured coalescent and birth–death models: A quantitative comparison 使用结构化聚合模型和出生-死亡模型估计病原体传播:定量比较。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-10-18 DOI: 10.1016/j.epidem.2024.100795
Sophie Seidel, Tanja Stadler , Timothy G. Vaughan
Elucidating disease spread between subpopulations is crucial in guiding effective disease control efforts. Genomic epidemiology and phylodynamics have emerged as key principles to estimate such spread from pathogen phylogenies derived from molecular data. Two well-established structured phylodynamic methodologies – based on the coalescent and the birth–death model – are frequently employed to estimate viral spread between populations. Nonetheless, these methodologies operate under distinct assumptions whose impact on the accuracy of migration rate inference is yet to be thoroughly investigated.
In this manuscript, we present a simulation study, contrasting the inferential outcomes of the structured coalescent model with constant population size and the multitype birth–death model with a constant rate. We explore this comparison across a range of migration rates in endemic diseases and epidemic outbreaks. The results of the epidemic outbreak analysis revealed that the birth–death model exhibits a superior ability to retrieve accurate migration rates compared to the coalescent model, regardless of the actual migration rate. Thus, to estimate accurate migration rates, the population dynamics have to be accounted for. On the other hand, for the endemic disease scenario, our investigation demonstrates that both models produce comparable coverage and accuracy of the migration rates, with the coalescent model generating more precise estimates. Regardless of the specific scenario, both models similarly estimated the source location of the disease.
This research offers tangible modelling advice for infectious disease analysts, suggesting the use of either model for endemic diseases. For epidemic outbreaks, or scenarios with varying population size, structured phylodynamic models relying on the Kingman coalescent with constant population size should be avoided as they can lead to inaccurate estimates of the migration rate. Instead, coalescent models accounting for varying population size or birth–death models should be favoured. Importantly, our study emphasises the value of directly capturing exponential growth dynamics which could be a useful enhancement for structured coalescent models.
阐明疾病在亚群之间的传播对于指导有效的疾病控制工作至关重要。基因组流行病学和系统动力学已成为从分子数据得出的病原体系统发育中估算这种传播的关键原则。基于聚合模型和出生-死亡模型的两种成熟的结构系统动力学方法经常被用来估算病毒在种群间的传播。然而,这些方法在不同的假设条件下运行,其对迁移率推断准确性的影响还有待深入研究。在本手稿中,我们进行了一项模拟研究,对比了具有恒定种群规模的结构化聚合模型和具有恒定迁移率的多型出生-死亡模型的推论结果。我们探讨了在地方病和流行病爆发的一系列迁移率下的这种比较。流行病爆发分析的结果表明,与凝聚模型相比,无论实际迁移率如何,出生-死亡模型在检索准确迁移率方面都表现出更强的能力。因此,要估算准确的迁移率,就必须考虑到人口动态。另一方面,对于地方病情景,我们的调查表明,两种模型的覆盖范围和迁移率的准确性相当,而凝聚模型的估计结果更为精确。无论具体情景如何,两种模型对疾病来源地点的估算结果相似。这项研究为传染病分析人员提供了切实可行的建模建议,建议对地方病使用两种模型中的任何一种。对于流行病爆发或人口规模变化的情况,应避免使用依赖于人口规模恒定的金曼聚合的结构化系统动力学模型,因为它们可能导致对迁移率的不准确估计。取而代之的是考虑不同种群规模的凝聚模型或出生-死亡模型。重要的是,我们的研究强调了直接捕捉指数增长动态的价值,这对结构化凝聚模型是一个有用的增强。
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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 : 2024-10-11 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
Impact of COVID-19 control measures on respiratory syncytial virus and hand-foot-and-mouth disease transmission in Hong Kong and South Korea COVID-19 控制措施对香港和韩国呼吸道合胞病毒和手足口病传播的影响。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-10-10 DOI: 10.1016/j.epidem.2024.100797
Yiu Chung Lau , Sukhyun Ryu , Zhanwei Du , Lin Wang , Peng Wu , Eric H.Y. Lau , Benjamin J. Cowling , Sheikh Taslim Ali
The public health and social measures (PHSMs) for mitigation/control of COVID-19 pandemic influenced the transmission dynamics of many other infectious diseases, including respiratory syncytial virus (RSV) infection, and hand, foot and mouth disease (HFMD) and their disease-burden. This study aimed to infer the transmission dynamics of these respiratory viruses and assess the impact of COVID-19 PHSMs on their community activity. We developed a compartmental framework to infer the transmission dynamics of RSV and HFMD in Hong Kong and South Korea from January 2014 to May 2024. We assessed the impact of PHSMs by comparing the change in virus transmissibility, reproduction number and population susceptibility before, during, and after the COVID-19 pandemic period. A significant reduction in RSV and HFMD activity was observed starting in January 2020, with a resurgence since late 2021. Transmissibility of both diseases decreased by 46 % - 95 % during the lull, while population susceptibility was estimated to increase by maximum of 19 %. On relaxation of the PHSMs, the transmissibility were recovered up to 70 % in Hong Kong and nearly 100 % in South Korea in 2023 with significant epidemics for these viruses. Strict implementation of COVID-19 PHSMs led to low RSV and HFMD activity, but the absence of community infection resulted in reductions in population immunity, and slightly larger epidemics when these diseases re-emerged following the COVID-19 pandemic.
为缓解/控制 COVID-19 大流行而采取的公共卫生和社会措施(PHSMs)影响了许多其他传染病的传播动态,包括呼吸道合胞病毒(RSV)感染和手足口病(HFMD)及其疾病负担。本研究旨在推断这些呼吸道病毒的传播动态,并评估 COVID-19 PHSMs 对其社区活动的影响。我们建立了一个分区框架,以推断 2014 年 1 月至 2024 年 5 月期间 RSV 和手足口病在香港和韩国的传播动态。我们通过比较 COVID-19 大流行之前、期间和之后病毒传播能力、繁殖数量和人群易感性的变化,评估了 PHSMs 的影响。从 2020 年 1 月开始,RSV 和手足口病的活动明显减少,2021 年下半年开始重新抬头。在低潮期,这两种疾病的传播率下降了 46% - 95%,而人群易感性估计最多增加了 19%。放宽PHSM后,2023年香港和韩国的传播率分别恢复到70%和近100%,这些病毒将出现显著流行。严格执行 COVID-19 PHSMs 可降低 RSV 和手足口病的活动性,但由于缺乏社区感染,导致人群免疫力下降,当这些疾病在 COVID-19 大流行后再次出现时,流行范围会稍大一些。
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引用次数: 0
The effects of HIV self-testing on HIV incidence and awareness of status among men who have sex with men in the United States: Insights from a novel compartmental model 艾滋病病毒自我检测对美国男男性行为者中艾滋病病毒感染率和对感染状况认识的影响:新颖分区模型的启示。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-10-05 DOI: 10.1016/j.epidem.2024.100796
Alex Viguerie , Chaitra Gopalappa , Cynthia M. Lyles , Paul G. Farnham

Background

The OraQuick In-Home HIV self-test represents a fast, inexpensive, and convenient method for users to assess their HIV status. If integrated thoughtfully into existing testing practices, accompanied by efficient pathways to formal diagnosis, self-testing could enhance both HIV awareness and reduce HIV incidence. However, currently available self-tests are less sensitive, particularly for recent infection, when compared to gold-standard laboratory tests. It is important to understand the impact if some portion of standard testing is replaced by self-tests. We used a compartmental model to evaluate the effects of self-testing in diverse scenarios among gay, bisexual and other men who have sex with men (MSM) in the United States for the period 2020–2030, and to understand which scenarios maximize the advantages of self-testing.

Methods

We introduced a novel 4-compartment model for HIV self-testing. We employed the model under different screening rates, self-test proportions, and delays to diagnosis for those identified through self-tests to determine the potential effects of self-testing on HIV incidence and awareness of status when applied to the US MSM population. We studied scenarios in which self-tests supplement laboratory-based tests, with no replacement, and scenarios in which some replacement occurs. We also examined how future improvements in self-test sensitivity may affect our results.

Results

When HIV self-tests are supplemental rather than substitutes for laboratory-based testing, self-testing can decrease HIV incidence among MSM in the US by up to 10 % and increase awareness of status among MSM from 85 % to 91 % over a 10-year period, provided linkage to care and formal diagnosis occur promptly following a positive self-test (90 days or less). As self-tests replace a higher percentage laboratory-based testing algorithms, increases in overall testing rates were necessary to ensure reductions in HIV incidence. However, such needed increases were relatively small (under 10 % for prompt engagement in care and moderate levels of replacement). Improvements in self-test sensitivity and/or decreases in the detection period may further reduce any necessary increases in overall testing by up to 40 %.

Conclusions

If properly utilized, self-testing can provide significant long-term reductions to HIV incidence and improve awareness of HIV status. Ensuring that self-testing increases overall testing and that formal diagnosis and engagement in care occur promptly following a positive self-test are necessary to maximize the benefits of self-testing. Future improvements in self-test sensitivity and reductions in the detection period would further reduce HIV incidence and the potential risks associated with replacing laboratory tests with self-tests.
背景:OraQuick 居家 HIV 自我检测是一种快速、廉价、方便的方法,用户可以通过它来评估自己的 HIV 感染状况。如果能将其与现有的检测方法周到地结合起来,并辅以高效的正规诊断途径,那么自我检测既能提高人们对艾滋病的认识,又能降低艾滋病的发病率。然而,与黄金标准的实验室检测相比,目前可用的自我检测灵敏度较低,尤其是对近期感染的检测。了解由自我检测取代部分标准检测的影响非常重要。我们使用了一个分室模型来评估 2020-2030 年期间在美国男同性恋、双性恋和其他男男性行为者(MSM)中不同情况下自我检测的影响,并了解哪种情况能最大限度地发挥自我检测的优势:方法:我们为 HIV 自我检测引入了一个新颖的四室模型。我们在不同的筛查率、自我检测比例以及通过自我检测发现者的诊断延迟条件下使用了该模型,以确定自我检测在应用于美国男男性行为人群时对 HIV 感染率和感染状况认知度的潜在影响。我们研究了自我检测作为实验室检测的补充(不存在替代)和存在一定替代的两种情况。我们还研究了未来自我检测灵敏度的提高会如何影响我们的结果:结果:如果艾滋病毒自我检测是实验室检测的补充而非替代,那么自我检测可在 10 年内将美国男男性行为者中的艾滋病毒发病率降低 10%,并将男男性行为者对自身状况的认知度从 85% 提高到 91%,前提是在自我检测呈阳性后(90 天或更短)及时联系医疗机构并进行正式诊断。由于自我检测取代了较高比例的实验室检测算法,因此有必要提高总体检测率,以确保降低艾滋病毒发病率。然而,这种所需的提高幅度相对较小(对于及时参与护理和中等程度的替代来说,低于 10%)。自我检测灵敏度的提高和/或检测期的缩短可能会进一步减少总体检测率的必要增长,增幅可达 40%:如果使用得当,自我检测可显著降低艾滋病的长期发病率,并提高人们对艾滋病状况的认识。要使自我检测的益处最大化,就必须确保自我检测能提高总体检测率,并在自我检测呈阳性后及时进行正式诊断和参与护理。未来自我检测灵敏度的提高和检测周期的缩短将进一步降低艾滋病毒的发病率,并降低用自我检测取代实验室检测的潜在风险。
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引用次数: 0
Wastewater-based epidemiology for COVID-19 surveillance and beyond: A survey 基于废水的流行病学,用于 COVID-19 监测及其他:调查。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-09-26 DOI: 10.1016/j.epidem.2024.100793
Chen Chen , Yunfan Wang , Gursharn Kaur , Aniruddha Adiga , Baltazar Espinoza , Srinivasan Venkatramanan , Andrew Warren , Bryan Lewis , Justin Crow , Rekha Singh , Alexandra Lorentz , Denise Toney , Madhav Marathe
The pandemic of COVID-19 has imposed tremendous pressure on public health systems and social economic ecosystems over the past years. To alleviate its social impact, it is important to proactively track the prevalence of COVID-19 within communities. The traditional way to estimate the disease prevalence is to estimate from reported clinical test data or surveys. However, the coverage of clinical tests is often limited and the tests can be labor-intensive, requires reliable and timely results, and consistent diagnostic and reporting criteria. Recent studies revealed that patients who are diagnosed with COVID-19 often undergo fecal shedding of SARS-CoV-2 virus into wastewater, which makes wastewater-based epidemiology for COVID-19 surveillance a promising approach to complement traditional clinical testing. In this paper, we survey the existing literature regarding wastewater-based epidemiology for COVID-19 surveillance and summarize the current advances in the area. Specifically, we have covered the key aspects of wastewater sampling, sample testing, and presented a comprehensive and organized summary of wastewater data analytical methods. Finally, we provide the open challenges on current wastewater-based COVID-19 surveillance studies, aiming to encourage new ideas to advance the development of effective wastewater-based surveillance systems for general infectious diseases.
在过去几年中,COVID-19 的流行给公共卫生系统和社会经济生态系统带来了巨大压力。为减轻其社会影响,必须积极跟踪 COVID-19 在社区内的流行情况。估算疾病流行率的传统方法是根据报告的临床检测数据或调查进行估算。然而,临床检测的覆盖范围往往有限,而且检测可能需要大量人力,需要可靠、及时的结果,以及一致的诊断和报告标准。最近的研究表明,确诊为 COVID-19 的患者通常会将 SARS-CoV-2 病毒随粪便排入废水中,这使得基于废水的 COVID-19 监测流行病学成为补充传统临床检测的一种可行方法。在本文中,我们调查了有关基于废水的 COVID-19 监测流行病学的现有文献,并总结了该领域的最新进展。具体而言,我们介绍了废水采样、样本检测的关键环节,并对废水数据分析方法进行了全面、有序的总结。最后,我们提出了当前基于废水的 COVID-19 监测研究面临的公开挑战,旨在鼓励新思路,推动基于废水的一般传染病有效监测系统的发展。
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引用次数: 0
Outbreak reconstruction with a slowly evolving multi-host pathogen: A comparative study of three existing methods on Mycobacterium bovis outbreaks 缓慢进化的多宿主病原体的疫情重建:对三种现有牛分枝杆菌疫情爆发方法的比较研究
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-09-21 DOI: 10.1016/j.epidem.2024.100794
Hélène Duault , Benoit Durand , Laetitia Canini
In a multi-host system, understanding host-species contribution to transmission is key to appropriately targeting control and preventive measures. Outbreak reconstruction methods aiming to identify who-infected-whom by combining epidemiological and genetic data could contribute to achieving this goal. However, the majority of these methods remain untested on realistic simulated multi-host data. Mycobacterium bovis is a slowly evolving multi-host pathogen and previous studies on outbreaks involving both cattle and wildlife have identified observation biases. Indeed, contrary to cattle, sampling wildlife is difficult. The aim of our study was to evaluate and compare the performances of three existing outbreak reconstruction methods (seqTrack, outbreaker2 and TransPhylo) on M. bovis multi-host data simulated with and without biases. Extending an existing transmission model, we simulated 30 bTB outbreaks involving cattle, badgers and wild boars and defined six sampling schemes mimicking observation biases. We estimated general and specific to multi-host systems epidemiological indicators. We tested four alternative transmission scenarios changing the mutation rate or the composition of the epidemiological system. The reconstruction of who-infected-whom was sensitive to the mutation rate and seqTrack reconstructed prolific super-spreaders. TransPhylo and outbreaker2 poorly estimated the contribution of each host-species and could not reconstruct the presence of a dead-end epidemiological host. However, the host-species of cattle (but not badger) index cases was correctly reconstructed by seqTrack and outbreaker2. These two specific indicators improved when considering an observation bias. We found an overall poor performance for the three methods on simulated biased and unbiased bTB data. This seemed partly attributable to the low evolutionary rate characteristic of M. bovis leading to insufficient genetic information, but also to the complexity of the simulated multi-host system. This study highlights the importance of an integrated approach and the need to develop new outbreak reconstruction methods adapted to complex epidemiological systems and tested on realistic multi-host data.
在多宿主系统中,了解宿主物种对传播的贡献是适当确定控制和预防措施目标的关键。疫情重建方法旨在通过结合流行病学和基因数据来确定谁感染了谁,有助于实现这一目标。然而,这些方法中的大多数仍未在现实的多宿主模拟数据中得到验证。牛分枝杆菌是一种进化缓慢的多宿主病原体,以往对牛和野生动物疫情的研究发现了观察偏差。事实上,与牛相反,对野生动物进行采样非常困难。我们研究的目的是评估和比较现有的三种疫情重建方法(seqTrack、outbreaker2 和 TransPhylo)在模拟有偏差和无偏差的牛口蹄疫多宿主数据上的性能。我们扩展了现有的传播模型,模拟了 30 次涉及牛、獾和野猪的牛结核病爆发,并定义了六种模拟观察偏差的采样方案。我们估算了多宿主系统的一般和特定流行病学指标。我们测试了改变变异率或流行病学系统组成的四种替代传播方案。谁感染谁的重建对突变率很敏感,seqTrack 重建了多产的超级传播者。TransPhylo 和 outbreaker2 对每种宿主的贡献估计不足,无法重建流行病学中存在的死亡宿主。然而,seqTrack 和 outbreaker2 能正确地重建牛(而不是獾)指数病例的宿主物种。在考虑观察偏差时,这两个特定指标都有所改善。我们发现这三种方法在模拟有偏差和无偏差的 bTB 数据上的总体表现不佳。这似乎部分归因于牛海绵状芽孢杆菌的低进化率特征导致遗传信息不足,但也归因于模拟多宿主系统的复杂性。这项研究强调了综合方法的重要性,以及开发适应复杂流行病学系统的新疫情重建方法并在现实的多宿主数据上进行测试的必要性。
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