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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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引用次数: 0
Directly observed social contact patterns among school children in rural Gambia 直接观察冈比亚农村学童的社会接触模式
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-09-11 DOI: 10.1016/j.epidem.2024.100790
Isaac Osei , Emmanuel Mendy , Kevin van Zandvoort , Olimatou Jobe , Golam Sarwar , Baleng Mahama Wutor , Stefan Flasche , Nuredin I. Mohammed , Jane Bruce , Brian Greenwood , Grant A. Mackenzie

Introduction

School-aged children play a major role in the transmission of many respiratory pathogens due to high rate of close contacts in schools. The validity and accuracy of proxy-reported contact data may be limited, particularly for children when attending school. We observed social contacts within schools and assessed the accuracy of proxy-reported versus observed physical contact data among students in rural Gambia.

Methods

We enrolled school children who had also been recruited to a survey of Streptococcus pneumoniae carriage and social contacts. We visited participants at school and observed their contact patterns within and outside the classroom for two hours. We recorded the contact type, gender and approximate age of the contactee, and class size. We calculated age-stratified contact matrices to determine in-school contact patterns. We compared proxy-reported estimated physical contacts for the subset of participants (18 %) randomised to be observed on the same day for which the parent or caregiver reported the school contacts.

Results

We recorded 3822 contacts for 219 participants from 114 schools. The median number of contacts was 15 (IQR: 11–20). Contact patterns were strongly age-assortative, and mainly involved physical touch (67.5 %). Those aged 5–9 years had the highest mean number of contacts [19.0 (95 %CI: 16.7–21.3)] while the ≥ 15-year age group had fewer contacts [12.8 (95 %CI: 10.9–14.7)]. Forty (18 %) participants had their school-observed contact data collected on the same day as their caregiver reported their estimated physical contacts at school; only 22.5 % had agreement within ±2 contacts between the observed and reported contacts. Fifty-eight percent of proxy-reported contacts were under-estimates.

Conclusions

Social contact rates observed among pupils at schools in rural Gambia were high, strongly age-assortative, and physical. Reporting of school contacts by proxies may underestimate the effect of school-age children in modelling studies of transmission of infections. New approaches are needed to quantify contacts within schools.

导言:由于学校中密切接触者较多,学龄儿童在许多呼吸道病原体的传播中扮演着重要角色。代理报告的接触数据的有效性和准确性可能有限,尤其是对上学的儿童而言。我们观察了学校内的社会接触情况,并评估了冈比亚农村地区学生的代理报告数据与观察到的身体接触数据的准确性。我们到学校探访了参与者,并在两个小时内观察了他们在教室内外的接触模式。我们记录了接触类型、接触者的性别和大致年龄以及班级人数。我们计算了年龄分层接触矩阵,以确定校内接触模式。我们比较了家长或看护人在报告校内接触的同一天随机接受观察的参与者(18%)的委托人报告的估计身体接触情况。接触次数的中位数为 15 次(IQR:11-20)。接触模式与年龄密切相关,主要涉及身体接触(67.5%)。5-9 岁年龄组的平均接触次数最多[19.0(95 %CI:16.7-21.3)],而≥15 岁年龄组的接触次数较少[12.8(95 %CI:10.9-14.7)]。有 40 名参与者(18%)的学校观察接触数据是在其看护人报告其估计的在校身体接触次数的同一天收集的;只有 22.5% 的参与者的观察接触次数与报告接触次数的一致性在 ±2 次以内。结论在冈比亚农村地区的学校中观察到的学生社会接触率很高,具有很强的年龄排序性和身体接触性。在对传染病传播进行模拟研究时,代理报告的学校接触率可能会低估学龄儿童的影响。需要新的方法来量化校内接触。
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引用次数: 0
The impact of household size on measles transmission: A long-term perspective 家庭规模对麻疹传播的影响:长期视角
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-09-06 DOI: 10.1016/j.epidem.2024.100791
Subekshya Bidari , Wan Yang

Households play an important role in the transmission of infectious diseases due to the close contact therein. Previous modeling studies on disease transmission with household-level mixing have explored the relationship between household size distribution and epidemic characteristics such as final epidemic sizes and the basic reproduction number but have not considered the epidemic impact of declining household sizes caused by demographic shifts. Here, we use a disease transmission model that incorporates demographic changes in household sizes to study the long-term transmission dynamics of measles in communities with varying household size distributions. We explore the impact of incorporating both household- and age-structured mixing on the dynamic properties of the transmission model and compare these dynamics across different household size distributions. Our analysis, based on the household- and age-structured model, shows that communities with larger household sizes require higher vaccination thresholds and bear a greater burden of infections. However, simulations show the apparent impact of changing household sizes is the combined result of changing birth rates and household mixing, and that changing birth rates likely play a larger role than changes in household mixing in shaping measles transmission dynamics (n.b, life-long immunity makes replenishment of population susceptibility from births a crucial transmission driver for measles). In addition, simulations of endemic transmission of measles within a hypothetical population formulated using aggregated world demographic data suggest the decline in household size (driven by changing fertility rates of the population), in addition to increasing vaccination coverage, could have had a significant impact on the incidence of measles over time.

由于住户之间的密切接触,住户在传染病的传播中发挥着重要作用。以往关于家庭层面混合的疾病传播模型研究探讨了家庭规模分布与最终流行病规模和基本繁殖数量等流行病特征之间的关系,但没有考虑人口结构变化导致家庭规模下降对流行病的影响。在此,我们使用一个包含家庭规模人口变化的疾病传播模型来研究麻疹在不同家庭规模分布社区的长期传播动态。我们探讨了家庭和年龄结构混合对传播模型动态特性的影响,并比较了不同家庭规模分布的动态特性。我们基于家庭和年龄结构模型的分析表明,家庭规模较大的社区需要更高的疫苗接种门槛,并承受更大的感染负担。然而,模拟结果表明,家庭规模变化的明显影响是出生率和家庭混合变化的综合结果,而且出生率的变化可能比家庭混合变化在影响麻疹传播动态方面发挥更大的作用(注:终身免疫使出生人口易感性的补充成为麻疹传播的关键驱动因素)。此外,利用世界人口总数数据模拟麻疹在假定人口中的地方性传播,结果表明,除了疫苗接种覆盖率的提高外,家庭规模的缩小(由人口生育率的变化驱动)也会对麻疹的发病率产生重大影响。
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引用次数: 0
Preface: COVID-19 Scenario Modeling Hubs 前言:COVID-19 情景建模中心。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-09-01 DOI: 10.1016/j.epidem.2024.100788
Sara L. Loo, Matteo Chinazzi, Ajitesh Srivastava, Srinivasan Venkatramanan, Shaun Truelove, Cecile Viboud
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引用次数: 0
Investigation of P. vivax elimination via mass drug administration: A simulation study 通过大规模给药消除间日疟原虫的研究:模拟研究
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-09-01 DOI: 10.1016/j.epidem.2024.100789
Md Nurul Anwar , James M. McCaw , Alexander E. Zarebski , Roslyn I. Hickson , Jennifer A. Flegg

Plasmodium vivax is the most geographically widespread malaria parasite. P. vivax has the ability to remain dormant (as a hypnozoite) in the human liver and subsequently reactivate, which makes control efforts more difficult. Given the majority of P. vivax infections are due to hypnozoite reactivation, targeting the hypnozoite reservoir with a radical cure is crucial for achieving P. vivax elimination. Stochastic effects can strongly influence dynamics when disease prevalence is low or when the population size is small. Hence, it is important to account for this when modelling malaria elimination. We use a stochastic multiscale model of P. vivax transmission to study the impacts of multiple rounds of mass drug administration (MDA) with a radical cure, accounting for superinfection and hypnozoite dynamics. Our results indicate multiple rounds of MDA with a high-efficacy drug are needed to achieve a substantial probability of elimination. This work has the potential to help guide P. vivax elimination strategies by quantifying elimination probabilities for an MDA approach.

间日疟原虫是地域分布最广的疟疾寄生虫。间日疟原虫能够在人的肝脏中保持休眠(作为下生虫),随后重新活化,这就增加了控制工作的难度。鉴于大多数间日疟原虫感染都是由次原虫再活化引起的,因此针对次原虫库的根治方法对于消灭间日疟原虫至关重要。当疾病流行率较低或种群规模较小时,随机效应会对动力学产生很大影响。因此,在建立消除疟疾模型时必须考虑到这一点。我们利用间日疟传播的随机多尺度模型,研究了多轮大规模用药(MDA)和根治的影响,并考虑了超级感染和低佐虫动态。我们的研究结果表明,需要使用高效药物进行多轮大规模给药,才能达到很高的根除概率。这项研究通过量化 MDA 方法的消除概率,有可能帮助指导消灭间日疟原虫的战略。
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引用次数: 0
The utility of whole-genome sequencing to identify likely transmission pairs for pathogens with slow and variable evolution 全基因组测序在确定进化缓慢且多变的病原体的可能传播配对方面的作用
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-08-23 DOI: 10.1016/j.epidem.2024.100787
A.J. Wood , C.H. Benton , R.J. Delahay , G. Marion , E. Palkopoulou , C.M. Pooley , G.C. Smith , R.R. Kao

Pathogen whole-genome sequencing (WGS) has been used to track the transmission of infectious diseases in extraordinary detail, especially for pathogens that undergo fast and steady evolution, as is the case with many RNA viruses. However, for other pathogens evolution is less predictable, making interpretation of these data to inform our understanding of their epidemiology more challenging and the value of densely collected pathogen genome data uncertain. Here, we assess the utility of WGS for one such pathogen, in the “who-infected-whom” identification problem. We study samples from hosts (130 cattle, 111 badgers) with confirmed infection of M. bovis (causing bovine Tuberculosis), which has an estimated clock rate as slow as 0.1–1 variations per year. For each potential pathway between hosts, we calculate the relative likelihood that such a transmission event occurred. This is informed by an epidemiological model of transmission, and host life history data. By including WGS data, we shrink the number of plausible pathways significantly, relative to those deemed likely on the basis of life history data alone. Despite our uncertainty relating to the evolution of M. bovis, the WGS data are therefore a valuable adjunct to epidemiological investigations, especially for wildlife species whose life history data are sparse.

病原体全基因组测序(WGS)已被用于非常详细地追踪传染病的传播情况,特别是对于像许多 RNA 病毒那样经历快速而稳定进化的病原体。然而,对于其他病原体来说,进化的可预测性较低,这就使得解释这些数据以帮助我们了解其流行病学更具挑战性,而且密集收集的病原体基因组数据的价值也不确定。在此,我们评估了 WGS 在 "谁感染了谁 "的鉴定问题中对此类病原体的实用性。我们研究了宿主(130 头牛、111 只獾)的样本,这些宿主确诊感染了牛结核杆菌(导致牛结核病),据估计其时钟频率慢至每年 0.1-1 次变化。对于宿主之间的每种潜在途径,我们都会计算发生这种传播事件的相对可能性。这一计算参考了流行病学传播模型和宿主生活史数据。通过纳入 WGS 数据,我们大大减少了可能传播途径的数量,而不是仅根据生活史数据来计算。尽管我们对牛海绵状芽孢杆菌的进化存在不确定性,但 WGS 数据仍是流行病学调查的重要辅助工具,特别是对于生活史数据稀少的野生动物物种。
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引用次数: 0
Improving the contribution of mathematical modelling evidence to guidelines and policy: Experiences from tuberculosis 提高数学建模证据对指导方针和政策的贡献:结核病方面的经验。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-08-06 DOI: 10.1016/j.epidem.2024.100786
C. Finn McQuaid , Nicolas A. Menzies , Rein M.G.J. Houben , Gabriella B. Gomez , Anna Vassall , Nimalan Arinaminpathy , Peter J. Dodd , Richard G. White

We read with great interest the recent paper by Lo et al., who argue that there is an urgent need to ensure the quality of modelling evidence used to support international and national guideline development. Here we outline efforts by the Tuberculosis Modelling and Analysis Consortium, together with the World Health Organization Global Task Force on Tuberculosis Impact Measurement, to develop material to improve the quality and transparency of country-level tuberculosis modelling to inform decision-making.

我们饶有兴趣地阅读了 Lo 等人最近发表的论文,他们认为迫切需要确保用于支持国际和国家指导方针制定的建模证据的质量。在此,我们简要介绍了结核病建模与分析联合会与世界卫生组织结核病影响测量全球工作组一起,为提高国家级结核病建模的质量和透明度,为决策提供信息而开发材料所做的努力。
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引用次数: 0
Dynamics of Neisseria gonorrhoeae transmission among female sex workers and clients: A mathematical modeling study 淋病奈瑟菌在女性性工作者和嫖客中的传播动态:数学模型研究。
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-08-05 DOI: 10.1016/j.epidem.2024.100785
Houssein H. Ayoub , Milan Tomy , Hiam Chemaitelly , Ryosuke Omori , Kent Buse , Nicola Low , Sarah Hawkes , Laith J. Abu-Raddad

Background

This study aimed to examine the transmission dynamics of Neisseria gonorrhoeae (NG) in heterosexual sex work networks (HSWNs) and the impact of variation in sexual behavior and interventions on NG epidemiology.

Methods

The study employed an individual-based mathematical model to simulate NG transmission dynamics in sexual networks involving female sex workers (FSWs) and their clients, primarily focusing on the Middle East and North Africa region. A deterministic model was also used to describe NG transmission from clients to their spouses.

Results

NG epidemiology in HSWNs displays two distinct patterns. In the common low-partner-number HSWNs, a significant proportion of NG incidence occurs among FSWs, with NG prevalence 13 times higher among FSWs than clients, and three times higher among clients than their spouses. Interventions substantially reduce incidence. Increasing condom use from 10 % to 50 % lowers NG prevalence among FSWs, clients, and their spouses from 12.2 % to 6.4 %, 1.2 % to 0.5 %, and 0.4 % to 0.2 %, respectively. Increasing symptomatic treatment coverage among FSWs from 0 % to 100 % decreases prevalence from 10.6 % to 4.5 %, 0.8 % to 0.4 %, and 0.3 % to 0.1 %, respectively. Increasing asymptomatic treatment coverage among FSWs from 0 % to 50 % decreases prevalence from 8.2 % to 0.4 %, 0.6 % to 0.1 %, and 0.2 % to 0.0 %, respectively, with very low prevalence when coverage exceeds 50 %. In high-partner-number HSWNs, prevalence among FSWs saturates at a high level, and the vast majority of incidence occurs among clients and their spouses, with a limited impact of incremental increases in interventions.

Conclusion

NG epidemiology in HSWNs is typically a "fragile epidemiology" that is responsive to a range of interventions even if the interventions are incremental, partially efficacious, and only applied to FSWs.

背景:本研究旨在探讨淋病奈瑟菌(NG)在异性性工作网络(HSWNs)中的传播动态,以及性行为和干预措施的变化对 NG 流行病学的影响:研究采用了基于个体的数学模型来模拟女性性工作者(FSWs)及其客户参与的性工作网络中的 NG 传播动态,主要侧重于中东和北非地区。此外,还使用了一个确定性模型来描述嫖客向其配偶传播 NG 的情况:性工作者中的 NG 流行病学显示出两种截然不同的模式。在常见的伴侣人数较少的 HSWNs 中,有很大一部分 NG 发生在 FSWs 中,FSWs 的 NG 感染率是客户的 13 倍,客户的 NG 感染率是其配偶的 3 倍。干预措施可大幅降低发病率。将安全套的使用率从 10% 提高到 50%,可将女性社会工作者、客户及其配偶的 NG 感染率分别从 12.2% 降至 6.4%、1.2% 降至 0.5%、0.4% 降至 0.2%。如果将女性外阴残割者的无症状治疗覆盖率从 0% 提高到 100%,感染率将分别从 10.6% 降至 4.5%、0.8% 降至 0.4%、0.3% 降至 0.1%。如果将对女性外阴残割者的无症状治疗覆盖率从 0% 提高到 50%,感染率将分别从 8.2% 降至 0.4%、0.6% 降至 0.1%、0.2% 降至 0.0%,当覆盖率超过 50%时,感染率将非常低。在性伴侣人数较多的 HSWN 中,FSW 的流行率在较高水平上达到饱和,绝大多数发病率发生在客户及其配偶中,干预措施的逐步增加影响有限:在 HSWNs 中,NG 流行病学是典型的 "脆弱流行病学",对一系列干预措施有反应,即使这些干预措施是渐进的、部分有效的,并且只适用于 FSWs。
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引用次数: 0
Inference of epidemic dynamics in the COVID-19 era and beyond COVID-19 时代及以后的流行病动态推断
IF 3 3区 医学 Q2 INFECTIOUS DISEASES Pub Date : 2024-07-31 DOI: 10.1016/j.epidem.2024.100784
Anne Cori , Adam Kucharski

The COVID-19 pandemic demonstrated the key role that epidemiology and modelling play in analysing infectious threats and supporting decision making in real-time. Motivated by the unprecedented volume and breadth of data generated during the pandemic, we review modern opportunities for analysis to address questions that emerge during a major modern epidemic. Following the broad chronology of insights required — from understanding initial dynamics to retrospective evaluation of interventions, we describe the theoretical foundations of each approach and the underlying intuition. Through a series of case studies, we illustrate real life applications, and discuss implications for future work.

COVID-19 大流行表明,流行病学和建模在分析传染病威胁和支持实时决策方面发挥着关键作用。大流行期间产生的数据量之大、范围之广前所未有,在此激励下,我们回顾了现代分析的机遇,以解决现代大流行期间出现的问题。从了解最初的动态到对干预措施的回顾性评估,我们按照所需的洞察力的时间顺序,描述了每种方法的理论基础和基本直觉。通过一系列案例研究,我们阐述了现实生活中的应用,并讨论了对未来工作的影响。
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引用次数: 0
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