Collaborative Research: RAPID: RTEM: Rapid Testing as Multi-fidelity Data Collection for Epidemic Modeling

新型冠状病毒(新冠肺炎)疫情正在产生重大的社会、经济和健康影响，并突显了实时分析新出现传染病的时空动态的重要性。2019年12月从中国武汉脱颖而出的新冠肺炎，目前正在多个国家传播。尤其令人关注的是，新型冠状病毒的病死率似乎高于季节性流感，尤其是对老年人和那些有心血管疾病和糖尿病等既往健康状况的人来说。任何遏制疫情的计划都必须建立在对高危人群所占比例的定量了解的基础上，这些高危人群需要得到有效控制措施的保护，才能充分和迅速地减少传播，使疫情得以结束。可用于帮助校准传播模型和预测疾病传播/严重程度的不同数据收集和测试模式和策略具有不同的成本、响应时间和准确性。在这项快速反应研究(RAPID)项目中，该团队将研究为新型冠状病毒快速检测建立最佳实践的问题。其结果将是流行病建模的快速测试，它将转化为对新冠肺炎疫情特征的科学预测，包括持续时间和总体规模，并有助于全球抗击该疾病的努力。实时新兴市场将填补新冠肺炎疫情期间数据驱动决策方面的一个重要空白，从而使服务能够对国家经济和健康产生重大影响。该项目的教育影响将是通过将研究挑战和成果纳入现有的本科生和研究生班级，对博士后和博士后研究人员的指导以及对课程的影响。新出现的传染病时空动态的计算模型以及疾病传播的数据和模型驱动的计算机模拟在预测流行病的地理时间演变以及设计、激活和调整流行病控制实践方面越来越重要。在这个项目中，研究人员解决了流行病建模的快速测试(RTEM)问题：给定一个部分已知的目标疾病模型和一组测试模式(从已知疾病热点的调查到监测测试)，具有不同的成本、精度和观测延迟，什么是帮助恢复潜在疾病模型的最佳快速测试策略？出现了几个科学问题：测试的价值是什么？是否应该只对病人进行病毒检测？应该投入什么水平的资源来开发高准确度的测试(低假阳性、低假阴性)？是只使用一种旨在实现最佳成本/效率权衡的测试类型更好，还是使用非同类测试策略更好？当然，这些问题需要在流行病学、计算机科学、机器学习、数学建模和统计学的界面上进行研究。作为工作的一部分，该团队将开发一个传输动力学和控制模型，该模型根据新冠肺炎的需要量身定做，以适应诊断测试的不同保真度和快速测试方案背后的延迟。研究人员将进一步将生成的RTEM-SEIR模型与EpiDMS和DataStorm集成，以执行连续的耦合模拟。该项目由传染病生态学和进化计划(环境生物学部门)和土木、机械和制造创新计划(工程)联合资助。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

The novel coronavirus (COVID-19) epidemic is generating significant social, economic, and health impacts and has highlighted the importance of real-time analysis of the spatio-temporal dynamics of emerging infectious diseases. COVID-19, which emerged out of the city of Wuhan in China in December 2019 is now spreading in multiple countries. It is particularly concerning that the case fatality rate appears to be higher for the novel coronavirus than for seasonal influenza, and especially so for older populations and those with prior health conditions such as cardiovascular disease and diabetes. Any plan for stopping the epidemic must be based on a quantitative understanding of the proportion of the at-risk population that needs to be protected by effective control measures in order for transmission to decline sufficiently and quickly enough for the epidemic to end. Different data collection and testing modalities and strategies available to help calibrate transmission models and predict the spread/severity of a disease, have variable costs, response times, and accuracies. In this Rapid Response Research (RAPID) project, the team will examine the problem of establishing optimal practices for rapid testing for the novel coronavirus. The result will be the Rapid Testing for Epidemic Modeling (RTEM), which will translate into science-based predictions of the COVID-19 epidemic's characteristics, including the duration and overall size, and help the global efforts to combat the disease. The RTEM will fill an important gap in data-driven decision making during the COVID-19 epidemic and, thus, will enable services with significant national economic and health impact. The educational impact of the project will be on mentoring of post-doctoral and PhD researchers and on curricula by incorporating research challenges and outcomes into existing undergraduate and graduate classes. Computational models for the spatio-temporal dynamics of emerging infectious diseases and data- and model-driven computer simulations for disease spreading are increasingly critical in predicting geo-temporal evolution of epidemics as well as designing, activating, and adapting practices for controlling epidemics. In this project, the researchers tackle a Rapid Testing for Epidemic Modeling (RTEM) problem: Given a partially known target disease model and a set of testing modalities (from surveys to surveillance testing at known disease hotspots), with varying costs, accuracies, and observational delays, what is the best rapid testing strategy that would help recover the underlying disease model? Several scientific questions arise: What is the value of testing? Should only sick people be tested for virus detection? What level of resources should be devoted to the development of highly accurate tests (low false positives, low false negatives)? Is it better to use only one type of test aiming at the best cost/effectiveness trade off, or a non-homogeneous testing policy? Naturally these questions need to be investigated at the interface of epidemiology, computer science, machine learning, mathematical modeling and statistics. As part of the work, the team will develop a model of transmission dynamics and control, tailored to COVID-19 in a way that accommodates diagnostic testing with varying fidelities and delays underlying a rapid testing regimen. The investigators will further integrate the resulting RTEM-SEIR model with EpiDMS and DataStorm for executing continuous coupled simulations. This project is jointly funded through the Ecology and Evolution of Infectious Diseases program (Division of Environmental Biology) and the Civil, Mechanical and Manufacturing Innovation program (Engineering).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.