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1. Estimation of heterogeneous instantaneous reproduction numbers with application to characterize SARS-CoV-2 transmission in Massachusetts counties

   https://doi.org/10.1371/journal.pcbi.1010434  

   Zhou, Zhenwei; Kolaczyk, Eric D.; Thompson, Robin N.; White, Laura F. (September 2022, PLOS Computational Biology)

   Wu, Joseph T. (Ed.)

   The reproductive number is an important metric that has been widely used to quantify the infectiousness of communicable diseases. The time-varying instantaneous reproductive number is useful for monitoring the real-time dynamics of a disease to inform policy making for disease control. Local estimation of this metric, for instance at a county or city level, allows for more targeted interventions to curb transmission. However, simultaneous estimation of local reproductive numbers must account for potential sources of heterogeneity in these time-varying quantities—a key element of which is human mobility. We develop a statistical method that incorporates human mobility between multiple regions for estimating region-specific instantaneous reproductive numbers. The model also can account for exogenous cases imported from outside of the regions of interest. We propose two approaches to estimate the reproductive numbers, with mobility data used to adjust incidence in the first approach and to inform a formal priori distribution in the second (Bayesian) approach. Through a simulation study, we show that region-specific reproductive numbers can be well estimated if human mobility is reasonably well approximated by available data. We use this approach to estimate the instantaneous reproductive numbers of COVID-19 for 14 counties in Massachusetts using CDC case report data and the human mobility data collected by SafeGraph. We found that, accounting for mobility, our method produces estimates of reproductive numbers that are distinct across counties. In contrast, independent estimation of county-level reproductive numbers tends to produce similar values, as trends in county case-counts for the state are fairly concordant. These approaches can also be used to estimate any heterogeneity in transmission, for instance, age-dependent instantaneous reproductive number estimates. As people are more mobile and interact frequently in ways that permit transmission, it is important to account for this in the estimation of the reproductive number. 

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2. COVID-19: Short term prediction model using daily incidence data

   https://doi.org/10.1371/journal.pone.0250110  

   Zhao, Hongwei; Merchant, Naveed N.; McNulty, Alyssa; Radcliff, Tiffany A.; Cote, Murray J.; Fischer, Rebecca S.; Sang, Huiyan; Ory, Marcia G. (April 2021, PLOS ONE)

   Schieffelin, John (Ed.)

   Background Prediction of the dynamics of new SARS-CoV-2 infections during the current COVID-19 pandemic is critical for public health planning of efficient health care allocation and monitoring the effects of policy interventions. We describe a new approach that forecasts the number of incident cases in the near future given past occurrences using only a small number of assumptions. Methods Our approach to forecasting future COVID-19 cases involves 1) modeling the observed incidence cases using a Poisson distribution for the daily incidence number, and a gamma distribution for the series interval; 2) estimating the effective reproduction number assuming its value stays constant during a short time interval; and 3) drawing future incidence cases from their posterior distributions, assuming that the current transmission rate will stay the same, or change by a certain degree. Results We apply our method to predicting the number of new COVID-19 cases in a single state in the U.S. and for a subset of counties within the state to demonstrate the utility of this method at varying scales of prediction. Our method produces reasonably accurate results when the effective reproduction number is distributed similarly in the future as in the past. Large deviations from the predicted results can imply that a change in policy or some other factors have occurred that have dramatically altered the disease transmission over time. Conclusion We presented a modelling approach that we believe can be easily adopted by others, and immediately useful for local or state planning. 

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3. Adaptive Ensemble Q-learning: Minimizing Estimation Bias via Error Feedback

   Wang, Hang; Lin, Sen; Zhang, Junshan (December 2021, AAdvances in Neural Information Processing Systems 34 (NeurIPS 2021))

   The ensemble method is a promising way to mitigate the overestimation issue in Q-learning, where multiple function approximators are used to estimate the action values. It is known that the estimation bias hinges heavily on the ensemble size (i.e., the number of Q-function approximators used in the target), and that determining the 'right' ensemble size is highly nontrivial, because of the time-varying nature of the function approximation errors during the learning process. To tackle this challenge, we first derive an upper bound and a lower bound on the estimation bias, based on which the ensemble size is adapted to drive the bias to be nearly zero, thereby coping with the impact of the time-varying approximation errors accordingly. Motivated by the theoretic findings, we advocate that the ensemble method can be combined with Model Identification Adaptive Control (MIAC) for effective ensemble size adaptation. Specifically, we devise Adaptive Ensemble Q-learning (AdaEQ), a generalized ensemble method with two key steps: (a) approximation error characterization which serves as the feedback for flexibly controlling the ensemble size, and (b) ensemble size adaptation tailored towards minimizing the estimation bias. Extensive experiments are carried out to show that AdaEQ can improve the learning performance than the existing methods for the MuJoCo benchmark. 

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4. Estimating unobserved SARS-CoV-2 infections in the United States

   https://doi.org/10.1073/pnas.2005476117  

   Perkins, T. Alex; Cavany, Sean M.; Moore, Sean M.; Oidtman, Rachel J.; Lerch, Anita; Poterek, Marya (September 2020, Proceedings of the National Academy of Sciences)

   null (Ed.)

   By March 2020, COVID-19 led to thousands of deaths and disrupted economic activity worldwide. As a result of narrow case definitions and limited capacity for testing, the number of unobserved severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections during its initial invasion of the United States remains unknown. We developed an approach for estimating the number of unobserved infections based on data that are commonly available shortly after the emergence of a new infectious disease. The logic of our approach is, in essence, that there are bounds on the amount of exponential growth of new infections that can occur during the first few weeks after imported cases start appearing. Applying that logic to data on imported cases and local deaths in the United States through 12 March, we estimated that 108,689 (95% posterior predictive interval [95% PPI]: 1,023 to 14,182,310) infections occurred in the United States by this date. By comparing the model’s predictions of symptomatic infections with local cases reported over time, we obtained daily estimates of the proportion of symptomatic infections detected by surveillance. This revealed that detection of symptomatic infections decreased throughout February as exponential growth of infections outpaced increases in testing. Between 24 February and 12 March, we estimated an increase in detection of symptomatic infections, which was strongly correlated (median: 0.98; 95% PPI: 0.66 to 0.98) with increases in testing. These results suggest that testing was a major limiting factor in assessing the extent of SARS-CoV-2 transmission during its initial invasion of the United States. 

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5. EFFECTS OF VACCINATION ON THE TRANSMISSION DYNAMICS OF COVID-19 IN DOUGHERTY COUNTY OF GEORGIA, USA

   https://doi.org/10.1142/S021833902250019X  

   PANTHA, BUDDHI; MOHAMMED-AWEL, JEMAL; VAIDYA, NAVEEN K. (September 2022, Journal of Biological Systems)

   Despite the significant progress in the development of vaccines, the COVID-19 pandemic still poses difficulty for its control because of many obstacles such as the proper implementation of vaccination, public hesitancy towards vaccines, dropping out from the second dose, and varying level of protection after the first and the second doses. In this study, we develop a novel mathematical model of COVID-19 transmission, including two separate vaccinated compartments (first dose and both doses). We parametrize and validate our model using data from Dougherty county of Georgia, USA, one of the most affected counties, where the transmission trend clearly is associated with various policies and public events. We analyze our model for stability of equilibria and persistence of the disease, and formulate expression for reproduction numbers. We estimate that the basic reproduction number in Dougherty county is 1.69, and the effective reproduction number during the study period ranges from 0.26 to 6.36. The number of daily undiagnosed cases peaked at 310 per day, resulting in the maximum number of active infectious individuals to be 2471. Our model predicts that in a high transmission scenario, the vaccination strategies should be combined with other non-pharmaceutical prevention strategies to ensure transmission control. Moreover, our results emphasize that completing both doses of vaccines on time is critical to achieve maximum benefits from the vaccination programs. 

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