Informing pandemic response in the face of uncertainty. An evaluation of the U.S. COVID-19 Scenario Modeling Hub (preprint)

Our ability to forecast epidemics more than a few weeks into the future is constrained by the complexity of disease systems, our limited ability to measure the current state of an epidemic, and uncertainties in how human action will affect transmission. Realistic longer-term projections (spanning more than a few weeks) may, however, be possible under defined scenarios that specify the future state of critical epidemic drivers, with the additional benefit that such scenarios can be used to anticipate the comparative effect of control measures. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make 6-month ahead projections of the number of SARS-CoV-2 cases, hospitalizations and deaths. The SMH released nearly 1.8 million national and state-level projections between February 2021 and November 2022. SMH performance varied widely as a function of both scenario validity and model calibration. Scenario assumptions were periodically invalidated by the arrival of unanticipated SARS-CoV-2 variants, but SMH still provided projections on average 22 weeks before changes in assumptions (such as virus transmissibility) invalidated scenarios and their corresponding projections. During these periods, before emergence of a novel variant, a linear opinion pool ensemble of contributed models was consistently more reliable than any single model, and projection interval coverage was near target levels for the most plausible scenarios (e.g., 79% coverage for 95% projection interval). SMH projections were used operationally to guide planning and policy at different stages of the pandemic, illustrating the value of the hub approach for long-term scenario projections.

Inter-rater reliability of the Infectious Disease Modeling Reproducibility Checklist (IDMRC) as applied to COVID-19 computational modeling research (preprint)

Background: Infectious disease computational modeling studies have been widely published during the coronavirus disease 2019 (COVID-19) pandemic, yet they have limited reproducibility. Developed through an iterative testing process with multiple reviewers, the Infectious Disease Modeling Reproducibility Checklist (IDMRC) enumerates the minimal elements necessary to support reproducible infectious disease computational modeling publications. The primary objective of this study was to assess the reliability of the IDMRC and to identify which reproducibility elements were unreported in a sample of COVID-19 computational modeling publications. Methods: Four reviewers used the IDMRC to assess 46 preprint and peer reviewed COVID-19 modeling studies published between March 13th, 2020, and July 31st, 2020. The inter-rater reliability was evaluated by mean percent agreement and Fleiss' kappa coefficients. Papers were ranked based on the average number of reported reproducibility elements, and average proportion of papers that reported each checklist item were tabulated. Results: Questions related to the computational environment (mean = 0.90, range = 0.90-0.90), analytical software (mean = 0.74, range = 0.68-0.82), model description (mean = 0.71, range = 0.58-0.84), model implementation (mean = 0.68, range = 0.39-0.86), and experimental protocol (mean = 0.63, range = 0.58-0.69) had moderate or greater (kappa > 0.41) inter-rater reliability. Questions related to data had the lowest values (mean = 0.37, range = 0.23-0.59). Reviewers ranked similar papers in the upper and lower quartiles based on the proportion of reproducibility elements each paper reported. While over 70% of the publications provided data used in their models, less than 30% provided the model implementation. Conclusions: The IDMRC is the first comprehensive, quality-assessed tool for guiding researchers in reporting reproducible infectious disease computational modeling studies. The inter-rater reliability assessment found that most scores were characterized by moderate or greater agreement. These results suggests that the IDMRC might be used to provide reliable assessments of the potential for reproducibility of published infectious disease modeling publications. Results of this evaluation identified opportunities for improvement to the model implementation and data questions that can further improve the reliability of the checklist.

COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support (preprint)

Policymakers make decisions about COVID-19 management in the face of considerable uncertainty. We convened multiple modeling teams to evaluate reopening strategies for a mid-sized county in the United States, in a novel process designed to fully express scientific uncertainty while reducing linguistic uncertainty and cognitive biases. For the scenarios considered, the consensus from 17 distinct models was that a second outbreak will occur within 6 months of reopening, unless schools and non-essential workplaces remain closed. Up to half the population could be infected with full workplace reopening; non-essential business closures reduced median cumulative infections by 82%. Intermediate reopening interventions identified no win-win situations; there was a trade-off between public health outcomes and duration of workplace closures. Aggregate results captured twice the uncertainty of individual models, providing a more complete expression of risk for decision-making purposes.