To increase situational awareness and support evidence-based policymaking, we formulated a mathematical model for coronavirus disease transmission within a regional population. This compartmental model accounts for quarantine, self-isolation, social distancing, a nonexponentially distributed incubation period, asymptomatic persons, and mild and severe forms of symptomatic disease. We used Bayesian inference to calibrate region-specific models for consistency with daily reports of confirmed cases in the 15 most populous metropolitan statistical areas in the United States. We also quantified uncertainty in parameter estimates and forecasts. This online learning approach enables early identification of new trends despite considerable variability in case reporting.

An important question, of whether the initiation of HIV treatment during ongoing TB treatment for HIV-TB co-infected individuals is appropriate, still remains unanswered; initiating HIV treatment at or soon after the start of the TB treatment course has some advantages including fewer HIV-related deaths and a lower risk of HIV transmission as well as some disadvantages including occurrence of Immune Reconstitution Inflammatory Syndrome (IRIS) due to a high pill burden. In this study, we develop a mathematical model to explore the effects of early and late HIV treatment, during the TB treatment course, on new HIV infections, HIV-related deaths, and IRIS cases. Mathematical analyses of our model indicate that co-infection treatment programs alone cannot eradicate the diseases; additional interventions and/or treatments targeting individuals infected with a single disease are necessary for successful disease eradication. Numerical computations of the model solution demonstrate that outcomes of the treatment programs aiming to reduce the total burden of this co-infection depend highly on both the strength and initiation timing of antiretroviral therapy (ART). Based on our model, we also formulate an optimal control problem and solve it using Pontryagin's Maximum Principle and an efficient numerical iterative method. Our numerical results of an optimal HIV-TB treatment protocol that yields a minimum burden from this co-infection indicates that each of the new HIV infections, HIV-related deaths and IRIS cases is important for achieving optimal benefits from the co-infection treatment programs.

Although many persons in the United States have acquired immunity to COVID-19, either through vaccination or infection with SARS-CoV-2, COVID-19 will pose an ongoing threat to non-immune persons so long as disease transmission continues. We can estimate when sustained disease transmission will end in a population by calculating the population-specific basic reproduction number , the expected number of secondary cases generated by an infected person in the absence of any interventions. The value of relates to a herd immunity threshold (HIT), which is given by . When the immune fraction of a population exceeds this threshold, sustained disease transmission becomes exponentially unlikely (barring mutations allowing SARS-CoV-2 to escape immunity). Here, we report state-level estimates obtained using Bayesian inference. Maximum a posteriori estimates range from 7.1 for New Jersey to 2.3 for Wyoming, indicating that disease transmission varies considerably across states and that reaching herd immunity will be more difficult in some states than others. estimates were obtained from compartmental models via the next-generation matrix approach after each model was parameterized using regional daily confirmed case reports of COVID-19 from 21 January 2020 to 21 June 2020. Our estimates characterize the infectiousness of ancestral strains, but they can be used to determine HITs for a distinct, currently dominant circulating strain, such as SARS-CoV-2 variant Delta (lineage B.1.617.2), if the relative infectiousness of the strain can be ascertained. On the basis of Delta-adjusted HITs, vaccination data, and seroprevalence survey data, we found that no state had achieved herd immunity as of 20 September 2021.

To increase situational awareness and support evidence-based policy-making, we formulated two types of mathematical models for COVID-19 transmission within a regional population. One is a fitting function that can be calibrated to reproduce an epidemic curve with two timescales (e.g., fast growth and slow decay). The other is a compartmental model that accounts for quarantine, self-isolation, social distancing, a non-exponentially distributed incubation period, asymptomatic individuals, and mild and severe forms of symptomatic disease. Using Bayesian inference, we have been calibrating our models daily for consistency with new reports of confirmed cases from the 15 most populous metropolitan statistical areas in the United States and quantifying uncertainty in parameter estimates and predictions of future case reports. This online learning approach allows for early identification of new trends despite considerable variability in case reporting. We infer new significant upward trends for five of the metropolitan areas starting between 19-April-2020 and 12-June-2020.

Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g., numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages.

The initial contagiousness of a communicable disease within a given population is quantified by the basic reproduction number, denoted R_0. The value of R_0 gives the expected number of new cases generated by an infectious person in a wholly susceptible population and depends on both pathogen and population properties. On the basis of compartmental models that reproduce Coronavirus Disease 2019 (COVID-19) surveillance data, we estimated region-specific R_0 values for 280 of 384 metropolitan statistical areas (MSAs) in the United States (US), which account for 95% of the US population living in urban areas and 82% of the total population. Our estimates range from 1.9 to 7.7 and quantify the relative susceptibilities of regional populations to spread of respiratory diseases.

Does the implementation of social distancing measures have merit in controlling the spread of the novel coronavirus? In this study, we develop a mathematical model to explore the effects of social distancing on new disease infections. Mathematical analyses of our model indicate that successful eradication of the disease is strongly dependent on the chosen preventive measure. Numerical computations of the model solution demonstrate that the ability to flatten the curve becomes easier as social distancing is strictly enforced. Based on our model, we also formulate an optimal control problem and solve it using Pontryagin's Maximum Principle and an efficient numerical iterative method. Our numerical results of an optimal 2019-nCoV treatment protocol that yields a minimum disease burden from this disease indicates that social distancing is vitally important.