Quantitative Biology

The novel coronavirus disease (COVID-19) is a public health problem once according to the World Health Organization up to June 10th, 2020, more than 7.1 million people were infected, and more than 400 thousand have died worldwide. In the current scenario, the Brazil and the United States of America present a high daily incidence of new cases and deaths. It is important to forecast the number of new cases in a time window of one week, once this can help the public health system developing strategic planning to deals with the COVID-19. In this paper, Bayesian regression neural network, cubist regression, k-nearest neighbors, quantile random forest, and support vector regression, are used stand-alone, and coupled with the recent pre-processing variational mode decomposition (VMD) employed to decompose the time series into several intrinsic mode functions. All Artificial Intelligence techniques are evaluated in the task of time-series forecasting with one, three, and six-days-ahead the cumulative COVID-19 cases in five Brazilian and American states up to April 28th, 2020. Previous cumulative COVID-19 cases and exogenous variables as daily temperature and precipitation were employed as inputs for all forecasting models. The hybridization of VMD outperformed single forecasting models regarding the accuracy, specifically when the horizon is six-days-ahead, achieving better accuracy in 70% of the cases. Regarding the exogenous variables, the importance ranking as predictor variables is past cases, temperature, and precipitation. Due to the efficiency of evaluated models to forecasting cumulative COVID-19 cases up to six-days-ahead, the adopted models can be recommended as a promising models for forecasting and be used to assist in the development of public policies to mitigate the effects of COVID-19 outbreak.

This paper has a twofold contribution. The first is a data driven approach for predicting the Covid 19 pandemic dynamics, based on data from more advanced countries. The second is to report and discuss the results obtained with this approach for Brazilian states, as of May 4th, 2020. We start by presenting preliminary results obtained by training an LSTM SAE network, which are somewhat disappointing. Then, our main approach consists in an initial clustering of the world regions for which data is available and where the pandemic is at an advanced stage, based on a set of manually engineered features representing a country response to the early spread of the pandemic. A Modified Auto-Encoder network is then trained from these clusters and learns to predict future data for Brazilian states. These predictions are used to estimate important statistics about the disease, such as peaks. Finally, curve fitting is carried out on the predictions in order to find the distribution that best fits the outputs of the MAE, and to refine the estimates of the peaks of the pandemic. Results indicate that the pandemic is still growing in Brazil, with most states peaks of infection estimated between the 25th of April and the 19th of May 2020. Predicted numbers reach a total of 240 thousand infected Brazilians, distributed among the different states, with São Paulo leading with almost 65 thousands estimated, confirmed cases. The estimated end of the pandemics (with 97 percent of cases reaching an outcome) starts as of May 28th for some states and rests through August 14th, 2020.

We present a compartmental SEIRD model aimed at forecasting hospital occupancy in metropolitan areas during the current COVID-19 outbreak. The model features asymptomatic and symptomatic infections with detailed hospital dynamics. We model explicitly branching probabilities and non exponential residence times in each latent and infected compartments. Using both hospital admittance confirmed cases and deaths we infer the contact rate and the initial conditions of the dynamical system, considering break points to model lockdown interventions. Our Bayesian approach allows us to produce timely probabilistic forecasts of hospital demand. The model has been used by the federal government of Mexico to assist public policy, and has been applied for the analysis of more than 70 metropolitan areas and the 32 states in the country.

The ongoing novel coronavirus epidemic has been announced a pandemic by the World Health Organization on March 11, 2020, and the Govt. of India has declared a nationwide lockdown from March 25, 2020, to prevent community transmission of COVID-19. Due to absence of specific antivirals or vaccine, mathematical modeling play an important role to better understand the disease dynamics and designing strategies to control rapidly spreading infectious diseases. In our study, we developed a new compartmental model that explains the transmission dynamics of COVID-19. We calibrated our proposed model with daily COVID-19 data for the four Indian provinces, namely Jharkhand, Gujarat, Andhra Pradesh, and Chandigarh. We study the qualitative properties of the model including feasible equilibria and their stability with respect to the basic reproduction number R 0 . The disease-free equilibrium becomes stable and the endemic equilibrium becomes unstable when the recovery rate of infected individuals increased but if the disease transmission rate remains higher then the endemic equilibrium always remain stable. For the estimated model parameters, R 0 >1 for all the four provinces, which suggests the significant outbreak of COVID-19. Short-time prediction shows the increasing trend of daily and cumulative cases of COVID-19 for the four provinces of India.

The infections and fatalities due to SARS-CoV-2 virus for cases specific to India have been studied using a deterministic susceptible-exposed-infected-recovered-dead (SEIRD) compartmental model. One of the most significant epidemiological parameter, namely the effective reproduction number of the infection is extracted from the daily growth rate data of reported infections and it is included in the model with a time variation. We evaluate the effect of control interventions implemented till now and estimate the case numbers for infections and deaths averted by these restrictive measures. We further provide a forecast on the extent of the future Covid-19 transmission in India and predict the probable numbers of infections and fatalities under various potential scenarios.

A fractional compartmental mathematical model for the spread of the COVID-19 disease is proposed. Special focus has been done on the transmissibility of super-spreaders individuals. Numerical simulations are shown for data of Galicia, Spain, and Portugal. For each region, the order of the Caputo derivative takes a different value, that is not close to one, showing the relevance of considering fractional models.

The novel coronavirus disease (COVID-19) is known as the causative virus of outbreak pneumonia initially recognized in the mainland of China, late December 2019. COVID-19 reaches out to many countries in the world, and the number of daily cases continues to increase rapidly. In order to simulate, track, and forecast the trend of the virus spread, several mathematical and statistical models have been developed. Susceptible-Exposed-Infected-Quarantined-Recovered-Death-Insusceptible (SEIQRDP) model is one of the most promising dynamic systems that has been proposed for estimating the transmissibility of the COVID-19. In the present study, we propose a Fractional-order SEIQRDP model to analyze the COVID-19 epidemic. The Fractional-order paradigm offers a flexible, appropriate, and reliable framework for pandemic growth characterization. In fact, fractional-order operator is not local and consider the memory of the variables. Hence, it takes into account the sub-diffusion process of confirmed and recovered cases growth. The results of the validation of the model using real COVID-19 data are presented, and the pertinence of the proposed model to analyze, understand, and predict the epidemic is discussed.

We present a unifying, tractable approach for studying the spread of viruses causing complex diseases that require to be modeled using a large number of types (e.g., infective stage, clinical state, risk factor class). We show that recording each infected individual's infection age, i.e., the time elapsed since infection, 1. The age distribution n(t,a) of the population at time t can be described by means of a first-order, one-dimensional partial differential equation (PDE) known as the McKendrick-von Foerster equation. 2. The frequency of type i at time t is simply obtained by integrating the probability p(a,i) of being in state i at age a against the age distribution n(t,a) . The advantage of this approach is three-fold. First, regardless of the number of types, macroscopic observables (e.g., incidence or prevalence of each type) only rely on a one-dimensional PDE "decorated" with types. This representation induces a simple methodology based on the McKendrick-von Foerster PDE with Poisson sampling to infer and forecast the epidemic. We illustrate this technique using a French data from the COVID-19 epidemic. Second, our approach generalizes and simplifies standard compartmental models using high-dimensional systems of ordinary differential equations (ODEs) to account for disease complexity. We show that such models can always be rewritten in our framework, thus, providing a low-dimensional yet equivalent representation of these complex models. Third, beyond the simplicity of the approach, we show that our population model naturally appears as a universal scaling limit of a large class of fully stochastic individual-based epidemic models, here the initial condition of the PDE emerges as the limiting age structure of an exponentially growing population starting from a single individual.

On June 24th, Governor Cooper announced that North Carolina will not be moving into Phase 3 of its reopening process at least until July 17th. Given the recent increases in daily positive cases and hospitalizations, this decision was not surprising. However, given the political and economic pressures which are forcing the state to reopen, it is not clear what actions will help North Carolina to avoid the worst. We use a compartmentalized model to study the effects of social distancing measures and testing capacity combined with contact tracing on the evolution of the pandemic in North Carolina until the end of the year. We find that going back to restrictions that were in place during Phase 1 will slow down the spread but if the state wants to continue to reopen or at least remain in Phase 2 or Phase 3 it needs to significantly expand its testing and contact tracing capacity. Even under our best-case scenario of high contact tracing effectiveness, the number of contact tracers the state currently employs is inadequate.

We introduce a parsimonious game-theoretic behavioral--epidemic model, in which an interplay of realistic factors shapes the co-evolution of individual decision-making and epidemics on a network. Although such a co-evolution is deeply intertwined in the real-world, existing models schematize population behavior as instantaneously reactive, thus being unable to capture human behavior in the long term. Our model offers a unified framework to model and predict complex emergent phenomena, including successful collective responses, periodic oscillations, and resurgent epidemic outbreaks, as illustrated through two real-world case studies.