Forecasting COVID-19 Chile' second outbreak by a generalized SIR model with constant time delays and a fitted positivity rate

An improved method of global dynamics: Analyzing the COVID-19 model with time delays and exposed infection

Considering the transmission characteristics of the coronavirus disease 2019 (COVID-19), there are certain time delays in the transition from susceptible individuals to exposed individuals after contact with exposed, symptomatically infected, and asymptomatically infected individuals. A COVID-19 model with time delays and exposed infection is developed and then the global dynamics of this model is investigated by an improved method; moreover, the numerical simulations are carried out. It is shown that the COVID-19-free equilibrium T0 is globally asymptotically stable (GAS) if and only if the control reproduction number Rc≤1, while T0 is unstable and the COVID-19 equilibrium T∗ is GAS if and only if Rc>1. The numerical results reveal that strengthening quarantine measures is helpful to control the COVID-19 epidemic in India. Furthermore, when Rc<1, the numbers of symptomatically infected, asymptomatically infected, and quarantined individuals eventually tend to the zero equilibrium state, and with the increase in the time delay, the three kinds of variables change faster and their peaks become larger; when Rc>1, the three kinds of variables eventually tend to the positive equilibrium state, which are oscillatory and the amplitudes of the oscillation enlarge as the value of time delay increases. The numerical results show that when Rc<1, the smaller the value of time delay, the smaller the final epidemic size. In short, the longer it takes time for susceptible individuals to transform exposed individuals, the harder COVID-19 will be controlled.

A general modeling framework for quantitative tracking, accurate prediction of ICU, and assessing vaccination for COVID-19 in Chile

Background

One of the main lessons of the COVID-19 pandemic is that we must prepare to face another pandemic like it. Consequently, this article aims to develop a general framework consisting of epidemiological modeling and a practical identifiability approach to assess combined vaccination and non-pharmaceutical intervention (NPI) strategies for the dynamics of any transmissible disease.

Materials and methods

Epidemiological modeling of the present work relies on delay differential equations describing time variation and transitions between suitable compartments. The practical identifiability approach relies on parameter optimization, a parametric bootstrap technique, and data processing. We implemented a careful parameter optimization algorithm by searching for suitable initialization according to each processed dataset. In addition, we implemented a parametric bootstrap technique to accurately predict the ICU curve trend in the medium term and assess vaccination.

Results

We show the framework's calibration capabilities for several processed COVID-19 datasets of different regions of Chile. We found a unique range of parameters that works well for every dataset and provides overall numerical stability and convergence for parameter optimization. Consequently, the framework produces outstanding results concerning quantitative tracking of COVID-19 dynamics. In addition, it allows us to accurately predict the ICU curve trend in the medium term and assess vaccination. Finally, it is reproducible since we provide open-source codes that consider parameter initialization standardized for every dataset.

Conclusion

This work attempts to implement a holistic and general modeling framework for quantitative tracking of the dynamics of any transmissible disease, focusing on accurately predicting the ICU curve trend in the medium term and assessing vaccination. The scientific community could adapt it to evaluate the impact of combined vaccination and NPIs strategies for COVID-19 or any transmissible disease in any country and help visualize the potential effects of implemented plans by policymakers. In future work, we want to improve the computational cost of the parametric bootstrap technique or use another more efficient technique. The aim would be to reconstruct epidemiological curves to predict the combined NPIs and vaccination policies' impact on the ICU curve trend in real-time, providing scientific evidence to help anticipate policymakers' decisions.

An innovative ensemble model based on multiple neural networks and a novel heuristic optimization algorithm for COVID-19 forecasting

During the global fight against the novel coronavirus pneumonia (COVID-19) epidemic, accurate outbreak trend forecasting has become vital for outbreak prevention and control. Effective COVID-19 outbreak trend prediction remains a complex and challenging issue owing to the significant fluctuations in the COVID-19 data series. Most previous studies have limitations only using individual forecasting methods for outbreak modeling, ignoring the combination of the advantages of different prediction methods, which may lead to insufficient results. Therefore, this paper develops a novel ensemble paradigm based on multiple neural networks and a novel heuristic optimization algorithm. First, a new hybrid sine cosine algorithm-whale optimization algorithm (SCWOA) is exercised on 15 benchmark tests. Second, four neural networks are used as predictors for the COVID-19 outbreak forecasting. Each predictor is given a weight, and the proposed SCWOA is used to optimize the best matching weights of the ensemble model. The daily COVID-19 series collected from three of the most-affected countries were taken as the test cases. The experimental results demonstrate that different neural network models have different performances in various complex epidemic prediction scenarios. The SCWOA-based ensemble model can outperform all comparable models with its high accuracy and robustness.

Global stability and analysing the sensitivity of parameters of a multiple-susceptible population model of SARS-CoV-2 emphasising vaccination drive

The study explores the dynamics of a COVID-19 epidemic in multiple susceptible populations, including the various stages of vaccination administration. In the model, there are eight human compartments: completely susceptible; susceptible with dose-1 vaccination; susceptible with dose-2 vaccination; susceptible with booster dose vaccination; exposed; infected with and without symptoms, and recovered compartments. The biological feasibility of the model is analysed. The threshold value,R 0 , is derived using the next-generation matrix. The stability analysis of the equilibrium points was performed locally and globally using the threshold parameter of the model. The conditions determining disease persistence is obtained. The model is subjected to sensitivity analysis, and the most sensitive parameters are identified. Also, MATLAB is used to verify the mathematical outcomes of the system's dynamic behaviour and suggests that necessary steps should be taken to keep the spread of the omicron variant infectious disease under control. The findings of this study could aid health officials in their efforts to combat the spread of COVID-19.

Modelling quarantine effects on SARS-CoV-2 epidemiological dynamics in Chilean communes and their relationship with the Social Priority Index

Background

An epidemiological model (susceptible, un-quarantined infected, quarantined infected, confirmed infected (SUQC)) was previously developed and applied to incorporate quarantine measures and calculate COVID-19 contagion dynamics and pandemic control in some Chinese regions. Here, we generalized this model to incorporate the disease recovery rate and applied our model to records of the total number of confirmed cases of people infected with the SARS-CoV-2 virus in some Chilean communes.

Methods

In each commune, two consecutive stages were considered: a stage without quarantine and an immediately subsequent quarantine stage imposed by the Ministry of Health. To adjust the model, typical epidemiological parameters were determined, such as the confirmation rate and the quarantine rate. The latter allowed us to calculate the reproduction number.

Results

The mathematical model adequately reproduced the data, indicating a higher quarantine rate when quarantine was imposed by the health authority, with a corresponding decrease in the reproduction number of the virus down to values that prevent or decrease its exponential spread. In general, during this second stage, the communes with the lowest social priority indices had the highest quarantine rates, and therefore, the lowest effective viral reproduction numbers. This study provides useful evidence to address the health inequity of pandemics. The mathematical model applied here can be used in other regions or easily modified for other cases of infectious disease control by quarantine.

Stochastic SIR model predicts the evolution of COVID-19 epidemics from public health and wastewater data in small and medium-sized municipalities: A one year study

The level of unpredictability of the COVID-19 pandemics poses a challenge to effectively model its dynamic evolution. In this study we incorporate the inherent stochasticity of the SARS-CoV-2 virus spread by reinterpreting the classical compartmental models of infectious diseases (SIR type) as chemical reaction systems modeled via the Chemical Master Equation and solved by Monte Carlo Methods. Our model predicts the evolution of the pandemics at the level of municipalities, incorporating for the first time (i) a variable infection rate to capture the effect of mitigation policies on the dynamic evolution of the pandemics (ii) SIR-with-jumps taking into account the possibility of multiple infections from a single infected person and (iii) data of viral load quantified by RT-qPCR from samples taken from Wastewater Treatment Plants. The model has been successfully employed for the prediction of the COVID-19 pandemics evolution in small and medium size municipalities of Galicia (Northwest of Spain).