Analytical Modeling of the Temporal Evolution of Epidemics Outbreaks Accounting for Vaccinations

Application and significance of SIRVB model in analyzing COVID-19 dynamics

In the summer of 2024, COVID-19 positive cases spiked in many countries, but it is no longer a deadly pandemic thanks to global herd immunity to the SARS-CoV-2 viruses. In our physical chemistry lab in spring 2024, students practice kinetic models, SIR (Susceptible, Infected, and Recovered) and SIRV (Susceptible, Infected, Recovered, Vaccinated) using COVID-19 positive cases and vaccination data from World Health Organization (WHO). In this report, we further introduce virus breakthrough to the existing model updating it the SIRVB (Susceptible, Infectious, Recovered, Vaccinated, Breakthrough) model. We believe this is the simplest model possible to explain the COVID-19 kinetics/dynamics in all countries in the past four years. Parameters obtained from such practice correlate with many indices of different countries. These models and parameters have significant value to researchers and policymakers in predicting the stages of future outbreaks of infectious diseases.

Application and Significance of SIRVB Model in Analyzing COVID-19 Dynamics

In the summer of 2024, COVID-19 positive cases spiked in many countries, but it is no longer a deadly pandemic thanks to global herd immunity to the SARS-CoV-2 viruses. In our physical chemistry lab in spring 2024, students practice kinetic models, SIR (Susceptible, Infected, and Recovered) and SIRV (Susceptible, Infected, Recovered, Vaccinated) using COVID-19 positive cases and vaccination data from World Health Organization (WHO). In this report, we further introduce virus breakthrough to the existing model updating it the SIRVB (Susceptible, Infectious, Recovered, Vaccinated, Breakthrough) model. We believe this is the simplest model possible to explain the COVID-19 kinetics in all countries in the past four years. Parameters obtained from such practice correlate with many indices of different countries. These models and parameters have significant value to researchers and policymakers in predicting the stages of future outbreaks of infectious diseases.

A unified stochastic SIR model driven by Lévy noise with time-dependency

We propose a unified stochastic SIR model driven by Lévy noise. The model is structural enough to allow for time-dependency, nonlinearity, discontinuity, demography, and environmental disturbances. We present concise results on the existence and uniqueness of positive global solutions and investigate the extinction and persistence of the novel model. Examples and simulations are provided to illustrate the main results.

Physical Chemistry Lab for Data Analysis of COVID-19 Spreading Kinetics in Different Countries

The COVID-19 pandemic has passed. It gives us a real-world example of kinetic data analysis practice for our undergraduate physical chemistry laboratory class. It is a great example to connect this seemingly very different problem to the kinetic theories for chemical reactions that the students have learned in the lecture class. At the beginning of the spring 2023 semester, we obtained COVID-19 kinetic data from the "Our World in Data" database, which summarizes the World Health Organization (WHO) data reported from different countries. We analyzed the effective spreading kinetics based on the susceptible-infectious-recovered-vaccinated (SIR-V) model. We then compared the effective rate constants represented by the real-time reproduction numbers (R t ) underlining the reported data for these countries and discussed the results and the limitations of the model with the students.

Numerical Scheme for Compartmental Models: New Matlab Software Codes for Numerical Simulation

Background: This paper presents a newly developed Matlab code for the numerical simulation of compartmental/deterministic models. It addresses modeling and simulation issues concerning compartmental models. The code is easy to understand and edit for the simulation of compartmental models. An alternative codes for statistical software package R has been proposed for the same model. R software is freely available for use. Methods: We proposed a basic SEIR model for illustration purposes. Matlab and R software codes are developed for the SEIR model which users can follow and easily understand the computations. Results: The two codes work on all Matlab and R versions. For models with more compartments, we suggest using higher version of Matlab and R. Matlab works on windows, Mac and Linux Conclusions: New Matlab software codes purposely for numerical simulations of classical deterministic models which can run on any version of Matlab has been introduced in this paper. This code can be edited/modify to suit any deterministic models and any desired output required. An alternative open source free version has been written in R has been provided as well.

Analysis of the COVID-19 pandemic using a compartmental model with time-varying parameters fitted by a genetic algorithm

Analyzing the COVID-19 pandemic is a critical factor in developing effective policies to deal with similar challenges in the future. However, many parameters (e.g., the actual number of infected people, the effectiveness of vaccination) are still subject to considerable debate because they are unobservable. To model a pandemic and estimate unobserved parameters, researchers use compartmental models. Most often, in such models, the transition rates are considered as constants, which allows simulating only one epidemiological wave. However, multiple waves have been reported for COVID-19 caused by different strains of the virus. This paper presents an approach based on the reconstruction of real distributions of transition rates using genetic algorithms, which makes it possible to create a model that describes several pandemic peaks. The model is fitted on registered COVID-19 cases in four countries with different pandemic control strategies (Germany, Sweden, UK, and US). Mean absolute percentage error (MAPE) was chosen as the objective function, the MAPE values of 2.168%, 2.096%, 1.208% and 1.703% were achieved for the listed countries, respectively. Simulation results are consistent with the empirical statistics of medical studies, which confirms the quality of the model. In addition to observables such as registered infected, the output of the model contains variables that cannot be measured directly. Among them are the proportion of the population protected by vaccines, the size of the exposed compartment, and the number of unregistered cases of COVID-19. According to the results, at the peak of the pandemic, between 14% (Sweden) and 25% (the UK) of the population were infected. At the same time, the number of unregistered cases exceeds the number of registered cases by 17 and 3.4 times, respectively. The average duration of the vaccine induced immune period is shorter than claimed by vaccine manufacturers, and the effectiveness of vaccination has declined sharply since the appearance of the Delta and Omicron strains. However, on average, vaccination reduces the risk of infection by about 65-70%.

Spatio-Temporal Patterns of the SARS-CoV-2 Epidemic in Germany

Results from an explorative study revealing spatio-temporal patterns of the SARS-CoV-2/ COVID-19 epidemic in Germany are presented. We dispense with contestable model assumptions and show the intrinsic spatio-temporal patterns of the epidemic dynamics. The analysis is based on COVID-19 incidence data, which are age-stratified and spatially resolved at the county level, provided by the Federal Government's Public Health Institute of Germany (RKI) for public use. Although the 400 county-related incidence time series shows enormous heterogeneity, both with respect to temporal features as well as spatial distributions, the counties' incidence curves organise into well-distinguished clusters that coincide with East and West Germany. The analysis is based on dimensionality reduction, multidimensional scaling, network analysis, and diversity measures. Dynamical changes are captured by means of difference-in-difference methods, which are related to fold changes of the effective reproduction numbers. The age-related dynamical patterns suggest a considerably stronger impact of children, adolescents and seniors on the epidemic activity than previously expected. Besides these concrete interpretations, the work mainly aims at providing an atlas for spatio-temporal patterns of the epidemic, which serves as a basis to be further explored with the expertise of different disciplines, particularly sociology and policy makers. The study should also be understood as a methodological contribution to getting a handle on the unusual complexity of the COVID-19 pandemic.

Adaptive SIR model with vaccination: simultaneous identification of rates and functions illustrated with COVID-19

An Adaptive Susceptible-Infected-Removed-Vaccinated (A-SIRV) epidemic model with time-dependent transmission and removal rates is constructed for investigating the dynamics of an epidemic disease such as the COVID-19 pandemic. Real data of COVID-19 spread is used for the simultaneous identification of the unknown time-dependent rates and functions participating in the A-SIRV system. The inverse problem is formulated and solved numerically using the Method of Variational Imbedding, which reduces the inverse problem to a problem for minimizing a properly constructed functional for obtaining the sought values. To illustrate and validate the proposed solution approach, the present study used available public data for several countries with diverse population and vaccination dynamics—the World, Israel, The United States of America, and Japan.

An extended epidemic model with vaccination: Weak-immune SIRVI

A new modification of the SIR epidemic model incorporating vaccination is proposed in the present paper. The recent trend of vaccinating against COVID-19 pandemic reveals a strong control of infectious disease. On the other hand, it is observed in some countries that, the vaccine application offers less control over the spread of virus, since some portion of vaccinated people is not totally protected/immuned and viable to infection again after a while due to weak/loss immunity offered by the vaccine. This requires transition from vaccinated department to infected for COVID-19. This character of COVID-19 helps us reconsideration of the vaccinated department by letting some part of it being exposed to the infection again. Taking this into account, as a result of modification of the SIR model, the epidemiology is now governed with three main epidemic dimensionless parameters, having provided an initial fraction of infected individuals. The dimensionless model with these parameters is analyzed initially from the stability point of view. The effects of weak immunity are then illustrated numerically on some chosen parameter range. How some of the countries applying the COVID-19 vaccine programs affected by weak/loss immunity is eventually examined with the modified model. The rate of vaccination as well as the basic Reproduction number are found to affect the epidemic demography of the population subject to weak or loss of immunity. In the case of a high vaccination rate, the countries are not anticipated to be highly influenced by the weak immunity of low level, whereas weak immunity prolongs the contagious disease by appearance of secondary multiple peaks in the epidemic compartments with relatively small vaccination rates and basic Reproductive numbers.

SIR-Solution for Slowly Time-Dependent Ratio between Recovery and Infection Rates

The temporal evolution of pandemics described by the susceptible-infectious-recovered (SIR)-compartment model is sensitively determined by the time dependence of the infection (a(t)) and recovery (μ(t)) rates regulating the transitions from the susceptible to the infected and from the infected to the recovered compartment, respectively. Here, approximated SIR solutions for different time dependencies of the infection and recovery rates are derived which are based on the adiabatic approximation assuming time-dependent ratios, k(t)=μ(t)/a(t), varying slowly in comparison with the typical time characteristics of the pandemic wave. For such slow variations, the available analytical approximations from the KSSIR-model, developed by us and valid for a stationary value of the ratio k, are used to insert a posteriori the adopted time-dependent ratio of the two rates. Instead of investigating endless different combinations of the time dependencies of the two rates a(t) and μ(t), a suitably parameterized reduced time, τ, dependence of the ratio k(τ) is adopted. Together with the definition of the reduced time, this parameterized ratio k(τ) allows us to cover a great variety of different time dependencies of the infection and recovery rates. The agreement between the solutions from the adiabatic approximation in its four different studied variants and the exact numerical solutions of the SIR-equations is tolerable providing confidence in the accuracy of the proposed adiabatic approximation.

Characterizing stages of COVID-19 epidemics: a nonlinear physics perspective based on amplitude equations

The relevant dynamics underlying COVID-19 waves is described from an amplitude space perspective. To this end, the amplitude dynamics of infected populations is considered in different stages of epidemic waves. Eigenvectors and their corresponding amplitudes are derived analytically for low-dimensional models and by means of computational methods for high-dimensional models. It is shown that the amplitudes of all eigenvectors as functions of time can be tracked through the diverse stages of COVID-19 waves featuring jumps at the stage boundaries. In particular, it is shown that under certain circumstances the initial, outbreak stage and the final, subsiding stage of an epidemic wave are primarily determined by the unstable eigenvector of the initial stage and its corresponding remnant vector of the final stage. The corresponding amplitude captures most of the dynamics of the emerging and subsiding epidemics such that the problem at hand effectively becomes one dimensional leading to a dramatic reduction of the complexity of the problem at hand. Explicitly demonstrated for the first-wave COVID-19 epidemics of the year 2020 in the state of New York and Pakistan are given.

Modeling of COVID-19 propagation with compartment models

The current pandemic is a great challenge for several research areas. In addition to virology research, mathematical models and simulations can be a valuable contribution to the understanding of the dynamics of the pandemic and can give recommendations to both physicians and politicians. In this paper we give an overview about mathematical models to describe the pandemic by differential equations. As a matter of principle the historic origin of the epidemic growth models will be remembered. Moreover we discuss models for the actual pandemic of 2020/2021. This will be done based on actual data of people infected with COVID-19 from the European Centre for Disease Prevention and Control (ECDC), input parameters of mathematical models will be determined and applied. These parameters will be estimated for the UK, Italy, Spain, and Germany and used in a SIR-type model. As a basis for the model's calibration, the initial exponential growth phase of the COVID-19 pandemic in the named countries is used. Strategies for the commencing and ending of social and economic shutdown measures are discussed. To respect heterogeneity of the people density in the different federal states of Germany diffusion effects are considered.

Explicit formulae for the peak time of an epidemic from the SIR model. Which approximant to use?

An analytic evaluation of the peak time of a disease allows for the installment of effective epidemic precautions. Recently, an explicit analytic, approximate expression (MT) for the peak time of the fraction of infected persons during an outbreak within the susceptible-infectious-recovered/removed (SIR) model had been presented and discussed (Turkyilmazoglu, 2021). There are three existing approximate solutions (SK-I, SK-II, and CG) of the semi-time SIR model in its reduced formulation that allow one to come up with different explicit expressions for the peak time of the infected compartment (Schlickeiser and Kröger, 2021; Carvalho and Gonçalves, 2021). Here we compare the four expressions for any choice of SIR model parameters and find that SK-I, SK-II and CG are more accurate than MT as long as the amount of population to which the SIR model is applied exceeds hundred by far (countries, ss, cities). For small populations with less than hundreds of individuals (families, small towns), however, the approximant MT outperforms the other approximants. To be able to compare the various approaches, we clarify the equivalence between the four-parametric dimensional SIR equations and their two-dimensional dimensionless analogue. Using Covid-19 data from various countries and sources we identify the relevant regime within the parameter space of the SIR model.

Verification of the accuracy of the SIR model in forecasting based on the improved SIR model with a constant ratio of recovery to infection rate by comparing with monitored second wave data

The temporal evolution of second and subsequent waves of epidemics such as Covid-19 is investigated. Analytic expressions for the peak time and asymptotic behaviours, early doubling time, late half decay time, and a half-early peak law, characterizing the dynamical evolution of number of cases and fatalities, are derived, where the pandemic evolution exhibiting multiple waves is described by the semi-time SIR model. The asymmetry of the epidemic wave and its exponential tail are affected by the initial conditions, a feature that has no analogue in the all-time SIR model. Our analysis reveals that the immunity is very strongly increasing in several countries during the second Covid-19 wave. Wave-specific SIR parameters describing infection and recovery rates we find to behave in a similar fashion. Still, an apparently moderate change of their ratio can have significant consequences. As we show, the probability of an additional wave is however low in several countries due to the fraction of immune inhabitants at the end of the second wave, irrespective of the ongoing vaccination efforts. We compare with alternate approaches and data available at the time of submission. Most recent data serves to demonstrate the successful forecast and high accuracy of the SIR model in predicting the evolution of pandemic outbreaks as long as the assumption underlying our analysis, an unchanged situation of the distribution of variants of concern and the fatality fraction, do not change dramatically during a wave. With the rise of the α variant at the time of submission the second wave did not terminate in some countries, giving rise to a superposition of waves that is not treated by the present contribution.

A Local and Time Resolution of the COVID-19 Propagation—A Two-Dimensional Approach for Germany Including Diffusion Phenomena to Describe the Spatial Spread of the COVID-19 Pandemic

The understanding of factors that affect the dissemination of a viral infection is fundamental to help combat it. For instance, during the COVID-19 pandemic that changed the lives of people all over the world, one observes regions with different incidences of cases. One can speculate that population density might be one of the variables that affect the incidence of cases. In populous areas, such as big cities or congested urban areas, higher COVID-19 incidences could be observed than in rural regions. It is natural to think that if population density is such an important factor, then a gradient or difference in population density might lead to a diffusion process that will proceed until equilibrium is reached. The aim of this paper consists of the inclusion of a diffusion concept into the COVID-19 modeling. With this concept, one covers a gradient-driven transfer of the infection next to epidemic growth models (SIR-type models). This is discussed for a certain period of the German situation based on the quite different incidence data for the different federal states of Germany. With this ansatz, some phenomena of the actual development of the pandemic are found to be confirmed. The model provides a possibility to investigate certain scenarios, such as border-crossings or local spreading events, and their influence on the COVID-19 propagation. The resulting information can be a basis for the decisions of politicians and medical persons in charge of managing a pandemic.