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A new mathematical model of Coronavirus (2019-nCov) using piecewise hybrid fractional order derivatives is given in this paper. Moreover, in order to be consistent with the physical model problem, a new parameter μ is presented. The boundedness, existence, and positivity of the solutions for the proposed model are discussed. Two improved numerical methods are presented in this paper. The Caputo proportional constant nonstandard modified Euler–Maruyama method is introduced to study the fractional stochastic model, and the Grünwald–Letnikov nonstandard finite difference method is presented to study the hybrid fractional order deterministic model. Comparative studies with real data from Spain and Wuhan are presented. [ABSTRACT FROM AUTHOR]

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Mycobacterium tuberculosis (Mtb) coinfection has been observed in a number of nations and it is connected with severe illness and death. The paper studies a reaction–diffusion within-host Mtb/SARS-CoV-2 coinfection model with immunity. This model explores the connections between uninfected epithelial cells, latently Mtb-infected epithelial cells, productively Mtb-infected epithelial cells, SARS-CoV-2-infected epithelial cells, free Mtb particles, free SARS-CoV-2 virions, and CTLs. The basic properties of the model's solutions are verified. All equilibrium points with the essential conditions for their existence are calculated. The global stability of these equilibria is established by adopting compatible Lyapunov functionals. The theoretical outcomes are enhanced by implementing numerical simulations. It is found that the equilibrium points mirror the single infection and coinfection states of SARS-CoV-2 with Mtb. The threshold conditions that determine the movement from the monoinfection to the coinfection state need to be tested when developing new treatments for coinfected patients. The impact of the diffusion coefficients should be monitored at the beginning of coinfection as it affects the initial distribution of particles in space. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID-19) is a respiratory disease that appeared in 2019 caused by a virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is still spreading and causing deaths around the world. There is a real concern of SARS-CoV-2 coinfection with other infectious diseases. Tuberculosis (TB) is a bacterial disease caused by Mycobacterium tuberculosis (Mtb). SARS-CoV-2 coinfection with TB has been recorded in many countries. It has been suggested that the coinfection is associated with severe disease and death. Mathematical modeling is an effective tool that can help understand the dynamics of coinfection between new diseases and well-known diseases. In this paper, we develop an in-host TB and SARS-CoV-2 coinfection model with cytotoxic T lymphocytes (CTLs). The model investigates the interactions between healthy epithelial cells (ECs), latent Mtb-infected ECs, active Mtb-infected ECs, SARS-CoV-2-infected ECs, free Mtb, free SARS-CoV-2, and CTLs. The model's solutions are proved to be nonnegative and bounded. All equilibria with their existence conditions are calculated. Proper Lyapunov functions are selected to examine the global stability of equilibria. Numerical simulations are implemented to verify the theoretical results. It is found that the model has six equilibrium points. These points reflect two states: the mono-infection state where SARS-CoV-2 or TB occurs as a single infection, and the coinfection state where the two infections occur simultaneously. The parameters that control the movement between these states should be tested in order to develop better treatments for TB and COVID-19 coinfected patients. Lymphopenia increases the concentration of SARS-CoV-2 particles and thus can worsen the health status of the coinfected patient. [ABSTRACT FROM AUTHOR]

The aim of the present paper is to formulate two new mathematical models to describe the co-dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human T-cell lymphotropic virus type-I (HTLV-I) in a host. The models characterizes the interplaying between seven compartments, uninfected ECs, latently SARS-CoV-2-infected ECs, actively SARS-CoV-2-infected ECs, free SARS-CoV-2 particles, uninfected CD4 + T cells, latently HTLV-I-infected CD4 + T cells and actively HTLV-I-infected CD4 + T cells. The models incorporate five intracellular time delays: (i) two delays in the formation of latently SARS-CoV-2-infected ECs and latently HTLV-I-infected CD4 + T cells, (ii) two delays in the reactivation of latently SARS-CoV-2-infected ECs and latently HTLV-I-infected CD4 + T cells, and (iii) maturation delay of new SARS-CoV-2 virions. We consider discrete-time delays and distributed-time delays in the first and second models, respectively. We first investigate the properties of the model's solutions, then we calculate all equilibria and study their global stability. The global asymptotic stability is examined by constructing Lyapunov functionals. The analytical findings are supported via numerical simulation. The impact of time delays on the coinfection progression is discussed. We found that, increasing time delays values can have an antiviral treatment-like impact. Our developed coinfection model can contribute to understand the SARS-CoV-2 and HTLV-I co-dynamics and help to select suitable treatment strategies for COVID-19 patients with HTLV-I. [ABSTRACT FROM AUTHOR]

According to the World Health Organization updates, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a pandemic between 2019 and 2022, with millions of confirmed cases and deaths worldwide. There are various approaches to predicting the suspected, infected, and recovered (SIR) cases with different factual or epidemiological models. Some of the recent approaches to predicting the COVID-19 outbreak have had positive impacts in specific nations. Results show that the SIR model is a significant tool to cast the dynamics and predictions of the COVID-19 outbreak compared to other epidemic models. In this paper, we employ the Monte Carlo simulation to predict the spread of COVID-19 in the United Arab Emirates. We study traditional SIR models in general and focus on a time-dependent SIR model, which has been proven more adaptive and robust in predicting the COVID-19 outbreak. We evaluate the time-dependent SIR model. Then, we implement a Monte Carlo model. The Monte Carlo model uses the parameters extracted from the Time-Dependent SIR Model. The Monte Carlo model exhibited a better prediction accuracy and resembles the data collected from the Ministry of Cabinet Affairs, United Arab Emirates, between April and July 2020. [ABSTRACT FROM AUTHOR]

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new virus which infects the respiratory system and causes the coronavirus disease 2019 (COVID-19). The coinfection between malaria and COVID-19 has been registered in many countries. This has risen an urgent need to understand the dynamics of coinfection. In this paper, we construct a reaction–diffusion in-host malaria/COVID-19 model. The model includes seven-dimensional partial differential equations that explore the interactions between seven compartments, healthy red blood cells (RBCs), infected RBCs, free merozoites, healthy epithelial cells (ECs), infected ECs, free SARS-CoV-2 particles, and antibodies. The biological validation of the model is confirmed by establishing the nonnegativity and boundedness of the model's solutions. All equilibrium points with the corresponding existence conditions are calculated. The global stability of all equilibria is proved by picking up appropriate Lyapunov functionals. Numerical simulations are used to enhance and visualize the theoretical results. We found that the equilibrium points show the different cases when malaria and SARS-CoV-2 infections occur as mono-infection or coinfection. The shared antibody immune response decreases the concentrations of SARS-CoV-2 and malaria merozoites. This can have an important role in reducing the severity of SARS-CoV-2 if the immune response works effectively. [ABSTRACT FROM AUTHOR]

Studies have reported several cases with respiratory viruses coinfection in hospitalized patients. Influenza A virus (IAV) mimics the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) with respect to seasonal occurrence, transmission routes, clinical manifestations and related immune responses. The present paper aimed to develop and investigate a mathematical model to study the dynamics of IAV/SARS-CoV-2 coinfection within the host. The influence of SARS-CoV-2-specific and IAV-specific antibody immunities is incorporated. The model simulates the interaction between seven compartments, uninfected epithelial cells, SARS-CoV-2-infected cells, IAV-infected cells, free SARS-CoV-2 particles, free IAV particles, SARS-CoV-2-specific antibodies and IAV-specific antibodies. The regrowth and death of the uninfected epithelial cells are considered. We study the basic qualitative properties of the model, calculate all equilibria and investigate the global stability of all equilibria. The global stability of equilibria is established using the Lyapunov method. We perform numerical simulations and demonstrate that they are in good agreement with the theoretical results. The importance of including the antibody immunity into the coinfection dynamics model is discussed. We have found that without modeling the antibody immunity, the case of IAV and SARS-CoV-2 coexistence is not observed. Finally, we discuss the influence of IAV infection on the dynamics of SARS-CoV-2 single-infection and vice versa. [ABSTRACT FROM AUTHOR]

The new COVID-19 variants of concern are causing more infections and spreading much faster than their predecessors. Recent cases show that even vaccinated people are highly affected by these new variants. The proactive nucleotide sequence prediction of possible new variants of COVID-19 and developing better healthcare plans to address their spread require a unified framework for variant classification and early prediction. This paper attempts to answer the following research questions: can a convolutional neural network with self-attention by extracting discriminative features from nucleotide sequences be used to classify COVID-19 variants? Second, is it possible to employ uncertainty calculation in the predicted probability distribution to predict new variants? Finally, can synthetic approaches such as variational autoencoder-decoder networks be employed to generate a synthetic new variant from random noise? Experimental results show that the generated sequence is significantly similar to the original coronavirus and its variants, proving that our neural network can learn the mutation patterns from the old variants. Moreover, to our knowledge, we are the first to collect data for all COVID-19 variants for computational analysis. The proposed framework is extensively evaluated for classification, new variant prediction, and new variant generation tasks and achieves better performance for all tasks. Our code, data, and trained models are available on GitHub (https://github.com/Aminullah6264/COVID19 , accessed on 16 September 2022). [ABSTRACT FROM AUTHOR]

The evolution of some epidemics, such as influenza, demonstrates common patterns both in different regions and from year to year. On the contrary, epidemics such as the novel COVID-19 show quite heterogeneous dynamics and are extremely susceptible to the measures taken to mitigate their spread. In this paper, we propose empirical dynamic modeling to predict the evolution of influenza in Spain's regions. It is a non-parametric method that looks into the past for coincidences with the present to make the forecasts. Here, we extend the method to predict the evolution of other epidemics at any other starting territory and we also test this procedure with Spanish COVID-19 data. We finally build influenza and COVID-19 networks to check possible coincidences in the geographical distribution of both diseases. With this, we grasp the uniqueness of the geographical dynamics of COVID-19. [ABSTRACT FROM AUTHOR]

The mathematical modeling and analysis of within-host or between-host coronavirus disease 2019 (COVID-19) dynamics are considered robust tools to support scientific research. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of COVID-19. This paper proposes and investigates a within-host COVID-19 dynamics model with latent infection, the logistic growth of healthy epithelial cells and the humoral (antibody) immune response. Time delays can affect the dynamics of SARS-CoV-2 infection predicted by mathematical models. Therefore, we incorporate four time delays into the model: (i) delay in the formation of latent infected epithelial cells, (ii) delay in the formation of active infected epithelial cells, (iii) delay in the activation of latent infected epithelial cells, and (iv) maturation delay of new SARS-CoV-2 particles. We establish that the model's solutions are non-negative and ultimately bounded. This confirms that the concentrations of the virus and cells should not become negative or unbounded. We deduce that the model has three steady states and their existence and stability are perfectly determined by two threshold parameters. We use Lyapunov functionals to confirm the global stability of the model's steady states. The analytical results are enhanced by numerical simulations. The effect of time delays on the SARS-CoV-2 dynamics is investigated. We observe that increasing time delay values can have the same impact as drug therapies in suppressing viral progression. This offers some insight useful to develop a new class of treatment that causes an increase in the delay periods and then may control SARS-CoV-2 replication. [ABSTRACT FROM AUTHOR]

Governments must consider different issues when deciding on the location of healthcare centers. In addition to the costs of opening such centers, three further elements should be addressed: accessibility, demand, and equity. Such locations must be chosen to meet the corresponding demand, so that they guarantee a socially equitable distribution, and to ensure that they are accessible to a sufficient degree. The location of the centers must be chosen from a set of possible facilities to guarantee certain minimum standards for the operational viability of the centers. Since the set of potential locations does not necessarily cover the demand of all geographical zones, the efficiency criterion must be maximized. However, the efficient distribution of resources does not necessarily meet the equity criterion. Thus, decision-makers must consider the trade-off between these two criteria: efficiency and equity. The described problem corresponds to the challenge that governments face in seeking to minimize the impact of the pandemic on citizens, where healthcare centers may be either public hospitals that care for COVID-19 patients or vaccination points. In this paper, we focus on the problem of a zone-divided region requiring the localization of healthcare centers. We propose a non-linear programming model to solve this problem based on a coverage formula using the Gini index to measure equity and accessibility. Then, we consider an approach using epsilon constraints that makes this problem solvable with mixed integer linear computations at each iteration. A simulation algorithm is also considered to generate problem instances, while computational experiments are carried out to show the potential use of the proposed mathematical programming model. The results show that the spatial distribution influences the coverage level of the healthcare system. Nevertheless, this distribution does not reduce inequity at accessible healthcare centers, as the distribution of the supply of health centers must be incorporated into the decision-making process. [ABSTRACT FROM AUTHOR]

In comparison with other respiratory viruses, the current COVID-19 pandemic's rapid seizing the world can be attributed to indirect (contact) way of transmission of SARS-CoV-2 virus in addition to the regular airborne way. A significant part of indirect transmission is made through cash bank notes. SARS-CoV-2 remains on cash paper money for period around four times larger than influenza A virus and is absorbed by cash notes two and a half times more effectively than influenza A (our model). During the pandemic, cryptocurrencies have gained attractiveness as an "epidemiologically safe" means of transactions. On the basis of the authors' gallop polls performed online with social networks users in 44 countries in 2020–2021 (the total number of clear responses after the set repair 32,115), around 14.7% of surveyed participants engaged in cryptocurrency-based transactions during the pandemic. This may be one of the reasons of significant rise of cryptocurrencies rates since mid-March 2020 till the end of 2021. The paper discusses the reasons for cryptocurrency attractiveness during the COVID-19 pandemic. Among them, there are fear of SARS-CoV-2 spread via cash contacts and the ability of the general population to mine cryptocurrencies. The article also provides a breakdown of the polled audience profile to determine the nationalities that have maximal level of trust to saving and transacting money as cryptocurrencies. [ABSTRACT FROM AUTHOR]

Since December 2019, the novel coronavirus (SARS-CoV-2) and its associated illness COVID-19 have rapidly spread worldwide. The Mexican government has implemented public safety measures to minimize the spread of the virus. In this paper, we used statistical models in two stages to estimate the total number of coronavirus (COVID-19) cases per day at the state and national levels in Mexico. In this paper, we propose two types of models. First, a polynomial model of the growth for the first part of the outbreak until the inflection point of the pandemic curve and then a second nonlinear growth model used to estimate the middle and the end of the outbreak. Model selection was performed using Vuong's test. The proposed models showed overall fit similar to predictive models (e.g., time series and machine learning); however, the interpretation of parameters is simpler for decisionmakers, and the residuals follow the expected distribution when fitting the models without autocorrelation being an issue. [ABSTRACT FROM AUTHOR]

COVID-19 is a disease occurring as a result of infection by a novel coronavirus called SARS-CoV-2. Since the WHO announced COVID-19 as a global pandemic, mathematical works have taken place to simulate infection scenarios at different scales even though the majority of these models only consider the temporal dynamics of SARS-COV-2. In this paper, we present a new spatio-temporal within-host mathematical model of COVID-19, accounting for the coupled dynamics of healthy cells, infected cells, SARS-CoV-2 molecules, chemokine concentration, effector T cells, regulatory T cells, B-lymphocytes cells and antibodies. We develop a computational framework involving discretisation schemes for diffusion and chemotaxis terms using central differences and midpoint approximations within two dimensional space combined with a predict–evaluate–correct mode for time marching. Then, we numerically investigate the model performance using a list of values simulating the baseline scenario for viral infection at a cellular scale. Moreover, we explore the model sensitivity via applying certain conditions to observe the model validity in a comparison with clinical outcomes collected from recent studies. In this computational investigation, we have a numerical range of 104 to 108 for the viral load peak, which is equivalent to what has been obtained from throat swab samples for many patients. [ABSTRACT FROM AUTHOR]

At the end of 2019, an outbreak of the novel coronavirus (COVID-19) made a profound impact on the country's production and people's daily lives. Up until now, COVID-19 has not been fully controlled all over the world. Based on the clinical research progress of infectious diseases, combined with epidemiological theories and possible disease control measures, this paper establishes a Susceptible Infected Recovered (SIR) model that meets the characteristics of the transmission of the new coronavirus, using the least square estimation (LSE) method to estimate the model parameters. The simulation results show that quarantine and containment measures as well as vaccine and drug development measures can control the spread of the epidemic effectively. As can be seen from the prediction results of the model, the simulation results of the epidemic development of the whole country and Nanjing are in agreement with the real situation of the epidemic, and the number of confirmed cases is close to the real value. At the same time, the model's prediction of the prevention effect and control measures have shed new light on epidemic prevention and control. [ABSTRACT FROM AUTHOR]

In this paper, a mathematical model was developed to simulate SARS-CoV-2 dynamics in infected patients. The model considers both the innate and adaptive immune responses and consists of healthy cells, infected cells, viral load, cytokines, natural killer cells, cytotoxic T-lymphocytes, B-lymphocytes, plasma cells, and antibody levels. First, a mathematical analysis was performed to discuss the model's equilibrium points and compute the basic reproduction number. The accuracy of such mathematical models may be affected by many sources of uncertainties due to the incomplete representation of the biological process and poorly known parameters. This may strongly limit their performance and prediction skills. A state-of-the-art data assimilation technique, the ensemble Kalman filter (EnKF), was then used to enhance the model's behavior by incorporating available data to determine the best possible estimate of the model's state and parameters. The proposed assimilation system was applied on the real viral load datasets of six COVID-19 patients. The results demonstrate the efficiency of the proposed assimilation system in improving the model predictions by up to 40 % . [ABSTRACT FROM AUTHOR]

The spread of the SARS-CoV-2 modeling is a challenging problem because of its complex nature and lack of information regarding certain aspects. In this paper, we explore a Digital Twin approach to model the pandemic situation in Catalonia. The Digital Twin is composed of three different dynamic models used to perform the validations by a Model Comparison approach. We detail how we use this approach to obtain knowledge regarding the effects of the nonpharmaceutical interventions and the problems we faced during the modeling process. We use Specification and Description Language (SDL) to represent the compartmental forecasting model for the SARS-CoV-2. Its graphical notation simplifies the different specialists' understanding of the model hypotheses, which must be validated continuously following a Solution Validation approach. This model allows the successful forecasting of different scenarios for Catalonia. We present some formalization details, discuss the validation process and present some results obtained from the validation model discussion, which becomes a digital twin of the pandemic in Catalonia. [ABSTRACT FROM AUTHOR]

COVID-19 infections have plagued the world and led to deaths with a heavy pneumonia manifestation. The main objective of this investigation is to evaluate the performance of certain economies during the crisis derived from the COVID-19 pandemic. The gross domestic product (GDP) and global health security index (GHSI) of the countries belonging–or not–to the Organization for Economic Cooperation and Development (OECD) are considered. In this paper, statistical models are formulated to study this performance. The models' specifications include, as the response variable, the GDP variation/growth percentage in 2020, and as the covariates: the COVID-19 disease rate from its start in March 2020 until 31 December 2020; the GHSI of 2019; the countries' risk by default spreads from July 2019 to May 2020; belongingness or not to the OECD; and the GDP per capita in 2020. We test the heteroscedasticity phenomenon present in the modeling. The variable "COVID-19 cases per million inhabitants" is statistically significant, showing its impact on each country's economy through the GDP variation. Therefore, we report that COVID-19 cases affect domestic economies, but that OECD membership and other risk factors are also relevant. [ABSTRACT FROM AUTHOR]

In this paper, an extended SEIR model with a vaccination compartment is proposed to simulate the novel coronavirus disease (COVID-19) spread in Saudi Arabia. The model considers seven stages of infection: susceptible (S), exposed (E), infectious (I), quarantined (Q), recovered (R), deaths (D), and vaccinated (V). Initially, a mathematical analysis is carried out to illustrate the non-negativity, boundedness, epidemic equilibrium, existence, and uniqueness of the endemic equilibrium, and the basic reproduction number of the proposed model. Such numerical models can be, however, subject to various sources of uncertainties, due to an imperfect description of the biological processes governing the disease spread, which may strongly limit their forecasting skills. A data assimilation method, mainly, the ensemble Kalman filter (EnKF), is then used to constrain the model outputs and its parameters with available data. We conduct joint state-parameters estimation experiments assimilating daily data into the proposed model using the EnKF in order to enhance the model's forecasting skills. Starting from the estimated set of model parameters, we then conduct short-term predictions in order to assess the predicability range of the model. We apply the proposed assimilation system on real data sets from Saudi Arabia. The numerical results demonstrate the capability of the proposed model in achieving accurate prediction of the epidemic development up to two-week time scales. Finally, we investigate the effect of vaccination on the spread of the pandemic. [ABSTRACT FROM AUTHOR]