scholarly journals Modifying the network-based stochastic SEIR model to account for quarantine: an application to COVID-19

2021 ◽  
Vol 10 (s1) ◽  
Author(s):  
Chris Groendyke ◽  
Adam Combs
Keyword(s):  
Network Model ◽  
Transmission Rate ◽  
Disease Spread ◽  
Contact Network ◽  
Model Parameters ◽  
Seir Model ◽  
Disease States ◽  
Potential Contact ◽  
The Mean ◽  
Infectious State

Abstract Objectives: Diseases such as SARS-CoV-2 have novel features that require modifications to the standard network-based stochastic SEIR model. In particular, we introduce modifications to this model to account for the potential changes in behavior patterns of individuals upon becoming symptomatic, as well as the tendency of a substantial proportion of those infected to remain asymptomatic. Methods: Using a generic network model where every potential contact exists with the same common probability, we conduct a simulation study in which we vary four key model parameters (transmission rate, probability of remaining asymptomatic, and the mean lengths of time spent in the exposed and infectious disease states) and examine the resulting impacts on various metrics of epidemic severity, including the effective reproduction number. We then consider the effects of a more complex network model. Results: We find that the mean length of time spent in the infectious state and the transmission rate are the most important model parameters, while the mean length of time spent in the exposed state and the probability of remaining asymptomatic are less important. We also find that the network structure has a significant impact on the dynamics of the disease spread. Conclusions: In this article, we present a modification to the network-based stochastic SEIR epidemic model which allows for modifications to the underlying contact network to account for the effects of quarantine. We also discuss the changes needed to the model to incorporate situations where some proportion of the individuals who are infected remain asymptomatic throughout the course of the disease.

scholarly journals Revealing mechanisms of infectious disease spread through empirical contact networks

2021 ◽  
Vol 17 (12) ◽  
pp. e1009604
Author(s):  
Pratha Sah ◽  
Michael Otterstatter ◽  
Stephan T. Leu ◽  
Sivan Leviyang ◽  
Shweta Bansal
Keyword(s):  
Infectious Disease ◽  
Incomplete Data ◽  
Model Comparison ◽  
Transmission Rate ◽  
Disease Spread ◽  
Contact Network ◽  
Statistical Tool ◽  
Contact Networks ◽  
Crithidia Bombi ◽  
Transmission Pathways

The spread of pathogens fundamentally depends on the underlying contacts between individuals. Modeling the dynamics of infectious disease spread through contact networks, however, can be challenging due to limited knowledge of how an infectious disease spreads and its transmission rate. We developed a novel statistical tool, INoDS (Identifying contact Networks of infectious Disease Spread) that estimates the transmission rate of an infectious disease outbreak, establishes epidemiological relevance of a contact network in explaining the observed pattern of infectious disease spread and enables model comparison between different contact network hypotheses. We show that our tool is robust to incomplete data and can be easily applied to datasets where infection timings of individuals are unknown. We tested the reliability of INoDS using simulation experiments of disease spread on a synthetic contact network and find that it is robust to incomplete data and is reliable under different settings of network dynamics and disease contagiousness compared with previous approaches. We demonstrate the applicability of our method in two host-pathogen systems: Crithidia bombi in bumblebee colonies and Salmonella in wild Australian sleepy lizard populations. INoDS thus provides a novel and reliable statistical tool for identifying transmission pathways of infectious disease spread. In addition, application of INoDS extends to understanding the spread of novel or emerging infectious disease, an alternative approach to laboratory transmission experiments, and overcoming common data-collection constraints.

scholarly journals Covid-19 mortality rates in Northamptonshire UK: initial sub-regional comparisons and provisional SEIR model of disease spread

2020 ◽  
Author(s):  
Nick Petford ◽  
Jackie Campbell
Keyword(s):  
Mortality Rate ◽  
Transmission Rate ◽  
Local Population ◽  
Mortality Rates ◽  
Disease Spread ◽  
Parameter Estimates ◽  
Deterministic Models ◽  
Seir Model ◽  
East Midlands ◽  
Public Health Practitioners

We analysed mortality rates in a non-metropolitan UK subregion (Northamptonshire) to understand SARS-CoV-2 disease fatalities at sub 1000000 population levels. A numerical (SEIR) model was then developed to predict the spread of Covid-19 in Northamptonshire. A combined approach using statistically-weighted data to fit the start of the epidemic to the mortality record. Parameter estimates were then derived for the transmission rate and basic reproduction number. Age standardised mortality rates are highest in Northampton (urban) and lowest in semi-rural districts. Northamptonshire has a statistically higher Covid-19 mortality rate than for the East Midlands and England as a whole. Model outputs suggest the number of infected individuals exceed official estimates, meaning less than 40 percent of the population may require immunisation. Combining published (sub-regional) mortality rate data with deterministic models on disease spread has the potential to help public health practitioners develop bespoke mitigations, guided by local population demographics.

scholarly journals An Extended SEIR Model with Vaccination for Forecasting the COVID-19 Pandemic in Saudi Arabia Using an Ensemble Kalman Filter

Mathematics ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 636
Author(s):  
Rabih Ghostine ◽  
Mohamad Gharamti ◽  
Sally Hassrouny ◽  
Ibrahim Hoteit
Keyword(s):  
Saudi Arabia ◽  
Kalman Filter ◽  
Ensemble Kalman Filter ◽  
Numerical Models ◽  
Parameters Estimation ◽  
Disease Spread ◽  
Model Parameters ◽  
Equilibrium Existence ◽  
Seir Model ◽  
Proposed Model

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.

scholarly journals Dynamic versus Continuous Interventions: Optimizing Lockdown Policies for COVID-19

2021 ◽  
Author(s):  
Kaan Akinci ◽  
Javier Fdez ◽  
Elena Peña-Tapia ◽  
Olaf Witkowski
Keyword(s):  
Transmission Rate ◽  
Optimal Strategies ◽  
Specific Model ◽  
Evolutionary Strategies ◽  
Model Parameters ◽  
Seir Model ◽  
Agent Based ◽  
Slowing Down ◽  
Using Data ◽  
Gradual Decay

In the context of the ongoing COVID-19 pandemic, while millions of people await the administration of a vaccine, social distancing remains the leading approach towards the effect commonly known as “flattening the curve” of infections. Over the last year, governmental administrations throughout the globe have implemented various lockdown policies in hopes of slowing down the transmission of the disease. However, the current lack of consensus on when and how these policies should be implemented reflects the need for further studies regarding these questions. In this paper, we tackle the issue of lockdown policy management, in particular in terms of lockdown placement (how often, when, and how long these periods should be), in order to minimize the peak of infections in a specific population. We introduce a novel combination of classic mathematical disease modelling using the equation-based SEIR model, and Evolutionary Strategies (ES) for optimizing the peak of infections. The method is evaluated using data collected in different countries, and a particular focus is placed on the study of the effect of specific model parameters on lockdown optimization, such as the transmission rate (β), of which 4 alternative modelling functions have been proposed and analyzed. Our results indicate that this transmission rate parameter significantly influences the resulting optimal strategies. In particular, the presence of a gradual decay of the rate of transmission during lockdown leads to longer, more sparsely placed confinement periods while an abrupt, instantaneous drop in the amount of contacts per person favors shorter but more frequent lockdowns. Although these results are limited by the scope of action provided by the simplicity of the SEIR model, they suggest that the influence of the evolution of the rate of transmission along the disease should be assessed in further studies with alternative optimization strategies (agent-based) and models (SEIRSHUD).

scholarly journals Network model and analysis of the spread of Covid-19 with social distancing

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Parul Maheshwari ◽  
Réka Albert
Keyword(s):  
Network Model ◽  
Transmission Rate ◽  
Real Data ◽  
Disease Spread ◽  
Prevention Measures ◽  
Social Distancing ◽  
Workplace Interactions ◽  
Human Interactions ◽  
Reproduction Numbers ◽  
Second Wave

AbstractThe first mitigation response to the Covid-19 pandemic was to limit person-to-person interaction as much as possible. This was implemented by the temporary closing of many workplaces and people were required to follow social distancing. Networks are a great way to represent interactions among people and the temporary severing of these interactions. Here, we present a network model of human–human interactions that could be mediators of disease spread. The nodes of this network are individuals and different types of edges denote family cliques, workplace interactions, interactions arising from essential needs, and social interactions. Each individual can be in one of four states: susceptible, infected, immune, and dead. The network and the disease parameters are informed by the existing literature on Covid-19. Using this model, we simulate the spread of an infectious disease in the presence of various mitigation scenarios. For example, lockdown is implemented by deleting edges that denote non-essential interactions. We validate the simulation results with the real data by matching the basic and effective reproduction numbers during different phases of the spread. We also simulate different possibilities of the slow lifting of the lockdown by varying the transmission rate as facilities are slowly opened but people follow prevention measures like wearing masks etc. We make predictions on the probability and intensity of a second wave of infection in each of these scenarios.

scholarly journals Impact of public health interventions to curb SARS-CoV-2 spread assessed by an evidence-educated Delphi panel and tailored SEIR model

2021 ◽  
Author(s):  
Bernd Brüggenjürgen ◽  
Hans-Peter Stricker ◽  
Lilian Krist ◽  
Miriam Ortiz ◽  
Thomas Reinhold ◽  
...  
Keyword(s):  
Public Health ◽  
Transmission Rate ◽  
Latency Period ◽  
Policy Decision ◽  
Sensitivity Analyses ◽  
Delphi Panel ◽  
Time Step ◽  
Seir Model ◽  
Health Policy Decision ◽  
The Impact

Abstract Aim To use a Delphi-panel-based assessment of the effectiveness of different non-pharmaceutical interventions (NPI) in order to retrospectively approximate and to prospectively predict the SARS-CoV-2 pandemic progression via a SEIR model (susceptible, exposed, infectious, removed). Methods We applied an evidence-educated Delphi-panel approach to elicit the impact of NPIs on the SARS-CoV-2 transmission rate R0 in Germany. Effectiveness was defined as the product of efficacy and compliance. A discrete, deterministic SEIR model with time step of 1 day, a latency period of 1.8 days, duration of infectiousness of 5 days, and a share of the total population of 15% assumed to be protected by immunity was developed in order to estimate the impact of selected NPI measures on the course of the pandemic. The model was populated with the Delphi-panel results and varied in sensitivity analyses. Results Efficacy and compliance estimates for the three most effective NPIs were as follows: test and isolate 49% (efficacy)/78% (compliance), keeping distance 42%/74%, personal protection masks (cloth masks or other face masks) 33%/79%. Applying all NPI effectiveness estimates to the SEIR model resulted in a valid replication of reported occurrence of the German SARS-CoV-2 pandemic. A combination of four NPIs at consented compliance rates might curb the CoViD-19 pandemic. Conclusion Employing an evidence-educated Delphi-panel approach can support SARS-CoV-2 modelling. Future curbing scenarios require a combination of NPIs. A Delphi-panel-based NPI assessment and modelling might support public health policy decision making by informing sequence and number of needed public health measures.

scholarly journals The Relationship between Inflammation Markers (CRP, IL-6, sCD40L) and Colorectal Cancer Stage, Grade, Size and Location

Diagnostics ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1382
Author(s):  
Olga Martyna Koper-Lenkiewicz ◽  
Violetta Dymicka-Piekarska ◽  
Anna Justyna Milewska ◽  
Justyna Zińczuk ◽  
Joanna Kamińska
Keyword(s):  
Colorectal Cancer ◽  
Linear Regression ◽  
Tumor Size ◽  
Distal Colon ◽  
Proximal Colon ◽  
Model Parameters ◽  
Grade Group ◽  
Who Grade ◽  
The Mean ◽  
Mean Concentration

The aim of the study was the evaluation whether in primary colorectal cancer (CRC) patients (n = 55): age, sex, TNM classification results, WHO grade, tumor location (proximal colon, distal colon, rectum), tumor size, platelet count (PLT), mean platelet volume (MPV), mean platelet component (MCP), levels of carcinoembryonic antigen (CEA), cancer antigen (CA 19-9), as well as soluble lectin adhesion molecules (L-, E-, and P-selectins) may influence circulating inflammatory biomarkers: IL-6, CRP, and sCD40L. We found that CRP concentration evaluation in routine clinical practice may have an advantage as a prognostic biomarker in CRC patients, as this protein the most comprehensively reflects clinicopathological features of the tumor. Univariate linear regression analysis revealed that in CRC patients: (1) with an increase in PLT by 10 × 103/μL, the mean concentration of CRP increases by 3.4%; (2) with an increase in CA 19-9 of 1 U/mL, the mean concentration of CRP increases by 0.7%; (3) with the WHO 2 grade, the mean CRP concentration increases 3.631 times relative to the WHO 1 grade group; (4) with the WHO 3 grade, the mean CRP concentration increases by 4.916 times relative to the WHO 1 grade group; (5) with metastases (T1-4N+M+) the mean CRP concentration increases 4.183 times compared to non-metastatic patients (T1-4N0M0); (6) with a tumor located in the proximal colon, the mean concentration of CRP increases 2.175 times compared to a tumor located in the distal colon; (7) in patients with tumor size > 3 cm, the CRP concentration is about 2 times higher than in patients with tumor size ≤ 3 cm. In the multivariate linear regression model, the variables that influence the mean CRP value in CRC patients included: WHO grade and tumor localization. R2 for the created model equals 0.50, which indicates that this model explains 50% of the variance in the dependent variable. In CRC subjects: (1) with the WHO 2 grade, the mean CRP concentration rises 3.924 times relative to the WHO 1 grade; (2) with the WHO 3 grade, the mean CRP concentration increases 4.721 times in relation to the WHO 1 grade; (3) with a tumor located in the rectum, the mean CRP concentration rises 2.139 times compared to a tumor located in the distal colon; (4) with a tumor located in the proximal colon, the mean concentration of CRP increases 1.998 times compared to the tumor located in the distal colon; if other model parameters are fixed.

Explanation Plus Prediction—The Logical Focus of Project Management Research

2021 ◽  
pp. 875697282199994
Author(s):  
Joseph F. Hair ◽  
Marko Sarstedt
Keyword(s):  
Project Management ◽  
Statistical Models ◽  
Predictive Power ◽  
Mean Absolute Error ◽  
Explanatory Power ◽  
Absolute Error ◽  
Model Parameters ◽  
Mean Square ◽  
Management Research ◽  
The Mean

Most project management research focuses almost exclusively on explanatory analyses. Evaluation of the explanatory power of statistical models is generally based on F-type statistics and the R 2 metric, followed by an assessment of the model parameters (e.g., beta coefficients) in terms of their significance, size, and direction. However, these measures are not indicative of a model’s predictive power, which is central for deriving managerial recommendations. We recommend that project management researchers routinely use additional metrics, such as the mean absolute error or the root mean square error, to accurately quantify their statistical models’ predictive power.

scholarly journals A modified SEIR model to predict the behavior of the early stage in coronavirus and coronavirus-like outbreaks

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wilfredo Angulo ◽  
José M. Ramírez ◽  
Dany De Cecchis ◽  
Juan Primera ◽  
Henry Pacheco ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Risk Perceptions ◽  
Transmission Rate ◽  
Early Stage ◽  
Individual Risk ◽  
Seir Model ◽  
Proposed Model ◽  
Probable Site ◽  
Adjusted Model ◽  
The Impact

AbstractCOVID-19 is a highly infectious disease that emerged in China at the end of 2019. The COVID-19 pandemic is the first known pandemic caused by a coronavirus, namely, the new and emerging SARS-CoV-2 coronavirus. In the present work, we present simulations of the initial outbreak of this new coronavirus using a modified transmission rate SEIR model that takes into account the impact of government actions and the perception of risk by individuals in reaction to the proportion of fatal cases. The parameters related to these effects were fitted to the number of infected cases in the 33 provinces of China. The data for Hubei Province, the probable site of origin of the current pandemic, were considered as a particular case for the simulation and showed that the theoretical model reproduces the behavior of the data, thus indicating the importance of combining government actions and individual risk perceptions when the proportion of fatal cases is greater than $$4\%$$ 4 % . The results show that the adjusted model reproduces the behavior of the data quite well for some provinces, suggesting that the spread of the disease differs when different actions are evaluated. The proposed model could help to predict outbreaks of viruses with a biological and molecular structure similar to that of SARS-CoV-2.

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