Estimation of time-varying reproduction numbers underlying epidemiological processes: A new statistical tool for the COVID-19 pandemic

Health information management systems and practices in conflict-affected settings: the case of northwest Syria

BACKGROUND

In conflict settings, as it is the case in Syria, it is crucial to enhance health information management to facilitate an effective and sustainable approach to strengthening health systems in such contexts. In this study, we aim to provide a baseline understanding of the present state of health information management in Northwest Syria (NWS) to better plan for strengthening the health information system of the area that is transitioning to an early-recovery stage.

METHODS

A combination of questionnaires and subsequent interviews was used for data collection. Purposive sampling was used to select twenty-one respondents directly involved in managing and directing different domains of health information in the NWS who worked with local NGOs, INGOs, UN-agencies, or part of the Health Working Group. A scoring system for each public health domain was constructed based on the number and quality of the available datasets for these domains, which were established by Checci and others.

RESULTS & CONCLUSIONS

Reliable and aggregate health information in the NWS is limited, despite some improvements made over the past decade. The conflict restricted and challenged efforts to establish a concentrated and harmonized HIS in the NWS, which led to a lack of leadership, poor coordination, and duplication of key activities. Although the UN established the EWARN and HeRAMS as common data collection systems in the NWS, they are directed toward advocacy and managed by external experts with little participation or access from local stakeholders to these datasets.

RECOMMENDATIONS

There is a need for participatory approaches and the empowerment of local actors and local NGOs, cooperation between local and international stakeholders to increase access to data, and a central domain for planning, organization, and harmonizing the process. To enhance the humanitarian health response in Syria and other crisis areas, it is imperative to invest in data collection and utilisation, mHealth and eHealth technologies, capacity building, and robust technical and autonomous leadership.

Detecting changes in the transmission rate of a stochastic epidemic model

Throughout the course of an epidemic, the rate at which disease spreads varies with behavioral changes, the emergence of new disease variants, and the introduction of mitigation policies. Estimating such changes in transmission rates can help us better model and predict the dynamics of an epidemic, and provide insight into the efficacy of control and intervention strategies. We present a method for likelihood-based estimation of parameters in the stochastic susceptible-infected-removed model under a time-inhomogeneous transmission rate comprised of piecewise constant components. In doing so, our method simultaneously learns change points in the transmission rate via a Markov chain Monte Carlo algorithm. The method targets the exact model posterior in a difficult missing data setting given only partially observed case counts over time. We validate performance on simulated data before applying our approach to data from an Ebola outbreak in Western Africa and COVID-19 outbreak on a university campus.

Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models

Compartmental models that describe infectious disease transmission across subpopulations are central for assessing the impact of non-pharmaceutical interventions, behavioral changes and seasonal effects on the spread of respiratory infections. We present a Bayesian workflow for such models, including four features: (1) an adjustment for incomplete case ascertainment, (2) an adequate sampling distribution of laboratory-confirmed cases, (3) a flexible, time-varying transmission rate, and (4) a stratification by age group. Within the workflow, we benchmarked the performance of various implementations of two of these features (2 and 3). For the second feature, we used SARS-CoV-2 data from the canton of Geneva (Switzerland) and found that a quasi-Poisson distribution is the most suitable sampling distribution for describing the overdispersion in the observed laboratory-confirmed cases. For the third feature, we implemented three methods: Brownian motion, B-splines, and approximate Gaussian processes (aGP). We compared their performance in terms of the number of effective samples per second, and the error and sharpness in estimating the time-varying transmission rate over a selection of ordinary differential equation solvers and tuning parameters, using simulated seroprevalence and laboratory-confirmed case data. Even though all methods could recover the time-varying dynamics in the transmission rate accurately, we found that B-splines perform up to four and ten times faster than Brownian motion and aGPs, respectively. We validated the B-spline model with simulated age-stratified data. We applied this model to 2020 laboratory-confirmed SARS-CoV-2 cases and two seroprevalence studies from the canton of Geneva. This resulted in detailed estimates of the transmission rate over time and the case ascertainment. Our results illustrate the potential of the presented workflow including stratified transmission to estimate age-specific epidemiological parameters. The workflow is freely available in the R package HETTMO, and can be easily adapted and applied to other infectious diseases.

Bayesian modeling of dynamic behavioral change during an epidemic

For many infectious disease outbreaks, the at-risk population changes their behavior in response to the outbreak severity, causing the transmission dynamics to change in real-time. Behavioral change is often ignored in epidemic modeling efforts, making these models less useful than they could be. We address this by introducing a novel class of data-driven epidemic models which characterize and accurately estimate behavioral change. Our proposed model allows time-varying transmission to be captured by the level of "alarm" in the population, with alarm specified as a function of the past epidemic trajectory. We investigate the estimability of the population alarm across a wide range of scenarios, applying both parametric functions and non-parametric functions using splines and Gaussian processes. The model is set in the data-augmented Bayesian framework to allow estimation on partially observed epidemic data. The benefit and utility of the proposed approach is illustrated through applications to data from real epidemics.

Estimating time-dependent contact: a multi-strain epidemiological model of SARS-CoV-2 on the island of Ireland

Mathematical modelling plays a key role in understanding and predicting the epidemiological dynamics of infectious diseases. We construct a flexible discrete-time model that incorporates multiple viral strains with different transmissibilities to estimate the changing patterns of human contact that generates new infections. Using a Bayesian approach, we fit the model to longitudinal data on hospitalisation with COVID-19 from the Republic of Ireland and Northern Ireland during the first year of the pandemic. We describe the estimated change in human contact in the context of government-mandated non-pharmaceutical interventions in the two jurisdictions on the island of Ireland. We take advantage of the fitted model to conduct counterfactual analyses exploring the impact of lockdown timing and introducing a novel, more transmissible variant. We found substantial differences in human contact between the two jurisdictions during periods of varied restriction easing and December holidays. Our counterfactual analyses reveal that implementing lockdowns earlier would have decreased subsequent hospitalisation substantially in most, but not all cases, and that an introduction of a more transmissible variant - without necessarily being more severe - can cause a large impact on the health care burden.

Impact of vaccination on the entire population and dose-response relation of COVID-19

Objective

The objective of this study is to develop a mathematical model for the COVID-19 pandemic including vaccination, the transmissibility of the virus-pathogen dose-response relationship, vaccine efficiency, and vaccination rate.

Methods

The Runge-Kutta (RK-45) method was applied to solve the proposed model with MATLAB code and the calculated results show the dynamics of the individuals in each compartment. The data of total death due to the COVID-19 pandemic in the case of the USA were collected from GitHub and the re-use of this data needs no ethical clearance. The control reproduction number was used to assess the dose-response relationship and critical vaccination coverage.

Results

We have calculated the probability of infection and the infection risk against the different exposure doses and the virus copies, respectively. The results show that the probability of infection increases with the increasing exposure dose for certain virus copies and the risk of infection decreases with the increasing of virus copies for a certain exposure dose. The results also show that the critical vaccination coverage demands increase with an increase in transmission rate and decrease with increasing vaccine efficacy.

Conclusions

It was seen that the critical vaccination coverage corresponding to an increased transmission rate rise sharply in the beginning and then reached a threshold. Moreover, the real data of the total death cases in the USA were compared with the fitted curved of the model which validated the proposed model. Vaccination against COVID-19 is essential to control the pandemic, and achieving high vaccine uptake in the population can reduce the pandemic as fast as possible.

Modeling the time-dependent transmission rate using gaussian pulses for analyzing the COVID-19 outbreaks in the world

In this work, an SEIR epidemic model with time-dependent transmission rate parameters for the multiple waves of COVID-19 infection was investigated. It is assumed that the transmission rate is determined by the superposition of the Gaussian pulses. The interaction of these dynamics is represented by recursive equations. Analysis of the overall dynamics of disease spread is determined by the effective reproduction number R_e(t) produced throughout the infection period. The study managed to show the evolution of the epidemic over time and provided important information about the occurrence of multiple waves of COVID-19 infection in the world and Indonesia.

Model Development and Prediction of Covid-19 Pandemic in Bangladesh with Nonlinear Incident

We introduce a SEIRD compartmental model to analyze the dynamics of the pandemic in Bangladesh. The multi-wave patterns of the new infective in Bangladesh from the day of the official confirmation to August 15, 2021, are simulated in the proposed SEIRD model. To solve the model equations numerically, we use the RK-45 method. Primarily, we establish some theorems including local and global stability for the proposed model. The analysis shows that the death curve simulated by the model provides a very good agreement with the officially confirmed death data for the Covid-19 pandemic in Bangladesh. Furthermore, the proposed model estimates the duration and peaks of Covid-19 in Bangladesh which are compared with the real data.

An SEIR Model with Time-Varying Coefficients for Analyzing the SARS-CoV-2 Epidemic

In this study, we propose a time-dependent susceptible-exposed-infected-recovered (SEIR) model for the analysis of the SARS-CoV-2 epidemic outbreak in three different countries, the United States, Italy, and Iceland using public data inherent the numbers of the epidemic wave. Since several types and grades of actions were adopted by the governments, including travel restrictions, social distancing, or limitation of movement, we want to investigate how these measures can affect the epidemic curve of the infectious population. The parameters of interest for the SEIR model were estimated employing a composite likelihood approach. Moreover, standard errors have been corrected for temporal dependence. The adoption of restrictive measures results in flatten epidemic curves, and the future evolution indicated a decrease in the number of cases.

Mathematical modeling to study the impact of immigration on the dynamics of the COVID-19 pandemic: A case study for Venezuela

We propose two different mathematical models to study the effect of immigration on the COVID-19 pandemic. The first model does not consider immigration, whereas the second one does. Both mathematical models consider five different subpopulations: susceptible, exposed, infected, asymptomatic carriers, and recovered. We find the basic reproduction number R₀ using the next-generation matrix method for the mathematical model without immigration. This threshold parameter is paramount because it allows us to characterize the evolution of the disease and identify what parameters substantially affect the COVID-19 pandemic outcome. We focus on the Venezuelan scenario, where immigration and emigration have been important over recent years, particularly during the pandemic. We show that the estimation of the transmission rates of the SARS-CoV-2 are affected when the immigration of infected people is considered. This has an important consequence from a public health perspective because if the basic reproduction number is less than unity, we can expect that the SARS-CoV-2 would disappear. Thus, if the basic reproduction number is slightly above one, we can predict that some mild non-pharmaceutical interventions would be enough to decrease the number of infected people. The results show that the dynamics of the spread of SARS-CoV-2 through the population must consider immigration to obtain better insight into the outcomes and create awareness in the population regarding the population flow.

A generalized epidemiological model with dynamic and asymptomatic population

In this paper, we develop an extension of compartmental epidemiological models which is suitable for COVID-19. The model presented in this paper comprises seven compartments in the progression of the disease. This model, named as the SINTRUE (Susceptible, Infected and pre-symptomatic, Infected and Symptomatic but Not Tested, Tested Positive, Recorded Recovered, Unrecorded Recovered, and Expired) model. The proposed model incorporates transmission due to asymptomatic carriers and captures the spread of the disease due to the movement of people to/from different administrative boundaries within a country. In addition, the model allows estimating the number of undocumented infections in the population and the number of unrecorded recoveries. The associated parameters in the model can help architect the public health policy and operational management of the pandemic. The results show that the testing rate of the asymptomatic patients is a crucial parameter to fight against the pandemic. The model is also shown to have a better predictive capability than the other epidemiological models.

Risk and the Republican National Convention: Application of the Novel COVID-19 Operational Risk Assessment

The United States Centers for Disease Control and Prevention and the World Health Organization broadly categorize mass gathering events as high risk for amplification of coronavirus disease 2019 (COVID-19) spread in a community due to the nature of respiratory diseases and the transmission dynamics. However, various measures and modifications can be put in place to limit or reduce the risk of further spread of COVID-19 for the mass gathering. During this pandemic, the Johns Hopkins University Center for Health Security produced a risk assessment and mitigation tool for decision-makers to assess SARS-CoV-2 transmission risks that may arise as organizations and businesses hold mass gatherings or increase business operations: The JHU Operational Toolkit for Businesses Considering Reopening or Expanding Operations in COVID-19 (Toolkit). This article describes the deployment of a data-informed, risk-reduction strategy that protects local communities, preserves local health-care capacity, and supports democratic processes through the safe execution of the Republican National Convention in Charlotte, North Carolina. The successful use of the Toolkit and the lessons learned from this experience are applicable in a wide range of public health settings, including school reopening, expansion of public services, and even resumption of health-care delivery.

Modeling the effects of the governmental responses to COVID-19 on transit demand: The case of Athens, Greece

Short-term demand forecasting is essential for the public transit system, allowing for effective operations planning. This is especially relevant in the highly uncertain environment created by the SARS‑CoV‑2 pandemic. In this paper, we attempt to develop accurate prediction models of transit ridership in Athens, Greece, using Autoregressive Fractional Integrated time series models enhanced with SARS‑CoV‑2-related exogenous variables. The selected exogenous variables are, from the one hand, the ratio of weekly SARS‑CoV‑2 infections over the infections 3 weeks before (capturing the dynamics of the pandemic, as a proxy for fear of transmitting the disease while commuting), and from the other hand, an index of the stringency of the government's SARS‑CoV‑2-related measures and regulations. The developed ARFIMAX models have been fitted separately on bus and metro ridership data and wield comparable and statistically significant results. In both models, the exogenous variables prove to be statistically significant and their values are intuitive, suggesting a linear interrelation between them and transit ridership.

Data analysis and prediction of the COVID-19 outbreak in the first and second waves for top 5 affected countries in the world

In this paper, we introduce a SEIATR compartmental model to analyze and predict the COVID-19 outbreak in the Top 5 affected countries in the world, namely the USA, India, Brazil, France, and Russia. The officially confirmed cases and death due to COVID-19 from the day of the official confirmation to June 30, 2021 are considered for each country. Primarily, we use the data to make a comparison between the cumulative cases and deaths due to COVID-19 among these five different countries. This analysis allows us to infer the key parameters associated with the dynamics of the disease for these five different countries. For example, the analysis reveals that the infection rate is much higher in the USA, Brazil, and France compared to that of India and Russia, while the recovery rate is found almost the same for these countries. Further, the death rate is measured higher in Brazil as opposed to India, where it is found much lower among the remaining countries. We then use the SEIART compartmental model to characterize the first and second waves of these countries, as well as to investigate and identify the influential model parameters and nature of the virus transmissibility in respective countries. Besides estimating the time-dependent reproduction number (Rt) for these countries, we also use the model to predict the peak size and the time occurring peak in respective countries. The analysis demonstrates that COVID-19 was observed to be much more infectious in the second wave than the first wave in all countries except France. The results also demonstrate that the epidemic took off very quickly in the USA, India, and Brazil compared to two other countries considered in this study. Furthermore, the prediction of the epidemic peak size and time produced by our model provides a very good agreement with the officially confirmed cases data for all countries expect Brazil.

Generalized SIR (GSIR) epidemic model: An improved framework for the predictive monitoring of COVID-19 pandemic

Novel coronavirus respiratory disease COVID-19 has caused havoc in many countries across the globe. In order to contain infection of this highly contagious disease, most of the world population is constrained to live in a complete or partial lockdown for months together with a minimal human-to-human interaction having far reaching consequences on countries' economy and mental well-being of their citizens. Hence, there is a need for a good predictive model for the health advisory bodies and decision makers for taking calculated proactive measures to contain the pandemic and maintain a healthy economy. This paper extends the mathematical theory of the classical Susceptible-Infected-Removed (SIR) epidemic model and proposes a Generalized SIR (GSIR) model that is an integrative model encompassing multiple waves of daily reported cases. Existing growth function models of epidemic have been shown as the special cases of the GSIR model. Dynamic modeling of the parameters reflect the impact of policy decisions, social awareness, and the availability of medication during the pandemic. GSIR framework can be utilized to find a good fit or predictive model for any pandemic. The study is performed on the COVID-19 data for various countries with detailed results for India, Brazil, United States of America (USA), and World. The peak infection, total expected number of COVID-19 cases and thereof deaths, time-varying reproduction number, and various other parameters are estimated from the available data using the proposed methodology. The proposed GSIR model advances the existing theory and yields promising results for continuous predictive monitoring of COVID-19 pandemic.

Khalil New Generalized Weibull Distribution Based on Ranked Samples: Estimation, Mathematical Properties, and Application to COVID-19 Data

In this paper, a five-parameter distribution, Khalil’s new generalized Weibull distribution, is defined and studied in detail. Some mathematical and statistical functions are studied. The effects of shape parameters on skewness and kurtosis are studied. Extensions for density and distribution functions are provided. Estimation of the intended model parameters based on ranked samples is investigated. The behavior of the maximum likelihood estimators is examined using a Monte Carlo simulation. In order to predict unique symmetric and asymmetric patterns and illustrate the applicability and potential of the intended distribution, a COVID-19 dataset is analyzed. The goodness-of-fit results of the new generalized Weibull model of Khalil are compared with some other models. Finally, we make some concluding remarks.

Time-discrete SIR model for COVID-19 in Fiji

Using the data provided by Fiji's ministry of health and medical services, we apply an implicit time-discrete SIR (susceptible people–infectious people–removed people) model that tracks the transmission and recovering rate at time, t to predict the trend of the coronavirus disease 2019 (COVID-19) pandemic in Fiji. The model implied time-varying transmission and recovery rates were calculated from 4 May 2021 to 9 October 2021. The estimator functions for these rates were determined, and a short-term (30 days) forecast was done. The model was validated with observed values of the active and recovered cases from 11 October 2021 to 9 December 2021. Statistical results reveal a good fit of profiles between model simulated and the reported COVID-19 data. The gradual decrease of the time-varying basic reproduction number with values below one towards the end of the study period suggest the government's success in controlling the epidemic. The mean reproduction number for the second wave of COVID-19 in Fiji was estimated as 2.7818. The results from this study can be used by researchers, the Fijian government, and the relevant health policy makers in making informed decisions should a third COVID-19 wave occur.

Modeling COVID-19 Incidence by the Renewal Equation after Removal of Administrative Bias and Noise

Simple Summary

In the past two years, the COVID-19 incidence curves and reproduction number Rt have been the main metrics used by policy makers and journalists to monitor the spread of this global pandemic. However, these metrics are not always reliable in the short term, because of a combination of delay in detection, administrative delays and random noise. In this article, we present a complete model of COVID-19 incidence, faithfully reconstructing the incidence curve and reproduction number from the renewal equation of the disease and precisely estimating the biases associated with periodic weekly bias, festive day bias and residual noise.

Abstract

The sanitary crisis of the past two years has focused the public’s attention on quantitative indicators of the spread of the COVID-19 pandemic. The daily reproduction number Rt, defined by the average number of new infections caused by a single infected individual at time t, is one of the best metrics for estimating the epidemic trend. In this paper, we provide a complete observation model for sampled epidemiological incidence signals obtained through periodic administrative measurements. The model is governed by the classic renewal equation using an empirical reproduction kernel, and subject to two perturbations: a time-varying gain with a weekly period and a white observation noise. We estimate this noise model and its parameters by extending a variational inversion of the model recovering its main driving variable Rt. Using Rt, a restored incidence curve, corrected of the weekly and festive day bias, can be deduced through the renewal equation. We verify experimentally on many countries that, once the weekly and festive days bias have been corrected, the difference between the incidence curve and its expected value is well approximated by an exponential distributed white noise multiplied by a power of the magnitude of the restored incidence curve.

Gauging the Impact of Artificial Intelligence and Mathematical Modeling in Response to the COVID-19 Pandemic: A Systematic Review

While the world continues to grapple with the devastating effects of the SARS-nCoV-2 virus, different scientific groups, including researchers from different parts of the world, are trying to collaborate to discover solutions to prevent the spread of the COVID-19 virus permanently. Henceforth, the current study envisions the analysis of predictive models that employ machine learning techniques and mathematical modeling to mitigate the spread of COVID-19. A systematic literature review (SLR) has been conducted, wherein a search into different databases, viz., PubMed and IEEE Explore, fetched 1178 records initially. From an initial of 1178 records, only 50 articles were analyzed completely. Around (64%) of the studies employed data-driven mathematical models, whereas only (26%) used machine learning models. Hybrid and ARIMA models constituted about (5%) and (3%) of the selected articles. Various Quality Evaluation Metrics (QEM), including accuracy, precision, specificity, sensitivity, Brier-score, F1-score, RMSE, AUC, and prediction and validation cohort, were used to gauge the effectiveness of the studied models. The study also considered the impact of Pfizer-BioNTech (BNT162b2), AstraZeneca (ChAd0x1), and Moderna (mRNA-1273) on Beta (B.1.1.7) and Delta (B.1.617.2) viral variants and the impact of administering booster doses given the evolution of viral variants of the virus.

Statistical Analysis of the People Fully Vaccinated against COVID-19 in Two Different Regions

Motivation. Currently, the COVID-19 pandemic represents a critical issue all over the world. On May 11, 2020, at 05 : 41 GMT, approximately 0.28 million individuals had perished because of the COVID-19 pandemic, and the figure is continuously growing rapidly. Unfortunately, millions of people have died due to this pandemic. As a result, this issue forced governments and other corresponding organizations to take significant action, such as the lockdown and vaccinations. Furthermore, scientists have developed several vaccinations, and the World Health Organization (WHO) has urged governments and people to get vaccinated to eradicate this pandemic. Consequently, the findings of any scientific research into this phenomenon are highly interesting. Problem Statement. To enhance individual protection, it is now critical to analyze and compare the percentage of people fully vaccinated against COVID-19. It is constantly of interest in the field of big data science and other related disciplines to provide the best analysis and modeling of COVID-19 data. Methodology. Through this paper, we aimed to compare individuals who have been completely vaccinated against COVID-19 in two locations: North American countries and Arabian Peninsula countries. Simple techniques for comparing individuals who have been completely vaccinated against COVID-19 have been applied, which may be used to generate the foundation for conclusions. Most significantly, a modern statistical model was created to present the best assessment of individuals completely vaccinated against COVID-19 data in nations in North America and the Arabian Peninsula. Some of the suggested statistical model features were proposed. Furthermore, the estimate of the model parameters was driven using the maximum likelihood estimation method. Results. The flexibility provided by the proposed statistical model is useful for describing the percentage of the individuals completely vaccinated against COVID-19, which provides a close fit with the COVID-19 data. Implications. The proposed statistical model can be used for statistics and generate new statistical distributions that can be used to compare and predict the process of people's willingness to vaccinate and take the vaccine to try to eliminate COVID-19.

The current COVID-19 pandemic in China: An overview and corona data analysis☆

At the end of December 2019, the Wuhan Municipal Health Commission, revealed several cases of pneumonia of unknown etiology. Later, this etiology was called the coronavirus disease 2019 (COVID-19). COVID-19 disease is rapidly spreading around the globe, affected millions of people, compelling governments to take serious actions. Due to this deadly disease, a number of deaths have been occurred and still increasing exponentially. In the practice and application of big data sciences, it is always of interest to provide the best description of the data. In this present article, the event background, symptoms, and preventions from COVID-19 are discussed. The steps were taken by the Chinese government to control the COVID-19 has also been discussed. Up to date, details, and data of daily discovered cases, total discovered cases, daily deaths, and total deaths around the world are presented. Moreover, a new statistical distribution is introduced to provide the best characterization of the survival times of the patients affected by the COVID-19 in China. By analyzing the survival times of the COVID-19 patient’s data, it is showed that the new model provides a closer fit to COVID-19 events.

Priority and age specific vaccination algorithm for the pandemic diseases: a comprehensive parametric prediction model

BACKGROUND

There have been several destructive pandemic diseases in the human history. Since these pandemic diseases spread through human-to-human infection, a number of non-pharmacological policies has been enforced until an effective vaccine has been developed. In addition, even though a vaccine has been developed, due to the challenges in the production and distribution of the vaccine, the authorities have to optimize the vaccination policies based on the priorities. Considering all these facts, a comprehensive but simple parametric model enriched with the pharmacological and non-pharmacological policies has been proposed in this study to analyse and predict the future pandemic casualties.

METHOD

This paper develops a priority and age specific vaccination policy and modifies the non-pharmacological policies including the curfews, lockdowns, and restrictions. These policies are incorporated with the susceptible, suspicious, infected, hospitalized, intensive care, intubated, recovered, and death sub-models. The resulting model is parameterizable by the available data where a recursive least squares algorithm with the inequality constraints optimizes the unknown parameters. The inequality constraints ensure that the structural requirements are satisfied and the parameter weights are distributed proportionally.

RESULTS

The results exhibit a distinctive third peak in the casualties occurring in 40 days and confirm that the intensive care, intubated, and death casualties converge to zero faster than the susceptible, suspicious, and infected casualties with the priority and age specific vaccination policy. The model also estimates that removing the curfews on the weekends and holidays cause more casualties than lifting the restrictions on the people with the chronic diseases and age over 65.

CONCLUSION

Sophisticated parametric models equipped with the pharmacological and non-pharmacological policies can predict the future pandemic casualties for various cases.

The propagation effect of commuting to work in the spatial transmission of COVID-19

This work is concerned with the spatiotemporal dynamics of the coronavirus disease 2019 (COVID-19) in Germany. Our goal is twofold: first, we propose a novel spatial econometric model of the epidemic spread across NUTS-3 regions to identify the role played by commuting-to-work patterns for spatial disease transmission. Second, we explore if the imposed containment (lockdown) measures during the first pandemic wave in spring 2020 have affected the strength of this transmission channel. Our results from a spatial panel error correction model indicate that, without containment measures in place, commuting-to-work patterns were the first factor to significantly determine the spatial dynamics of daily COVID-19 cases in Germany. This indicates that job commuting, particularly during the initial phase of a pandemic wave, should be regarded and accordingly monitored as a relevant spatial transmission channel of COVID-19 in a system of economically interconnected regions. Our estimation results also provide evidence for the triggering role of local hot spots in disease transmission and point to the effectiveness of containment measures in mitigating the spread of the virus across German regions through reduced job commuting and other forms of mobility.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10109-021-00349-3.

Hybrid deep learning of social media big data for predicting the evolution of COVID-19 transmission

In this study, a hybrid deep-learning model termed as ODANN, built upon neural networks (NN) coupled with data assimilation and natural language processing (NLP) features extraction methods, has been constructed to concurrently process daily COVID-19 time-series records and large volumes of COVID-19 related Twitter data, as representative of the global community's aggregated emotional responses towards the current pandemic, to model the growth rate in the number of confirmed COVID-19 cases globally via a proposed G parameter. Overall, there were 3 key components to ODANN's development phase, namely: (i) data hydration and pre-processing were performed on COVID-19 related Twitter data ranging between 23 January 2020 and 10 May 2020, which amounted to over 100 million Tweets written in English language; (ii) multiple NLP features extraction methods were subsequently leveraged to encode the hydrated Twitter data into useful semantic word vectors for training ODANN under an optimal set of hyperparameters; and (iii) historical time-series data of defined characteristics were also assimilated into ODANN's selected hidden layer(s) to model the G parameter daily with a lead-time of 1 day. By far, our experimental results demonstrated that by adopting a rolling time-window size of 5 days, with respect to the number of historical time-series records for assimilating different data features, enabled ODANN to outperform other traditional time-series models and recent studies, in terms of the computed RMSE and MAE scores attained from the model's testing step. Overall, the summarized results from ODANN demonstrated its competitive edge in modelling and forecasting the growth rate in the number of COVID-19 cases globally.

Influenza viruses and coronaviruses: Knowns, unknowns, and common research challenges

The development of safe and effective vaccines in a record time after the emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a remarkable achievement, partly based on the experience gained from multiple viral outbreaks in the past decades. However, the Coronavirus Disease 2019 (COVID-19) crisis also revealed weaknesses in the global pandemic response and large gaps that remain in our knowledge of the biology of coronaviruses (CoVs) and influenza viruses, the 2 major respiratory viruses with pandemic potential. Here, we review current knowns and unknowns of influenza viruses and CoVs, and we highlight common research challenges they pose in 3 areas: the mechanisms of viral emergence and adaptation to humans, the physiological and molecular determinants of disease severity, and the development of control strategies. We outline multidisciplinary approaches and technological innovations that need to be harnessed in order to improve preparedeness to the next pandemic.

Does the data tell the true story? A modelling assessment of early COVID-19 pandemic suppression and mitigation strategies in Ghana

This paper uses publicly available data and various statistical models to estimate the basic reproduction number (R0) and other disease parameters for Ghana's early COVID-19 pandemic outbreak. We also test the effectiveness of government imposition of public health measures to reduce the risk of transmission and impact of the pandemic, especially in the early phase. R0 is estimated from the statistical model as 3.21 using a 0.147 estimated growth rate [95% C.I.: 0.137-0.157] and a 15-day time to recovery after COVID-19 infection. This estimate of the initial R0 is consistent with others reported in the literature from other parts of Africa, China and Europe. Our results also indicate that COVID-19 transmission reduced consistently in Ghana after the imposition of public health interventions-such as border restrictions, intra-city movement, quarantine and isolation-during the first phase of the pandemic from March to May 2020. However, the time-dependent reproduction number (Rt) beyond mid-May 2020 does not represent the true situation, given that there was not a consistent testing regime in place. This is also confirmed by our Jack-knife bootstrap estimates which show that the positivity rate over-estimates the true incidence rate from mid-May 2020. Given concerns about virus mutations, delays in vaccination and a possible new wave of the pandemic, there is a need for systematic testing of a representative sample of the population to monitor the reproduction number. There is also an urgent need to increase the availability of testing for the general population to enable early detection, isolation and treatment of infected individuals to reduce progression to severe disease and mortality.

Explaining Causal Influence of External Factors on Incidence Rate of Covid-19

Classical susceptible-infected-removed model with constant transmission rate and removal rate may not capture real world dynamics of epidemic due to complex influence of multiple external factors on the spread and spatio-temporal variation of transmission rate. Also, explainability of a model is of prime necessity to understand the influence of multiple factors on transmission rate. Thus, we modified discrete global susceptible-infected-removed model with time-varying transmission rate, recovery rate and multiple spatially local models. We have derived the criteria for disease-free equilibrium within a specific time period. A convolutional LSTM model is created and trained to map multiple spatiotemporal features to transmission rate. The model achieved 8.39% mean absolute percent error in terms of cumulative infection cases in each locality in a region in USA for a 10-day prediction period. Comparison with current state of the art methods reveals performance superiority of the proposed method. A perturbation-based spatio-temporal model interpretation method is proposed which generates spatio-temporal local interpretations. Global interpretations are generated by statistically accumulating the local interpretations. Global interpretations of transmission rate for a region in USA shows consistent positive influence of population density, whereas, temperature and humidity have very minor influence. An experiment with what-if scenario reveals locality specific quick identification of positive cases, rapid isolation and improving healthcare facilities are keys to rapid convergence to disease-free equilibrium. A long-term forecasting of 160 days predicts new infection cases in a region in USA with a median error of 455 cases.

Underdetection in a stochastic SIR model for the analysis of the COVID-19 Italian epidemic

We propose a way to model the underdetection of infected and removed individuals in a compartmental model for estimating the COVID-19 epidemic. The proposed approach is demonstrated on a stochastic SIR model, specified as a system of stochastic differential equations, to analyse data from the Italian COVID-19 epidemic. We find that a correct assessment of the amount of underdetection is important to obtain reliable estimates of the critical model parameters. The adaptation of the model in each time interval between relevant government decrees implementing contagion mitigation measures provides short-term predictions and a continuously updated assessment of the basic reproduction number.

Nine-month Trend of Time-Varying Reproduction Numbers of COVID-19 in West of Iran

BACKGROUND

The basic reproduction number (R0) is an important concept in infectious disease epidemiology and the most important parameter to determine the transmissibility of a pathogen. This study aimed to estimate the nine-month trend of time-varying R of COVID-19 epidemic using the serial interval (SI) and Markov Chain Monte Carlo in Lorestan, west of Iran.

STUDY DESIGN

Descriptive study.

METHODS

This study was conducted based on a cross-sectional method. The SI distribution was extracted from data and log-normal, Weibull, and Gamma models were fitted. The estimation of time-varying R0, a likelihood-based model was applied, which uses pairs of cases to estimate relative likelihood.

RESULTS

In this study, Rt was estimated for SI 7-day and 14-day time-lapses from 27 February-14 November 2020. To check the robustness of the R0 estimations, sensitivity analysis was performed using different SI distributions to estimate the reproduction number in 7-day and 14-day time-lapses. The R0 ranged from 0.56 to 4.97 and 0.76 to 2.47 for 7-day and 14-day time-lapses. The doubling time was estimated to be 75.51 days (95% CI: 70.41, 81.41).

CONCLUSION

Low R0 of COVID-19 in some periods in Lorestan, west of Iran, could be an indication of preventive interventions, namely quarantine and isolation. To control the spread of the disease, the reproduction number should be reduced by decreasing the transmission and contact rates and shortening the infectious period.

Self-driven criticality in a stochastic epidemic model

We present a generic epidemic model with stochastic parameters in which the dynamics self-organize to a critical state with suppressed exponential growth. More precisely, the dynamics evolve into a quasi-steady state, where the effective reproduction rate fluctuates close to the critical value 1 for a long period, as indeed observed for different epidemics. The main assumptions underlying the model are that the rate at which each individual becomes infected changes stochastically in time with a heavy-tailed steady state. The critical regime is characterized by an extremely long duration of the epidemic. Its stability is analyzed both numerically and analytically in different models.

Quality-Adjusted Life-Year Losses Averted With Every COVID-19 Infection Prevented in the United States

OBJECTIVE

To estimate the overall quality-adjusted life-years (QALYs) gained by averting 1 coronavirus disease 2019 (COVID-19) infection over the duration of the pandemic.

METHODS

A cohort-based probabilistic simulation model, informed by the latest epidemiological estimates on COVID-19 in the United States provided by the Centers for Disease Control and Prevention and literature review. Heterogeneity of parameter values across age group was accounted for. The main outcome studied was QALYs for the infected patient, patient's family members, and the contagion effect of the infected patient over the duration of the pandemic.

RESULTS

Averting a COVID-19 infection in a representative US resident will generate an additional 0.061 (0.016-0.129) QALYs (for the patient: 0.055, 95% confidence interval [CI] 0.014-0.115; for the patient's family members: 0.006, 95% CI 0.002-0.015). Accounting for the contagion effect of this infection, and assuming that an effective vaccine will be available in 3 months, the total QALYs gains from averting 1 single infection is 1.51 (95% CI 0.28-4.37) accrued to patients and their family members affected by the index infection and its sequelae. These results were robust to most parameter values and were most influenced by effective reproduction number, probability of death outside the hospital, the time-varying hazard rates of hospitalization, and death in critical care.

CONCLUSION

Our findings suggest that the health benefits of averting 1 COVID-19 infection in the United States are substantial. Efforts to curb infections must weigh the costs against these benefits.

Risk and the Republican National Convention: Application of the Novel COVID-19 Operational Risk Assessment

The United States Centers for Disease Control and Prevention and the World Health Organization broadly categorize mass gathering events as high risk for amplification of coronavirus disease 2019 (COVID-19) spread in a community due to the nature of respiratory diseases and the transmission dynamics. However, various measures and modifications can be put in place to limit or reduce the risk of further spread of COVID-19 for the mass gathering. During this pandemic, the Johns Hopkins University Center for Health Security produced a risk assessment and mitigation tool for decision-makers to assess SARS-CoV-2 transmission risks that may arise as organizations and businesses hold mass gatherings or increase business operations: The JHU Operational Toolkit for Businesses Considering Reopening or Expanding Operations in COVID-19 (Toolkit). This article describes the deployment of a data-informed, risk-reduction strategy that protects local communities, preserves local health-care capacity, and supports democratic processes through the safe execution of the Republican National Convention in Charlotte, North Carolina. The successful use of the Toolkit and the lessons learned from this experience are applicable in a wide range of public health settings, including school reopening, expansion of public services, and even resumption of health-care delivery.

A Framework for a Statistical Characterization of Epidemic Cycles: COVID-19 Case Study

Background

Since the beginning of the COVID-19 pandemic, researchers and health authorities have sought to identify the different parameters that drive its local transmission cycles to make better decisions regarding prevention and control measures. Different modeling approaches have been proposed in an attempt to predict the behavior of these local cycles.

Objective

This paper presents a framework to characterize the different variables that drive the local, or epidemic, cycles of the COVID-19 pandemic, in order to provide a set of relatively simple, yet efficient, statistical tools to be used by local health authorities to support decision making.

Methods

Virtually closed cycles were compared to cycles in progress from different locations that present similar patterns in the figures that describe them. With the aim to compare populations of different sizes at different periods of time and locations, the cycles were normalized, allowing an analysis based on the core behavior of the numerical series. A model for the reproduction number was derived from the experimental data, and its performance was presented, including the effect of subnotification (ie, underreporting). A variation of the logistic model was used together with an innovative inventory model to calculate the actual number of infected persons, analyze the incubation period, and determine the actual onset of local epidemic cycles.

Results

The similarities among cycles were demonstrated. A pattern between the cycles studied, which took on a triangular shape, was identified and used to make predictions about the duration of future cycles. Analyses on effective reproduction number (R_t) and subnotification effects for Germany, Italy, and Sweden were presented to show the performance of the framework introduced here. After comparing data from the three countries, it was possible to determine the probable dates of the actual onset of the epidemic cycles for each country, the typical duration of the incubation period for the disease, and the total number of infected persons during each cycle. In general terms, a probable average incubation time of 5 days was found, and the method used here was able to estimate the end of the cycles up to 34 days in advance, while demonstrating that the impact of the subnotification level (ie, error) on the effective reproduction number was <5%.

Conclusions

It was demonstrated that, with relatively simple mathematical tools, it is possible to obtain a reliable understanding of the behavior of COVID-19 local epidemic cycles, by introducing an integrated framework for identifying cycle patterns and calculating the variables that drive it, namely: the R_t, the subnotification effects on estimations, the most probable actual cycles start dates, the total number of infected, and the most likely incubation period for SARS-CoV-2.

Linking dynamic patterns of COVID-19 spreads in Italy with regional characteristics: a two level longitudinal modelling approach

The current statistical modeling of coronavirus (COVID-19) spread has mainly focused on spreading patterns and forecasting of COVID-19 development; these patterns have been found to vary among locations. As the survival time of coronaviruses on surfaces depends on temperature, some researchers have explored the association of daily confirmed cases with environmental factors. Furthermore, some researchers have studied the link between daily fatality rates with regional factors such as health resources, but found no significant factors. As the spreading patterns of COVID-19 development vary a lot among locations, fitting regression models of daily confirmed cases or fatality rates directly with regional factors might not reveal important relationships. In this study, we investigate the link between regional spreading patterns of COVID-19 development in Italy and regional factors in two steps. First, we characterize regional spreading patterns of COVID-19 daily confirmed cases by a special patterned Poisson regression model for longitudinal count; the varying growth and declining patterns as well as turning points among regions in Italy have been well captured by regional regression parameters. We then associate these regional regression parameters with regional factors. The effects of regional factors on spreading patterns of COVID-19 daily confirmed cases have been effectively evaluated.

An epidemic model for non-first-order transmission kinetics

Compartmental models in epidemiology characterize the spread of an infectious disease by formulating ordinary differential equations to quantify the rate of disease progression through subpopulations defined by the Susceptible-Infectious-Removed (SIR) scheme. The classic rate law central to the SIR compartmental models assumes that the rate of transmission is first order regarding the infectious agent. The current study demonstrates that this assumption does not always hold and provides a theoretical rationale for a more general rate law, inspired by mixed-order chemical reaction kinetics, leading to a modified mathematical model for non-first-order kinetics. Using observed data from 127 countries during the initial phase of the COVID-19 pandemic, we demonstrated that the modified epidemic model is more realistic than the classic, first-order-kinetics based model. We discuss two coefficients associated with the modified epidemic model: transmission rate constant k and transmission reaction order n. While k finds utility in evaluating the effectiveness of control measures due to its responsiveness to external factors, n is more closely related to the intrinsic properties of the epidemic agent, including reproductive ability. The rate law for the modified compartmental SIR model is generally applicable to mixed-kinetics disease transmission with heterogeneous transmission mechanisms. By analyzing early-stage epidemic data, this modified epidemic model may be instrumental in providing timely insight into a new epidemic and developing control measures at the beginning of an outbreak.

Towards Providing Effective Data-Driven Responses to Predict the Covid-19 in São Paulo and Brazil

São Paulo is the most populous state in Brazil, home to around 22% of the country's population. The total number of Covid-19-infected people in São Paulo has reached more than 1 million, while its total death toll stands at 25% of all the country's fatalities. Joining the Brazilian academia efforts in the fight against Covid-19, in this paper we describe a unified framework for monitoring and forecasting the Covid-19 progress in the state of São Paulo. More specifically, a freely available, online platform to collect and exploit Covid-19 time-series data is presented, supporting decision-makers while still allowing the general public to interact with data from different regions of the state. Moreover, a novel forecasting data-driven method has also been proposed, by combining the so-called Susceptible-Infectious-Recovered-Deceased model with machine learning strategies to better fit the mathematical model's coefficients for predicting Infections, Recoveries, Deaths, and Viral Reproduction Numbers. We show that the obtained predictor is capable of dealing with badly conditioned data samples while still delivering accurate 10-day predictions. Our integrated computational system can be used for guiding government actions mainly in two basic aspects: real-time data assessment and dynamic predictions of Covid-19 curves for different regions of the state. We extend our analysis and investigation to inspect the virus spreading in Brazil in its regions. Finally, experiments involving the Covid-19 advance in other countries are also given.

The Interplay of Demographic Variables and Social Distancing Scores in Deep Prediction of U.S. COVID-19 Cases

With the severity of the COVID-19 outbreak, we characterize the nature of the growth trajectories of counties in the United States using a novel combination of spectral clustering and the correlation matrix. As the U.S. and the rest of the world are experiencing a severe second wave of infections, the importance of assigning growth membership to counties and understanding the determinants of the growth are increasingly evident. Subsequently, we select the demographic features that are most statistically significant in distinguishing the communities. Lastly, we effectively predict the future growth of a given county with an LSTM using three social distancing scores. This comprehensive study captures the nature of counties' growth in cases at a very micro-level using growth communities, demographic factors, and social distancing performance to help government agencies utilize known information to make appropriate decisions regarding which potential counties to target resources and funding to.

Mathematical modelling of the second wave of COVID-19 infections using deterministic and stochastic SIDR models

Recently, various countries from across the globe have been facing the second wave of COVID-19 infections. In order to understand the dynamics of the spread of the disease, much effort has been made in terms of mathematical modeling. In this scenario, compartmental models are widely used to simulate epidemics under various conditions. In general, there are uncertainties associated with the reported data, which must be considered when estimating the parameters of the model. In this work, we propose an effective methodology for estimating parameters of compartmental models in multiple wave scenarios by means of a dynamic data segmentation approach. This robust technique allows the description of the dynamics of the disease without arbitrary choices for the end of the first wave and the start of the second. Furthermore, we adopt a time-dependent function to describe the probability of transmission by contact for each wave. We also assess the uncertainties of the parameters and their influence on the simulations using a stochastic strategy. In order to obtain realistic results in terms of the basic reproduction number, a constraint is incorporated into the problem. We adopt data from Germany and Italy, two of the first countries to experience the second wave of infections. Using the proposed methodology, the end of the first wave (and also the start of the second wave) occurred on 166 and 187 days from the beginning of the epidemic, for Germany and Italy, respectively. The estimated effective reproduction number for the first wave is close to that obtained by other approaches, for both countries. The results demonstrate that the proposed methodology is able to find good estimates for all parameters. In relation to uncertainties, we show that slight variations in the design variables can give rise to significant changes in the value of the effective reproduction number. The results provide information on the characteristics of the epidemic for each country, as well as elements for decision-making in the economic and governmental spheres.

Estimated prevalence and viral transmissibility in subjects with asymptomatic SARS-CoV-2 infections in Wuhan, China

The role of subjects with asymptomatic SARS-CoV-2 infection in the current pandemic is not well-defined. Based on two different approaches to estimate the culminative attack rate (seroprevalence of antibodies against SARS-CoV-2, and a four compartment mathematical model) and the reported number of patients with COVID-19, the ratio of asymptomatic versus symptomatic SARS-CoV-2 infection was estimated to be 7 (95% CI: 2.8–12.4) in Wuhan, Hubei, China, the first epicenter of this pandemic, which has settled with no new cases. Together with detailed recording of the contact sources in a cohort of patients, and applying the estimations to an established mathematical model, the viral transmissibility of the subjects with asymptomatic SARS-CoV-2 infection is around 10% of that of the symptomatic patients (95% CI: 7.6%–12.3%). Public health measures/policies should address this important pool of infectious source in combat against this viral pandemic.

Simulating the progression of the COVID-19 disease in Cameroon using SIR models

This paper analyses the evolution of COVID-19 in Cameroon over the period March 6-April 2020 using SIR models. Specifically, we 1) evaluate the basic reproduction number of the virus, 2) determine the peak of the infection and the spread-out period of the disease, and 3) simulate the interventions of public health authorities. Data used in this study is obtained from the Cameroonian Public Health Ministry. The results suggest that over the identified period, the reproduction number of COVID-19 in Cameroon is about 1.5, and the peak of the infection should have occurred at the end of May 2020 with about 7.7% of the population infected. Furthermore, the implementation of efficient public health policies could help flatten the epidemic curve.