Correlates of the country differences in the infection and mortality rates during the first wave of the COVID-19 pandemic: Evidence from Bayesian model averaging
Viktor Stojkoski, Zoran Utkovski, Petar Jolakoski, Dragan Tevdovski, Ljupco Kocarev
In the initial wave of the COVID-19 pandemic we observed great discrepancies in both infection and mortality rates between countries. Besides the biological and epidemiological factors, a multitude of social and economic criteria also influence the extent to which these discrepancies appear. Consequently, there is an active debate regarding the critical socio-economic and health factors that correlate with the infection and mortality rates outcome of the pandemic. Here, we leverage Bayesian model averaging techniques and country level data to investigate the potential of 28 variables, describing a diverse set of health and socio-economic characteristics, in being correlates of the final number of infections and deaths during the first wave of the coronavirus pandemic. We show that only few variables are able to robustly correlate with these outcomes. To understand the relationship between the potential correlates in explaining the infection and death rates, we create a Jointness Space. Using this space, we conclude that the extent to which each variable is able to provide a credible explanation for the COVID-19 infections/mortality outcome varies between countries because of their heterogeneous features.
We propose a probabilistic mortality forecasting model that can be applied to derive forecasts for populations with regular and irregular mortality developments. Our model (1) uses rates of mortality improvement to model dynamic age patterns of mortality change and it can (2) optionally complement the mortality trend of a country of interest with that of at least one reference country. Retrospective mortality forecasts for British and Danish women from 1991 to 2011 suggest that our model can generate smaller forecast errors than other widely accepted approaches like, for instance, the Lee-Cart…
Estimating the true mortality burden of COVID-19 for every country in the world is a difficult, but crucial, public health endeavor. Attributing deaths, direct or indirect, to COVID-19 is problematic. A more attainable target is the "excess deaths", the number of deaths in a particular period, relative to that expected during "normal times", and we estimate this for all countries on a monthly time scale for 2020 and 2021. The excess mortality requires two numbers, the total deaths and the expected deaths, but the former is unavailable for many countries, and so modeling is required for these c…
The number of new infections per day is a key quantity for effective epidemic management. It can be estimated relatively directly by testing of random population samples. Without such direct epidemiological measurement, other approaches are required to infer whether the number of new cases is likely to be increasing or decreasing: for example, estimating the pathogen effective reproduction number, R, using data gathered from the clinical response to the disease. For Covid-19 (SARS-CoV-2) such R estimation is heavily dependent on modelling assumptions, because the available clinical case data a…
Civil registration vital statistics (CRVS) data are used to produce national estimates of maternal mortality, but are often subject to substantial reporting errors due to misclassification of maternal deaths. The accuracy of CRVS systems can be assessed by comparing CRVS-based counts of maternal and non-maternal deaths to those obtained from specialized studies, which are rigorous assessments of maternal mortality for a given country-period. We developed a Bayesian bivariate random walk model to estimate sensitivity and specificity of the reporting on maternal mortality in CRVS data, and assoc…
IMEDACS；Vivace Health Solutions Inc（Vivace健康解决方案公司）；Johns Hopkins University（约翰斯·霍普金斯大学）；Scripps Memorial Hospital - Encinitas（斯克里普斯恩西尼塔斯纪念医院）
Although timely sepsis diagnosis and prompt interventions in Intensive Care Unit (ICU) patients are associated with reduced mortality, early clinical recognition is frequently impeded by non-specific signs of infection and failure to detect signs of sepsis-induced organ dysfunction in a constellation of dynamically changing physiological data. The goal of this work is to identify patient at risk of life-threatening sepsis utilizing a data-centered and machine learning-driven approach. We derive a mortality risk predictive dynamic Bayesian network (DBN) guided by a customized sepsis knowledgeba…
Acute infection, if not rapidly and accurately detected, can lead to sepsis, organ failure and even death. Current detection of acute infection as well as assessment of a patient's severity of illness are imperfect. Characterization of a patient's immune response by quantifying expression levels of specific genes from blood represents a potentially more timely and precise means of accomplishing both tasks. Machine learning methods provide a platform to leverage this 'host response' for development of deployment-ready classification models. Prioritization of promising classifiers is dependent, …
Reliable mortality estimates at the subnational level are essential in the study of health inequalities within a country. One of the difficulties in producing such estimates is the presence of small populations, where the stochastic variation in death counts is relatively high, and so the underlying mortality levels are unclear. We present a Bayesian hierarchical model to estimate mortality at the subnational level. The model builds on characteristic age patterns in mortality curves, which are constructed using principal components from a set of reference mortality curves. Information on morta…
In this paper, we estimate the seroprevalence against COVID-19 by country and derive the seroprevalence over the world. To estimate seroprevalence, we use serological surveys (also called the serosurveys) conducted within each country. When the serosurveys are incorporated to estimate world seroprevalence, there are two issues. First, there are countries in which a serological survey has not been conducted. Second, the sample collection dates differ from country to country. We attempt to tackle these problems using the vaccination data, confirmed cases data, and national statistics. We constru…
In this work we present a spatial approach to model and investigate mortality data referenced over a Lexis structure. We decompose the force of mortality into two interpretable components: a Markov random field, smooth with respect to time, age and cohort which explains the main pattern of mortality; and a secondary component of independent shocks, accounting for additional non-smooth mortality. Inference is based on a hierarchical Bayesian approach with Markov chain Monte Carlo computations. We present an extensive application to data from the Human Mortality Database about 37 countries. For …
This paper presents a novel approach for modeling mortality rates above age 70 by proposing a mixture-based model. This model is compared to four other widely used models: the Beard, Gompertz, Makeham, and Perks models. Our model can capture the complex behavior of mortality rates at all ages, providing a more accurate representation of the data. To evaluate the performance of our model, we applied it to two countries with different data quality: Japan and Brazil. Our results show that the proposed model outperforms the other models in both countries, particularly in Japan where it obtained an…
In recent years, much of the focus in monitoring child mortality has been on assessing changes in the under-five mortality rate (U5MR). However, as the U5MR decreases, the share of neonatal deaths (within the first month) tends to increase, warranting increased efforts in monitoring this indicator in addition to the U5MR. A Bayesian splines regression model is presented for estimating neonatal mortality rates (NMR) for all countries. In the model, the relationship between NMR and U5MR is assessed and used to inform estimates, and spline regression models are used to capture country-specific tr…
Imperial College London（伦敦帝国理工学院）；National University of Singapore（新加坡国立大学）；University of Copenhagen（哥本哈根大学）
The COVID-19 pandemic has caused over 6.4 million registered deaths to date and has had a profound impact on economic activity. Here, we study the interaction of transmission, mortality, and the economy during the SARS-CoV-2 pandemic from January 2020 to December 2022 across 25 European countries. We adopt a Bayesian Mixed Effects model with auto-regressive terms. We find that increases in disease transmission intensity decreases Gross domestic product (GDP) and increases daily excess deaths, with a longer lasting impact on excess deaths in comparison to GDP, which recovers more rapidly. Broad…
Estimates of the under-five mortality rate (U5MR) are used to track progress in reducing child mortality and to evaluate countries' performance related to Millennium Development Goal 4. However, for the great majority of developing countries without well-functioning vital registration systems, estimating the U5MR is challenging due to limited data availability and data quality issues. We describe a Bayesian penalized B-spline regression model for assessing levels and trends in the U5MR for all countries in the world, whereby biases in data series are estimated through the inclusion of a multil…
The maternal mortality ratio (MMR) is defined as the number of maternal deaths in a population per 100,000 live births. Country-specific MMR estimates are published on a regular basis by the United Nations Maternal Mortality Estimation Inter-agency Group (UN MMEIG) to track progress in reducing maternal deaths and to evaluate regional and national performance related to Millennium Development Goal (MDG) 5, which calls for a 75% reduction in the MMR between 1990 and 2015. Until 2014, the UN MMEIG used a multilevel regression model for producing estimates for countries without sufficient data fr…
Accurate estimates of the under-5 mortality rate (U5MR) in a developing world context are a key barometer of the health of a nation. This paper describes new models to analyze survey data on mortality in this context. We are interested in both spatial and temporal description, that is, wishing to estimate U5MR across regions and years, and to investigate the association between the U5MR and spatially-varying covariate surfaces. We illustrate the methodology by producing yearly estimates for subnational areas in Kenya over the period 1980 - 2014 using data from demographic health surveys (DHS).…
Human mortality data sets can be expressed as multiway data arrays, the dimensions of which correspond to categories by which mortality rates are reported, such as age, sex, country and year. Regression models for such data typically assume an independent error distribution or an error model that allows for dependence along at most one or two dimensions of the data array. However, failing to account for other dependencies can lead to inefficient estimates of regression parameters, inaccurate standard errors and poor predictions. An alternative to assuming independent errors is to allow for dep…
The number of corona virus (COVID-19) infections grows worldwide. In order to create short term predictions to prepare for the extent of the global pandemic we analyze infection data from the top 25 affected countries. It is shown that all country-specific infection rates follow a power law growth behavior and the scaling exponents per country are calculated. We find two different growth patterns: either steady power law growth from the very beginning with moderate scaling exponents of 3-5 or explosive power law growth with dramatic scaling exponents of 8-11. In the case of the USA we even fin…
Covid-19 is raging a devastating trail with the highest mortality-to-infected ratio ever for a pandemic. Lack of vaccine and therapeutic has rendered social exclusion through lockdown as the singular mode of containment. Harnessing the predictive powers of Machine Learning within a 6 dimensional infection kinetic model, depicting interactive evolution of 6 infection stages - healthy susceptible ($H$), predisposed comorbid susceptible ($P$), infected ($I$), recovered ($R$), herd immunized ($V$) and mortality ($D$) - the model, PHIRVD, provides the first accurate mortality prediction of 18 count…
This paper introduces new methods to analyze the changing progression of COVID-19 cases to deaths in different waves of the pandemic. First, an algorithmic approach partitions each country or state's COVID-19 time series into a first wave and subsequent period. Next, offsets between case and death time series are learned for each country via a normalized inner product. Combining these with additional calculations, we can determine which countries have most substantially reduced the mortality rate of COVID-19. Finally, our paper identifies similarities in the trajectories of cases and deaths fo…
This paper compares and contrasts the spread and impact of COVID-19 in the three countries most heavily impacted by the pandemic: the United States (US), India and Brazil. All three of these countries have a federal structure, in which the individual states have largely determined the response to the pandemic. Thus, we perform an extensive analysis of the individual states of these three countries to determine patterns of similarity within each. First, we analyse structural similarity and anomalies in the trajectories of cases and deaths as multivariate time series. Next, we study the lengths …
In this paper, we propose a general framework for optimal control measures, which follows the evolution of COVID-19 infection counts collected by Surveillance Units on a country level. We employ an autoregressive model that allows to decompose the mean number of infections into three components that describe: intra-locality infections, inter-locality infections, and infections from other sources such as travelers arriving to a country from abroad. We identify the inter-locality term as a time-evolving network and when it drives the dynamics of the disease we focus on its properties. Tools from…
The COVID-19 pandemic has affected all countries of the world producing a substantial number of fatalities accompanied by a major disruption in their social, financial, and educational organization. The strict disciplinary measures implemented by China were very effective and thus were subsequently adopted by most world countries to various degrees. The infection duration and number of infected persons are of critical importance for the battle against the pandemic. We use the quantitative landscape of the disease spreading in China as a benchmark and utilize infection data from eight countries…
This study analyzed the morbidity and mortality rates of the COVID-19 pandemic in different prefectures of Japan. Under the constraint that daily maximum confirmed deaths and daily maximum cases should exceed 4 and 10, respectively, 14 prefectures were included, and cofactors affecting the morbidity and mortality rates were evaluated. In particular, the number of confirmed deaths was assessed excluding the cases of nosocomial infections and nursing home patients. A mild correlation was observed between morbidity rate and population density (R2=0.394). In addition, the percentage of the elderly…
Epidemic spread on networks is one of the most studied dynamics in network science and has important implications in real epidemic scenarios. Nonetheless, the dynamics of real epidemics and how it is affected by the underline structure of the infection channels are still not fully understood. Here we apply the SIR model and study analytically and numerically the epidemic spread on a recently developed spatial modular model imitating the structure of cities in a country. The model assumes that inside a city the infection channels connect many different locations, while the infection channels be…
The noise in daily infection counts of an epidemic should be super-Poissonian due to intrinsic epidemiological and administrative clustering. Here, we use this clustering to classify the official national SARS-CoV-2 daily infection counts and check for infection counts that are unusually anti-clustered. We adopt a one-parameter model of $ϕ'_i$ infections per cluster, dividing any daily count $n_i$ into $n_i/ϕ'_i$ 'clusters', for 'country' $i$. We assume that $n_i/ϕ'_i$ on a given day $j$ is drawn from a Poisson distribution whose mean is robustly estimated from the four neighbouring days, and …
The influence of per capita income on life expectancy is well documented, mostly through studies of multinational samples. However, one expects fairly weak correlations at both ends of the life span, that is to say in early infancy and in age groups of elderly from 85 to 100 years. The reason is that at both ends mortality is largely controled by biological factors rather than by socio-economic conditions. In order to test this conjecture, we explore the influence of income on age groups, separately in France, the United States and South Korea. More precisely in each country we compare income …
The spread of COVID-19 during the initial phase of the first half of 2020 was curtailed to a larger or lesser extent through measures of social distancing imposed by most countries. In this work, we link directly, through machine learning techniques, infection data at a country level to a single number that signifies social distancing effectiveness. We assume that the standard SIR model gives a reasonable description of the dynamics of spreading, and thus the social distancing aspect can be modeled through time-dependent infection rates that are imposed externally. We use an exponential ansatz…
In this paper, we introduce a novel modeling framework for incorporating fear of infection and frustration with social distancing into disease dynamics. We show that the resulting SEIR behavior-perception model has three principal modes of qualitative behavior---no outbreak, controlled outbreak, and uncontrolled outbreak. We also demonstrate that the model can produce transient and sustained waves of infection consistent with secondary outbreaks. We fit the model to cumulative COVID-19 case and mortality data from several regions. Our analysis suggests that regions which experience a significa…
There has been considerable public debate about whether the economic impact of the current COVID19 restrictions are worth the costs. Although the potential impact of COVID19 has been modelled extensively, very few numbers have been presented in the discussions about potential economic impacts. For a good answer to the question - will the restrictions cause as much harm as COVID19? - credible evidence-based estimates are required, rather than simply rhetoric. Here we provide some preliminary estimates to compare the impact of the current restrictions against the direct impact of the virus. Sinc…
We adapt a SEIRD differential model with asymptomatic population and Covid deaths, which we call SEAIRD, to simulate the evolution of COVID-19, and add a control function affecting both the diffusion of the virus and GDP, featuring all direct and indirect containment policies; to model feasibility, the control is assumed to be a piece-wise linear function satisfying additional constraints. We describe the joint dynamics of infection and the economy and discuss the trade-off between production and fatalities. In particular, we carefully study the conditions for the existence of the optimal poli…
We investigate patterns of COVID-19 mortality across 20 Italian regions and their association with mobility, positivity, and socio-demographic, infrastructural and environmental covariates. Notwithstanding limitations in accuracy and resolution of the data available from public sources, we pinpoint significant trends exploiting information in curves and shapes with Functional Data Analysis techniques. These depict two starkly different epidemics; an "exponential" one unfolding in Lombardia and the worst hit areas of the north, and a milder, "flat(tened)" one in the rest of the country -- inclu…
We develop an agent-based model to assess the cumulative number of deaths during hypothetical Covid-19-like epidemics for various non-pharmaceutical intervention strategies. We consider local and non-local modes of disease transmission. The first simulates transmission through social contacts in the vicinity of the place of residence while the second through social contacts in public places: schools, hospitals, airports, etc., where many people meet, who live in remote geographic locations. Epidemic spreading is modeled as a discrete-time stochastic process on random geometric networks. We use…
We model the spreading of a crisis by constructing a global economic network and applying the Susceptible-Infected-Recovered (SIR) epidemic model with a variable probability of infection. The probability of infection depends on the strength of economic relations between the pair of countries, and the strength of the target country. It is expected that a crisis which originates in a large country, such as the USA, has the potential to spread globally, like the recent crisis. Surprisingly we show that also countries with much lower GDP, such as Belgium, are able to initiate a global crisis. Usin…
Factors such as non-uniform definitions of mortality, uncertainty in disease prevalence, and biased sampling complicate the quantification of fatality during an epidemic. Regardless of the employed fatality measure, the infected population and the number of infection-caused deaths need to be consistently estimated for comparing mortality across regions. We combine historical and current mortality data, a statistical testing model, and an SIR epidemic model, to improve estimation of mortality. We find that the average excess death across the entire US is 13$\%$ higher than the number of reporte…
In this paper we explore a time-depended SEIR model, in which the dynamics of the infection in four groups from a selected target group (population), divided according to the infection, are modeled by a system of nonlinear ordinary differential equations. Several basic parameters are involved in the model: coefficients of infection rate, incubation rate, recovery rate. The coefficients are adaptable to each specific infection, for each individual country, and depend on the measures to limit the spread of the infection and the effectiveness of the methods of treatment of the infected people in …
An epidemic carries human and fiscal costs. In the case of imported pandemics, the first-best solution is to restrict national borders to identify and isolate infected individuals. However, when that opportunity is not fully seized and there is no preventative intervention available, second-best options must be chosen. In this article we develop a system of differential equations that simulate both the fiscal and human costs associated to different mitigation measurements. After simulating several scenarios, we conclude that herd immunity (or unleashing the pandemic) is the worst policy in ter…
During the COVID-19 pandemic, we witnessed a disproportionate infection rate among marginalized and low-income groups. Despite empirical evidence suggesting that structural inequalities in society contribute to health disparities, there has been little attempt to offer a computational and theoretical explanation to establish its plausibility and quantitative impact. This paper combines an agent-based network model and a compartmental susceptible-infectious-removed model (SIR) to explain how socioeconomic inequalities affect the dynamics of disease spreading. Specifically, we focus on two aspec…
Motivated by COVID-19, we develop and analyze a simple stochastic model for a disease spread in human population. We track how the number of infected and critically ill people develops over time in order to estimate the demand that is imposed on the hospital system. To keep this demand under control, we consider a class of simple policies for slowing down and reopening the society and we compare their efficiency in mitigating the spread of the virus from several different points of view. We find that in order to avoid overwhelming of the hospital system, a policy must impose a harsh lockdown o…
Background: During 2021 several new variants of the SARS-CoV-2 virus appeared with both increased levels of transmissibility and virulence with respect to the original wild variant. The Delta (B.1.617.2) variation, first seen in India, dominates COVID-19 infections in several large countries including the United States and India. Most recently, the Lambda variant of interest with increased resistance to vaccines has spread through much of South America. Objective: This research explores the degree to which new variants of concern 1) generate spikes and waves of fluctuations in the daily case f…
Assessing the economic impact of COVID-19 pandemic and public health policies is essential for a rapid recovery. In this paper, we analyze the impact of mobility contraction on furloughed workers and excess deaths in Italy. We provide a link between the reduction of mobility and excess deaths, confirming that the first countrywide lockdown has been effective in curtailing the COVID-19 epidemics. Our analysis points out that a mobility contraction of 10% leads to a mortality reduction of 5% whereas it leads to an increase of 50% in full time equivalent furloughed workers. Based on our results, …
Many countries have passed their first COVID-19 epidemic peak. Traditional epidemiological models describe this as a result of non-pharmaceutical interventions that pushed the growth rate below the recovery rate. In this new phase of the pandemic many countries show an almost linear growth of confirmed cases for extended time-periods. This new containment regime is hard to explain by traditional models where infection numbers either grow explosively until herd immunity is reached, or the epidemic is completely suppressed (zero new cases). Here we offer an explanation of this puzzling observati…
In this study, we formulate a mathematical model incorporating age specific transmission dynamics of COVID-19 to evaluate the role of vaccination and treatment strategies in reducing the size of COVID-19 burden. Initially, we establish the positivity and boundedness of the solutions of the model and calculate the basic reproduction number. We then formulate an optimal control problem with vaccination and treatment as control variables. Optimal vaccination and treatment policies are analysed for different values of the weight constant associated with the cost of vaccination and different transm…
Understanding Covid-19 lethality and its variation from country to country is essential for supporting governments in the choice of appropriate strategies. Adopting correct indicators to monitor the lethality of the infection in the course of the outbreak is a crucial issue. This works highlights how far the time-dependent case fatality rate is a misleading indicator for estimating the fatality in the course of the outbreak, even if our attention is only restricted to the subset of confirmed cases. Our analysis proves that the final case fatality ratio for several major European countries is b…
In this paper we find common features between the equations that are used for pandemic or epidemic modeling and the renormalization group equations that are used in high energy physics. Some of these features include the relation of contact matrices in pandemic modeling and operator mixing in the renormalization group equations. Another common feature are the use of flow diagrams and the study of fixed points both in pandemic modeling and in evolution under renormalization group equations. We illustrate these relations through the study of some cases of interest to the current COVID-19 pandemi…
We study the effectiveness of tracking and testing in mitigating or suppressing epidemic outbreaks, in combination with or as an alternative to quarantines and global lockdowns. We study these intervention methods on a network-based SEIR model, augmented with an additional probability to model symptomatic, asymptomatic and pre-symptomatic cases. Our focus is on the basic trade-offs between economic costs and human lives lost, and how these trade-offs change under different lockdown, quarantine, tracking and testing policies. Our main findings are as follows: (i) Tests combined with patient qua…
The COVID-19 pandemic has caused major disturbance to human life. An important reason behind the widespread social anxiety is the huge uncertainty about the pandemic. A fundamental uncertainty is how many or what percentage of people have been infected. There are published and frequently updated data on various statistics of the pandemic, at local, country or global level. However, due to various reasons, many cases were not included in those reported numbers. We propose a structured approach for the estimation of the number of unreported cases, where we distinguish cases that arrive late in t…
This contribution analyzes the COVID-19 outbreak by comparably simple mathematical and numerical methods. The final goal is to predict the peak of the epidemic outbreak per country with a reliable technique. This is done by an algorithm motivated by standard SIR models and aligned with the standard data provided by the Johns Hopkins University. To reconstruct data for the unregistered Infected, the algorithm uses current values of the infection fatality rate and a data-driven estimation of a specific form of the recovery rate. All other ingredients are data-driven as well. Various examples of …
University of Cambridge（剑桥大学）；UNC-Chapel Hill（北卡罗来纳大学教堂山分校）；UNC Gilling School of Global Public Health（北卡罗来纳大学吉林斯全球公共卫生学院）；Canadian Institute for Theoretical Astrophysics（加拿大理论天体物理研究所）；University of Toronto（多伦多大学）；Canadian Institute for Advanced Research（加拿大高等研究院）；California State University Fullerton（加州州立大学富勒顿分校）；Oberlin College（欧柏林学院）
We present a new mathematical model to explicitly capture the effects that the three restriction measures: the lockdown date and duration, social distancing and masks, and, schools and border closing, have in controlling the spread of COVID-19 infections $i(r, t)$. Before restrictions were introduced, the random spread of infections as described by the SEIR model grew exponentially. The addition of control measures introduces a mixing of order and disorder in the system's evolution which fall under a different mathematical class of models that can eventually lead to critical phenomena. A gener…
Since the outbreak of COVID-19, many data analyses have been done. Some of them are based on the classical epidemiological approach that assumes an exponential growth, but a few studies report that a power-law scaling may provide a better fit to the currently available data. Hereby, we examine the data in China (01/20/2020--02/24/2020), and indeed find that the growth closely follows a power-law kinetics over a significantly wide time period. The exponents are $2.48(20)$, $2.21(6)$ and $4.26(12)$ for the number of confirmed infections, deaths and cured cases, respectively, indicating an underl…
