In this paper, we use SEIR equations to make predictions for the number of mortality due to COVID-19 in İstanbul. Using excess mortality method, we find the number of mortality for the previous three waves in 2020 and 2021. We show that the predictions of our model is consistent with number of moralities for each wave. Furthermore, we predict the number of mortality for the second wave of 2021. We also extend our analysis for Germany, Italy and Turkey to compare the basic reproduction number $R_0$ for Istanbul. Finally, we calculate the number of infected people in Istanbul for herd immunity.
I present three types of applications of generalized additive models (GAMs) to COVID-19 mortality rates in the US for the purpose of advancing methods to document inequities with respect to which communities suffered disproportionate COVID-19 mortality rates at specific times during the first three years of the pandemic. First, GAMs can be used to describe the changing relationship between COVID-19 mortality and county-level covariates (sociodemographic, economic, and political metrics) over time. Second, GAMs can be used to perform spatiotemporal smoothing that pools information over time and…
We present an extension of the Li and Lee model to quantify mortality in five European countries during the COVID-19 pandemic. The first two factors are used to model the pre-COVID mortality, with the first layer modelling the common trend and the second layer the country-specific deviation from the common trend. We add a third layer to capture the country-specific impact of COVID-19 in 2020 and 2021 in excess of the pre-COVID trend. We use weekly mortality data from the Short Term Mortality Fluctuations Database to calibrate this third factor, and we use a more granular dataset for deaths in …
The current outbreak of COVID-19 has called renewed attention to the need for sound statistical analysis for monitoring mortality patterns and trends over time. Excess mortality has been suggested as the most appropriate indicator to measure the overall burden of the pandemic on mortality. As such, excess mortality has received considerable interest during the first months of the COVID-19 pandemic. Previous approaches to estimate excess mortality are somewhat limited, as they do not include sufficiently long-term trends, correlations among different demographic and geographic groups, and the a…
The subset selection problem of linear algebra is applied to identify independent patterns of COVID-19 evolution within Brazil. The data consist of a set of mortality curves in states of Brazil. A subset of the most independent curves is selected by using a functional version of the QR matrix decomposition technique with column pivoting. The selected subset is used next as a basis to represent the remaining curves filtering out any data redundancy. For each independent curve, an associated epidemiological region of influence is defined. The results show two main independent curves with a simil…
Coronavirus disease 2019 (COVID-19) is associated with a very high number of casualties in the general population. Assessing the exact magnitude of this number is a non-trivial problem, as relying only on officially reported COVID-19 associated fatalities runs the risk of incurring in several kinds of biases. One of the ways to approach the issue is to compare overall mortality during the pandemic with expected mortality computed using the observed mortality figures of previous years. In this paper, we build on existing methodology and propose two ways to compute expected as well as excess mor…
Currently, Brazil has one of the fastest increasing COVID-19 epidemics in the world, that has caused at least 94 thousand confirmed deaths until now. The city of Sao Paulo is particularly vulnerable because it is the most populous in the country. Analyzing the spatiotemporal dynamics of COVID-19 is important to help the urgent need to integrate better actions to face the pandemic. Thus, this study aimed to analyze the COVID-19 mortality, from March to July 2020, considering the spatio-time architectures, the socio-economic context of the population, and using a fine granular level, in the most…
In this article, we deal with COVID-19 data to study the trend of the epidemic at the global situation. Choosing the mortality rate as an appropriate metric which measures the relative relation between the cumulative confirmed cases and death cases, we utilize the modified kernel estimator for random density function (Petersen and Muller, 2016) to obtain the density of the mortality rate, and apply Frechet change point detection (Dubey and Muller, 2020) to check if there is any significant change on the dynamic pattern of COVID-19 deaths. The analysis shows that the pattern of global COVID-19 …
The COVID-19 pandemic has placed forecasting models at the forefront of health policy making. Predictions of mortality and hospitalization help governments meet planning and resource allocation challenges. In this paper, we consider the weekly forecasting of the cumulative mortality due to COVID-19 at the national and state level in the U.S. Optimal decision-making requires a forecast of a probability distribution, rather than just a single point forecast. Interval forecasts are also important, as they can support decision making and provide situational awareness. We consider the case where pr…
The ongoing COVID-19 pandemic has brought science to the fore of the public discourse and considering the complexity of the issues involved, with it also the challenge of effective and informative science communication. A particularly contentious topic, in that it is both highly emotional in and of itself, as well as in that it sits at the nexus of the decision-making process regarding the handling of the pandemic, which has effected lockdowns, social behaviour measures, business closures, and others, concerns the recording and the reporting of the disease mortality. To clarify a point which h…
COVID-19 related deaths underestimate the pandemic burden on mortality because they suffer from completeness and accuracy issues. Excess mortality is a popular alternative, as it compares observed with expected deaths based on the assumption that the pandemic did not occur. Expected deaths had the pandemic not occurred depend on population trends, temperature, and spatio-temporal patterns. In addition to this, high geographical resolution is required to examine within country trends and the effectiveness of the different public health policies. In this tutorial, we propose a framework using R …
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…
We aim to assess the impact of a pandemic data point on the calibration of a stochastic multi-population mortality projection model and its resulting projections for future mortality rates. Throughout the paper we put focus on the Li & Lee mortality model, which has become a standard for projecting mortality in Belgium and the Netherlands. We calibrate this mortality model on annual deaths and exposures at the level of individual ages. This type of mortality data is typically collected, produced and reported with a significant delay of -- for some countries -- several years on a platform such …
Widespread vaccination campaigns have changed the landscape for COVID-19, vastly altering symptoms and reducing morbidity and mortality. We estimate trends in mortality by month of admission and vaccination status among those hospitalised with COVID-19 in England between March 2020 to September 2021, controlling for demographic factors and hospital load. Among 259,727 hospitalised COVID-19 cases, 51,948 (20.0%) experienced mortality in hospital. Hospitalised fatality risk ranged from 40.3% (95% confidence interval 39.4-41.3%) in March 2020 to 8.1% (7.2-9.0%) in June 2021. Older individuals and…
The first cases of COVID-19 in France were detected on January 24, 2020. The number of screening tests carried out and the methodology used to target the patients tested do not allow for a direct computation of the real number of cases and the mortality rate.In this report, we develop a 'mechanistic-statistical' approach coupling a SIR ODE model describing the unobserved epidemiological dynamics, a probabilistic model describing the data acquisition process and a statistical inference method. The objective of this model is not to make forecasts but to estimate the real number of people infecte…
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…
F. Hoffmann-La Roche Ltd（罗氏制药公司）；Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）；ETH Zurich（苏黎世联邦理工学院）；John A. Paulson School of Engineering and Applied Sciences, Harvard University（哈佛大学约翰·A·保尔森工程与应用科学学院）；Beth Israel Deaconess Medical Center, Harvard Medical School（哈佛医学院贝斯以色列女执事医疗中心）；MIT Critical Data, Laboratory for Computational Physiology, Institute for Medical Engineering and Science, Harvard-MIT Health Sciences & Technology（哈佛-麻省理工健康科学与技术研究所医学工程与科学研究所计算生理学实验室MIT关键数据）；University Hospital of Tübingen（蒂宾根大学医院）；Kantonsspital Winterthur（温特图尔州立医院）
Coronavirus Disease 2019 (COVID-19) is an emerging respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with rapid human-to-human transmission and a high case fatality rate particularly in older patients. Due to the exponential growth of infections, many healthcare systems across the world are under pressure to care for increasing amounts of at-risk patients. Given the high number of infected patients, identifying patients with the highest mortality risk early is critical to enable effective intervention and optimal prioritisation of care. Here, we pre…
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, describi…
A multiple objective space-time forecasting approach is presented involving cyclical curve log-regression, and multivariate time series spatial residual correlation analysis. Specifically, the mean quadratic loss function is minimized in the framework of trigonometric regression. While, in our subsequent spatial residual correlation analysis, maximization of the likelihood allows us to compute the posterior mode in a Bayesian multivariate time series soft-data framework. The presented approach is applied to the analysis of COVID-19 mortality in the first wave affecting the Spanish Communities,…
Updating observations of a signal due to the delays in the measurement process is a common problem in signal processing, with prominent examples in a wide range of fields. An important example of this problem is the nowcasting of COVID-19 mortality: given a stream of reported counts of daily deaths, can we correct for the delays in reporting to paint an accurate picture of the present, with uncertainty? Without this correction, raw data will often mislead by suggesting an improving situation. We present a flexible approach using a latent Gaussian process that is capable of describing the chang…
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 coronavirus disease (COVID-19) has spread worldwide with an unprecedented impact on society. In the Philippines, several interventions such as mobility restrictions for different age groups and vaccination prioritization programs have been implemented to reduce the risks of infections and mortality. This study aimed to identify age-sex composition with greater susceptibility, longer hospitalization and higher fatality. The COVID-19 cases from March 2020 to April 2021 provided by the Department of Health Davao Region in the Philippines were analyzed. A Chi-square test was used to determine …
Respiratory complications due to coronavirus disease COVID-19 have claimed tens of thousands of lives in 2020. Many cases of COVID-19 escalate from Severe Acute Respiratory Syndrome (SARS-CoV-2) to viral pneumonia to acute respiratory distress syndrome (ARDS) to death. Extracorporeal membranous oxygenation (ECMO) is a life-sustaining oxygenation and ventilation therapy that may be used for patients with severe ARDS when mechanical ventilation is insufficient to sustain life. While early planning and surgical cannulation for ECMO can increase survival, clinicians report the lack of a risk score…
Mixed Time Series Quasi-Likelihood Models for Uncovering Covid-19 Viral Load and Mortality Dynamics
Loyola University Chicago（芝加哥洛约拉大学）；Southern Methodist University（南方卫理公会大学）；Queen Mary University of London（伦敦大学玛丽女王学院）；University College Dublin（都柏林大学学院）
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…
In the United States, from the start of the COVID-19 pandemic to December 31, 2020, 341,199 deaths and more than 19,663,976 infections were recorded. Recent literature establishes that communities with poverty-related health problems, such as obesity, cardiovascular disease, diabetes, and hypertension, are more susceptible to mortality from SARS-CoV-2 infection. Additionally, controversial public health policies implemented by the nation's political leaders have highlighted the socioeconomic inequalities of minorities. Therefore, through multivariate correlational analysis using machine learni…
Covid-19 is responsible for high mortality in all countries, with the maternal population it is no different. Countries with a high rate of maternal mortality have deficiencies in the health care of pregnant women and women who have recently given birth, which will certainly be enhanced in a situation of overload in the health system, as occurred in this pandemic. Understanding the impact of the pandemic on maternal health is essential to discuss public policies and assist in solutions to future crises. With that in mind, we present the Brazilian Obstetric Observatory COVID-19 (OOBr COVID-19).…
Currently, there are 14 ongoing clinical studies on low dose radiotherapy (LDRT) for COVID-19 pneumonia. An underlying assumption is that irradiation of about 1 Gy is effective at ameliorating viral pneumonia. Its rationale, however, relies on early human case series or animal studies mostly obtained in the pre-antibiotic era, where rigorous statistical analyses were not performed. It therefore remains unclear whether those early data support such assumptions. With standard statistical survival models, and based on a systematic literature review, we re-analyzed 14 radiobiological animal datase…
We analyse the temporal and regional structure in mortality rates related to COVID-19 infections. We relate the fatality date of each deceased patient to the corresponding day of registration of the infection, leading to a nowcasting model which allows us to estimate the number of present-day infections that will, at a later date, prove to be fatal. The numbers are broken down to the district level in Germany. Given that death counts generally provide more reliable information on the spread of the disease compared to infection counts, which inevitably depend on testing strategy and capacity, t…
This article explores the territorial differences in the onset and spread of COVID-19 and the excess mortality associated with the pandemic, across the European NUTS3 regions and US counties. Both in Europe and in the US, the pandemic arrived earlier and recorded higher Rt values in urban regions than in intermediate and rural ones. A similar gap is also found in the data on excess mortality. In the weeks during the first phase of the pandemic, urban regions in EU countries experienced excess mortality of up to 68pp more than rural ones. We show that, during the initial days of the pandemic, t…
Understanding differences in hospital case-fatality rates (HCFRs) of coronavirus disease (COVID-19) may help evaluate its severity and the capacity of the healthcare system to reduce mortality. We examined the variability in HCFRs of COVID-19 in relation to spatial inequalities in socioeconomic factors across the city of Sao Paulo, Brazil. We found that HCFRs were higher for men and for individuals aged 60 years and older. Our models identified per capita income as a significant factor that is negatively associated with the HCFRs of COVID-19, even after adjusting by age, sex and presence of ri…
Predicting the evolution of mortality rates plays a central role for life insurance and pension funds.Various stochastic frameworks have been developed to model mortality patterns taking into account the main stylized facts driving these patterns. However, relying on the prediction of one specific model can be too restrictive and lead to some well documented drawbacks including model misspecification, parameter uncertainty and overfitting. To address these issues we first consider mortality modelling in a Bayesian Negative-Binomial framework to account for overdispersion and the uncertainty ab…
The COVID-19 pandemic has created unprecedented challenges worldwide. Strained healthcare providers make difficult decisions on patient triage, treatment and care management on a daily basis. Policy makers have imposed social distancing measures to slow the disease, at a steep economic price. We design analytical tools to support these decisions and combat the pandemic. Specifically, we propose a comprehensive data-driven approach to understand the clinical characteristics of COVID-19, predict its mortality, forecast its evolution, and ultimately alleviate its impact. By leveraging cohort-leve…
