Objective: To estimate the number of deaths in Peru due to COVID-19. Design: With a priori information obtained from the daily number of deaths due to CODIV-19 in China and data from the Peruvian authorities, we constructed a predictive Bayesian non-linear model for the number of deaths in Peru. Exposure: COVID-19. Outcome: Number of deaths. Results: Assuming an intervention level similar to the one implemented in China, the total number of deaths in Peru is expected to be 612 (95%CI: 604.3 - 833.7) persons. Sixty four days after the first reported death, the 99% of expected deaths will be observed. The inflexion point in the number of deaths is estimated to be around day 26 (95%CI: 25.1 - 26.8) after the first reported death. Conclusion: These estimates can help authorities to monitor the epidemic and implement strategies in order to manage the COVID-19 pandemic.
The COVID-19 pandemic has caused severe public health consequences in the United States. In this study, we use a hierarchical Bayesian model to estimate the age-specific COVID-19 attributable deaths over time in the United States. The model is specified by a novel non-parametric spatial approach, a low-rank Gaussian Process (GP) projected by regularised B-splines. We show that this projection defines a new GP with attractive smoothness and computational efficiency properties, derive its kernel function, and discuss the penalty terms induced by the projected GP. Simulation analyses and benchmar…
Multiple studies have suggested the spread of COVID-19 is affected by factors such as climate, BCG vaccinations, pollution and blood type. We perform a joint study of these factors using the death growth rates of 40 regions worldwide with both machine learning and Bayesian methods. We find weak, non-significant (< 3$σ$) evidence for temperature and relative humidity as factors in the spread of COVID-19 but little or no evidence for BCG vaccination prevalence or $\text{PM}_{2.5}$ pollution. The only variable detected at a statistically significant level (>3$σ$) is the rate of positive COVID-19 …
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 effective reproduction number is a key figure to monitor the course of the COVID-19 pandemic. In this study we consider a retrospective modelling approach for estimating the effective reproduction number based on death counts during the first year of the pandemic in Germany. The proposed Bayesian hierarchical model incorporates splines to estimate reproduction numbers flexibly over time while adjusting for varying effective infection fatality rates. The approach also provides estimates of dark figures regarding undetected infections over time. Results for Germany illustrate that estimated …
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…
The Covid-19 pandemic has spread across the world since the beginning of 2020. Many regions have experienced its effects. The state of South Carolina in the USA has seen cases since early March 2020 and a primary peak in early April 2020. A lockdown was imposed on April 6th but lifting of restrictions started on April 24th. The daily case and death data as reported by NCHS (deaths) via the New York Times GitHUB repository have been analyzed and approaches to modeling of the data are presented. Prediction is also considered and the role of asymptomatic transmission is assessed as a latent unobs…
A finite mixture model is used to learn trends from the currently available data on coronavirus (COVID-19). Data on the number of confirmed COVID-19 related cases and deaths for European countries and the United States (US) are explored. A semi-supervised clustering approach with positive equivalence constraints is used to incorporate country and state information into the model. The analysis of trends in the rates of cases and deaths is carried out jointly using a mixture of multivariate Gaussian non-linear regression models with a mean trend specified using a generalized logistic function. T…
In this report we fit a semi-mechanistic Bayesian hierarchical model to describe the Mexican COVID-19 epidemic. We obtain two epidemiological measures: the number of infections and the reproduction number. Estimations are based on death data. Hence, we expect our estimates to be more accurate than the attack rates estimated from the reported number of cases.
Faced with the 2020 SARS-CoV2 epidemic, public health officials have been seeking models that could be used to predict not only the number of new cases but also the levels of hospitalisation, critical care and deaths. In this paper we present a stochastic compartmental model capable of real-time monitoring and forecasting of the pandemic incorporating multiple streams of real-world data, reported cases, testing intensity, deaths, hospitalisations and critical care occupancy. Model parameters are estimated via a Bayesian particle filtering technique. The model successfully tracks the key variab…
This paper aims to develop a global perspective of the complexity of the relationship between the standardised per-capita growth rate of Covid-19 cases, deaths, and the OxCGRT Covid-19 Stringency Index, a measure describing a country's stringency of lockdown policies. To achieve our goal, we use a heterogeneous intrinsic dimension estimator implemented as a Bayesian mixture model, called Hidalgo. We identify that the Covid-19 dataset may project onto two low-dimensional manifolds without significant information loss. The low dimensionality suggests strong dependency among the standardised grow…
Emerging at the end of 2019, COVID-19 has become a public health threat to people worldwide. Apart from the deaths who tested positive for COVID-19, many others have died from causes indirectly related to COVID-19. Therefore, the COVID-19 confirmed deaths underestimate the influence of the pandemic on the society; instead, the measure of `excess deaths' is a more objective and comparable way to assess the scale of the epidemic and formulate lessons. One common practical issue in analyzing the impact of COVID-19 is to determine the `pre-COVID-19' period and the `post-COVID-19' period. We apply …
Background: Most COVID-19 deaths occur among adults, not children, and attention has focused on mitigating COVID-19 burden among adults. However, a tragic consequence of adult deaths is that high numbers of children might lose their parents and caregivers to COVID-19-associated deaths. Methods: We quantified COVID-19-associated caregiver loss and orphanhood in the US and for each state using fertility and excess and COVID-19 mortality data. We assessed burden and rates of COVID-19-associated orphanhood and deaths of custodial and co-residing grandparents, overall and by race/ethnicity. We furt…
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 analysis of complex longitudinal data such as COVID-19 deaths is challenging due to several inherent features: (i) Similarly-shaped profiles with different decay patterns; (ii) Unexplained variation among repeated measurements within each country, these repeated measurements may be viewed as clustered data since they are taken on the same country at roughly the same time; (iii) Skewness, outliers or skew-heavy-tailed noises are possibly embodied within response variables. This article formulates a robust nonlinear mixed-effects model based in the class of scale mixtures of skew-normal dist…
The emergence of the novel coronavirus (COVID-19) has generated a need to quickly and accurately assemble up-to-date information related to its spread. While it is possible to use deaths to provide a reliable information feed, the latency of data derived from deaths is significant. Confirmed cases derived from positive test results potentially provide a lower latency data feed. However, the sampling of those tested varies with time and the reason for testing is often not recorded. Hospital admissions typically occur around 1-2 weeks after infection and can be considered out of date in relation…
Official counts of COVID-19 deaths have been criticized for potentially including people who did not die of COVID-19 but merely died with COVID-19. I address that critique by fitting a generalized additive model to weekly counts of all deaths registered in England and Wales during the 2010s. The model produces baseline rates of death registrations expected without the COVID-19 pandemic, and comparing those baselines to recent counts of registered deaths exposes the emergence of excess deaths late in March 2020. By April's end, England and Wales registered 45,300 $\pm$ 3200 excess deaths of adu…
We analysed publicly available data on place of occurrence of COVID-19 deaths from national statistical agencies in the UK between March 9 2020 and February 28 2021. We introduce a modified Weibull model that describes the deaths due to COVID-19 at a national and place of occurrence level. We observe similar trends in the UK where deaths due to COVID-19 first peak in Homes, followed by Hospitals and Care Homes 1-2 weeks later in the first and second waves. This is in line with the infectious period of the disease, indicating a possible transmission vehicle between the settings. Our results sho…
Objective: To make an estimate of the excess deaths caused by COVID-19 in the non-violent mortality of Peru, controlling for the effect of quarantine. Methods: Analysis of longitudinal data from the departments of Peru using official public information from the National Death Information System and the Ministry of Health of Peru. The analysis is performed between January 1, 2018 and June 23, 2020 (100 days of quarantine). The daily death rate per million inhabitants has been used. The days in which the departments were quarantined with a limit number of accumulated cases of COVID-19 were used …
Since the beginning of the COVID-19 pandemic, many dashboards have emerged as useful tools to monitor the evolution of the pandemic, inform the public, and assist governments in decision making. Our goal is to develop a globally applicable method, integrated in a twice daily updated dashboard that provides an estimate of the trend in the evolution of the number of cases and deaths from reported data of more than 200 countries and territories, as well as a seven-day forecast. One of the significant difficulties to manage a quickly propagating epidemic is that the details of the dynamic needed t…
The crisis caused by COVID-19 revealed the global unpreparedness to handle the impact of a pandemic. In this paper, we present a statistical analysis of the data related to the COVID-19 outbreak in China, specifically the infection speed, death and fatality rates in Hubei province. By fitting distributions of these quantities we design a parametric reinsurance contract whose trigger and cap are based on the probability distributions of the infection speed, death and fatality rates. In particular, fitting the distribution for the infection speed and death rates we provide a measure of the effec…
The difference in COVID 19 death rates across political regimes has caught a lot of attention. The "efficient autocracy" view suggests that autocracies may be more efficient at putting in place policies that contain COVID 19 spread. On the other hand, the "biasing autocracy" view underlines that autocracies may be under reporting their COVID 19 data. We use fixed effect panel regression methods to discriminate between the two sides of the debate. Our results show that a third view may in fact be prevailing: once pre-determined characteristics of countries are accounted for, COVID 19 death rate…
In this paper, we apply statistical methods for functional data to explain the heterogeneity in the evolution of number of deaths of Covid-19 over different regions. We treat the cumulative daily number of deaths in a specific region as a curve (functional data) such that the data comprise of a set of curves over a cross-section of locations. We start by using clustering methods for functional data to identify potential heterogeneity in the curves and their functional derivatives. This first stage is an unconditional descriptive analysis, as we do not use any covariate to estimate the clusters…
Political affiliation has emerged as a potential risk factor for COVID-19, amid evidence that Republican-leaning counties have had higher COVID-19 death rates than Democrat-leaning counties and evidence of a link between political party affiliation and vaccination views. This study constructs an individual-level dataset with political affiliation and excess death rates during the COVID-19 pandemic via a linkage of 2017 voter registration in Ohio and Florida to mortality data from 2018 to 2021. We estimate substantially higher excess death rates for registered Republicans when compared to regis…
As the COVID-19 ravaging through the globe, accurate forecasts of the disease spread is crucial for situational awareness, resource allocation, and public health decision-making. Alternative to the traditional disease surveillance data collected by the United States (US) Centers for Disease Control and Prevention (CDC), big data from Internet such as online search volumes has been previously shown to contain valuable information for tracking infectious disease dynamics. In this study, we evaluate the feasibility of using Internet search volume of relevant queries to track and predict COVID-19 …
The coronavirus which appeared in December 2019 in Wuhan has spread out worldwide and caused the death of more than 280,000 people (as of May, 11 2020). Since February 2020, doubts were raised about the numbers of confirmed cases and deaths reported by the Chinese government. In this paper, we examine data available from China at the city and provincial levels and we compare them with Canadian provincial data, US state data and French regional data. We consider cumulative and daily numbers of confirmed cases and deaths and examine these numbers through the lens of their first two digits and in…
The evolution of the COVID-19 epidemic has been accompanied by accumulating evidence on the underlying epidemiological parameters. Hence there is potential for models providing mid-term forecasts of the epidemic trajectory using such information. The effectiveness of lockdown interventions can also be assessed by modelling later epidemic stages, possibly using a multiphase epidemic model. Commonly applied methods to analyze epidemic trajectories include phenomenological growth models (e.g. the Richards), and variants of the susceptible-infected-recovered (SIR) compartment model. Here we focus …
Since December 2019, the world has been witnessing the gigantic effect of an unprecedented global pandemic called Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) - COVID-19. So far, 38,619,674 confirmed cases and 1,093,522 confirmed deaths due to COVID-19 have been reported. In the United States (US), the cases and deaths are recorded as 7,833,851 and 215,199. Several timely researches have discussed the local and global effects of the confounding factors on COVID-19 casualties in the US. However, most of these studies considered little about the time varying associations between an…
We develop a novel temporal complex network approach to quantify the US county level spread dynamics of COVID-19. The objective is to study the effects of the local spread dynamics, COVID-19 cases and death, and Google search activities on the US stock market. We use both conventional econometric and Machine Learning (ML) models. The results suggest that COVID-19 cases and deaths, its local spread, and Google searches have impacts on abnormal stock prices between January 2020 to May 2020. In addition, incorporating information about local spread significantly improves the performance of foreca…
Determining who is at risk from a disease is important in order to protect vulnerable subpopulations during an outbreak. We are currently in a SARS-COV-2 (commonly referred to as COVID-19) pandemic which has had a massive impact across the world, with some communities and individuals seen to have a higher risk of severe outcomes and death from the disease compared to others. These risks are compounded for people of lower socioeconomic status, those who have limited access to health care, higher rates of chronic diseases, such as hypertension, diabetes (type-2), obesity, likely due to the chron…
At a national-level, we sought to investigate the effect of public masking mandates on COVID-19 in Fall 2020. Specifically, we aimed to evaluate how the relative growth of COVID-19 cases and deaths would have differed if all states had issued a mandate to mask in public by September 1, 2020 versus if all states had delayed issuing such a mandate. To do so, we applied the Causal Roadmap, a formal framework for causal and statistical inference. The outcome was defined as the state-specific relative increase in cumulative cases and in cumulative deaths {21, 30, 45, 60}-days after September 1. Des…
In this paper, we show a strong correlation between turnstile usage data of the New York City subway provided by the Metropolitan Transport Authority of New York City and COVID-19 deaths and cases reported by the New York City Department of Health. The turnstile usage data not only indicate the usage of the city's subway but also people's activity that promoted the large prevalence of COVID-19 city dwellers experienced from March to May of 2020. While this correlation is apparent, no proof has been provided before. Here we demonstrate this correlation through the application of a long short-te…
Motivated by the current Coronavirus Disease (COVID-19) pandemic, which is due to the SARS-CoV-2 virus, and the important problem of forecasting daily deaths and cumulative deaths, this paper examines the construction of prediction regions or intervals under the Poisson regression model and for an over-dispersed Poisson regression model. For the Poisson regression model, several prediction regions are developed and their performance are compared through simulation studies. The methods are applied to the problem of forecasting daily and cumulative deaths in the United States (US) due to COVID-1…
This study explored how population mobility flows form commuting networks across US counties and influence the spread of COVID-19. We utilized 3-level mixed effects negative binomial regression models to estimate the impact of network COVID-19 exposure on county confirmed cases and deaths over time. We also conducted weighting-based analyses to estimate the causal effect of network exposure. Results showed that commuting networks matter for COVID-19 deaths and cases, net of spatial proximity, socioeconomic, and demographic factors. Different local racial and ethnic concentrations are also asso…
Redlining is the discriminatory practice whereby institutions avoided investment in certain neighborhoods due to their demographics. Here we explore the lasting impacts of redlining on the spread of COVID-19 in New York City (NYC). Using data available through the Home Mortgage Disclosure Act, we construct a redlining index for each NYC census tract via a multi-level logistical model. We compare this redlining index with the COVID-19 statistics for each NYC Zip Code Tabulation Area. Accurate mappings of the pandemic would aid the identification of the most vulnerable areas and permit the most …
Knowledge of the current state of economies, how they respond to COVID-19 mitigations and indicators, and what the future might hold for them is important. We use recently-developed generalised network autoregressive (GNAR) models, using trade-determined networks, to model and forecast the Purchasing Managers' Indices for a number of countries. We use networks that link countries where the links themselves, or their weights, are determined by the degree of export trade between the countries. We extend these models to include node-specific time series exogenous variables (GNARX models), using t…
The COVID-19 pandemic has highlighted delayed reporting as a significant impediment to effective disease surveillance and decision-making. In the absence of timely data, statistical models which account for delays can be adopted to nowcast and forecast cases or deaths. We discuss the four key sources of systematic and random variability in available data for COVID-19 and other diseases, and critically evaluate current state-of-the-art methods with respect to appropriately separating and capturing this variability. We present a general spatio-temporal hierarchical framework for correcting delay…
We analyze the data about casualties in Italy in the period 01/01/2015 to 30/09/2020 released by the Italian National Institute of Statistics (ISTAT). The data exhibit a clear sinusoidal behavior, whose fit allows for a robust subtraction of the baseline trend of casualties in Italy, with a surplus of mortality in correspondence to the flu epidemics in winter and to the hottest periods in summer. While these peaks are symmetric in shape, the peak in coincidence with the COVID-19 pandemics is asymmetric and more pronounced. We fit the former with a Gaussian function and the latter with a Gomper…
We assess the impact of COVID-19 response measures implemented in Germany and Switzerland on cumulative COVID-19-related hospitalization and death rates. Our analysis exploits the fact that the epidemic was more advanced in some regions than in others when certain lockdown measures came into force, based on measuring health outcomes relative to the region-specific start of the epidemic and comparing outcomes across regions with earlier and later start dates. When estimating the effect of the relative timing of measures, we control for regional characteristics and initial epidemic trends by lin…
University of California, Berkeley（加利福尼亚大学伯克利分校）；University of California, San Francisco（加利福尼亚大学旧金山分校）；Chan Zuckerberg Biohub（陈·扎克伯格生物中心）
As the COVID-19 outbreak evolves, accurate forecasting continues to play an extremely important role in informing policy decisions. In this paper, we present our continuous curation of a large data repository containing COVID-19 information from a range of sources. We use this data to develop predictions and corresponding prediction intervals for the short-term trajectory of COVID-19 cumulative death counts at the county-level in the United States up to two weeks ahead. Using data from January 22 to June 20, 2020, we develop and combine multiple forecasts using ensembling techniques, resulting…
The novel coronavirus disease 2019 COVID-19 has been leading the world into a prominent crisis. As of May 19, 2020, the virus had spread to 215 countries with more than 4,622,001 confirmed cases and 311,916 reported deaths worldwide, including Algeria with 7201 cases and 555 deaths. Analyze and forecast COVID-19 cases and deaths growth could be useful in many ways, governments could estimate medical equipment and take appropriate policy responses, and experts could approximate the peak and the end of the disease. In this work, we first train a time series Prophet model to analyze and forecast …
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 …
In this paper we develop statistical methods for causal inference in epidemics. Our focus is in estimating the effect of social mobility on deaths in the Covid-19 pandemic. We propose a marginal structural model motivated by a modified version of a basic epidemic model. We estimate the counterfactual time series of deaths under interventions on mobility. We conduct several types of sensitivity analyses. We find that the data support the idea that reduced mobility causes reduced deaths, but the conclusion comes with caveats. There is evidence of sensitivity to model misspecification and unmeasu…
The choices that researchers make while conducting a statistical analysis usually have a notable impact on the results. This fact has become evident in the ongoing research of the association between the environment and the evolution of the COVID-19 pandemic, in light of the hundreds of contradictory studies that have already been published on this issue in just a few months. In this paper, a COVID-19 dataset containing the number of daily cases registered in the regions of Catalonia (Spain) since the start of the pandemic is analysed. Specifically, the possible effect of several environmental…
This paper evaluates the dynamic impact of various policies adopted by US states on the growth rates of confirmed Covid-19 cases and deaths as well as social distancing behavior measured by Google Mobility Reports, where we take into consideration people's voluntarily behavioral response to new information of transmission risks. Our analysis finds that both policies and information on transmission risks are important determinants of Covid-19 cases and deaths and shows that a change in policies explains a large fraction of observed changes in social distancing behavior. Our counterfactual exper…
To capture the death rates and strong weekly, biweekly and probably monthly patterns in the Canada COVID-19, we utilize the generalized additive models in the absence of direct statistically based measurement of infection rates. By examining the death rates of Canada in general and Quebec, Ontario and Alberta in particular, one can easily figured out that there are substantial overdispersion relative to the Poisson so that the negative binomial distribution is an appropriate choice for the analysis. Generalized additive models (GAMs) are one of the main modeling tools for data analysis. GAMs c…
Are COVID-19 fatalities large when a federal government does not enforce containment policies and instead allow states to implement their own policies? We answer this question by developing a stochastic extension of a SIRD epidemiological model for a country composed of multiple states. Our model allows for interstate mobility. We consider three policies: mask mandates, stay-at-home orders, and interstate travel bans. We fit our model to daily U.S. state-level COVID-19 death counts and exploit our estimates to produce various policy counterfactuals. While the restrictions imposed by some state…
We demonstrate from first principles a core fallacy employed by a coterie of authors who claim that data from the Vaccine Adverse Reporting System (VAERS) show that hundreds of thousands of U.S. deaths are attributable to COVID vaccination.
This work systematically conducts a data analysis based on the numbers of both cumulative and daily confirmed COVID-19 cases and deaths in a time span through April 2020 to June 2022 for over 200 countries around the world. Such research feature aims to reveal the temporal and spatial evolution of the country-level distribution observed in COVID-19 pandemic, and obtains some interesting results as follows. (1) The distributions of the numbers for cumulative confirmed cases and deaths obey power-law in early stages of COVID-19 and stretched exponential function in subsequent course. (2) The dis…
We introduce a minimalist outbreak forecasting model that combines data-driven parameter estimation with variational data assimilation. By focusing on the fundamental components of nonlinear disease transmission and representing data in a domain where model stochasticity simplifies into a process with independent increments, we design an approach that only requires four core parameters to be estimated. We illustrate this novel methodology on COVID-19 forecasts. Results include case count and deaths predictions for the US and all of its 50 states, the District of Columbia, and Puerto Rico. The …
In this paper, we model the trajectory of the cumulative confirmed cases and deaths of COVID-19 (in log scale) via a piecewise linear trend model. The model naturally captures the phase transitions of the epidemic growth rate via change-points and further enjoys great interpretability due to its semiparametric nature. On the methodological front, we advance the nascent self-normalization (SN) technique (Shao, 2010) to testing and estimation of a single change-point in the linear trend of a nonstationary time series. We further combine the SN-based change-point test with the NOT algorithm (Bara…
