Bayesian nowcasting with leading indicators applied to COVID-19 fatalities in Sweden.

The real-time analysis of infectious disease surveillance data is essential in obtaining situational awareness about the current dynamics of a major public health event such as the COVID-19 pandemic. This analysis of e.g., time-series of reported cases or fatalities is complicated by reporting delays that lead to under-reporting of the complete number of events for the most recent time points. This can lead to misconceptions by the interpreter, for instance the media or the public, as was the case with the time-series of reported fatalities during the COVID-19 pandemic in Sweden. Nowcasting methods provide real-time estimates of the complete number of events using the incomplete time-series of currently reported events and information about the reporting delays from the past. In this paper we propose a novel Bayesian nowcasting approach applied to COVID-19-related fatalities in Sweden. We incorporate additional information in the form of time-series of number of reported cases and ICU admissions as leading signals. We demonstrate with a retrospective evaluation that the inclusion of ICU admissions as a leading signal improved the nowcasting performance of case fatalities for COVID-19 in Sweden compared to existing methods.

On assessing excess mortality in Germany during the COVID-19 pandemic

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 mortality, namely at the weekly and at the yearly level. Particular focus is put on the role of age, which plays a central part in both COVID-19-associated and overall mortality. We illustrate our methods by making use of age-stratified mortality data from the years 2016 to 2020 in Germany to compute age group-specific excess mortality during the COVID-19 pandemic in 2020.Die Corona-Pandemie (COVID-19) ist mit einer erhöhten Zahl an Todesfällen in der Bevölkerung verbunden. Die Quantifizierung der Übersterblichkeit ist ein nicht triviales Problem, denn wenn man sich nur auf die öffentlich gemeldeten COVID-19-assoziierten Todesfälle stützt, besteht die Gefahr von Verzerrungen. Eine Möglichkeit, das Problem zu umgehen, ist der Vergleich der Gesamtsterblichkeit während der Pandemie mit der erwarteten Sterblichkeit, welche aus den beobachteten Sterblichkeitszahlen der Vorjahre berechnet werden kann. In unserem Artikel bauen wir auf dieser Methodik auf und schlagen zwei Methoden zur Berechnung der erwarteten Sterblichkeit und damit der Übersterblichkeit vor, nämlich auf wöchentlicher und auf Jahresebene. Besonderes Augenmerk liegt auf dem Einfluss des Alters auf die Sterblichkeit, welches eine zentrale Rolle bei COVID-19-assoziierten Todesfällen spielt. Wir veranschaulichen unsere Methoden anhand von Sterbedaten aus den Jahren 2016 bis 2020 in Deutschland und zeigen wie altersgruppenspezifischen Übersterblichkeit während der COVID-19-Pandemie im Jahr 2020 berechnet werden kann.

On assessing excess mortality in Germany during the COVID-19 pandemic Zur Berechnung der Übersterblichkeit in Deutschland während der COVID-19-Pandemie

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 mortality, namely at the weekly and at the yearly level. Particular focus is put on the role of age, which plays a central part in both COVID-19-associated and overall mortality. We illustrate our methods by making use of age-stratified mortality data from the years 2016 to 2020 in Germany to compute age group-specific excess mortality during the COVID-19 pandemic in 2020.

Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection.

As several countries gradually release social distancing measures, rapid detection of new localized COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (automatic selection of models and outlier detection for epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterize the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggests ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. As such, our method could be of wider use for infectious disease surveillance. We illustrate ASMODEE using publicly available data of National Health Service (NHS) Pathways reporting potential COVID-19 cases in England at a fine spatial scale, showing that the method would have enabled the early detection of the flare-ups in Leicester and Blackburn with Darwen, two to three weeks before their respective lockdown. ASMODEE is implemented in the free R package trendbreaker. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.

Analysis of the early COVID-19 epidemic curve in Germany by regression models with change points.

We analysed the coronavirus disease 2019 epidemic curve from March to the end of April 2020 in Germany. We use statistical models to estimate the number of cases with disease onset on a given day and use back-projection techniques to obtain the number of new infections per day. The respective time series are analysed by a trend regression model with change points. The change points are estimated directly from the data. We carry out the analysis for the whole of Germany and the federal state of Bavaria, where we have more detailed data. Both analyses show a major change between 9 and 13 March for the time series of infections: from a strong increase to a decrease. Another change was found between 25 March and 29 March, where the decline intensified. Furthermore, we perform an analysis stratified by age. A main result is a delayed course of the pandemic for the age group 80 + resulting in a turning point at the end of March. Our results differ from those by other authors as we take into account the reporting delay, which turned out to be time dependent and therefore changes the structure of the epidemic curve compared to the curve of newly reported cases.

Analysis of Asymptomatic and Presymptomatic Transmission in SARS-CoV-2 Outbreak, Germany, 2020.

We determined secondary attack rates (SAR) among close contacts of 59 asymptomatic and symptomatic coronavirus disease case-patients by presymptomatic and symptomatic exposure. We observed no transmission from asymptomatic case-patients and highest SAR through presymptomatic exposure. Rapid quarantine of close contacts with or without symptoms is needed to prevent presymptomatic transmission.

Nowcasting the COVID-19 pandemic in Bavaria.

To assess the current dynamics of an epidemic, it is central to collect information on the daily number of newly diseased cases. This is especially important in real-time surveillance, where the aim is to gain situational awareness, for example, if cases are currently increasing or decreasing. Reporting delays between disease onset and case reporting hamper our ability to understand the dynamics of an epidemic close to now when looking at the number of daily reported cases only. Nowcasting can be used to adjust daily case counts for occurred-but-not-yet-reported events. Here, we present a novel application of nowcasting to data on the current COVID-19 pandemic in Bavaria. It is based on a hierarchical Bayesian model that considers changes in the reporting delay distribution over time and associated with the weekday of reporting. Furthermore, we present a way to estimate the effective time-varying case reproduction number Re(t) based on predictions of the nowcast. The approaches are based on previously published work, that we considerably extended and adapted to the current task of nowcasting COVID-19 cases. We provide methodological details of the developed approach, illustrate results based on data of the current pandemic, and evaluate the model based on synthetic and retrospective data on COVID-19 in Bavaria. Results of our nowcasting are reported to the Bavarian health authority and published on a webpage on a daily basis (https://corona.stat.uni-muenchen.de/). Code and synthetic data for the analysis are available from https://github.com/FelixGuenther/nc_covid19_bavaria and can be used for adaption of our approach to different data.