A statistical model for the dynamics of COVID-19 infections and their case detection ratio in 2020

Effect of vaccinations and school restrictions on the spread of COVID-19 in different age groups in Germany

With the emergence of SARS-CoV-2, various non-pharmaceutical interventions were adopted to control virus transmission, including school closures. Subsequently, the introduction of vaccines mitigated not only disease severity but also the spread of SARS-CoV-2. This study leveraged an adapted SIR model and non-linear mixed-effects modeling to quantify the impact of remote learning, school holidays, the emergence of Variants of Concern (VOCs), and the role of vaccinations in controlling SARS-CoV-2 spread across 16 German federal states with an age-stratified approach. Findings highlight a significant inverse correlation (Spearman's ρ = -0.92, p < 0.001) between vaccination rates and peak incidence rates across all age groups. Model-parameter estimation using the observed number of cases stratified by federal state and age allowed to assess the effects of school closure and holidays, considering adjustments for vaccinations and spread of VOCs over time. Here, modeling revealed significant (p < 0.001) differences in the virus's spread among pre-school children (0-4), children (5-11), adolescents (12-17), adults (18-59), and the elderly (60+). The transition to remote learning emerged as a critical measure in significantly reducing infection rates among children and adolescents (p < 0.001), whereas an increased infection risk was noted among the elderly during these periods, suggesting a shift in infection networks due to altered caregiving roles. Conversely, during school holiday periods, infection rates among adolescents mirrored those observed when schools were open. Simulation exercises based on the model provided evidence that COVID-19 vaccinations might serve a dual purpose: they protect the vaccinated individuals and contribute to the broader community's safety.

Bayesian hierarchical spatiotemporal models for prediction of (under)reporting rates and cases: COVID-19 infection among the older people in the United States during the 2020-2022 pandemic

The gap between the reported and actual COVID-19 infection cases has been an issue of concern. Here, we present Bayesian hierarchical spatiotemporal disease mapping models for state-level predictions of COVID-19 infection risks and (under)reporting rates among people aged 65 and above during the first two years of the pandemic in the United States. With prior elicitation based on recent prevalence studies, the study suggests that the median state-level reporting rate of COVID-19 infection was 90% (interquartile range: [78%, 96%]). Our study uncovers spatiotemporal variations and dynamics in state-level infection risks and (under)reporting rates, suggesting time-varying associations between higher population density, higher percentage of minorities, and higher percentage of vaccination and increased risks of COVID-19 infection, as well as an association between more easily accessible tests and higher reporting rates. With sensitivity analyses, we highlight the impact and importance of incorporating covariates information and objective prior references for evaluating the issue of underreporting.

Dynamic parameterization of a modified SEIRD model to analyze and forecast the dynamics of COVID-19 outbreaks in the United States

The rapid spread of the numerous outbreaks of the coronavirus disease 2019 (COVID-19) pandemic has fueled interest in mathematical models designed to understand and predict infectious disease spread, with the ultimate goal of contributing to the decision making of public health authorities. Here, we propose a computational pipeline that dynamically parameterizes a modified SEIRD (susceptible-exposed-infected-recovered-deceased) model using standard daily series of COVID-19 cases and deaths, along with isolated estimates of population-level seroprevalence. We test our pipeline in five heavily impacted states of the US (New York, California, Florida, Illinois, and Texas) between March and August 2020, considering two scenarios with different calibration time horizons to assess the update in model performance as new epidemiologic data become available. Our results show a median normalized root mean squared error (NRMSE) of 2.38% and 4.28% in calibrating cumulative cases and deaths in the first scenario, and 2.41% and 2.30% when new data are assimilated in the second scenario, respectively. Then, 2-week (4-week) forecasts of the calibrated model resulted in median NRMSE of cumulative cases and deaths of 5.85% and 4.68% (8.60% and 17.94%) in the first scenario, and 1.86% and 1.93% (2.21% and 1.45%) in the second. Additionally, we show that our method provides significantly more accurate predictions of cases and deaths than a constant parameterization in the second scenario (p < 0.05). Thus, we posit that our methodology is a promising approach to analyze the dynamics of infectious disease outbreaks, and that our forecasts could contribute to designing effective pandemic-arresting public health policies.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00366-023-01816-9.

Automation, organizational ambidexterity and the stability of employee relations: new tensions arising between corporate entrepreneurship, innovation management and stakeholder management

While previous entrepreneurship research has only seldom drawn on organizational ambidexterity, the analysis of the important contemporary tensions among entrepreneurship, innovation management and strategic management issues may be facilitated by more closely analysing organizational ambidexterity in entrepreneurial settings. In this paper, we follow this thinking and more closely analyse an often applied form of corporate entrepreneurship: automation. Such automation is transferring work that was formerly conducted by humans to machines and may thus result in new tensions between corporate entrepreneurship, innovation management and the management of organizational stakeholders such as employees. The present paper investigates whether increased automation lowers the stability of firms' relationships with their employees. In addition, we expect that this relationship is moderated by organizational ambidexterity, as employees may have perceived ambidexterity as a signal that their firm will not overly invest in exploitation only, but maintain a balance between exploitation and exploration. Drawing on stakeholder theory, previous insights into corporate entrepreneurship and a survey of German Mittelstand firms, our findings show that highly ambidextrous firms are indeed more vulnerable to automation, leading to lower employee relational stability. Our findings thus suggest that in highly ambidextrous firms, novel tensions around automation-related corporate entrepreneurship will be detrimental to the stability of the firm's relations with one of its key stakeholder groups: employees.

Deaths during the first year of the COVID-19 pandemic: insights from regional patterns in Germany and Poland

BACKGROUND

Given the nature of the spread of SARS-CoV-2, strong regional patterns in the fatal consequences of the COVID-19 pandemic related to local characteristics such as population and health care infrastructures were to be expected. In this paper we conduct a detailed examination of the spatial correlation of deaths in the first year of the pandemic in two neighbouring countries - Germany and Poland, which, among high income countries, seem particularly different in terms of the death toll associated with the COVID-19 pandemic. The analysis aims to yield evidence that spatial patterns of mortality can provide important clues as to the reasons behind significant differences in the consequences of the COVID-19 pandemic in these two countries.

METHODS

Based on official health and population statistics on the level of counties, we explore the spatial nature of mortality in 2020 in the two countries - which, as we show, reflects important contextual differences. We investigate three different measures of deaths: the officially recorded COVID-19 deaths, the total values of excessive deaths and the difference between the two. We link them to important pre-pandemic regional characteristics such as population, health care and economic conditions in multivariate spatial autoregressive models. From the point of view of pandemic related fatalities we stress the distinction between direct and indirect consequences of COVID-19, separating the latter further into two types, the spatial nature of which is likely to differ.

RESULTS

The COVID-19 pandemic led to much more excess deaths in Poland than in Germany. Detailed spatial analysis of deaths at the regional level shows a consistent pattern of deaths officially registered as related to COVID-19. For excess deaths, however, we find strong spatial correlation in Germany but little such evidence in Poland.

CONCLUSIONS

In contrast to Germany, for Poland we do not observe the expected spatial pattern of total excess deaths and the excess deaths over and above the official COVID-19 deaths. This difference cannot be explained by pre-pandemic regional factors such as economic and population structures or by healthcare infrastructure. The findings point to the need for alternative explanations related to the Polish policy reaction to the pandemic and failures in the areas of healthcare and public health, which resulted in a massive loss of life.

A novel method to monitor COVID-19 fatality rate in real-time, a key metric to guide public health policy

An accurate estimator of the real-time fatality rate is warranted to monitor the progress of ongoing epidemics, hence facilitating the policy-making process. However, most of the existing estimators fail to capture the time-varying nature of the fatality rate and are often biased in practice. A simple real-time fatality rate estimator with adjustment for reporting delays is proposed in this paper using the fused lasso technique. This approach is easy to use and can be broadly applied to public health practice as only basic epidemiological data are required. A large-scale simulation study suggests that the proposed estimator is a reliable benchmark for formulating public health policies during an epidemic with high accuracy and sensitivity in capturing the changes in the fatality rate over time, while the other two commonly-used case fatality rate estimators may convey delayed or even misleading signals of the true situation. The application to the COVID-19 data in Germany between January 2020 and January 2022 demonstrates the importance of the social restrictions in the early phase of the pandemic when vaccines were not available, and the beneficial effects of vaccination in suppressing the fatality rate to a low level since August 2021 irrespective of the rebound in infections driven by the more infectious Delta and Omicron variants during the fourth wave.

Statistical modelling of COVID-19 data: Putting generalized additive models to work

Over the course of the COVID-19 pandemic, Generalized Additive Models (GAMs) have been successfully employed on numerous occasions to obtain vital data-driven insights. In this article we further substantiate the success story of GAMs, demonstrating their flexibility by focusing on three relevant pandemic-related issues. First, we examine the interdepency among infections in different age groups, concentrating on school children. In this context, we derive the setting under which parameter estimates are independent of the (unknown) case-detection ratio, which plays an important role in COVID-19 surveillance data. Second, we model the incidence of hospitalizations, for which data is only available with a temporal delay. We illustrate how correcting for this reporting delay through a nowcasting procedure can be naturally incorporated into the GAM framework as an offset term. Third, we propose a multinomial model for the weekly occupancy of intensive care units (ICU), where we distinguish between the number of COVID-19 patients, other patients and vacant beds. With these three examples, we aim to showcase the practical and ‘off-the-shelf’ applicability of GAMs to gain new insights from real-world data.

Advancing Precision Vaccinology by Molecular and Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 in Germany, 2021

BACKGROUND

Comprehensive pathogen genomic surveillance represents a powerful tool to complement and advance precision vaccinology. The emergence of the Alpha variant in December 2020 and the resulting efforts to track the spread of this and other severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern led to an expansion of genomic sequencing activities in Germany.

METHODS

At Robert Koch Institute (RKI), the German National Institute of Public Health, we established the Integrated Molecular Surveillance for SARS-CoV-2 (IMS-SC2) network to perform SARS-CoV-2 genomic surveillance at the national scale, SARS-CoV-2-positive samples from laboratories distributed across Germany regularly undergo whole-genome sequencing at RKI.

RESULTS

We report analyses of 3623 SARS-CoV-2 genomes collected between December 2020 and December 2021, of which 3282 were randomly sampled. All variants of concern were identified in the sequenced sample set, at ratios equivalent to those in the 100-fold larger German GISAID sequence dataset from the same time period. Phylogenetic analysis confirmed variant assignments. Multiple mutations of concern emerged during the observation period. To model vaccine effectiveness in vitro, we employed authentic-virus neutralization assays, confirming that both the Beta and Zeta variants are capable of immune evasion. The IMS-SC2 sequence dataset facilitated an estimate of the SARS-CoV-2 incidence based on genetic evolution rates. Together with modeled vaccine efficacies, Delta-specific incidence estimation indicated that the German vaccination campaign contributed substantially to a deceleration of the nascent German Delta wave.

CONCLUSIONS

SARS-CoV-2 molecular and genomic surveillance may inform public health policies including vaccination strategies and enable a proactive approach to controlling coronavirus disease 2019 spread as the virus evolves.

Estimating the course of the COVID-19 pandemic in Germany via spline-based hierarchical modelling of death counts

We consider a retrospective modelling approach for estimating effective reproduction numbers based on death counts during the first year of the COVID-19 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. Results for Germany illustrate that our estimates based on death counts are often similar to classical estimates based on confirmed cases; however, considering death counts allows to disentangle effects of adapted testing policies from transmission dynamics. In particular, during the second wave of infections, classical estimates suggest a flattening infection curve following the “lockdown light” in November 2020, while our results indicate that infections continued to rise until the “second lockdown” in December 2020. This observation is associated with more stringent testing criteria introduced concurrently with the “lockdown light”, which is reflected in subsequently increasing dark figures of infections estimated by our model. In light of progressive vaccinations, shifting the focus from modelling confirmed cases to reported deaths with the possibility to incorporate effective infection fatality rates might be of increasing relevance for the future surveillance of the pandemic.

Estimating COVID-19-induced excess mortality in Lombardy, Italy

We compare the expected all-cause mortality with the observed one for different age classes during the pandemic in Lombardy, which was the epicenter of the epidemic in Italy. The first case in Italy was found in Lombardy in early 2020, and the first wave was mainly centered in Lombardy. The other three waves, in Autumn 2020, March 2021 and Summer 2021 are also characterized by a high number of cases in absolute terms. A generalized linear mixed model is introduced to model weekly mortality from 2011 to 2019, taking into account seasonal patterns and year-specific trends. Based on the 2019 year-specific conditional best linear unbiased predictions, a significant excess of mortality is estimated in 2020, leading to approximately 35000 more deaths than expected, mainly arising during the first wave. In 2021, instead, the excess mortality is not significantly different from zero, for the 85+ and 15-64 age classes, and significant reductions with respect to the 2020 estimated excess mortality are estimated for other age classes.