Exploring COVID-19 daily records of diagnosed cases and fatalities based on simple nonparametric methods

Abstract

Containment strategies to combat epidemics such as SARS-CoV-2/COVID-19 require the availability of epidemiological parameters, e.g., the effective reproduction number. Parametric models such as the commonly used susceptible-infected-removed (SIR) compartment models fitted to observed incidence time series have limitations due to the time-dependency of the parameters. Furthermore, fatalities are delayed with respect to the counts of new cases, and the reproduction cycle leads to periodic patterns in incidence time series. Therefore, based on comprehensible nonparametric methods including time-delay correlation analyses, estimates of crucial parameters that characterise the COVID-19 pandemic with a focus on the German epidemic are presented using publicly available time-series data on prevalence and fatalities. The estimates for Germany are compared with the results for seven other countries (France, Italy, the United States of America, the United Kingdom, Spain, Switzerland, and Brazil). The duration from diagnosis to death resulting from delay-time correlations turns out to be 13 days with high accuracy for Germany and Switzerland. For the other countries, the time-to-death durations have wider confidence intervals. With respect to the German data, the two time series of new cases and fatalities exhibit a strong coherence. Based on the time lag between diagnoses and deaths, properly delayed asymptotic as well as instantaneous fatality–case ratios are calculated. The temporal median of the instantaneous fatality–case ratio with time lag of 13 days between cases and deaths for Germany turns out to be 0.02. Time courses of asymptotic fatality–case ratios are presented for other countries, which substantially differ during the first half of the pandemic but converge to a narrow range with standard deviation 0.0057 and mean 0.024. Similar results are obtained from comparing time courses of instantaneous fatality–case ratios with optimal delay for the 8 exemplarily chosen countries. The basic reproduction number, R0, for Germany is estimated to be between 2.4 and 3.4 depending on the generation time, which is estimated based on a delay autocorrelation analysis. Resonances at about 4 days and 7 days are observed, partially attributable to weekly periodicity of sampling. The instantaneous (time-dependent) reproduction number is estimated from the incident (counts of new) cases, thus allowing us to infer the temporal behaviour of the reproduction number during the epidemic course. The time course of the reproduction number turns out to be consistent with the time-dependent per capita growth.