Data-driven case fatality rate estimation for the primary lineage of SARS-CoV-2 in Poland

Abstract

After more than one and a half year since the COVID-19 pandemics outbreak the scientific world is constantly trying to understand its dynamics. In this paper of the case fatality rates (CFR) for COVID-19 we study the historic data regarding mortality in Poland during the first six months of pandemic, when no SARS-CoV-2 variants of concern were present among infected. To this end, we apply competing risk models to perform both uni- and multivariate analyses on specific subpopulations selected by different factors including the key indicators: age, sex, hospitalization. The study explores the case fatality rate to find out its decreasing trend in time. Furthermore, we describe the differences in mortality among hospitalized and other cases indicating a sudden increase of mortality among hospitalized cases at the end of the 2020 spring season. Exploratory and multivariate analysis revealed the real impact of each variable and besides the expected factors indicating increased mortality (age, comorbidities) we track more non-obvious indicators. Recent medical care as well as the identification of the source contact, independently of the comorbidities, significantly impact an individual mortality risk. As a result, the study provides a twofold insight into the COVID-19 mortality in Poland. On one hand we explore mortality in different groups with respect to different variables, on the other we indicate novel factors that may be crucial in reducing mortality. The later can be coped, e.g. by more efficient contact tracing and proper organization and management of the health care system to accompany those who need medical care independently of comorbidities or COVID-19 infection.

Keywords: COVID-19; Case fatality rate; Mortality in Poland; Original SARS-CoV-2 lineage.

Fig. 1

Workflow diagram visualizing all of the steps that were taken to obtain the final results in the article.

Fig. 2

Phylogenetic tree for 50 randomly selected samples collected in Poland during the year 2020 (red circles). Samples from other European countries are randomly selected from the B.1.1.7 lineage.

Fig. 3

Frequency of reported symptoms, by outcome (Recovery, Death, Censored) and by hospital treatment (All cases, Hospitalized). The percent in each cell corresponds to the fraction of patients of given sex and outcome that showed a given symptom, e.g. the value in the first row in the first column is understood as 49.93% of all cases who have censored outcome were symptomatic (showed some symptoms). The analogous figure describing symptoms among different age groups as well as onset months can be found in the Supplementary S2 and S3.

Fig. 4

The comparison of CFR values within different categories (left-hand side) determined by various factors(right-hand side). Each CFR is calculated for both all cases and hospitalized (orange and blue boxes, respectively). Each box corresponds to quartiles, the line to 95% confidence interval and points to outlier observations. Each horizontal line in the middle of the box corresponds to the median CFR value.