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.

Non-HIV-related comorbidities and uncontrolled HIV replication are independent factors increasing the odds of hospitalization due to COVID-19 among HIV-positive patients in Poland

“…Overall mortality reported in our analysis (6 out of 173 patients, 3.47%) is consistent with the results of the large meta-analysis, where 1416 out of 41,113 (3.44%) HIV–SARS-CoV-2-coinfected individuals died [ 21 ] and slightly lower than the overall case-fatality ratio of 5.43% estimated by a large Polish study conducted in the first months of pandemic, before the first variants of concern were identified [ 22 ].…”

Computational methods and strategies for combating COVID-19

“…Mutation points as single nucleotide polymorphisms (SNPs) are identified in each virus clade detected through this phylogenetic analysis. These global dataset analyses further reveal that climatic and socio-demographic conditions have a more significant role in the spread of COVID-19, highlighted in the following works of Chatterjee et al [2] and Gogolewski et al [3] . In the work of Chatterjee et al [2] , the relationship of socio-demographic conditions, such as temperature, humidity, and population density of the regions, with the region-specific outbreak intensity of COVID-19 has been identified by the application of fuzzy association rule mining on COVID and social data collected from different countries.…”

“…In the work of Chatterjee et al [2] , the relationship of socio-demographic conditions, such as temperature, humidity, and population density of the regions, with the region-specific outbreak intensity of COVID-19 has been identified by the application of fuzzy association rule mining on COVID and social data collected from different countries. While in the work of Gogolewski et al [3] , case fatality rates (CFR) for COVID-19 have been extensively studied based on the historical data regarding mortality in Poland during the first six months of the pandemic, when no SARS-CoV-2 variants of concern were present among infected. It leads to the CFR's exploration to find its decreasing trend in time.…”

Differentiation of SARS-CoV-2 Variants Using RT-qPCRs by Targeting Recurrent Mutation Sites: A Diagnostic Laboratory Experience from Multi-Center Regional Study, August 2020–December 2021, Poland

“…There are only few publications tracing SARS-CoV-2 variants in Poland [ 29 , 34 , 35 , 36 , 37 ]. Most of them based on analysis of viral genomic data deposited at the Global Initiative on Sharing All Influenza Data (GISAID) [ 5 ]; it currently contains 83,764 sequences from Poland [ 5 ].…”

“…The first VOC, Alpha variant, was identified in a sample collected in October 2020. Interestingly, previous data reported that this variant appeared in Poland in December 2020 [ 37 , 42 ]. Since its emergence, the Alpha variant has gradually increased its proportion in the following months, as we already observed in our previous survey [ 29 ].…”