SARS-CoV-2 testing in the Slovak Republic from March 2020 to September 2022 - summary of the pandemic trends

Abstract

The COVID-19 pandemic has been part of Slovakia since March 2020. Intensive laboratory testing ended in October 2022, when the number of tests dropped significantly, but the state of the pandemic continues to this day. For the management of COVID-19, it is important to find an indicator that can predict pandemic changes in the community. The average daily/weekly Ct value with a certain time delay can predict changes in the number of cases of SARS-CoV-2 infection, which can be a useful indicator for the healthcare system. The study analyzed the results of 1,420,572 RT-qPCR tests provided by one accredited laboratory during the ongoing pandemic in Slovakia from March 2020 to September 2022. The total positivity of the analyzed tests was 24.64%. The average Ct values found were the highest in the age group of 3-5 years, equal to the number 30.75; the lowest were in the age group >65 years, equal to the number 27. The average weekly Ct values ranged from 22.33 (pandemic wave week) to 30.12 (summer week). We have summarized the results of SARS-CoV-2 diagnostic testing in Slovakia with the scope defined by the rate and positivity of tests carried out at Medirex a.s. laboratories.

Keywords: COVID-19; Ct value; RT-qPCR; Slovakia; age groups; pandemic; statistics.

Figure 1

Geographical classification of the examined and positively tested population according to the districts of Slovakia. (A) On the map, each district has a colored representation (log² scale) corresponding to the number of tests performed. For each color of the scale, the number of tests corresponding to each color is indicated. (B) Each district has a colored representation (linear scale) on the map that corresponds to the total positivity of the district. For each color of the scale, the positivity rate (%) corresponding to the individual colors is given. Non-representative districts with insufficient sample representation (less than 50 samples) to calculate total positivity are shown in gray. (C) Each district has a color representation on the map (log² scale) that corresponds to the rate of tests performed per district population. For each color of the scale, the rate of frequency (%) corresponding to individual colors is given. (D) Each district has a representation on the map (log² scale) corresponding to the rate of positive tests for the population of individual districts of Slovakia. For each color of the scale, the positivity rate (%) corresponding to the individual colors is given.

Figure 2

(A) Geographical visualization of individual regions of the Slovak Republic. BA, Bratislava region; TT, Trnava region; NR, Nitra region; TN, Trencin region; ZA, Zilina region; BB, Banska Bystrica region; KE, Kosice region; PO, Presov region (17). (B) Distribution of Ct values of positive diagnostic tests of individual regions of Slovakia shown as boxplots, supplemented by median Ct values (orange segments).

Figure 3

(A) Distribution of study PCR diagnostic tests performed per day (blue curve), corresponding number of positive study tests per day (red curve), compared with (B) distribution of all diagnostic tests performed per day within the Slovakian PCR testing (blue curve), corresponding number of positive tests within the Slovakian PCR testing (red curve) (5). (A,B) Graphs show the date range 2020-03-19 to 2022-09-29.

Figure 4

(A) Distribution of proportion of positive diagnostic tests of study performed per day, compared with (B) distribution of proportion of all positive tests per day within the Slovakian PCR testing (18). Graph (A) and the parallel yellow lines of graph (B) define the period from 2020-03-19 to 2022-09-29.

Figure 5

(A) Age distribution of all tested individuals (blue curve), positively tested individuals (red curve). (B) Age distribution of all tested females (green curve), positive tested females (red curve), all tested males (blue curve), positive tested males (pink curve). (C) Ct distribution of all positive diagnostic tests (black curve), positive tests performed in females (red curve) and positive tests performed in males (blue curve). (D) Ct distribution of all positive diagnostic tests. The data is broken down by the age of the individuals. (A–D) Data are displayed as density plots.

Figure 6

(A) Ct distributions of positive diagnostic tests shown as boxplots, supplemented by Ct median values (orange segments), boxplots representing the week with the lowest (red color)/ highest (green color) average Ct values are highlighted. (B) Time course of median Ct per day. (C) Change of ratio of positive tests per day with one week delay. (A–C) Graphs define the period from 2020-12-03 to 2022-09-29. Gaps in the graphs reconstruct pandemic days/weeks with an insufficient number of samples (less than 50 performed PCR tests) non-representative results not included in the evaluation.

Figure 7

(A) Distribution of Ct for positive diagnostic tests in different age groups. Data are displayed as violin charts and notched boxplots supplemented with Ct median values (orange segments). (B) Distribution of positivity rate by age of individuals (green curve) and distribution of number of tests by age of individuals (blue curve).