Can variants, reinfection, symptoms and test types affect COVID-19 diagnostic performance? A large-scale retrospective study of AG-RDTs during circulation of Delta and Omicron variants, Czechia, December 2021 to February 2022.

BackgroundThe sensitivity and specificity of selected antigen detection rapid diagnostic tests (AG-RDTs) for SARS-CoV-2 were determined in the unvaccinated population when the Delta variant was circulating. Viral loads, dynamics, symptoms and tissue tropism differ between Omicron and Delta.AimWe aimed to compare AG-RDT sensitivity and specificity in selected subgroups during Omicron vs Delta circulation.MethodsWe retrospectively paired AG-RDT results with PCRs registered in Czechia's Information System for Infectious Diseases from 1 to 25 December 2021 (Delta, n = 20,121) and 20 January to 24 February 2022 (Omicron, n = 47,104).ResultsWhen confirmatory PCR was conducted on the same day as AG-RDT as a proxy for antigen testing close to peak viral load, the average sensitivity for Delta was 80.4% and for Omicron 81.4% (p < 0.05). Sensitivity in vaccinated individuals was lower for Omicron (OR = 0.94; 95% confidence interval (CI): 0.87-1.03), particularly in reinfections (OR = 0.83; 95% CI: 0.75-0.92). Saliva AG-RDT sensitivity was below average for both Delta (74.4%) and Omicron (78.4%). Tests on the European Union Category A list had higher sensitivity than tests in Category B. The highest sensitivity for Omicron (88.5%) was recorded for patients with loss of smell or taste, however, these symptoms were almost 10-fold less common than for Delta. The sensitivity of AG-RDTs performed on initially asymptomatic individuals done 1, 2 or 3 days before a positive PCR test was consistently lower for Omicron compared with Delta.ConclusionSensitivity for Omicron was lower in subgroups that may become more common if SARS-CoV-2 becomes an endemic virus.

Comparison of COVID-19 epidemic among Czech dentists and the Czech general population.

Dentists are one of the professional groups most at risk for COVID-19 infection. Enhanced protective measures in dentistry have been adopted worldwide; however, it is unclear to what extent they were sufficient. To assess whether the protective measures outweighed the high infection risk, we compared COVID-19-related data between Czech dentists and the general Czech population. The data was obtained through a survey study attended by 15.8% of Czech Dental Chamber members. Data of the general population were acquired from the Czech Ministry of Health database. By the end of May 2022, COVID-19 full vaccination and 1st booster dose rates among study participants were 85.8% and 70.1%, respectively, which is significantly higher (p < 0.0001) compared to the Czech general population aged over 24 years (74.9% and 49.4%, respectively). To the same date, PCR/Antigen test verified COVID-19 prevalence among participants was 41.7%, and 49.9% among the general population (p < 0.0001). Prevalence and reinfection rates among individuals who received the 1st booster were significantly lower than among individuals without the booster or full vaccination (p < 0.0001). Persons who received the booster showed a faster return to work, shorter and different types of complications. Willingness to future vaccination was positive among 79.7% of respondents. Mandatory vaccination for healthcare workers and the general population was supported by 62.0% and 49.0%, respectively. The results showed that the high risk of COVID-19 infection associated with dentistry did not lead to higher COVID-19 prevalence among respondents compared to the general population.

COVID-19 vaccine booster significantly decreases the risk of intensive care unit hospitalization in heart failure patients during the Omicron variant wave: A population-based study.

Background: Heart failure (HF) patients are at higher risk of severe coronavirus disease 2019 (COVID-19). The Omicron variant has many novel mutations including those in the spike protein, leading to questions about vaccine effectiveness. The aim of this analysis was to evaluate the effectiveness of the COVID-19 vaccine with or without a booster (i.e., after the third dose) during the Omicron variant wave. Methods: Chronic heart failure patients in the Czech Republic were included in the analysis. COVID-19 infection was monitored from January 1st 2022 to March 31st 2022. The analysis was conducted on data collected in the National Health Information System. Vaccine effectiveness of vaccinated (with or without booster) vs. unvaccinated patients was analyzed for incidence of COVID-19, COVID-19-related hospitalizations, COVID-19 related intensive care unit admissions, and COVID-19 related mechanical ventilation/extracorporeal membrane oxygenation treatment. Findings: From a total 165,453 HF patients in the Czech Republic, 9,728 contracted COVID-19 (22.9% of them not vaccinated, 23.2% vaccinated and 53.8% vaccinated and boosted). Risk of intensive care unit (ICU) hospitalization was 7.6% in the unvaccinated group, 4.8% in the vaccinated group and 2.9% in the boosted group. The calculated effectiveness of the COVID-19 vaccine in prevention of ICU hospitalization in the vaccinated group was 41.9 and 76.6% in the boosted group. Interpretation: The results demonstrated moderate vaccine effectiveness in the prevention of severe COVID-19 in vaccinated but not boosted HF patients. Much stronger effectiveness was found in those who were vaccinated and boosted.

Sharing datasets of the COVID-19 epidemic in the Czech Republic.

At the time of the COVID-19 pandemic, providing access to data (properly optimised regarding personal data protection) plays a crucial role in providing the general public and media with up-to-date information. Open datasets also represent one of the means for evaluation of the pandemic on a global level. The primary aim of this paper is to describe the methodological and technical framework for publishing datasets describing characteristics related to the COVID-19 epidemic in the Czech Republic (epidemiology, hospital-based care, vaccination), including the use of these datasets in practice. Practical aspects and experience with data sharing are discussed. As a reaction to the epidemic situation, a new portal COVID-19: Current Situation in the Czech Republic (https://onemocneni-aktualne.mzcr.cz/covid-19) was developed and launched in March 2020 to provide a fully-fledged and trustworthy source of information for the public and media. The portal also contains a section for the publication of (i) public open datasets available for download in CSV and JSON formats and (ii) authorised-access-only section where the authorised persons can (through an online generated token) safely visualise or download regional datasets with aggregated data at the level of the individual municipalities and regions. The data are also provided to the local open data catalogue (covering only open data on healthcare, provided by the Ministry of Health) and to the National Catalogue of Open Data (covering all open data sets, provided by various authorities/publishers, and harversting all data from local catalogues). The datasets have been published in various authentication regimes and widely used by general public, scientists, public authorities and decision-makers. The total number of API calls since its launch in March 2020 to 15 December 2020 exceeded 13 million. The datasets have been adopted as an official and guaranteed source for outputs of third parties, including public authorities, non-governmental organisations, scientists and online news portals. Datasets currently published as open data meet the 3-star open data requirements, which makes them machine-readable and facilitates their further usage without restrictions. This is essential for making the data more easily understandable and usable for data consumers. In conjunction with the strategy of the MH in the field of data opening, additional datasets meeting the already implemented standards will be also released, both on COVID-19 related and unrelated topics.