Covid-19 antigen testing: better than we know? A test accuracy study.

BACKGROUND: Antigen testing for SARS-CoV-2 is considered to be less sensitive than the standard reference method - real-time PCR (RT-PCR). It has been suggested that many patients with positive RT-PCR 'missed' by antigen testing might be non-infectious. METHODS: In a real-world high-throughput setting for asymptomatic or mildly symptomatic patients, 494 patients were tested using RT-PCR as well as a single lateral flow antigen test (Ecotest, AssureTech, China). Where the results differed, virus viability was evaluated by cell culture. The test parameters were calculated with RT-PCR and RT-PCR adjusted on viability as reference standards. RESULTS: The overall sensitivity of the used antigen test related to the RT-PCR only was 76.2%, specificity was 97.3%. However, 36 out of 39 patients 'missed' by the antigen test contained no viable virus. After adjusting on that, the sensitivity grew to 97.7% and, more importantly for disease control purposes, the negative predictive value reached 99.2%. CONCLUSIONS: We propose that viability testing should be always performed when evaluating a new antigen test. A well-chosen and validated antigen test provides excellent results in identifying patients who are shedding viable virus (although some caveats still remain) in the real-world high-throughput setting of asymptomatic or mildly symptomatic individuals.

Five Antigen Tests for SARS-CoV-2: Virus Viability Matters.

Antigen testing for SARS-CoV-2 (AGT) is generally considered inferior to RT-PCR testing in terms of sensitivity. However, little is known about the infectiousness of RT-PCR positive patients who pass undetected by AGT. In a screening setting for mildly symptomatic or asymptomatic patients with high COVID-19 prevalence (30-40%), 1141 patients were tested using one of five AGTs and RT-PCR. Where the results differed, virus viability in the samples was tested on cell culture (CV-1 cells). The test battery included AGTs by JOYSBIO, Assure Tech, SD Biosensor, VivaChek Biotech and NDFOS. Sensitivities of the ATGs compared to RT-PCR ranged from 42% to 76%. The best test yielded a 76% sensitivity, 97% specificity, 92% positive, and 89% negative predictive values, respectively. However, in the best performing ATG tests, almost 90% of samples with "false negative" AGT results contained no viable virus. Corrected on the virus viability, sensitivities grew to 81-97% and, with one exception, the tests yielded high specificities >96%. Performance characteristics of the best test after adjustment were 96% sensitivity, 97% specificity, 92% positive, and 99% negative predictive values (high prevalence population). We, therefore, believe that virus viability should be considered when assessing the AGT performance. Also, our results indicate that a well-performing antigen test could in a high-prevalence setting serve as an excellent tool for identifying patients shedding viable virus. We also propose that the high proportion of RT-PCR-positive samples containing no viable virus in the group of "false negatives" of the antigen test should be further investigated with the aim of possibly preventing needless isolation of such patients.

Complex Reporting of Coronavirus Disease (COVID-19) Epidemic in the Czech Republic: Use of Interactive Web-Based Application in Practice

BACKGROUND: The beginning of the COVID-19 epidemic dates back to December 31, 2019, when first cases were reported in the People's Republic of China. In the Czech Republic, the first three cases of infection with the novel coronavirus were confirmed on March 1, 2020. The joint effort of state authorities and researchers gave rise to a unique team, which combines methodical knowledge of real-world processes with the know-how needed for effective processing, analysis and online visualization of data. OBJECTIVE: Due to an urgent need for a tool which would make it possible to present important reports, and which would be based on valid data sources only, a team of government experts together with researchers focused on the design and development of a web application intended to provide a regularly updated overview of COVID-19 epidemiology in the Czech Republic to the general public. METHODS: The CRISP-DM (CRoss-Industry Standard Process for Data Mining) standardized methodology for knowledge mining from database structures was chosen for the complex solution of analytical processing and visualization of data, which provides validated information on the COVID-19 epidemic across the Czech Republic. Great emphasis was put on the understanding and a correct implementation of all six steps (business understanding, data understanding, data preparation, modelling, evaluation and deployment) needed in the process, including the infrastructure of a nationwide information system, the methodological setting of communication channels between all involved stakeholders, as well as data collection, processing, analysis, validation and visualization. RESULTS: The web-based overview of the current spread of COVID-19 in the Czech Republic has been developed as an online platform providing a set of outputs in the form of tables, graphs and maps intended for the general public. On March 12, 2020, the first version of the web portal, containing fourteen overviews divided into five topical sections, was released. The web portal's primary objective is to publish a well-arranged visualization and clear explanation of basic information consisting of the overall numbers of performed tests, confirmed cases of COVID-19, and COVID-19-related deaths together with the daily and cumulative overviews of COVID-19-positive persons, performed tests, location and country of infection of COVID-19-positive persons, hospitalizations of COVID-19 patients, and distribution of personal protective equipment. CONCLUSIONS: The online interactive overview of the current spread of COVID-19 in the Czech Republic was launched on March 11, 2020, and has immediately become the primary communication channel employed by the health care sector to present the current situation regarding the COVID-19 epidemic. This complex reporting of the coronavirus disease epidemic in the Czech Republic also shows an effective way how to interconnect knowledge held by various specialists, such as regional and national methodology experts, who report positive cases of the disease on a daily basis, with knowledge held by developers of central registries, analysts, developers of web applications and leadership in the health care sector. CLINICALTRIAL: