# Developing molecular surveillance of SARS-CoV-2 in the Czech Republic (2021–2022) **Authors:** Timotej Šúri, Lucie Pfeiferová, Matěj Bezdíček, Jan Svatoň, Vladimír Hampl, Karel Berka, Helena Jiřincová, Martina Lengerová, Martin Kolísko, Alexander Nagy, Ruth Tachezy, Timotej Šúri, Timotej Šúri, Lucie Pfeiferová, Matěj Bezdíček, Jan Svatoň, Vladimír Hampl, Karel Berka, Helena Jiřincová, Martina Lengerová, Martin Kolísko, Alexander Nagy, Ruth Tachezy, Jan Bartoš, Petr Brož, Vojtěch Bystrý, Martin Čech, Monika Čechová, Jiří Černý, Kateřina Chudějová, Iva Dolinová, Pavel Dřevínek, Edvard Ehler, Alena Fialová, Filip Franko, Viktor Furman, Zoltán Füssy, Markéta Gančarčíková, Alejandro Jiménez González, Marián Hajdúch, Blanka Hamplová, Václav Hejret, Petr Holub, Patrik Horna, Miluše Hradilová, Štěpánka Hrdá, Magdalena Jančářová, Michaela Jaroměřská, Eduard Ježo, Daniel Klimeš, Šárka Kocourková, Jana Kozáková, Martin Kracík, Jan Kubovčiak, Jana Fialová Kučerová, Jan Kynčl, Matej Lexa, Monika Liptáková, Jan Macháň, Barbora Macková, Marek Malý, Kateřina Matějová, Luděk Matyska, Hana Medová, Ondřej Moravčík, Jakub Mrázek, Serafim Nenarokov, Eva Niklova, Marian Novotný, Jaroslav Nunvář, Adam Obr, Hana Orlíková, Josef Pasulka, Helena Paszeková, Ingrid Poláková, Martin Pospíšek, Miroslav Ruda, Jana Šáchová, Eric Salomaki, Jeffrey Silberman, Radek Šíma, Branislav Šiška, Rastislav Slavkovský, Klára Sobotíková, Kateřina Štillerová, Viktor Stránecký, Alexander Tice, Boris Tichý, Markéta Tomková, Karolína Trachtová, Sebastian Cristian Treitli, Jaromíra Večeřová, David Vostřák, Jan Vrbský, Monika Wisniewska, Artsemi Yushkevich, Tomáš Zajíc, Martin Zmuda, Michal Kolář, Jan Pačes, Michal Kolář, Jan Pačes PMC · DOI: 10.1038/s41598-025-01074-3 · Scientific Reports · 2025-06-04 ## TL;DR The paper describes how the Czech Republic used molecular surveillance to track SARS-CoV-2 variants during 2021–2022, helping inform public health responses. ## Contribution The study evaluates the effectiveness of molecular surveillance methods, including WGS and VD-PCR, in tracking SARS-CoV-2 variants in the Czech Republic. ## Key findings - VD-PCR results were available within 48 hours for 81.5% of cases during the Delta/Omicron transition. - WGS detected low-frequency novel variants in infection clusters and identified community spread of AY.20.1 in the Czech Republic. ## Abstract Molecular surveillance was widely used during the COVID-19 pandemic to detect rapidly emerging variants and monitor the transmission of SARS-CoV-2 within communities. In 2021, the Czech COVID-19 Genomics Consortium (COG-CZ) was set up to coordinate a new SARS-CoV-2 molecular surveillance network. In the Czech Republic, molecular surveillance employed whole genome sequencing (WGS) and variant discrimination polymerase chain reaction (VD-PCR) on samples collected through passive, active and sentinel surveillance. All WGS data was uploaded to GISAID and the PANGO lineages used by GISAID were compared to the main variants determined by VD-PCR. To assess the effectiveness and reliability of the gathered data in adapting pandemic responses, the capabilities and turnaround times of the molecular surveillance methods are evaluated. VD-PCR results were available within 48 h of sample collection for 81.5% of cases during the Delta/Omicron transition. WGS enabled the detection of low-frequency novel variants in infection clusters. WGS surveillance showed there was community spread of AY.20.1, a variant that gained novel mutations within the Czech Republic. Molecular surveillance informed the implementation of public health measures; temporal comparisons of restrictions and outcomes are described. Further areas for improvement have been identified for monitoring and managing future pandemics. The online version contains supplementary material available at 10.1038/s41598-025-01074-3. ## Linked entities - **Diseases:** SARS-CoV-2 (MONDO:0100096), COVID-19 (MONDO:0100096) ## Full-text entities - **Diseases:** COVID-19 (MESH:D000086382), infection (MESH:D007239) - **Species:** Severe acute respiratory syndrome coronavirus 2 (no rank) [taxon 2697049] ## Full text _Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC12137580/full.md ## Figures 7 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12137580/full.md ## References 8 references — full list in the complete paper: https://tomesphere.com/paper/PMC12137580/full.md --- Source: https://tomesphere.com/paper/PMC12137580