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.

Biological Center of the Academy of Sciences of the Czech Republic České Budějovice Czech Republic

CEITEC Masaryk University Brno Czech Republic

Department of Physical Chemistry Faculty of Science Palacký University in Olomouc Olomouc Czech Republic

Faculty of Science Charles University BIOCEV Prague Czech Republic

Institute of Molecular Genetics of the Czech Academy of Sciences Prague Czech Republic

National Institute of Public Health Prague Czech Republic

State Veterinary Institute Prague Czech Republic

University Hospital Brno and Faculty of Medicine Masaryk University Brno Czech Republic

University of Chemistry and Technology Prague Czech Republic

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