Developing molecular surveillance of SARS-CoV-2 in the Czech Republic (2021–2022)

Molecular surveillance was widely used during the COVID-19 pandemic to rapidly detect 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 enabled accurate detection of changes in major variant dominance within 48 h of sample collection during the Delta/Omicron transition. WGS detected novel mutations and infection clusters, including several genetic lineages and clades of the virus, some of which were unique to the Czech Republic, such as AY.20.1. Molecular surveillance informed the implementation of public health measures and contributed to reduced cases and mortality, however further areas for improvement have been identified for monitoring and managing future pandemics.