Developing molecular surveillance of SARS-CoV-2 in the Czech Republic (2021–2022)
Abstract
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.
Article Details
Authors (88)
Timotej Šúri
Lucie Pfeiferova
Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences
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 Drevinek
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 Kolar
Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences
Jan Pačes