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

T Timotej Šúri L Lucie Pfeiferova (Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences) M Matěj Bezdíček J Jan Svatoň V Vladimír Hampl K Karel Berka H Helena Jiřincová M Martina Lengerová M Martin Kolísko A Alexander Nagy R Ruth Tachezy J Jan Bartoš P Petr Brož V Vojtěch Bystrý M Martin Čech M Monika Čechová J Jiří Černý K Kateřina Chudějová I Iva Dolinová P Pavel Drevinek E Edvard Ehler A Alena Fialová F Filip Franko V Viktor Furman Z Zoltán Füssy M Markéta Gančarčíková A Alejandro Jiménez González M Marián Hajdúch B Blanka Hamplová V Václav Hejret P Petr Holub P Patrik Horna M Miluše Hradilová Štěpánka Hrdá M Magdalena Jančářová M Michaela Jaroměřská E Eduard Ježo D Daniel Klimeš Šárka Kocourková J Jana Kozáková M Martin Kracík J Jan Kubovčiak J Jana Fialová Kučerová J Jan Kynčl M Matej Lexa M Monika Liptáková J Jan Macháň B Barbora Macková M Marek Malý K Kateřina Matějová L Luděk Matyska H Hana Medová O Ondřej Moravčík J Jakub Mrázek S Serafim Nenarokov E Eva Niklova M Marian Novotný J Jaroslav Nunvář A Adam Obr H Hana Orlíková J Josef Pasulka H Helena Paszeková I Ingrid Poláková M Martin Pospíšek M Miroslav Ruda J Jana Šáchová E Eric Salomaki J Jeffrey Silberman R Radek Šíma B Branislav Šiška R Rastislav Slavkovský K Klára Sobotíková K Kateřina Štillerová V Viktor Stránecký A Alexander Tice B Boris Tichý M Markéta Tomková K Karolína Trachtová S Sebastian Cristian Treitli J Jaromíra Večeřová D David Vostřák J Jan Vrbský M Monika Wisniewska A Artsemi Yushkevich T Tomáš Zajíc M Martin Zmuda M Michal Kolar (Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences) J Jan Pačes

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

Volume / Issue Vol. 15, Issue 1
Published June 04, 2025
ISSN 2045-2322
Publisher Nature Portfolio

Journal Info

Scientific Reports

Nature Portfolio

ISSN: 2045-2322 Open Access Life Sciences

Authors (88)

T

Timotej Šúri

L

Lucie Pfeiferova

Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences

M

Matěj Bezdíček

J

Jan Svatoň

V

Vladimír Hampl

K

Karel Berka

H

Helena Jiřincová

M

Martina Lengerová

M

Martin Kolísko

A

Alexander Nagy

R

Ruth Tachezy

J

Jan Bartoš

P

Petr Brož

V

Vojtěch Bystrý

M

Martin Čech

M

Monika Čechová

J

Jiří Černý

K

Kateřina Chudějová

I

Iva Dolinová

P

Pavel Drevinek

E

Edvard Ehler

A

Alena Fialová

F

Filip Franko

V

Viktor Furman

Z

Zoltán Füssy

M

Markéta Gančarčíková

A

Alejandro Jiménez González

M

Marián Hajdúch

B

Blanka Hamplová

V

Václav Hejret

P

Petr Holub

P

Patrik Horna

M

Miluše Hradilová

Štěpánka Hrdá

M

Magdalena Jančářová

M

Michaela Jaroměřská

E

Eduard Ježo

D

Daniel Klimeš

Šárka Kocourková

J

Jana Kozáková

M

Martin Kracík

J

Jan Kubovčiak

J

Jana Fialová Kučerová

J

Jan Kynčl

M

Matej Lexa

M

Monika Liptáková

J

Jan Macháň

B

Barbora Macková

M

Marek Malý

K

Kateřina Matějová

L

Luděk Matyska

H

Hana Medová

O

Ondřej Moravčík

J

Jakub Mrázek

S

Serafim Nenarokov

E

Eva Niklova

M

Marian Novotný

J

Jaroslav Nunvář

A

Adam Obr

H

Hana Orlíková

J

Josef Pasulka

H

Helena Paszeková

I

Ingrid Poláková

M

Martin Pospíšek

M

Miroslav Ruda

J

Jana Šáchová

E

Eric Salomaki

J

Jeffrey Silberman

R

Radek Šíma

B

Branislav Šiška

R

Rastislav Slavkovský

K

Klára Sobotíková

K

Kateřina Štillerová

V

Viktor Stránecký

A

Alexander Tice

B

Boris Tichý

M

Markéta Tomková

K

Karolína Trachtová

S

Sebastian Cristian Treitli

J

Jaromíra Večeřová

D

David Vostřák

J

Jan Vrbský

M

Monika Wisniewska

A

Artsemi Yushkevich

T

Tomáš Zajíc

M

Martin Zmuda

M

Michal Kolar

Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics, Czech Academy of Sciences

J

Jan Pačes