Distribution of SARS-CoV-2 Lineages in the Czech Republic,
Analysis of Data from the First Year of the Pandemic

J 2021

Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic

KLEMPT, Petr, Ondrej BRZON, Martin KASNY, Katerina KVAPILOVA, Petr HUBACEK et. al.

Basic information

Original name

Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic

Authors

KLEMPT, Petr (203 Czech Republic, guarantor), Ondrej BRZON (203 Czech Republic), Martin KASNY (203 Czech Republic), Katerina KVAPILOVA (203 Czech Republic), Petr HUBACEK (203 Czech Republic), Ales BRIKSI (203 Czech Republic), Matěj BEZDÍČEK (203 Czech Republic, belonging to the institution), Vladimira KOUDELAKOVA (203 Czech Republic), Martina LENGEROVÁ (203 Czech Republic, belonging to the institution), Marian HAJDUCH (203 Czech Republic), Pavel DREVINEK (203 Czech Republic), Šárka POSPÍŠILOVÁ (203 Czech Republic, belonging to the institution), Eva KRIEGOVA (203 Czech Republic), Milan MACEK (203 Czech Republic) and Petr KVAPIL (203 Czech Republic)

Edition

Microorganisms, Basel, MDPI, 2021, 2076-2607

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10606 Microbiology

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.926

RIV identification code

RIV/00216224:14110/21:00124061

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.3390/microorganisms9081671

UT WoS

000689471800001

Keywords in English

SARS-CoV-2; metagenomics; variants; phylogeny; massively parallel sequencing

Abstract

V originále

In the Czech Republic, the current pandemic led to over 1.67 million SARS-CoV-2- positive cases since the recording of the first case on 1 March 2020. SARS-CoV-2 genome analysis is an important tool for effective real-time quantitative PCR (RT-qPCR) diagnostics, epidemiology monitoring, as well as vaccination strategy. To date, there is no comprehensive report on the distribution of SARS-CoV-2 genome variants in either the Czech Republic, including Central and Eastern Europe in general, during the first year of pandemic. In this study, we have analysed a representative cohort of SARS-CoV-2 genomes from 229 nasopharyngeal swabs of COVID-19 positive patients collected between March 2020 and February 2021 using validated reference-based sequencing workflow. We document the changing frequency of dominant variants of SARS-CoV-2 (from B.1 -> B.1.1.266 -> B.1.258 -> B.1.1.7) throughout the first year of the pandemic and list specific variants that could impact the diagnostic efficiency RT-qPCR assays. Moreover, our reference-based workflow provided evidence of superinfection in several samples, which may have contributed to one of the highest per capita numbers of COVID-19 cases and deaths during the first year of the pandemic in the Czech Republic.

Links

EF16_026/0008448, research and development project

Name: Analýza českých genomů pro teranostiku

LM2018132, research and development project

Name: Národní centrum lékařské genomiky (Acronym: NCLG)

Investor: Ministry of Education, Youth and Sports of the CR, National Center for Medical Genomics

LM2018133, research and development project

Name: Český národní uzel Evropské infrastruktury pro translační medicínu (Acronym: EATRIS-ERIC-CZ)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

KLEMPT, Petr, Ondrej BRZON, Martin KASNY, Katerina KVAPILOVA, Petr HUBACEK, Ales BRIKSI, Matěj BEZDÍČEK, Vladimira KOUDELAKOVA, Martina LENGEROVÁ, Marian HAJDUCH, Pavel DREVINEK, Šárka POSPÍŠILOVÁ, Eva KRIEGOVA, Milan MACEK and Petr KVAPIL. Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic. Microorganisms. Basel: MDPI, 2021, vol. 9, No 8, p. 1-12. ISSN 2076-2607. Available from: https://dx.doi.org/10.3390/microorganisms9081671.

@article{1831970,
   author = {Klempt, Petr and Brzon, Ondrej and Kasny, Martin and Kvapilova, Katerina and Hubacek, Petr and Briksi, Ales and Bezdíček, Matěj and Koudelakova, Vladimira and Lengerová, Martina and Hajduch, Marian and Drevinek, Pavel and Pospíšilová, Šárka and Kriegova, Eva and Macek, Milan and Kvapil, Petr},
   article_location = {Basel},
   article_number = {8},
   doi = {http://dx.doi.org/10.3390/microorganisms9081671},
   keywords = {SARS-CoV-2; metagenomics; variants; phylogeny; massively parallel sequencing},
   language = {eng},
   issn = {2076-2607},
   journal = {Microorganisms},
   title = {Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic},
   url = {https://www.mdpi.com/2076-2607/9/8/1671},
   volume = {9},
   year = {2021}
}

TY  - JOUR
ID  - 1831970
AU  - Klempt, Petr - Brzon, Ondrej - Kasny, Martin - Kvapilova, Katerina - Hubacek, Petr - Briksi, Ales - Bezdíček, Matěj - Koudelakova, Vladimira - Lengerová, Martina - Hajduch, Marian - Drevinek, Pavel - Pospíšilová, Šárka - Kriegova, Eva - Macek, Milan - Kvapil, Petr
PY  - 2021
TI  - Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic
JF  - Microorganisms
VL  - 9
IS  - 8
SP  - 1-12
EP  - 1-12
PB  - MDPI
SN  - 20762607
KW  - SARS-CoV-2
KW  - metagenomics
KW  - variants
KW  - phylogeny
KW  - massively parallel sequencing
UR  - https://www.mdpi.com/2076-2607/9/8/1671
N2  - In the Czech Republic, the current pandemic led to over 1.67 million SARS-CoV-2- positive cases since the recording of the first case on 1 March 2020. SARS-CoV-2 genome analysis is an important tool for effective real-time quantitative PCR (RT-qPCR) diagnostics, epidemiology monitoring, as well as vaccination strategy. To date, there is no comprehensive report on the distribution of SARS-CoV-2 genome variants in either the Czech Republic, including Central and Eastern Europe in general, during the first year of pandemic. In this study, we have analysed a representative cohort of SARS-CoV-2 genomes from 229 nasopharyngeal swabs of COVID-19 positive patients collected between March 2020 and February 2021 using validated reference-based sequencing workflow. We document the changing frequency of dominant variants of SARS-CoV-2 (from B.1 -> B.1.1.266 -> B.1.258 -> B.1.1.7) throughout the first year of the pandemic and list specific variants that could impact the diagnostic efficiency RT-qPCR assays. Moreover, our reference-based workflow provided evidence of superinfection in several samples, which may have contributed to one of the highest per capita numbers of COVID-19 cases and deaths during the first year of the pandemic in the Czech Republic.
ER  -

KLEMPT, Petr, Ondrej BRZON, Martin KASNY, Katerina KVAPILOVA, Petr HUBACEK, Ales BRIKSI, Matěj BEZDÍČEK, Vladimira KOUDELAKOVA, Martina LENGEROVÁ, Marian HAJDUCH, Pavel DREVINEK, Šárka POSPÍŠILOVÁ, Eva KRIEGOVA, Milan MACEK and Petr KVAPIL. Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic. \textit{Microorganisms}. Basel: MDPI, 2021, vol.~9, No~8, p.~1-12. ISSN~2076-2607. Available from: https://dx.doi.org/10.3390/microorganisms9081671.

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