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.

Základní údaje

Originální název

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

Autoři

Vydání

Microorganisms, Basel, MDPI, 2021, 2076-2607

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10606 Microbiology

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.926

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14110/21:00124061

Organizační jednotka

Lékařská fakulta

Klíčová slova anglicky

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

Štítky

14110212, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 7. 2. 2022 09:26, Mgr. Tereza Miškechová

Anotace

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.

Návaznosti

EF16_026/0008448, projekt VaV

Název: Analýza českých genomů pro teranostiku

LM2018132, projekt VaV

Název: Národní centrum lékařské genomiky (Akronym: NCLG)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Národní centrum lékařské genomiky

LM2018133, projekt VaV

Název: Český národní uzel Evropské infrastruktury pro translační medicínu (Akronym: EATRIS-ERIC-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Involvement of Czech Translational Medicine Infrastructure to the European Advanced Translational Research Infrastructure in Medicine

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 a 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, roč. 9, č. 8, s. 1-12. ISSN 2076-2607. Dostupné z: https://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 = {https://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 a 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, roč.~9, č.~8, s.~1-12. ISSN~2076-2607. Dostupné z: https://doi.org/10.3390/microorganisms9081671.

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