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

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 v...

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Autores principales: Klempt, Petr, Brzoň, Ondřej, Kašný, Martin, Kvapilová, Kateřina, Hubáček, Petr, Briksi, Aleš, Bezdíček, Matěj, Koudeláková, Vladimira, Lengerová, Martina, Hajdúch, Marian, Dřevínek, Pavel, Pospíšilová, Šárka, Kriegová, Eva, Macek, Milan, Kvapil, Petr
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8397935/
https://www.ncbi.nlm.nih.gov/pubmed/34442750
http://dx.doi.org/10.3390/microorganisms9081671
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author Klempt, Petr
Brzoň, Ondřej
Kašný, Martin
Kvapilová, Kateřina
Hubáček, Petr
Briksi, Aleš
Bezdíček, Matěj
Koudeláková, Vladimira
Lengerová, Martina
Hajdúch, Marian
Dřevínek, Pavel
Pospíšilová, Šárka
Kriegová, Eva
Macek, Milan
Kvapil, Petr
author_facet Klempt, Petr
Brzoň, Ondřej
Kašný, Martin
Kvapilová, Kateřina
Hubáček, Petr
Briksi, Aleš
Bezdíček, Matěj
Koudeláková, Vladimira
Lengerová, Martina
Hajdúch, Marian
Dřevínek, Pavel
Pospíšilová, Šárka
Kriegová, Eva
Macek, Milan
Kvapil, Petr
author_sort Klempt, Petr
collection PubMed
description 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.
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spelling pubmed-83979352021-08-29 Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic Klempt, Petr Brzoň, Ondřej Kašný, Martin Kvapilová, Kateřina Hubáček, Petr Briksi, Aleš Bezdíček, Matěj Koudeláková, Vladimira Lengerová, Martina Hajdúch, Marian Dřevínek, Pavel Pospíšilová, Šárka Kriegová, Eva Macek, Milan Kvapil, Petr Microorganisms Article 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. MDPI 2021-08-05 /pmc/articles/PMC8397935/ /pubmed/34442750 http://dx.doi.org/10.3390/microorganisms9081671 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Klempt, Petr
Brzoň, Ondřej
Kašný, Martin
Kvapilová, Kateřina
Hubáček, Petr
Briksi, Aleš
Bezdíček, Matěj
Koudeláková, Vladimira
Lengerová, Martina
Hajdúch, Marian
Dřevínek, Pavel
Pospíšilová, Šárka
Kriegová, Eva
Macek, Milan
Kvapil, Petr
Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic
title Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic
title_full Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic
title_fullStr Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic
title_full_unstemmed Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic
title_short Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic
title_sort distribution of sars-cov-2 lineages in the czech republic, analysis of data from the first year of the pandemic
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8397935/
https://www.ncbi.nlm.nih.gov/pubmed/34442750
http://dx.doi.org/10.3390/microorganisms9081671
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