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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...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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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. |
format | Online Article Text |
id | pubmed-8397935 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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