{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Klempt P"],"funding":["MSMT.cz"],"pagination":["1671"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8397935"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["9(8)"],"pubmed_abstract":["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."],"journal":["Microorganisms"],"pubmed_title":["Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic."],"pmcid":["PMC8397935"],"funding_grant_id":["00064203/6003","Ministry of Health, Czech Republic","CZ.02.1.01/0.0/0.0/16_026/000844, LM2018132"],"pubmed_authors":["Drevinek P","Bezdicek M","Koudelakova V","Macek M","Kvapilova K","Briksi A","Kasny M","Kvapil P","Brzon O","Lengerova M","Pospisilova S","Hubacek P","Klempt P","Hajduch M","Kriegova E"],"additional_accession":[]},"is_claimable":false,"name":"Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic.","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.","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Aug","modification":"2024-02-16T04:28:12.197Z","creation":"2022-02-11T09:59:21.488Z"},"accession":"S-EPMC8397935","cross_references":{"pubmed":["34442750"],"doi":["10.3390/microorganisms9081671"]}}