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

P. Klempt, O. Brzoň, M. Kašný, K. Kvapilová, P. Hubáček, A. Briksi, M. Bezdíček, V. Koudeláková, M. Lengerová, M. Hajdúch, P. Dřevínek, Š. Pospíšilová, E. Kriegová, M. Macek, P. Kvapil

. 2021 ; 9 (8) : . [pub] 20210805

Jazyk angličtina Země Švýcarsko

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/bmc21024207

Grantová podpora
CZ.02.1.01/0.0/0.0/16_026/000844, LM2018132 MSMT.cz
00064203/6003 MZCR.cz
Ministry of Health, Czech Republic RVO FNBr, 65269705

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.

Citace poskytuje Crossref.org

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