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 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.
['Klempt|Petr|P|', 'Brzoň|Ondřej|O|', 'Kašný|Martin|M|', 'Kvapilová|Kateřina|K|', 'Hubáček|Petr|P|', 'Briksi|Aleš|A|', 'Bezdíček|Matěj|M|0000-0002-5833-8325', 'Koudeláková|Vladimira|V|', 'Lengerová|Martina|M|', 'Hajdúch|Marian|M|', 'Dřevínek|Pavel|P|0000-0002-8994-5240', 'Pospíšilová|Šárka|Š|', 'Kriegová|Eva|E|0000-0002-8969-4197', 'Macek|Milan|M|', 'Kvapil|Petr|P|']
SARS-CoV-2 variants massively parallel sequencing metagenomics phylogeny