Systematic Genomic Surveillance of SARS-CoV-2 Virus on Illumina Sequencing Platforms in the Slovak Republic-One Year Experience.

Autor: Rusňáková D; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia.; Geneton Ltd., 841 04 Bratislava, Slovakia., Sedláčková T; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Geneton Ltd., 841 04 Bratislava, Slovakia., Radvák P; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Slovak Centre of Scientific and Technical Information, 840 05 Bratislava, Slovakia., Böhmer M; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Geneton Ltd., 841 04 Bratislava, Slovakia.; Public Health Authority of the Slovakia, 826 45 Bratislava, Slovakia., Mišenko P; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Geneton Ltd., 841 04 Bratislava, Slovakia., Budiš J; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Geneton Ltd., 841 04 Bratislava, Slovakia.; Slovak Centre of Scientific and Technical Information, 840 05 Bratislava, Slovakia., Bokorová S; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Geneton Ltd., 841 04 Bratislava, Slovakia., Lipková N; Geneton Ltd., 841 04 Bratislava, Slovakia., Forgáčová-Jakúbková M; Comenius University Science Park, 841 04 Bratislava, Slovakia., Sládeček T; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Geneton Ltd., 841 04 Bratislava, Slovakia., Sitarčík J; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Geneton Ltd., 841 04 Bratislava, Slovakia.; Slovak Centre of Scientific and Technical Information, 840 05 Bratislava, Slovakia., Krampl W; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia.; Geneton Ltd., 841 04 Bratislava, Slovakia., Gažiová M; Geneton Ltd., 841 04 Bratislava, Slovakia., Kaliňáková A; Public Health Authority of the Slovakia, 826 45 Bratislava, Slovakia., Staroňová E; Public Health Authority of the Slovakia, 826 45 Bratislava, Slovakia., Tichá E; Public Health Authority of the Slovakia, 826 45 Bratislava, Slovakia., Vrábľová T; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia.; Public Health Authority of the Slovakia, 826 45 Bratislava, Slovakia., Ševčíková L; Public Health Authority of the Slovakia, 826 45 Bratislava, Slovakia., Kotvasová B; Public Health Authority of the Slovakia, 826 45 Bratislava, Slovakia., Maďarová L; Regional Public Health Authority with the Seat in Banská Bystrica, 975 56 Banská Bystrica, Slovakia., Feiková S; Regional Public Health Authority with the Seat in Banská Bystrica, 975 56 Banská Bystrica, Slovakia., Beňová K; Regional Public Health Authority with the Seat in Trenčín, 911 01 Trenčín, Slovakia., Reizigová L; Regional Public Health Authority with the Seat in Trenčín, 911 01 Trenčín, Slovakia., Onderková Z; Regional Public Health Authority with the Seat in Košice, 040 11 Košice, Slovakia., Ondrušková D; Regional Public Health Authority with the Seat in Košice, 040 11 Košice, Slovakia., Loderer D; Biomedical Centre Martin, Jesseniuss Faculty of Medicine, Comenius University, 036 01 Martin, Slovakia., Škereňová M; Biomedical Centre Martin, Jesseniuss Faculty of Medicine, Comenius University, 036 01 Martin, Slovakia., Danková Z; Biomedical Centre Martin, Jesseniuss Faculty of Medicine, Comenius University, 036 01 Martin, Slovakia., Janíková K; Biomedical Centre Martin, Jesseniuss Faculty of Medicine, Comenius University, 036 01 Martin, Slovakia., Halašová E; Biomedical Centre Martin, Jesseniuss Faculty of Medicine, Comenius University, 036 01 Martin, Slovakia., Nováková E; Department of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University, 036 01 Martin, Slovakia., Turňa J; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia.; Slovak Centre of Scientific and Technical Information, 840 05 Bratislava, Slovakia., Szemes T; Comenius University Science Park, 841 04 Bratislava, Slovakia.; Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia.; Geneton Ltd., 841 04 Bratislava, Slovakia.
Jazyk: angličtina
Zdroj: Viruses [Viruses] 2022 Nov 02; Vol. 14 (11). Date of Electronic Publication: 2022 Nov 02.
DOI: 10.3390/v14112432
Abstrakt: To explore a genomic pool of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the pandemic, the Ministry of Health of the Slovak Republic formed a genomics surveillance workgroup, and the Public Health Authority of the Slovak Republic launched a systematic national epidemiological surveillance using whole-genome sequencing (WGS). Six out of seven genomic centers implementing Illumina sequencing technology were involved in the national SARS-CoV-2 virus sequencing program. Here we analyze a total of 33,024 SARS-CoV-2 isolates collected from the Slovak population from 1 March 2021, to 31 March 2022, that were sequenced and analyzed in a consistent manner. Overall, 28,005 out of 30,793 successfully sequenced samples met the criteria to be deposited in the global GISAID database. During this period, we identified four variants of concern (VOC)-Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529). In detail, we observed 165 lineages in our dataset, with dominating Alpha, Delta and Omicron in three major consecutive incidence waves. This study aims to describe the results of a routine but high-level SARS-CoV-2 genomic surveillance program. Our study of SARS-CoV-2 genomes in collaboration with the Public Health Authority of the Slovak Republic also helped to inform the public about the epidemiological situation during the pandemic.
Databáze: MEDLINE
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