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

Abstract

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.

MGA Biobank - A Multispecialistic Project Biobank in Slovakia

“…At the same time, we plan to continue the realization of biomedical studies focused primarily on the field of civilization and oncological diseases in order to develop and support cooperation between the health sector (hospitals, clinics) and the academic sector (universities, scientific research institutions) in Slovakia. Up to now, MGA Biobank efficiently supported research in Slovakia with more than 2,500 samples released to participating partner´s organizations in the past year, which supported studies with results recently published [9,10].…”

Neighbourhood watch: genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020–2022

“…In the following third wave, some Delta lineages (AY.122, B.1.617.2, AY.43 and AY.4) seemed to be more resilient than other Delta variants as they were detected in constant high proportions until December 2021 ( Figure 5 ). The same observations were also made in countries surrounding Germany, further suggesting a constant introduction of these lineages to M-V during the holiday season [ 27-29 ]. Other lineages occurred in higher proportions only for one to two months (AY.9.2 July/August 2021 and AY.98.1 September 2021) and many remaining Delta strains with low proportions occurred either mainly in July (cluster 6), September (cluster 7), August-December (cluster 8) or October-December 2021 (cluster 9) ( Figure 5 ).…”

Influence of the SARS-CoV-2 Omicron (B.1.1.529) variant and booster vaccine doses on the seroprevalence of specific IgG antibodies in the staff of the Slovak Academy of Sciences

“…Subsequently, the omicron variant (BA.1) spread gradually from December 2021, quickly displacing the delta variant. At the end of January 2022, it already dominated the sequenced samples in Slovakia (Rusňáková et al, 2022). According to the current sequencing data (March 2023) Omicron BA.5 subvariant dominated in Slovakia at the end of the year 2022.…”