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. 2023 Feb;28(8):2200451.
doi: 10.2807/1560-7917.ES.2023.28.8.2200451.

SARS-CoV-2 molecular epidemiology in Slovenia, January to September 2021

Sandra Janezic  1 , Aleksander Mahnic  1 , Urška Kuhar  2 , Jernej Kovač  3 , Barbara Jenko Bizjan  3 , Tom Koritnik  1 , Tine Tesovnik  3 , Robert Šket  3 , Uroš Krapež  4 , Brigita Slavec  4 , Tadej Malovrh  2 , Tadej Battelino  3 , Maja Rupnik  1 , Tjasa Zohar Cretnik  1 ; NLZOH COVID-19 team  5 ; CISLD NGS team  6 ; Members of the NLZOH COVID-19 team Members of the CISLD NGS team, UMC Ljubljana
Collaborators, Affiliations

SARS-CoV-2 molecular epidemiology in Slovenia, January to September 2021

Sandra Janezic et al. Euro Surveill. 2023 Feb.

Abstract

BackgroundSequencing of SARS-CoV-2 PCR-positive samples was introduced in Slovenia in January 2021. Our surveillance programme comprised three complementary schemes: (A) non-targeted sequencing of at least 10% of samples, (B) sequencing of samples positive after PCR screening for variants of concern (VOC) and (C) sequencing as per epidemiological indication.AimWe present the analysis of cumulative data of the non-targeted surveillance of SARS-CoV-2 and variant-dependent growth kinetics for the five most common variants in Slovenia for the first 9 months of 2021.MethodsSARS-CoV-2 PCR-positive samples, from January to September 2021, were selected for sequencing according to the national surveillance plan. Growth kinetics studies were done on Vero E6 cells.ResultsAltogether 15,175 genomes were sequenced and 64 variants were detected, of which three successively prevailed. Variant B.1.258.17 was detected in ca 80% of samples in January and was replaced, within 9 weeks, by the Alpha variant. The number of cases decreased substantially during the summer of 2021. However, the introduction of the Delta variant caused a fourth wave and completely outcompeted other variants. Other VOC were only detected in small numbers. Infection of Vero E6 cells showed higher replication rates for the variants Alpha and Delta, compared with B.1.258.17, B.1.258, and B.1.1.70, which dominated in Slovenia before the introduction of the Alpha and Delta variants.ConclusionInformation on SARS-CoV-2 variant diversity provided context to the epidemiological data of PCR-positive cases, contributed to control of the initial spread of known VOC and influenced epidemiological measures.

Keywords: Alpha variant; B.1.258.17 variant; Delta variant; SARS-CoV-2 genomic surveillance; Slovenia; Virus growth kinetics.

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Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
Distribution of SARS-CoV-2 variants, Slovenia, January–September 2021 (n = 15,175)
Figure 2
Figure 2
Prevalence of N439K amino acid substitution in the SARS-CoV-2 B.1.258.17 lineage over 19 weeks, Slovenia, January–May 2021 (n = 2,641)
Figure 3
Figure 3
Growth kinetics in Vero E6 cells of the most common SARS-CoV-2 variants, Slovenia, March and July 2021 (n = 21)
See this image and copyright information in PMC

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Supplementary concepts