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Abstract

Background

Sequencing 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.

Aim

We 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.

Methods

SARS-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.

Results

Altogether 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.

Conclusion

Information 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.

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This work is licensed under a Creative Commons Attribution 4.0 International License.
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2023-02-23
2024-11-21
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2023.28.8.2200451
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SARS-CoV-2 molecular epidemiology in Slovenia, January to September 2021
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Sandra+Janezic&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Janezic Sandra</a>, <a href="/search?value1=Aleksander+Mahnic&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Mahnic Aleksander</a>, <a href="/search?value1=Ur%C5%A1ka+Kuhar&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kuhar Urška</a>, <a href="/search?value1=Jernej+Kova%C4%8D&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kovač Jernej</a>, <a href="/search?value1=Barbara+Jenko+Bizjan&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Jenko Bizjan Barbara</a>, <a href="/search?value1=Tom+Koritnik&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Koritnik Tom</a>, <a href="/search?value1=Tine+Tesovnik&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Tesovnik Tine</a>, <a href="/search?value1=Robert+%C5%A0ket&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Šket Robert</a>, <a href="/search?value1=Uro%C5%A1+Krape%C5%BE&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Krapež Uroš</a>, <a href="/search?value1=Brigita+Slavec&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Slavec Brigita</a>, <a href="/search?value1=Tadej+Malovrh&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Malovrh Tadej</a>, <a href="/search?value1=Tadej+Battelino&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Battelino Tadej</a>, <a href="/search?value1=Maja+Rupnik&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Rupnik Maja</a>, <a href="/search?value1=Tjasa+Zohar+Cretnik&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Zohar Cretnik Tjasa</a>, <a href="/search?value1=NLZOH+COVID-19+team&option1=author&noRedirect=true" class="nonDisambigAuthorLink">NLZOH COVID-19 team</a>, <a href="/search?value1=CISLD+NGS+team&option1=author&noRedirect=true" class="nonDisambigAuthorLink">CISLD NGS team</a></span>. SARS-CoV-2 molecular epidemiology in Slovenia, January to September 2021. <a href="/content/ecdc">Euro Surveill.</a> 2023;28(8):pii=2200451. <a href="https://doi.org/10.2807/1560-7917.ES.2023.28.8.2200451" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2023.28.8.2200451</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 01 Jun 2022;&nbsp;&nbsp; <span class="generated">Accepted</span>: 01 Sept 2022 </span> </p>
/content/10.2807/1560-7917.ES.2023.28.8.2200451
/content/10.2807/1560-7917.ES.2023.28.8.2200451
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