Citation: Ferenˇ cak, I.; Obrovac, M.; Žmak, L.; Kuzle, J.; Petrovi´ c, G.; Vilibi´ c- ˇ Cavlek, T.; Juri´ c, D.; Juri´ c, A.; Hruškar, Ž.; Capak, K.; et al. SARS-CoV-2 Omicron Variant in Croatia—Rapid Detection of the First Case and Cross-Border Spread. Pathogens 2022, 11, 511. https:// doi.org/10.3390/pathogens11050511 Academic Editor: Dan O¸ telea Received: 31 March 2022 Accepted: 24 April 2022 Published: 26 April 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). pathogens Communication SARS-CoV-2 Omicron Variant in Croatia—Rapid Detection of the First Case and Cross-Border Spread Ivana Ferenˇ cak 1 , Mihaela Obrovac 1 , Ljiljana Žmak 1,2 , Josipa Kuzle 1 , Goranka Petrovi´ c 3 , Tatjana Vilibi´ c- ˇ Cavlek 1,2, * , Dragan Juri´ c 1 , Anita Juri´ c 1 , Željka Hruškar 1 , Krunoslav Capak 4 , Vladimir Stevanovi´ c 5 , Maja Milanovi´ c 6 , Marija Govedarica 6 , Danijela Vujoševi´ c 6 and Irena Tabain 1 1 Department of Microbiology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; ivana.ferencak@hzjz.hr (I.F.); mihaela.obrovac@hzjz.hr (M.O.); ljiljana.zmak@hzjz.hr (L.Ž.); josipa.kuzle@hzjz.hr (J.K.); dragan.juric@hzjz.hr (D.J.); misicanita1@gmail.com (A.J.); zeljka.hruskar@hzjz.hr (Ž.H.); irena.tabain@hzjz.hr (I.T.) 2 Department of Microbiology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia 3 Department of Epidemiology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; goranka.petrovic@hzjz.hr 4 Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; kcapak@hzjz.hr 5 Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; vladostevanovic@gmail.com 6 Department of Epidemiology, Institute of Public Health, 81110 Podgorica, Montenegro; maja.milanovic@ijzcg.me (M.M.); marija.govedarica@ijzcg.me (M.G.); danijela.vujosevic@ijzcg.me (D.V.) * Correspondence: tatjana.vilibic-cavlek@hzjz.hr Abstract: Background: Due to rapid spread, the Omicron variant has become the dominant SARS- CoV-2 variant responsible for infections worldwide. We present the first detection of the Omicron variant in Croatia which resulted in rapid cross-border spreading. Methods: Whole-genome se- quencing was performed using the Illumina MiniSeq sequencing system. SARS-CoV-2 lineages were identified using the PANGOLIN and GISAID databases. Results: The first case of the Omicron variant (BA.1.17) emerged in Croatia after a workshop held in Zagreb in November 2021. The patient reported a history of previous COVID-19 and received two doses of an mRNA vaccine. Three additional cases were detected among Croatian participants of the workshop. At the beginning of December, SARS-CoV-2 infection was confirmed in one participant from Montenegro and her husband. Phyloge- netic analysis showed that the detected Omicron variants were closely related to the first Croatian case, confirming the connection with the workshop outbreak and rapid cross-border spreading. Subsequent analyses of SARS-CoV-2 positive samples in Croatia showed the rapid introduction of the Omicron variant and depletion of the Delta variant resulting in the fifth pandemic wave. Conclusions: Genomic monitoring and early detection of novel SARS-CoV-2 variants are essential to implement timely epidemiological interventions and reduce further transmission in the population. Keywords: SARS-CoV-2; Omicron variant; whole-genome sequencing; surveillance; Croatia 1. Introduction During the past two years, from the beginning of the coronavirus disease (COVID-19) pandemic, the World Health Organization (WHO) categorised five severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants to be variants of concern (VOC) [1]. These variants possess concerning characteristics, including increased transmissibility or/and dis- ease severity, reduction in neutralisation by antibodies produced during previous infection or vaccination, as well as reduced effectiveness of treatments or diagnostic testing [1]. How- ever, no variant has caused as much concern as the last variant identified on 24 November 2021, in South Africa, named Omicron, after the 15th letter in the Greek alphabet [2]. Only two days after the identification of this new variant, the WHO designated it as a VOC [1] due to a high number of mutations in the spike protein [3]. Omicron harbours around 30 Pathogens 2022, 11, 511. https://doi.org/10.3390/pathogens11050511 https://www.mdpi.com/journal/pathogens