SARS-CoV-2 Omicron Variant in Croatia—Rapid Detection of the First Case and Cross-Border Spread

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 sequencing was performed using...

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Veröffentlicht in:	Pathogens (Basel) Jg. 11; H. 5; S. 511
Hauptverfasser:	Ferenčak, Ivana, Obrovac, Mihaela, Žmak, Ljiljana, Kuzle, Josipa, Petrović, Goranka, Vilibić-Čavlek, Tatjana, Jurić, Dragan, Jurić, Anita, Hruškar, Željka, Capak, Krunoslav, Stevanović, Vladimir, Milanović, Maja, Govedarica, Marija, Vujošević, Danijela, Tabain, Irena
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	Switzerland MDPI AG 26.04.2022 MDPI
Schlagworte:	Communication Contact tracing Coronaviruses COVID-19 COVID-19 vaccines Croatia Depletion Disease transmission Epidemics Epidemiology Gene sequencing Influenza Laboratories Medical research mRNA Mutation Omicron variant Pandemics Patients Phylogenetics Phylogeny SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 surveillance Viral diseases Whole genome sequencing Workshops South Africa Montenegro Croatia Omicron variant SARS-CoV-2 surveillance whole-genome sequencing Croatia
ISSN:	2076-0817, 2076-0817
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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 sequencing 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. Phylogenetic 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.
AbstractList	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. Whole-genome sequencing was performed using the Illumina MiniSeq sequencing system. SARS-CoV-2 lineages were identified using the PANGOLIN and GISAID databases. 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. Phylogenetic 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. 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. 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 sequencing 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. Phylogenetic 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. 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.BACKGROUNDDue 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.Whole-genome sequencing was performed using the Illumina MiniSeq sequencing system. SARS-CoV-2 lineages were identified using the PANGOLIN and GISAID databases.METHODSWhole-genome sequencing was performed using the Illumina MiniSeq sequencing system. SARS-CoV-2 lineages were identified using the PANGOLIN and GISAID databases.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. Phylogenetic 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.RESULTSThe 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. Phylogenetic 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.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.CONCLUSIONSGenomic monitoring and early detection of novel SARS-CoV-2 variants are essential to implement timely epidemiological interventions and reduce further transmission in the population.
Author	Capak, Krunoslav Stevanović, Vladimir Vujošević, Danijela Tabain, Irena Govedarica, Marija Petrović, Goranka Žmak, Ljiljana Obrovac, Mihaela Ferenčak, Ivana Hruškar, Željka Jurić, Dragan Milanović, Maja Kuzle, Josipa Vilibić-Čavlek, Tatjana Jurić, Anita
AuthorAffiliation	2 Department of Microbiology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia 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.) 5 Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; vladostevanovic@gmail.com 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.) 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.h
AuthorAffiliation_xml	– name: 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.) – name: 3 Department of Epidemiology, Croatian Institute of Public Health, 10000 Zagreb, Croatia; goranka.petrovic@hzjz.hr – name: 5 Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia; vladostevanovic@gmail.com – name: 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.) – name: 4 Environmental Health Department, Croatian Institute of Public Health, 10000 Zagreb, Croatia; kcapak@hzjz.hr – name: 2 Department of Microbiology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
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Snippet	Background: Due to rapid spread, the Omicron variant has become the dominant SARS-CoV-2 variant responsible for infections worldwide. We present the first... 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...
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SubjectTerms	Communication Contact tracing Coronaviruses COVID-19 COVID-19 vaccines Croatia Depletion Disease transmission Epidemics Epidemiology Gene sequencing Influenza Laboratories Medical research mRNA Mutation Omicron variant Pandemics Patients Phylogenetics Phylogeny SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 surveillance Viral diseases Whole genome sequencing Workshops
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Title	SARS-CoV-2 Omicron Variant in Croatia—Rapid Detection of the First Case and Cross-Border Spread
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