Diverse SARS-CoV-2 variants preceded the initial COVID-19 outbreak in Croatia

Rokić, Filip; Trgovec-Greif, Lovro; Sučić, Neven; Čemeljić, Noa; Grbeša, Đurđica Cekinović; Svedružić, Željko; Rukavina, Tomislav; Vugrek, Oliver; Jurak, Igor

We developed a next-generation SARS-CoV-2 sequencing platform and obtained the first SARS-CoV-2 sequences from patients in Croatia at the beginning of the COVID-19 outbreak in the spring of 2020. Integrating the sequencing and the epidemiological data, we show that patients were infected with different SARS-CoV-2 variants belonging to different clades (mostly G and GH). This result confirms that there was widespread virus transmission early in 2020. Interestingly, we identified a unique mutation resulting in a V13I substitution in Nsp5A, the main viral protease, in a patient who had not received antiviral therapy. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00705-021-05029-7.