Visualisation of sequenced SARS-CoV-2 samples in Croatia

As part of the European preparedness plan for biological threats associated with new variants of SARS-CoV-2 entitled the “HERA Incubator”, the Republic of Croatia has strengthened its national capacities for whole-genome sequencing (WGS) in order to be able to monitor the emergence and spread of new variants of the SARS-CoV-2 virus in its territory. For this purpose, a visualisation tool was created that uses the open code of the Nextstrain project (Hadfield, James et al. “Nextstrain: real-time tracking of pathogen evolution.” Bioinformatics (Oxford, England) vol. 34,23 (2018): 4121- 4123. doi:10.1093/bioinformatics/bty407).

The visualisation tool shows the results obtained from the analysis of whole-genome sequences of SARS-CoV-2 virus stored in the SARS-CoV-2 GISAID Database (Khare, Shruti et al. “GISAID’s Role in Pandemic Response.” China CDC weekly vol. 3,49 (2021): 1049-1051. doi:10.46234/ccdcw2021.255) and, for this reason, the analytical results and additional data are presented in English. Filters were used to select those sequences from the database with high coverage (read depth) and enter the sampling date.

The analyses were performed using tools from the Nextstrain platform, and the data will be updated twice a month to provide easier access to the sequencing results for the scientific community and general public. For access to the visualisation tool, visit HERE.