Unsupervised genome-wide cluster analysis: nucleotide sequences of the omicron variant of SARS-CoV-2 are similar to sequences from early 2020 [article]

Georg Hahn, Sanghun Lee, Dmitry Prokopenko, Tanya Novak, Julian Hecker, Surender Khurana, Lindsey R. Baden, Adrienne G. Randolph, Scott T. Weiss, Christoph Lange
2021 bioRxiv   pre-print
The GISAID database contains more than 100,000 SARS-CoV-2 genomes, including sequences of the recently discovered SARS-CoV-2 omicron variant and of prior SARS-CoV-2 strains that have been collected from patients around the world since the beginning of the pandemic. We applied unsupervised cluster analysis to the SARS-CoV-2 genomes, assessing their similarity at a genome-wide level based on the Jaccard index and principal component analysis. Our analysis results show that the omicron variant
more » ... ences are most similar to sequences that have been submitted early in the pandemic around January 2020. Furthermore, the omicron variants in GISAID are spread across the entire range of the first principal component, suggesting that the strain has been in circulation for some time. This observation supports a long-term infection hypothesis as the omicron strain origin.
doi:10.1101/2021.12.29.474469 fatcat:7qwrlauew5f37bf62gtomix4vm