A COVID-19 virus mutation tracker system (CovMT; appendix) based on SARS-CoV-2 isolate genomes deposited to GISAID to track the worldwide sequencing efforts and the evolution of the mutational landscape of this virus. CovMT, which is updated daily, summarises mutations from more than 450 000 isolates into groups of generic virus clades, lineages, and more specific mutation sets we call mutation fingerprints.