Using the CDC-classified SARS-CoV-2 VOC (B.1.1.7, B.1.351, B.1.427, B.1.429, and P.1), identified in Hawai’i as an example, we demonstrate a method to define the origin of SARS-CoV-2 lineages and VOC. This method works using either open-source or licensed software with either a personal computer or a supercomputer.