Evolutionary trajectory estimation via replication simulation of coronavirus spike gene based on random mutation and similarity-based selection.

ABSTRACT: Viruses exhibit rapid evolutionary dynamics through random mutations and selection, driving their adaptation and cross-species transmission. To investigate these mechanisms, we designed a simulation framework with a graphical user interface (GUI), implementing random mutation and similarity-based selection. This system models the evolution of a user-supplied viral sequence toward a designated target by recursively selecting the top-N amino acid sequences with the greatest similarity in each replication cycle. Simulations tracking the evolution of SARS-CoV-2 Wuhan-Hu-1 toward the Omicron variant (BA.1) displayed plateau-like similarity trajectories, where increased substitution rates resulted in a more rapid attainment of the plateau stage. The model-generated intermediate spike sequences e

SUBMITTER: Kim MC 

PROVIDER: S-EPMC12395072 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature