Stochastic Mutation Theory of SARS-CoV-2 Variants

Abstract: Predicting the future evolutionary trajectory of SARS-CoV-2 remains a critical challenge, particularly due to the pivotal role of spike protein mutations. Developing an evolutionary model capable of continuously integrating new experimental data is an urgent priority. By employing well-founded assumptions for mutant representation (four-letter and two-letter formats) and the n-mer distance algorithm, we constructed an evolutionary tree of SARS-CoV-2 mutations that accurately reflects observed viral strain evolution. We introduce a stochastic method for generating new strains on this tree based on spike protein mutations. For a given set A of existing mutation sites, we define a set X of x randomly generated sites on the spike protein. Our analysis reveals that the position of a generated strain on the tree is determined by x. Through large-scale stochastic sampling, we predict the emergence of new macro-lineages. As x increases, the proportions of macro-lineages shift: lineage O surpasses lineage N, lineage P overtakes O, and ultimately, new lineage Q surpasses P. We identified threshold values of x that distinguish between macro-lineages. Furthermore, we demonstrate that the linear regression of the number of mutated sites (x) against sample collection dates (t) provides a robust approximation, enabling the prediction of new lineage emergence based on the x-t relationship. To conclude, we demonstrated that the SARS-CoV-2 evolution adheres to statistical principles: the emergence of new strains on the evolutionary tree can be driven by randomly generated spike protein sites; and the large-scale stochastic sampling uncovers evolutionary patterns governing the emergence of diverse macro-lineages.