Exploring the dynamic variations of viral genomes via a novel genetic network.

[Display omitted] • A novel cluster approach is conducted a phylogenetic network analysis of viral genomes that provides insights into the dynamic variations for SARS-CoV-2 genomes. • It is elucidated that our genetic network can describe the relationships of viral genomes, modulate the spread tendencies of pandemic, and reflect the fluidity of mutations. • K-mer natural vector has the ability not only to capture the established hotspots of diversities in viral genomes, but also to deal with the cases with recombination and deletions, as well as sequencing errors. Exploring the dynamic variations of viral genomes utilizing with a phylogenetic analysis is vital to control the pandemic and stop its waves. Genetic network can be applied to depict the complicated evolution relationships of viral genomes. However, current phylogenetic methods cannot handle the cases with deletions effectively. Therefore, the k-mer natural vector is employed to characterize the compositions and distribution features of k-mers occurring in a viral genome, and construct a one-to-one relationship between a viral genome and its k-mer natural vector. Utilizing the k-mer natural vector, we proposed a novel genetic network to investigate the variations of viral genomes in transmission among humans. With the assistance of genetic network, we identified the super-spreaders that were responsible for the pandemic outbreaks all over the world and chose the parental strains to evaluate the effectiveness of diagnostics, therapeutics, and vaccines. The obtaining results fully demonstrated that our genetic network can truly describe the relationships of viral genomes, effectively simulate virus spread tendency, and trace the transmission routes precisely. In addition, this work indicated that the k-mer natural vector has the ability to capture established hotspots of diversities existing in the viral genomes and understand how genomic contents change over time. [ABSTRACT FROM AUTHOR]