Genome organization and packaging, mutation impacts and quasi-periodic patterns in viral genomes

A method described in this publication is able (i) to display features related to the general genome organization and packaging; (ii) to identify explicitly motifs responsible for these features and the distribution of motifs over the genome; the most pronounced motifs can be screened against available databases for further studies; (iii) to assess the impact of mutations; the salient mutations can be tried experimentally and used for genome editing; and (iv) to quantify the information that can be insightful for general studies of molecular evolution of living organisms. The method is based on the transitional genome mapping that may be considered as an extension and adaptation of the general correlation technique and is aimed at displaying significant correlations throughout all genome scales. Combining this method with a correlation entropy as the output variables extends significantly its abilities. The relevant theory was developed and tested for the assessment of statistical significance of the striking features in correlation characteristics. The particular applications are illustrated with the genomes of satellite tobacco mosaic virus, coronaviruses SARS-CoV-2 and SARS-CoV, hepatitis delta virus and viroid representatives from two main families. As shown, the genome editing with salient ordering mutations strengthens significantly the features related to the genome packaging and organization. The relevant underlying quasi-periodic patterns can be reconstructed explicitly. The resulting edited viral sequences can potentially be used for the development of vaccines, drug targeting and for the general studies of underlying molecular mechanisms.