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A method of Transitional Automorphic Mapping of the Genome on Itself (TAMGI)is aimed at combining detection and reconstruction of correlational andquasi-periodic motifs in the viral genomic RNA/DNA sequences. The motifsreconstructed by TAMGI are robust with respect to indels and point mutationsand can be tried as putative therapeutic targets. We developed and tested therelevant theory and statistical criteria for TAMGI applications. Theapplications of TAMGI are illustrated by the study of motifs in the genomes ofthe severe acute respiratory syndrome coronaviruses SARS-CoV and SARS-CoV-2(the latter coronavirus SARS-CoV-2 being responsible for the COVID-19 pandemic)packaged within filament-like helical capsid. Such ribonucleocapsid istransported into spherical membrane envelope with incorporated spikeglycoproteins. Two other examples concern the genomes of viruses withicosahedral capsids, satellite tobacco mosaic virus (STMV) and bacteriophagePHIX174. A part of the quasi-periodic motifs in these viral genomes was evolveddue to weakly specific cooperative interaction between genomic ssRNA/ssDNA andnucleocapsid proteins. The symmetry of the capsids leads to the naturalselection of specific quasi-periodic motifs in the related genomic sequences.Generally, TAMGI provides a convenient tool for the study of numerous molecularmechanisms with participation of both quasi-periodic motifs and completerepeats, the genome organization, contextual analysis of cis/trans regulatoryelements, data mining, and correlations in the genomic sequences.

journal of integrated omics

Combining detection and reconstruction of correlational and  quasi-periodic motifs in viral genomic sequences with transitional genome  mapping: Application to COVID-19