  The assembly and maturation of viruses with icosahedral capsids must be
coordinated with icosahedral symmetry. The icosahedral symmetry imposes also
the restrictions on the cooperative specific interactions between genomic
RNA/DNA and coat proteins that should be reflected in quasi-regular
segmentation of viral genomic sequences. Combining discrete direct and double
Fourier transforms, we studied the quasi-regular large-scale segmentation in
genomic sequences of different ssRNA, ssDNA, and dsDNA viruses. The particular
representatives included satellite tobacco mosaic virus and the strains of
satellite tobacco necrosis virus, STNV-C, STNV-1, STNV-2, Escherichia phages
MS2, phiX174, alpha3, and HK97, and Simian virus 40. In all their genomes, we
found the significant quasi-regular segmentation of genomic sequences related
to the virion assembly and the genome packaging within icosahedral capsid. We
also found good correspondence between our results and available cryo-electron
microscopy data on capsid structures and genome packaging in these viruses.
Fourier analysis of genomic sequences provides the additional insight into
mechanisms of hierarchical genome packaging and may be used for verification of
the concepts of 3-fold or 5-fold intermediates in virion assembly. The results
of sequence analysis should be taken into account at the choice of models and
data interpretation. They also may be helpful for the development of antiviral
drugs.
