Hamiltonian path analysis of viral genomes

A multiscale model of virus pandemic: Heterogeneous interactive entities in a globally connected world

“…For RNA viruses, such as SARS-CoV-2, that package their genomes during particle assembly, an understanding of viral geometry is important. This is because the geometric shapes of the structural proteins and their assembly properties are intimately linked, 129,130 and also affect other aspects of the viral life cycle, such as the structural transitions that in some viruses are important for infection. 77 In particular, in order to attribute as little coding sequence as possible to the viral capsid -a phenomenon called the principle of genetic economy -viruses encode blueprints of only a minimal number of distinct proteins (as small as one for the simplest form of virus), that are then repeatedly synthesised from the same genome segment, thus delivering multiple identical copies for virus assembly.…”

A modelling paradigm for RNA virus assembly

“…The (local) geometric properties of these paths can be classified for different types of capsid geometries. These local properties of the paths (as illustrated in Figure 4 b for MS2) can then be used, in combination with a bioinformatics search for potential PS candidates, to identify the likely PS distribution [ 32 , 46 , 47 •• ]. Note that it is not necessary for all binding sites to be occupied, and that the Hamiltonian path constraints can be more restrictive in some regions of the genome than in others.…”

A coarse-grained model of the expansion of the human rhinovirus 2 capsid reveals insights in genome release

“…Conformational changes in CP in response to contact with an RNA stem-loop have been reported in other viruses before, such as the allosteric conformer switch in MS2 that is a prerequisite for capsid assembly [20,21]. Also, in human parechovirus (HPeV), a different picornavirus that does not cleave its VP0 into VP2 and VP4, we have recently shown that there are multiple dispersed RNA sequence/structure motifs in the viral genome with affinity for CP that we termed packaging signals due to their role in capsid formation [22,23]. Cryo-electron microscopy studies of rhinovirus also show multiple dispersed contacts between genomic RNA and capsid, with a change in the contact pattern upon expansion [12].…”