Fig. 3: Virus genotypic complexity: from the hypercube to the ultracube.

a Classical view of quasispecies evolution in a hypercube for 4-bit sequences. Each node of the network connects two genotypes via a single-point mutation. Sequences evolve to first neighbors by single-bit (nucleotide) substitutions during replication. Homologous recombination may allow genotypes to jump to further neighbors (blue arrow). b Example of a sequence space for binary genomes of length five considering deletions (blue dashed arrows) and insertions (green solid arrows) during replication. These processes produce mutants and connect hypercubes of different dimensions, giving rise to a more complex sequence space that we label ultracube and which can be conceived as a multiplex network. For clarity, we do not display all the nodes but exemplify some processes of deletion and insertion, which give rise to a set of connected hypercubes of dimensions 5 (gray), 4 (black), 3 (blue), 2 (red), and 1 (orange). c Schematic diagram of connected hypercubes of different dimensions illustrated schematically as multilayered networks.