Viral quasispecies profiles as the result of the interplay of competition and cooperation

Using this novel combination of RME plus the ecological concept of niche overlapping for describing a quasispecies we explore the population distributions of viral variants that emerge, as well as the corresponding dynamics. We observe that the population distribution requires very long transients both to A) reach equilibrium and B) to show a clear dominating master sequence. Based on different independent and recent experimental evidence, we find that when some cooperation or facilitation between variants is included in appropriate doses we can solve both A) and B). We show that a useful quantity to calibrate the degree of cooperation is the Shannon entropy.In order to get a typical quasispecies profile, at least within the considered mathematical approach, it seems that pure competition is not enough. Some dose of cooperation among viral variants is needed. This has several biological implications that might contribute to shed light on the mechanisms operating in quasispecies dynamics and to understand the quasispecies as a whole entity.The concept of quasispecies [1] refers to the equilibrium spectrum of closely related mutants, dominated by a master sequence, generated by a mutation-selection process. It has become an adequate descriptor of RNA viruses at the population level [2,3] and provides natural links between population biology and virology.Competitive exclusion and displacement when two viral populations with nearly equal starting fitness compete has been observed [4]. Thus, a challenging puzzle is how so many (sometimes very similar) variants can coexist in nature. In the case of ordinary ecosystems niche differentiation is obviously an important aspect to promote biodiversity [5]. However, the often striking similarity in coexisting variants suggests that other mechanisms must be involved.An infected individual can harbor several genetically related variants of the same species (assuming that this concept is valid for RNA viruses), and thus the host ca