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

TL;DR

This paper combines ecological niche theory with the replicator-mutator equation to better understand viral quasispecies, highlighting the importance of cooperation among variants for realistic population dynamics and profiles.

Contribution

It introduces a novel approach integrating ecological concepts into viral quasispecies modeling, emphasizing the role of cooperation in population distribution and dynamics.

Findings

Long transients to equilibrium and dominant sequences in QS models

Cooperation among variants shortens transient times and shapes population profiles

Shannon entropy effectively calibrates the degree of cooperation

Abstract

Viral quasispecies can be regarded as a swarm of genetically related mutants or a quasispecies (QS). A common formalism to approach QS is the replicator-mutator equation (RME). However, a problem with the RME is how to quantify the interaction coefficients between viral variants. Here, this is addressed by adopting an ecological perspective and resorting to the niche theory of competing communities, which assumes that the utilization of resources primarily determines ecological segregation between competing individuals (the different viral variants that constitute the QS). Using this novel combination of RME plus the ecological concept of niche overlapping, for describing QS, 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. Therefore, in order to get a typical quasispecies profile, it seems that pure competition is not enough. Rather, some degree of cooperation among viral variants is needed. This has several biological implications that might contribute to shed light on the mechanisms operating in QS dynamics and to understand the QS as a whole entity.