Viral quasispecies profiles as the result of the interplay of competition and cooperation.
BACKGROUND
Viral quasispecies can be regarded as a swarm of genetically related mutants. A common approach employed to describe viral quasispecies is by means of the quasispecies equation (QE). However, a main criticism of QE is its lack of frequency-dependent selection. This can be overcome by an alternative formulation for the evolutionary dynamics: the replicator-mutator equation (RME). In turn, 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 quasispecies). This provides a theoretical framework to estimate quantitatively the fitness landscape.


RESULTS
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.


CONCLUSIONS
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.
Arbiza
Juan
J
Instituto de Física, Facultad de Ciencias, Iguá 4225, Universidad de República, Montevideo, Uruguay.
Mirazo
Santiago
S
Fort
Hugo
H
D019143:Evolution, Molecular; D005828:Genetics, Population; D016679:Genome, Viral; D008957:Models, Genetic; D009154:Mutation; D012367:RNA, Viral; D014780:Viruses / Q000235:genetics*
D012367:RNA, Viral
J Virol. 2000 Sep;74(18):8316-23
10954530
J Theor Biol. 2002 Nov 7;219(1):93-8
12392978
Nature. 2006 Jan 19;439(7074):344-8
16327776
FASEB J. 1996 Jun;10(8):859-64
8666162
J Mol Biol. 2007 Jun 15;369(4):985-1000
17481660
Proc Natl Acad Sci U S A. 1994 May 24;91(11):4821-4
8197141
Science. 2001 Jan 5;291(5501):114-8
11141560
Proc Natl Acad Sci U S A. 2006 Apr 18;103(16):6230-5
16585519
Naturwissenschaften. 1977 Nov;64(11):541-65
593400
Nature. 1999 Apr 1;398(6726):441-3
10201376
PLoS Pathog. 2005 Oct;1(2):e11
16220146
Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4448-52
15767582
Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13910-3
10570172
J Virol. 2004 Apr;78(7):3319-24
15016853
Genetics. 1998 Oct;150(2):523-32
9755186
Am Nat. 2003 Mar;161(3):497-505
12699226