Intermezzo+2

__**NOTE: THE INFORMATION ON THIS PAGE IS NO LONGER PART OF THE COURSE (removed from main wiki, 2014-2015)**__

=Intermezzo 2: Influenza virus and evolutionary signatures=

At this stage we make one more intermezzo from our story on hyper-cycles in order to further explore CAs and spiral patterns as a paradigm system. Once more we take to the world of infectious diseases and consider [|human], [|swine] and [|bird] [|influenzas] which are somewhat related, although bird influenzas are rarely transferred to human and pigs.

When [|sequence analysis] of the viruses is conducted of time two interesting patterns emerge of relatedness between viruses:
 * In humans and swine one observes a lopsided, asymmetric [|phylogenetic tree] with always one dominant strain. This implies a lot of selection and [|Red Queen]-like [|evolutionary dynamics]. Moreover if one would use a [|molecular clock] and date the [|common ancestor] of pigs and human virus one comes up with 1917 as the date: this is just about when the [|Spanish flu] broke out which caused more deaths that [|WW2]! This means that perhaps at this stage there was a transmission from birds.
 * In birds there is instead a very static pattern of phylogeny without a certain selection direction, although there is high diversity.

//So, does the host affect the evolution of the virus in a certain way?//

To study this issue Hogeweg ([|2002]?) developed a CA model in which infectivity declines in time and the chance of infection depends on protein distance of previous infections, where the virus is modelled as an [|amino-acid] sequence (this allows for phylogenetic analysis). Moreover hosts die and are born and there is a certain field size. The results show that in human-like conditions (low death rate / small field / long immunity) the system shows Red Queen-like dynamics. In contrast, with bird-like conditions (high death / large field / short immunity) the system shows a static pattern. So we obtain a very good match just by considering a few extracted differences between humans and birds (there are of course more).

//So why these results?// Well, **spirals**! For intermediate conditions (i.e. between humans and birds) we obtain intermediate spirals. For a while we get 2 interlocked spirals (2 virus strains). Most mutants cannot get in the spiral core and die out after a disturbance. When they do get in the core they also die out because the other virus is always more different than it is: i.e. if there is already variation in viruses, new variants have a harder time to get established (they are highly related to one strain). So after fast initial speciation, the system quickly established two strains. This can be disrupted, which causes fast evolution and thereafter stabilization again. Such evolution has been called **[|epochal evolution]**. In this case it is structured by mesoscale patterns. The width of the spirals depends on host decay rates and the infection duration. Hence in humans less than one spiral fits in the system resulting in non-stable spirals and Red Queen fast evolution. In bird conditions, one obtains stable spirals and speciation within spirals and between spirals (faster death allows for more phases within spirals).

The results illustrate once again how easily spirals arise, and how they affect the evolution of the entities that the spirals are made up of. Moreover, in terms of evolution, this intermezzo also demonstrates that mutants may have less chance to invade if there is population-based diversity, because other variants are more distant.

 **P Hogeweg** (2002) Multilevel processes in evolution and development: computational models and biological insights. In: Lässig M. & Valleriani A., eds., //Biological Evolution and Statistical Physics//, Springer lecture notes in physics 585, pp. 217-239. Springer Verlag. [|DownLoad PDF].
 * References**