Altogether, this indicates that the properties of the HD = 1 mutational neighborhood of the master sequence are evolved and that the master sequence is selected for its mutational neighborhood which minimizes neutrality and frequency of parasites, as well as maximizes the amount of helpers.
Independent HCV isolates of a given subtype typically differ by 6%to10%0%, and genetic variation between viral genomes within an individual is usually 1%to3%3% because of the replication of HCV as a quasispecies (that is, a collection of genetic variants that clusters around a master sequence and that evolves as a unit [ 4]).
Units of replication arise as mutants of the evolved master sequence, and, in turn, make more mutants.
Here we analyze the distribution of such classes in the mutational neighborhood of the master sequence, to conclude that the evolved quasispecies is selected for the peculiar distribution of its mutants.
Altogether, we conclude that stallers are an intrinsic problem for the system, and that the master sequence of the full model has evolved some "mutational control" over them.
As in quasispecies theory fitness is defined (solely) by replication rate, we calculate the replication rate of the master sequence and analyze to which extent it is maximized in the evolved quasispecies.
Altogether, the evolved quasispecies is under the mutational control of the master sequence, which minimizes the competition with other units of replication by its low degree of neutrality, minimizes the hinder from stallers whereas it maximizes the help received.
Contrary to expectations, we find that quasispecies evolving at high mutation rates are steep and characterized by one master sequence.
The sequencing revealed only one master sequence with a few point mutations (Supplementary Figure S1C).
First, the master sequence, i.e. the sequence with the highest replicative ability, is lost [ 1].
