Basically I am looking for a way to create a new form of human due to the infection of this virus.
If I understand correctly, you want your virus to guide/affect this humanoid's evolution after it has spread to every individual of the species without noticeable effects. There are some important issues in this scenario:
1. Why would a virus produce such effects, assuming it's not an artificial creation? In what way does changing these humanoids increases the virus' efficiency (which is measured in how many cells it infects and how many virsuses are produced per infected cell)?
2. When physical changes happen in the evolution of a species, they are a response to enviromental pressure. Big arms would evolve if an increased arm size would give a small survival/mating success advantage. But if everyone has the virus, everyone receives its DNA influence, meaning they are on equal footing. This implies that the rest of the enviroment (such as climate) will shape most of the humanoids' physical characteristicss, as opposed to the virus itself. This is why your virus needs to infect only a certain group of individuals, affect them in such a way that they gain survival advantages and then let nature take its course (they have more and healthier children which, in time, eliminate the normal members of the species which were unaffected by the virus).
3. Viruses don't have "dormant" characteristics. Think of a virus as a Tweet, you only have room for 140 characters and, in order to create something that makes sense, you can't afford to leave 20 characters in a state of dormancy, you use them all for maximum efficiency. Furthermore, viruses constantly change, mutate, create new strains with or without their hosts, I just don't how a dormant (and thus currently useless) characteristic could be copied succesfully after trillions and trillions of replications.
Assuming the scenario I hypothesized in my second point, depending on how many individuals of the species exist and if they aren't separated by large oceans, I would estimate that a set of significant physical changes can become dominant in 500k-1m years.