genogroup and genotype - (Mar/09/2013 )
These two are used to group virus belongs to one genus. How to decide the virus belong to one genogroup and genotype? How much sequence variation is in the genogroup and genotype?
Genotype would be the equivalent of a species, but genogroup could include other closely related species. The sequence variation would depend on the relatedness of a particular strain and the mutation rate (e.g. compare ssRNA viruses with dsDNA viruses in terms of mutation rate).
I think there must be a percentage for describing the sequence variance or similarity. For two sequences, how much similarity and variance decide that the two belong to different genogroup and how much further decide if they belong to same or different genotype.