Are there specified reference genotypes for genotyping of new torque teno virus isolates? Most studies on this virus are not clear about the reference sequences they have used and their phylogenic trees are not clear enough as someone can find out to which genotype the new isolates are fallen.
It looks like a mess, to me. I have no experience with Torque teno virus, I just searched for a few genomes, and aligned them (using MAFFT) to a set that was listed in the attached publication as being representative of genotypes 1 to 5.
I still can't make sense of it. But a quick look at the "genogroups 1 - 5"
data makes me think that AB060597 should be classified as genogroup 3 and not genogroup 2.
Some manuscripts have said that this virus has more than 39 genotypes but some other sources have specified 5 genotypes for this virus. May be those 5 strains are main genotypes and the 39 strains are subgenotypes of this virus. Can any one describe the problem obviously?
I think the 5 genotypes are the ones that are common among humans and fall in the Betatquevirus clade shown in fig 2 of the ChimpGorilla_TTV_2015. pdf file attached above. The 39 genotypes include other human and nonhuman viruses in the other clades.
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