Limited variation during circulation of a polyomavirus in the human population involves the COCO-VA toggling site of Middle and Alternative T-antigen(s)

•This study represents TSPyVs of about 40% reported TS cases from three continents.•TSPyVs genome sequences, phylogenetic distribution and evolution have been assessed.•Thirty substitutions and two deletions accumulated along three phylogenetic lineages of 13 TSPyVs.•Three out of four non-synonymous substitutions (NSS) were found in MT/ALTO protein.•A NSS that may have been fixed most early in MT/ALTO shows codon-constrained Val-Ala (COCO-VA) toggling.•Three sets of covarying genome sites have been identified.

We have recently shown that the trichodysplasia spinulosa-associated polyomavirus (TSPyV) belongs to a large monophyletic group of mammalian polyomaviruses that experienced accelerated codon-constrained Val-Ala (COCO-VA) toggling at a protein site common to both Middle and Alternative T-antigens (MT/ALTO). Here we analyzed thirteen, mostly newly sequenced TSPyV genomes, representing ~40% of reported TS disease cases world-wide. We found two deletions and 30 variable sites (≤0.6%) that included only four sites with non-synonymous substitutions (NSS). One NSS site was under positive selection in the exon shared by Small and Middle T antigens, while three others were segregated in MT/ALTO. Two MT/ALTO sites covaried with five sites elsewhere in the genome and determined separation of twelve TSPyVs into two most populous phylogenetic lineages. The other, most distant TSPyV was distinguished by NSS at the COCO-VA site, observed for the first time during intra-species evolution. Our findings reveal a connection between micro- and macro-evolution of polyomaviruses.