Background <p>Tamarillo or tree tomato (<i>Solanum betaceum</i> Cav.) is a fruit tree species of Andean origin with cultural and economic relevance in Colombia. The high incidence of complex viral diseases termed “virosis” in all tamarillo-growing regions of the country leads to huge production losses and seriously threatens its cultivation.</p> Methods <p>RNA-seq libraries were constructed for symptomatic samples from eight tamarillo-growing locations across the Department of Nariño (Colombia). Their virus diversity was characterized using the Genome Detective software. The identified PVY isolate was subsequently subjected to RT-PCR validation and phylogenetic analysis.</p> Results <p>Several virus species belonging to the genera <i>Torradovirus</i>, <i>Potyvirus</i> and <i>Polerovirus</i> were identified in mixed infections in tamarillo. Full- or nearly full-length genomes were generated for tomato torrado virus (ToTV), physalis torrado virus (PhyTV), potato leafroll virus (PLRV), and a novel isolate of potato virus Y-Tamarillo (PVY-Tam). When present, PVY-Tam seems to synergistically boost the accumulation of unrelated viruses, therefore contributing to the severity of the infections. Nucleotide sequence analysis suggests that the PVY-Tam from Nariño originated in South America by a recent divergence of the PVY^N lineage, and possibly by the recombination of geographically close isolates. Moreover, P3N-PIPO, a frameshift product from the potyviral P3 gene, shows variations in protein lenght between PVY isolates that might be involved with host-specific adaptations.</p> Conclusions <p>We provide evidence of a novel PVY-Tam isolate in the Andean region that might promote the severity of unrelated virus partners in field-grown tamarillo. Our findings contribute to understanding tamarillo virosis for the development of effective diagnostic and control strategies.</p>