A Divergent Variant of the Eleventh Human Polyomavirus Species, Saint Louis Polyomavirus

The number of known human polyomavirus (HPyV) species has been expanding rapidly in recent years. Several HPyVs, including BK polyomavirus (BKV or BKPyV), JC polyomavirus (JCV or JCPyV), Merkel cell polyomavirus (MCV or MCPyV), and trichodysplasia spinulosa-associated polyomavirus (TSV or TSPyV), are known to cause disease in immunocompromised individuals(1).OtherrecentlydiscoveredHPyVspecieshavenotyet been clearly associated with any disease. Saint Louis polyomavirus (STLPyV) was recently discovered in human fecal samples collected in Malawi, the United States, and the Gambia (2). It is currently uncertain whether STLPyV is a bona fide human-tropic polyomavirus species or was instead derived from a dietary source. In this genome announcement, we report a divergent variant of STLPyV isolated from condylomas (skin warts) surgically removed from the buttocks of a patient suffering from the primary immunodeficiency warts hypogammaglobulinemia infections and myelokathexis syndrome (WHIMS). Observation of STLPyV in a surface-sanitizedtissuespecimenstronglysuggeststhatSTLPyVproductively infects humans and thus can be considered the eleventh known HPyV. WepreviouslydiscoveredHPyV10inthissamesurgicalsample (3).ForHPyV10identification,thewartsweremincedandtreated withdetergentsandnucleases,andvirionswerepurifiedoutofthe resulting extract by ultracentrifugation. DNA was extracted from thepurifiedvirionsandsubjectedtorandom-primedrollingcircle amplification (RCA) (Templiphi, GE). Restriction fragments of the RCA product were subjected to plasmid-based cloning. This cloning-based approach revealed the presence of three viral species: human papillomavirus type 6 (HPV6), HPV124, and HPyV10. For discovery of the STLPyV variant, a portion of the RCA product was processed using Nextera reagents (Illumina) and subjected to deep sequencing (Illumina, Miseq), generating a total of 269,313 paired-end-reads. Of these reads, 2% showed homologytoknownhumanorbacterialsequenceswhenanalyzed