title: A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms.
abstract: Recent studies have established that the human urine contains a complex microbiome, including a virome about which little is known. Following immunosuppression in kidney transplant patients, BK polyomavirus (BKV) has been shown to induce nephropathy (BKVN), decreasing graft survival. In this study we investigated the urine virome profile of BKV+ and BKV- kidney transplant recipients. Virus-like particles were stained to confirm the presence of VLP in the urine samples. Metagenomic DNA was purified, and the virome profile was analyzed using metagenomic shotgun sequencing. While the BK virus was predominant in the BKV+ group, it was also found in the BKV- group patients. Additional viruses were also detected in all patients, notably including JC virus (JCV) and Torque teno virus (TTV) and interestingly, we detected multiple subtypes of the BKV, JCV and TTV. Analysis of the BKV subtypes showed that nucleotide polymorphisms were detected in the VP1, VP2 and Large T Antigen proteins, suggesting potential functional effects for enhanced pathogenicity. Our results demonstrate a complex urinary virome in kidney transplant patients with multiple viruses with several distinct subtypes warranting further analysis of virus subtypes in immunosuppressed hosts.
authors.affiliation: Department of Medicine, University of Illinois, Chicago, IL 60612, USA.
authors.forename: Asha
authors.initials: A
authors.lastname: Rani
authors.affiliation: Department of Medicine, University of Illinois, Chicago, IL 60612, USA.
authors.forename: Ravi
authors.initials: R
authors.lastname: Ranjan
authors.affiliation: Department of Medicine, University of Illinois, Chicago, IL 60612, USA.
authors.forename: Halvor S
authors.initials: HS
authors.lastname: McGee
authors.affiliation: Department of Medicine, University of Illinois, Chicago, IL 60612, USA.|Department of Bioengineering, University of Illinois, Chicago, IL 60612, USA.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Metwally
authors.affiliation: Department of Medicine, University of Illinois, Chicago, IL 60612, USA.
authors.forename: Zahraa
authors.initials: Z
authors.lastname: Hajjiri
authors.affiliation: Division of Renal Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Brennan
authors.affiliation: Department of Medicine, University of Illinois, Chicago, IL 60612, USA.
authors.forename: Patricia W
authors.initials: PW
authors.lastname: Finn
authors.affiliation: Department of Medicine, University of Illinois, Chicago, IL 60612, USA.|Department of Bioengineering, University of Illinois, Chicago, IL 60612, USA.|Department of Surgery, University of Illinois, Chicago, IL 60612, USA.
authors.forename: David L
authors.initials: DL
authors.lastname: Perkins
mesh_terms: D000328:Adult; D000368:Aged; D001739:BK Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D015331:Cohort Studies; D004266:DNA Virus Infections / Q000175:diagnosis / Q000276:immunology / Q000821:virology; D004279:DNA, Viral / Q000235:genetics*; D005260:Female; D005838:Genotype; D006801:Humans; D016867:Immunocompromised Host; D007166:Immunosuppressive Agents / Q000008:administration & dosage; D007577:JC Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D007676:Kidney Failure, Chronic / Q000601:surgery / Q000628:therapy; D016030:Kidney Transplantation; D008297:Male; D054892:Metagenome; D008875:Middle Aged; D010802:Phylogeny; D011110:Polymorphism, Genetic; D027601:Polyomavirus Infections / Q000175:diagnosis / Q000276:immunology / Q000821:virology; D017422:Sequence Analysis, DNA; D022783:Torque teno virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D014412:Tumor Virus Infections / Q000175:diagnosis / Q000276:immunology / Q000821:virology; D014556:Urine / Q000821:virology*
chemical_list: D004279:DNA, Viral; D007166:Immunosuppressive Agents