Emerg Infect DisEmerging Infect. DisEIDEmerging Infectious Diseases1080-60401080-6059Centers for Disease Control and Prevention23017293347162712-035910.3201/eid1810.120359DispatchDispatchHuman Polyomaviruses in Children Undergoing Transplantation, United States, 2008–2010Polyomaviruses in Children Undergoing TransplantationSiebrasseErica A.BauerIrmaHoltzLori R.LeBinh-minhLassa-ClaxtonSherryCanterCharlesHmielPaulShenoyShaliniSweetStuartTurmelleYumirleShepherdRossWangDavidWashington University School of Medicine, St. Louis, Missouri, USAAddress for correspondence: David Wang, Washington University School of Medicine, Campus Box 8230, 660 S. Euclid Ave, St. Louis, MO 63110, USA; email: davewang@borcim.wustl.edu102012181016761679

Immunocompromised patients are at risk for disease caused by infection by some polyomaviruses. To define the prevalence of polyomaviruses in children undergoing transplantation, we collected samples from a longitudinal cohort and tested for the 9 known human polyomaviruses. All were detected; several were present in previously unreported specimen types.

Keywords: transplantpolyomavirusimmunosuppressionPolyomaviridaeviruseschildrenpediatric

BK and JC polyomaviruses (BKPyV, JCPyV) cause disease in immunocompromised persons. Both are double-stranded DNA viruses in the family Polyomaviridae. Seven additional human polyomaviruses were discovered during 2007–2011: KI polyomavirus (KIPyV) (1), WU polyomavirus (WUPyV) (2), Merkel cell polyomavirus (MCPyV) (3), human polyomavirus 6 (HPyV6) (4), human polyomavirus 7 (HPyV7) (4), trichodysplasia spinulosa-associated polyomavirus (TSPyV) (5), and human polyomavirus 9 (HPyV9) (6).

The 7 novel polyomaviruses have been detected in various specimen types; detection has been extensively reviewed for KIPyV, WUPyV, and MCPyV (7). Polyomaviruses HPyV6, HPyV7, TSPyV, and HPyV9 have been detected in skin (4,5,8); TSPyV and HPyV9 have also been detected in urine, and HPyV9 was detected in serum (6). However, only 2 of these recently identified viruses have been specifically implicated in human diseases; MCPyV is associated with Merkel cell carcinoma (3), and TSPyV has been linked to trichodysplasia spinulosa (5). Immunosuppression is a likely cofactor in both diseases. The potential pathogenicity of the other 5 novel polyomaviruses is unknown. As a first step toward exploring their disease potential, we sought to define their prevalence in immunocompromised transplant recipients. To this end, we established a longitudinal cohort of children undergoing transplantation at St. Louis Children’s Hospital, St. Louis, Missouri, USA.

The Study

We recruited 32 patients who were scheduled to receive transplants (2 lung, 11 liver, 5 heart, 2 kidney, 1 liver/lung, and 11 bone marrow transplants) during October 2008–April 2010. The Human Research Protection Office of Washington University in St. Louis approved this study. The mean age of enrolled patients was 5.8 years, and the median age was 3.1 years. Thirty patients received transplants and were studied for 1 year after transplantation. We collected 716 clinical specimens (160 nasopharyngeal swab, 169 urine, 122 fecal, 265 plasma) during 265 patient visits. We collected 298 specimens from patients during symptomatic episodes, which were defined as having >1 of the following: fever, respiratory symptoms, or gastrointestinal symptoms. We collected clinical data using a questionnaire and the medical records.

Fecal material was diluted 1:6 in phosphate-buffered saline and filtered through 0.45-μm membranes. For all specimens, we extracted total nucleic acids using an Ampliprep Cobas extractor (Roche, Branchburg, NJ, USA). We used published real-time PCRs for WUPyV (9), KIPyV (9), TSPyV (5), MCPyV (10), BKPyV (11), and JCPyV (12) (Table 1). We developed assays for HPyV6, HPyV7, and HPyV9 using Primer Express software (Applied Biosystems, Carlsbad, CA, USA) (Table 1). To assess the performance of each assay, we used serial dilutions (5 to 5 × 106 copies/reaction) of a plasmid containing the target sequence. All 3 assays demonstrated a sensitivity of ≈5 copies/reaction and yielded linear curves with R2 values >0.99.

Real-time PCR assays to detect human polyomaviruses in children undergoing transplants, United States, 2008–2010*
VirusTargetPrimers, 5′ → 3′Probe, 5′ → 3′
WUPyVNCCRWU-C-4824-F: GGCACGGCGCCAACTWU-C-4861-TM: FAM-TGCCATACCAACACAGCTGCTGAGC-TAMRA-3′
WU-C-4898-R: CCTGTTGTAGGCCTTACTTACCTGTA
KIPyVLTAgKI-B-4603-F: GAATGCATTGGCATTCGTGAKI-B-4632-TM: FAM-TGTAGCCATGAATGCATACATCCCACTGC-TAMRA
KI-B-4668-R: GCTGCAATAAGTTTAGATTAGTTGGTGC
TSPyVLTAgLTF: TGTGTTTGGAAACCAGAATCATTTGLTP: FAM-TTCTTCTTCCTCCTCATCCTCCACCTCAAT-TAMRA
LTR: TGCTACCTTGCTATTAAATGTGGAG
MCPyVLTAgLT.1F: CCACAGCCAGAGCTCTTCCTLT probe: FAM-TCCTTCTCAGCGTCCCAGGCTTCA-TAMRA
LT.1R: TGGTGGTCTCCTCTCTGCTACTG
HPyV6VP1ES011F: GCCTGGAAGGGCCTAGTAAAGES024: FAM-ACCAACCATCTGTTGCAGGCATTAAAGCTA-TAMRA
ES012R: ATTGGCAGCTGTAACTTGTTTTCTG
HPyV7VP1ES017F: GGTCCAGGCAATACTGATGTAGCTAES025: FAM-CCTGCAAGCCCTCAGAAAGCAAGTAAATG-TAMRA
ES018R: TCTGCAACCCAGAGCTCTACTG
HPyV9LTAgES026F: GAAGACCCTGATCCTGAGGAAGAES031: FAM-TGGATCATCCCAGAGTTCATTTACCTGCA-TAMRA
ES027R: CTCTGGAGTATTAGGTTCAGGCTTCT
BKPyVLTAgBK-Deg-F: AGCAGGCAAGRGTTCTATTACTAAATBk-Deg-P: FAM-AAGACCCTAAAGACTTTCCYTCTGATCTACACCAGTTT-TAMRA
BK-Deg-R: GARGCAACAGCAGATTCYCAACA
JCPyVVP2/3JL1 (F): AAGGGAGGGAACCTATATTTCTTTTGJL1 (P): FAM-CTCATACACCCAAAGTATAGATGATGCAGACAGCA-TAMRA
JL1 (R): TCTAGCCTTTGGGTAACTTCTTGAA

*WUPyV, WU polyomavirus; NCCR, non-coding control region; KIPyV, KI polyomavirus; LTAg, large T antigen; TSPyV, trichodysplasia spinulosa polyomavirus; MCPyV, Merkel cell polyomavirus; HPyV, human polyomavirus; VP, virion protein; BKPyV, BK polyomavirus; JCPyV, JC polyomavirus.

Each of the 25-μl quantitative PCRs included 5 μL of extracted sample, 12.5 pmol of each primer, and 4 pmol of probe. The MCPyV primers and probe were used as described (10). We tested samples in a 96-well plate format, with 8 water negative controls and 1 positive control/plate. Reactions were cycled as recommended using either an ABI 7500 real-time thermocycler (Applied Biosystems) or a CFX96 real-time thermocycler (BioRad, Hercules, CA, USA). The threshold of all plates was set at a standard value, and samples were counted as positive if their cycle threshold was <37.00.

All 716 specimens were tested for each virus (Table 2). The most frequently detected virus was BKPyV, which was found primarily in urine as expected. JCPyV was detected in 1 plasma sample. HPyV6, HPyV7, MCPyV, and TSPyV were detected in specimen types not previously reported. HPyV6 and TSPyV were detected in fecal samples and nasopharyngeal swab samples, and HPyV7 was detected in a nasopharyngeal swab and urine. One fecal sample was positive for MCPyV. Because HPyV6, HPyV7, and MCPyV have been previously detected in skin, we cannot rule out the possibility that their presence in specimens could have been caused by shedding from skin.

Polyomaviruses detected among specimens from children undergoing transplants, United States, 2008–2010*
VirusSpecimen typeTransplantCtPatient IDDate of collection, time elapsed from transplant
HPyV6FecesBMT32.1930112012 Jun 06, 1 mo after transplant
HPyV6NPHeart36.1340052010 Nov 25, 7 mo after transplant
HPyV6FecesLung36.9550012010 Aug 17, 1 mo after transplant
HPyV7NPLiver34.5710022009 Jun 16, 7 mo after transplant
HPyV7UrineLiver36.5410022009 Jul 15, 8 mo after transplant
HPyV9UrineLiver36.7210092010 Feb 09, 1 wk after transplant
KIPyVNPBMT16.2830012009 Jul 07, 3 mo after transplant
KIPyVNPBMT36.0730012009 May 19, 1 mo after transplant
KIPyVNPBMT33.3730082009 Nov 12, before transplant
KIPyVNPBMT31.0430092010 Jul 30, 6 mo after transplant
MCPyVNPBMT36.2930112010 Apr 15, before transplant
MCPyVFecesBMT34.563011 2010 Jul 02, 2 mo after transplant
TSPyVNPHeart32.9840012009 May 29, 1 wk after transplant
TSPyVNPHeart30.7440012009 Jun 18, 1 mo after transplant
TSPyVFecesHeart33.8940012009 May 29, 1 wk after transplant
WUPyVNPBMT36.6230052009 Jul 15, before transplant
WUPyVNPBMT28.8130072009 Nov 06, 2 mo after transplant
JCPyVPlasmaBMT36.1230112010 Aug 24, 3 mo after transplant
BKPyVUrineBMT15.8330102010 Apr 15, 1 mo after transplant
BKPyVUrineKidney36.6720222010 Jul 01, 10 mo after transplant
BKPyVUrineBMT30.8030112010 Aug 24, 3 mo after transplant
BKPyVUrineHeart25.8440012009 Aug 14, 2 mo after transplant
BKPyVUrineHeart35.8940032009 Dec 23, 2 mo after transplant
BKPyVUrineHeart24.3740012009 Sep 23, 4 mo after transplant
BKPyVUrineLiver28.5610102009 Nov 23, 1 wk after transplant
BKPyVUrineLung33.1350022011 May 03, 1 year after transplant
BKPyVUrineLung25.2550022011 Feb 08, 10 mo after transplant
BKPyVUrineKidney9.9720022010 Mar 04, 6 mo after transplant
BKPyVUrineBMT30.1030092010 Mar 05, 2 mo after transplant
BKPyVUrineLiver22.891001 2009 Jan 07, 3 mo after transplant
BKPyVUrineKidney34.4120022010 May 13, 8 mo after transplant
BKPyVNPKidney35.9320022010 Mar 04, 6 mo after transplant
BKPyVFecesKidney33.1520022010 Mar 04, 6 mo after transplant
BKPyVFecesLiver33.3310012008 Dec18, 2 mo after transplant
BKPyVFecesLiver34.8410012009 Jan 07, 3 mo after transplant

*Ct, cycle threshold; ID, identification; HPyV, human polyomavirus; BMT, bone marrow transplant; NP, nasopharyngeal; KIPyV, KI polyomavirus; MCPyV, Merkel cell polyomavirus; TSPyV, trichodysplasia spinulosa polyomavirus; WUPyV, WU polyomavirus; JCPyV, JC polyomavirus; BKPyV, BK polyomavirus

We collected 2 serial nasopharyngeal samples that were positive for KIPyV from patient 3001 (Table 2), a 1-year-old child who had received a bone marrow transplant as treatment for Fanconi anemia. The first sample, a nasopharyngeal swab obtained 1 month after transplant, had low levels of KIPyV. To determine the viral load of the second nasopharyngeal swab specimen collected 2 months later, we reanalyzed the sample in triplicate; on the basis of extrapolation of the standard curve run in parallel, we estimated the viral load to be 1.3 × 109 genome copies/mL of nasopharyngeal swab transport media. This patient’s course was complicated by graft-versus-host disease of the gut and skin, renal failure requiring dialysis, and recurrent pulmonary hemorrhage. The patient was critically ill and had experienced multiorgan failure at the time of the second sampling. Other microbiological test results were negative at that time, including PCR for Epstein-Barr virus, cytomegalovirus, human herpesvirus-6, and adenovirus in the blood; aspergillus antigen detection in blood; and bacterial cultures of blood, tracheal aspirate, urine, and peritoneal fluid. The fecal specimen collected at this time was negative for KIPyV; plasma and urine were not available for this study. The patient died of acute respiratory failure and extensive pulmonary hemorrhage 24 days after collection of this specimen. Despite the frequent detection of KIPyV in respiratory specimens, no studies have definitively linked infection with respiratory disease. Titers of KIPyV were high in the nasopharyngeal swab sample from this patient 3 weeks before respiratory failure. Although this observation does not necessarily implicate KIPyV infection as a contributing factor in the death of the patient, it suggests a poorly controlled KIPyV infection in the respiratory tract.

Three specimens collected from patient 4001, a 13-year-old heart transplant recipient, were positive for TSPyV (Figure), but the patient did not have trichodysplasia spinulosa. At 1 week after transplant, the nasopharyngeal swab and fecal samples were positive for TSPyV. At 1 month after transplant, the nasopharyngeal swab sample was again positive for TSPyV, with a viral load of ≈2.3 × 104 genome copies/mL of transport media. There is currently only 1 TSPyV sequence in GenBank (accession no. GU989205). We used 4 primer pairs to amplify the complete genome of TSPyV from the nasopharyngeal swab taken 1 month after transplant. PCR products were cloned, and the complete genome was sequenced to 3× coverage (GenBank accession no. JQ723730) and compared with the other TSPyV sequence. There were 5 nt substitutions: 3 in noncoding regions and 2 synonymous mutations.

Samples tested for TSV (trichodysplasia spinulosa polyomavirus) during May–June 2009 from patient 4001, a 13-year-old heart transplant recipient at St. Louis Children’s Hospital, St. Louis, Missouri, USA. Samples tested at each time point are indicated by white squares. Black squares represent positive samples. NP, nasopharyngeal.

Although serologic studies have demonstrated that ≈70% of adults in Europe have been infected by TSPyV (13), its mode of transmission is unknown. The detection of TSPyV in nasopharyngeal swab and fecal samples raises the possibility that it may be transmitted by a respiratory or fecal–oral route. Furthermore, in the current study, 2 sequential nasopharyngeal swab samples taken 20 days apart were positive for TSPyV, suggesting it may persist for extended periods in the respiratory tract, at least in immunosuppressed persons.

Conclusions

Our goals were to establish a longitudinal repository of different specimens types from transplant recipients and to define the prevalence of polyomaviruses in these patients. We detected all 9 polyomaviruses in at least 1 specimen. Although the prevalence of each virus was generally low, TSPyV, HPyV6, HPyV7, and MCPyV were detected in specimen types not previously reported. These observations expand understanding of the recently identified polyomaviruses and the tissue and organ systems they may infect and suggest possible modes of transmission. Further studies to define their possible roles in human diseases are needed.

Suggested citation for this article: Siebrasse EA, Bauer I, Holtz LR, Le B, Lassa-Claxton S, Canter C, et al. Human polyomaviruses in children undergoing transplantation, United States, 2008–2010. Emerg Infect Dis [Internet]. 2012 Oct [date cited]. http://dx.doi.org/10.3201/eid1810.120359

Acknowledgments

We thank Angel Chen and Adira Vinograd for their help in compiling the clinical data for this study. We also thank M.C.W. Feltkamp for the TSPyV-positive control and Christopher Buck for the HPyV6-, HPyV7-, and MCPyV-positive controls (AddGene plasmids 24727–24729, respectively; addgene.org).

This study was supported by a grant from the Children’s Discovery Institute. E.A.S. was supported by the Department of Defense through the National Defense Science & Engineering Graduate Fellowship Program. L.R.H. is supported by ULIRR024992 subaward KL2RR024994 from the National Institutes of Health, National Center for Research Resources.

Ms Siebrasse is a graduate student at Washington University in St. Louis, Missouri. Her research focuses on the discovery and characterization of novel polyomaviruses.

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