1
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Zanella MC, Vu DL, Hosszu-Fellous K, Neofytos D, Van Delden C, Turin L, Poncet A, Simonetta F, Masouridi-Levrat S, Chalandon Y, Cordey S, Kaiser L. Longitudinal Detection of Twenty DNA and RNA Viruses in Allogeneic Hematopoietic Stem Cell Transplant Recipients Plasma. Viruses 2023; 15:v15040928. [PMID: 37112908 PMCID: PMC10142697 DOI: 10.3390/v15040928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Metagenomics revealed novel and routinely overlooked viruses, representing sources of unrecognized infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aim to describe DNA and RNA virus prevalence and kinetics in allo-HSCT recipients' plasma for one year post HSCT. We included 109 adult patients with first allo-HSCT from 1 March 2017 to 31 January 2019 in this observational cohort study. Seventeen DNA and three RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays using plasma samples collected at 0, 1, 3, 6, and 12 months post HSCT. TTV infected 97% of patients, followed by HPgV-1 (prevalence: 26-36%). TTV (median 3.29 × 105 copies/mL) and HPgV-1 (median 1.18 × 106 copies/mL) viral loads peaked at month 3. At least one Polyomaviridae virus (BKPyV, JCPyV, MCPyV, HPyV6/7) was detected in >10% of patients. HPyV6 and HPyV7 prevalence reached 27% and 12% at month 3; CMV prevalence reached 27%. HSV, VZV, EBV, HHV-7, HAdV and B19V prevalence remained <5%. HPyV9, TSPyV, HBoV, EV and HPg-V2 were never detected. At month 3, 72% of patients had co-infections. TTV and HPgV-1 infections were highly prevalent. BKPyV, MCPyV and HPyV6/7 were frequently detected relative to classical culprits. Further investigation is needed into associations between these viral infections and immune reconstitution or clinical outcomes.
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Affiliation(s)
- Marie-Céline Zanella
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Diem-Lan Vu
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Krisztina Hosszu-Fellous
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
| | - Dionysios Neofytos
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Chistian Van Delden
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Lara Turin
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Antoine Poncet
- Center for Clinical Research, Department of Health and Community Medicine, University of Geneva, 1206 Geneva, Switzerland
- Division of Clinical Epidemiology, Department of Health and Community Medicine, University Hospital of Geneva, 1211 Geneva, Switzerland
| | - Federico Simonetta
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Stavroula Masouridi-Levrat
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Yves Chalandon
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
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2
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Zanella MC, Pastor D, Feltkamp MCW, Hadaya K, Cordey S, Toutous Trellu L. Sustained Trichodysplasia Spinulosa Polyomavirus Viremia Illustrating a Primary Disseminated Infection in a Kidney Transplant Recipient. Microorganisms 2021; 9:microorganisms9112298. [PMID: 34835424 PMCID: PMC8624465 DOI: 10.3390/microorganisms9112298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/08/2023] Open
Abstract
Novel human polyomaviruses (HPyV) have been recently identified in solid organ transplant recipients. Trichodysplasia spinulosa (TS) is a rare disease associated with immunosuppression and induced by a polyomavirus (TSPyV). We report here a case of primary and disseminated TSPyV infection after kidney transplantation with extensive skin lesions, sustained viremia, and high viral loads in urine specimens, anal, nasal and throat swabs, assessed via specific real-time PCR for TSPyV during a follow-up period of 32 months after transplantation. The detection of TSPyV with a high viral load in respiratory and anal swab samples is compatible with viral replication and thus may suggest potential respiratory and oro-fecal routes of transmission.
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Affiliation(s)
- Marie-Céline Zanella
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland;
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
- Correspondence:
| | - Damien Pastor
- Department of Dermatology, Geneva University Hospitals, 1205 Geneva, Switzerland; (D.P.); (L.T.T.)
| | - Mariet C. W. Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands;
| | - Karine Hadaya
- Department of Nephrology and Hypertension, Geneva University Hospitals, 1205 Geneva, Switzerland;
| | - Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland;
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Laurence Toutous Trellu
- Department of Dermatology, Geneva University Hospitals, 1205 Geneva, Switzerland; (D.P.); (L.T.T.)
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Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients. Clin Microbiol Rev 2020; 33:33/4/e00027-20. [PMID: 32847820 DOI: 10.1128/cmr.00027-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.
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4
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Narayanan D, Rady PL, Tyring SK. Recent developments in trichodysplasia spinulosa disease. Transpl Infect Dis 2020; 22:e13434. [PMID: 32748541 DOI: 10.1111/tid.13434] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 12/22/2022]
Abstract
Trichodysplasia Spinulosa (TS) is a rare proliferative skin disease that occurs primarily in immunocompromised patients, specifically organ transplant recipients. TS is characterized by uncontrolled inner root sheath cell proliferation and folliculocentric papular eruption that can progress to disfiguring leonine facies when left untreated. TS presents with distinct histological features including the presence of large eosinophilic, trichohyaline granules within hyperproliferating inner root sheath cells of the hair bulb. The discovery of the Trichodysplasia Spinulosa Polyomavirus (TSPyV) and recent studies highlighting the role of TSPyV tumor antigens in cell proliferation pathways have provided new insight into the mechanisms of TS development. In this review, we discuss the expansion of our understanding of TS, specifically over the past 5 years. We summarize novel cases of TS and recent developments in the mechanisms underlying TSPyV-mediated disease progression. We also evaluate advancements in diagnostic methods and treatment options. As the incidence of TS continues to rise, it is becoming critical for clinicians to understand the clinical features of TS and emerging research regarding pathogenesis and therapeutics for early treatment of this potentially disfiguring disease.
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Affiliation(s)
- Deepika Narayanan
- Department of Dermatology, The University of Texas McGovern Medical School, Houston, TX, USA
| | - Peter L Rady
- Department of Dermatology, The University of Texas McGovern Medical School, Houston, TX, USA
| | - Stephen K Tyring
- Department of Dermatology, The University of Texas McGovern Medical School, Houston, TX, USA
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Pierrotti LC, Urbano PRP, Nali LHDS, Romano CM, Bicalho CDS, Arnone M, Valente NS, Pannuti CS, David-Neto E, Azevedo LS. Viremia and viruria of trichodysplasia spinulosa-associated polyomavirus before the development of clinical disease in a kidney transplant recipient. Transpl Infect Dis 2019; 21:e13133. [PMID: 31233669 DOI: 10.1111/tid.13133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/13/2019] [Accepted: 05/12/2019] [Indexed: 12/01/2022]
Abstract
Trichodysplasia spinulosa (TS) is a rare disease associated with immunosuppression and induced by a polyomavirus denominated Tricodisplasia Polyomavirus (TSPyV). We report a case of TS 6 months after kidney transplantation in a 65 years-old woman under immunosuppression therapy with prednisone, mycophenolate and tacrolimus. The patient developed follicular papules on the face with a thickening of the skin and alopecia of the eyebrows, leading to distortion of the face and a leonine appearance characteristic of the disease. The skin biopsy confirmed the clinical diagnosis and the presence of TSPyV DNA in the skin was detected. Staining for SV40 was positive. Immunosuppression was changed: mycophenolate was withdrawn, tacrolimus reduced and everolimus added. Intravenous cidofovir and later on leflunomide were added. Although the literature has reported clinical success with topical cidofovir, we were unable to use it because this drug is not available. There was an improvement of skin lesions and on cosmetic appearance. The patient had three rejections (one clinically diagnosed and two other biopsy proven), progressed with renal failure and graft loss. Retrospective analysis of stored urine and blood samples detected TSPyV DNA in some of those samples two months before the TS clinical development. This case highlights the TSPyV detection in blood and urine samples before the development of skin lesions.
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Affiliation(s)
- Ligia Camera Pierrotti
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Camila Malta Romano
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil
| | - Camila da Silva Bicalho
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil
| | - Marcelo Arnone
- Departamento de Dermatologia, Faculdade de Medicina, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil
| | - Neusa Sakai Valente
- Departamento de Dermatologia, Faculdade de Medicina, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil
| | - Cláudio Sérgio Pannuti
- Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil
| | - Elias David-Neto
- Divisão de Clínica Urológica, Faculdade de Medicina, Serviço de Transplante Renal, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil
| | - Luiz Sérgio Azevedo
- Divisão de Clínica Urológica, Faculdade de Medicina, Serviço de Transplante Renal, Hospital das Clínicas, Universidade de São Paulo, São Paulo, Brazil
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6
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Waldvogel-Abramowski S, Taleb S, Alessandrini M, Preynat-Seauve O. Viral Metagenomics of Blood Donors and Blood-Derived Products Using Next-Generation Sequencing. Transfus Med Hemother 2019; 46:87-93. [PMID: 31191194 DOI: 10.1159/000499088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/21/2019] [Indexed: 12/16/2022] Open
Abstract
Transfusion-transmitted infections remain a permanent threat in medicine. It keeps the burden of the past, marked by serious infections transmitted by transfusion, and is constantly threatened by emerging viruses. The global rise of immunosuppression among patients undergoing frequent transfusions exacerbates this problem. Over the past decade, criteria for donor selection have become increasingly more stringent. Although routine nucleic acid testing (NAT) for virus-specific detection has become more sensitive, these safety measures are only valuable for a limited number of select viruses. The scientific approach to this is however changing, with the goal of trying to identify infectious agents in donor units as early as possible to mitigate the risk of a clinically relevant infection. To this end, and in addition to an epidemiological surveillance of the general population, researchers are adopting new methods to discover emerging infectious agents, while simultaneously screening for an extended number of viruses in donors. Next-generation sequencing (NGS) offers the opportunity to explore the entire viral landscape in blood donors, the so-called metagenomics, to investigate severe transfusion reactions of unknown etiology. In the not too distant future, one could imagine this platform being used for routine testing of donated blood products.
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Affiliation(s)
- Sophie Waldvogel-Abramowski
- Laboratory of Immunohematology, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.,Blood Transfusion Center, Department of Medical Specialties, Geneva University Hospitals, Geneva, Switzerland
| | - Sofiane Taleb
- Laboratory of Clinical Biology, Foch University Hospitals, Suresnes, France
| | - Marco Alessandrini
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Olivier Preynat-Seauve
- Laboratory of Therapy and Stem Cells, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.,Department of Medical Specialties of internal Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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7
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van Rijn AL, Wunderink HF, de Brouwer CS, van der Meijden E, Rotmans JI, Feltkamp MCW. Impact of HPyV9 and TSPyV coinfection on the development of BK polyomavirus viremia and associated nephropathy after kidney transplantation. J Med Virol 2019; 91:1142-1147. [PMID: 30624811 PMCID: PMC6590353 DOI: 10.1002/jmv.25397] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/16/2018] [Accepted: 12/09/2018] [Indexed: 11/12/2022]
Abstract
Background BK polyomavirus (BKPyV) persistently infects the urinary tract and causes viremia and nephropathy in kidney transplantation (KTx), recipients. In a previous study, we observed an increased incidence and load of BKPyV viremia in KTx patients coinfected with human polyomavirus 9 (HPyV9). Here we sought confirmation of this observation and explored whether novel HPyVs that have been detected in urine (HPyV9 and trichodysplasia spinulosa polyomavirus [TSPyV]) potentially aggravate BKPyV infection. Methods A well‐characterized cohort of 209 KTx donor‐recipient pairs was serologically and molecularly analyzed for HPyV9 and TSPyV coinfection. These data were correlated with the occurrence of BKPyV viremia and BKPyVAN in the recipients within a year after KTx. Results Seropositivity for HPyV9 (19%) and TSPyV (89%) was comparable between donors and recipients and did not correlate with BKPyV viremia and BKPyVAN that developed in 25% and 3% of the recipients, respectively. Two recipients developed TSPyV viremia and none HPyV9 viremia. Modification of the predictive effect of donor BKPyV seroreactivity on recipient BKPyV viremia by HPyV9 and TSPyV was not observed. Conclusions Our data provide no evidence for a promoting effect of HPyV9 and TSPyV on BKPyV infection and BKPyVAN in renal allograft patients. Therefore, we do not recommend including HPyV9 and TSPyV screening in KTx patients.
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Affiliation(s)
- Aline L van Rijn
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Herman F Wunderink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline S de Brouwer
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Els van der Meijden
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Joris I Rotmans
- Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Mariet C W Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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8
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Nguyen KD, Chamseddin BH, Cockerell CJ, Wang RC. The Biology and Clinical Features of Cutaneous Polyomaviruses. J Invest Dermatol 2018; 139:285-292. [PMID: 30470393 DOI: 10.1016/j.jid.2018.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/07/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022]
Abstract
Human polyomaviruses are double-stand DNA viruses with a conserved genomic structure, yet they present with diverse tissue tropisms and disease presentations. Merkel cell polyomavirus, trichodysplasia spinulosa polyomavirus, human polyomavirus 6 and 7, and Malawi polyomavirus are shed from the skin, and Merkel cell polyomavirus, trichodysplasia spinulosa polyomavirus, human polyomavirus 6 and 7 have been linked to specific skin diseases. We present an update on the genomic and clinical features of these cutaneous polyomaviruses.
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Affiliation(s)
- Khang D Nguyen
- Department of Dermatology, The University of Texas Southwestern Medical Center, Department of Dermatology, Dallas, Texas, USA
| | - Bahir H Chamseddin
- Department of Dermatology, The University of Texas Southwestern Medical Center, Department of Dermatology, Dallas, Texas, USA
| | - Clay J Cockerell
- Department of Dermatology, The University of Texas Southwestern Medical Center, Department of Dermatology, Dallas, Texas, USA
| | - Richard C Wang
- Department of Dermatology, The University of Texas Southwestern Medical Center, Department of Dermatology, Dallas, Texas, USA.
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9
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van der Meijden E, Horváth B, Nijland M, de Vries K, Rácz EK, Diercks GF, de Weerd AE, Clahsen-van Groningen MC, van der Blij-de Brouwer CS, van der Zon AJ, Kroes ACM, Hedman K, van Kampen JJA, Riezebos-Brilman A, Feltkamp MCW. Primary Polyomavirus Infection, Not Reactivation, as the Cause of Trichodysplasia Spinulosa in Immunocompromised Patients. J Infect Dis 2017; 215:1080-1084. [PMID: 27578847 DOI: 10.1093/infdis/jiw403] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/19/2016] [Indexed: 11/13/2022] Open
Abstract
Classic human polyomaviruses (JC and BK viruses) become pathogenic when reactivating from latency. For the rare skin disease trichodysplasia spinulosa, we show that manifestations of the causative polyomavirus (TSPyV) occur during primary infection of the immunosuppressed host. High TSPyV loads in blood and cerebrospinal fluid, sometimes coinciding with cerebral lesions and neuroendocrine symptoms, marked the acute phase of trichodysplasia spinulosa, whereas initiation and maturation of TSPyV seroresponses occurred in the convalescent phase. TSPyV genomes lacked the rearrangements typical for reactivating polyomaviruses. These findings demonstrate the clinical importance of primary infection with this rapidly expanding group of human viruses and explain the rarity of some novel polyomavirus-associated diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Aloys C M Kroes
- Department of Medical Microbiology, Leiden University Medical Center
| | - Klaus Hedman
- Department of Virology, University of Helsinki and Helsinki University Hospital, Finland
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10
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Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A. The blood DNA virome in 8,000 humans. PLoS Pathog 2017; 13:e1006292. [PMID: 28328962 PMCID: PMC5378407 DOI: 10.1371/journal.ppat.1006292] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/03/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023] Open
Abstract
The characterization of the blood virome is important for the safety of blood-derived transfusion products, and for the identification of emerging pathogens. We explored non-human sequence data from whole-genome sequencing of blood from 8,240 individuals, none of whom were ascertained for any infectious disease. Viral sequences were extracted from the pool of sequence reads that did not map to the human reference genome. Analyses sifted through close to 1 Petabyte of sequence data and performed 0.5 trillion similarity searches. With a lower bound for identification of 2 viral genomes/100,000 cells, we mapped sequences to 94 different viruses, including sequences from 19 human DNA viruses, proviruses and RNA viruses (herpesviruses, anelloviruses, papillomaviruses, three polyomaviruses, adenovirus, HIV, HTLV, hepatitis B, hepatitis C, parvovirus B19, and influenza virus) in 42% of the study participants. Of possible relevance to transfusion medicine, we identified Merkel cell polyomavirus in 49 individuals, papillomavirus in blood of 13 individuals, parvovirus B19 in 6 individuals, and the presence of herpesvirus 8 in 3 individuals. The presence of DNA sequences from two RNA viruses was unexpected: Hepatitis C virus is revealing of an integration event, while the influenza virus sequence resulted from immunization with a DNA vaccine. Age, sex and ancestry contributed significantly to the prevalence of infection. The remaining 75 viruses mostly reflect extensive contamination of commercial reagents and from the environment. These technical problems represent a major challenge for the identification of novel human pathogens. Increasing availability of human whole-genome sequences will contribute substantial amounts of data on the composition of the normal and pathogenic human blood virome. Distinguishing contaminants from real human viruses is challenging. Novel sequencing technologies offer insight into the virome in human samples. Here, we identify the viral DNA sequences in blood of over 8,000 individuals undergoing whole genome sequencing. This approach serves to identify 94 viruses; however, many are shown to reflect widespread DNA contamination of commercial reagents or of environmental origin. While this represents a significant limitation to reliably identify novel viruses infecting humans, we could confidently detect sequences and quantify abundance of 19 human viruses in 42% of individuals. Ancestry, sex, and age were important determinants of viral prevalence. This large study calls attention on the challenge of interpreting next generation sequencing data for the identification of novel viruses. However, it serves to categorize the abundance of human DNA viruses using an unbiased technique.
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Affiliation(s)
- Ahmed Moustafa
- Human Longevity Inc., San Diego, California, United States of America
| | - Chao Xie
- Human Longevity Singapore Pte. Ltd., Singapore
| | - Ewen Kirkness
- Human Longevity Inc., San Diego, California, United States of America
| | - William Biggs
- Human Longevity Inc., San Diego, California, United States of America
| | - Emily Wong
- Human Longevity Inc., San Diego, California, United States of America
| | | | - Kenneth Bloom
- Human Longevity Inc., San Diego, California, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Karen E. Nelson
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - J. Craig Venter
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
| | - Amalio Telenti
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
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11
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Barton M, Lockhart S, Sidbury R, Wang R, Brandling-Bennett H. Trichodysplasia Spinulosa in a 7-Year-Old Boy Managed Using Physical Extraction of Keratin Spicules. Pediatr Dermatol 2017; 34:e74-e76. [PMID: 27990673 PMCID: PMC5788291 DOI: 10.1111/pde.13045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Trichodysplasia spinulosa (TS) is an uncommon skin disease characterized by a folliculocentric papular eruption and keratin spine formation, classically appearing on the central face and ears. It occurs in immunosuppressed patients and is linked to a viral etiology. Diagnostic tests including polymerase chain reaction (PCR) are available for detection of the TS-associated polyomavirus. Effective treatment options include topical cidofovir and oral valganciclovir. We present a case diagnosed using PCR with skin scrapings and treated using physical extraction of the keratin spicules. Significant improvement was noted, suggesting a safe, cost-effective treatment alternative.
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Affiliation(s)
- Michael Barton
- Billings Clinic Internal Medicine Residency, Billings, Montana
| | - Suing Lockhart
- Pediatric Dermatology, University of Washington, Seattle, Washington
| | - Robert Sidbury
- Pediatric Dermatology, University of Washington, Seattle, Washington
| | - Richard Wang
- University of Texas Southwestern Medical Center, Dallas, Texas
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12
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Pedergnana V, Martel-Jantin C, Nicol JTJ, Leblond V, Tortevoye P, Coursaget P, Touzé A, Abel L, Gessain A. Trichodysplasia Spinulosa Polyomavirus Infection Occurs during Early Childhood with Intrafamilial Transmission, Especially from Mother to Child. J Invest Dermatol 2017; 137:1181-1183. [PMID: 28108298 DOI: 10.1016/j.jid.2016.12.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/14/2016] [Accepted: 12/23/2016] [Indexed: 11/16/2022]
Affiliation(s)
- Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Claire Martel-Jantin
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France; CNRS, UMR3569, Paris, France; Université Paris Diderot, Cellule Pasteur, Paris, France
| | - Jérôme T J Nicol
- Université F Rabelais, Faculté des Sciences Pharmaceutiques, Tours, France; INRA UMR 1282, Infectiologie et Santé Publique, Tours, France
| | - Valérie Leblond
- Université F Rabelais, Faculté des Sciences Pharmaceutiques, Tours, France; INRA UMR 1282, Infectiologie et Santé Publique, Tours, France
| | - Patricia Tortevoye
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France; CNRS, UMR3569, Paris, France
| | - Pierre Coursaget
- Université F Rabelais, Faculté des Sciences Pharmaceutiques, Tours, France
| | - Antoine Touzé
- Université F Rabelais, Faculté des Sciences Pharmaceutiques, Tours, France; INRA UMR 1282, Infectiologie et Santé Publique, Tours, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Antoine Gessain
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Paris, France; CNRS, UMR3569, Paris, France.
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URBANO PR, OLIVEIRA ACSD, ROMANO CM. ALTERNATIVE METHODS FOR SEQUENCING FULL TSPyV GENOMES USING SANGER OR NGS. Rev Inst Med Trop Sao Paulo 2016; 58:92. [PMID: 27982358 PMCID: PMC5147722 DOI: 10.1590/s1678-9946201658092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/26/2016] [Indexed: 11/22/2022] Open
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