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Sahragard I, Yaghobi R, Mohammadi A, Afshari A, Pakfetrat M, Hossein Karimi M, Reza Pourkarim M. Impact of BK Polyomavirus NCCR variations in post kidney transplant outcomes. Gene 2024; 913:148376. [PMID: 38490510 DOI: 10.1016/j.gene.2024.148376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
The human BK Polyomavirus (BKPyV) is a DNA virus that is prevalent in 80 % of the population. Infection with this virus may begin in childhood, followed by asymptomatic persistence in the urinary tract. However, in immunocompromised individuals, especially kidney transplant recipients (KTRs), heightened replication of BKPyV can lead to severe complications. The genome of this virus is divided into three parts; the early and late region, and the non-coding control region (NCCR). Mutations in the NCCR can change the archetype strain to the rearranged strain, and NCCR rearrangements play a significant in virus pathogenesis. Interestingly, diverse types of NCCR block rearrangement result in significant differences in conversion potential and host cell viability in the infected cells. A correlation has been detected between increased viral replication potential and pathogenesis in BKPyV-infected KTRs with specific NCCR rearrangements. The objective of this review study was to examine the disease-causing and clinical consequences of variations in the NCCR in BKPyV-infected KTRs such as virus-associated nephropathy (BKPyVAN).
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Affiliation(s)
- Ilnaz Sahragard
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Ramin Yaghobi
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Ali Mohammadi
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Afsoon Afshari
- Shiraz Nephro-Urology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Pakfetrat
- Shiraz Nephro-Urology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Mahmoud Reza Pourkarim
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, Herestraat 49 BE-3000, Leuven, Belgium
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Passerini S, Prezioso C, Prota A, Babini G, Coppola L, Lodi A, Epifani AC, Sarmati L, Andreoni M, Moens U, Pietropaolo V, Ciotti M. Detection Analysis and Study of Genomic Region Variability of JCPyV, BKPyV, MCPyV, HPyV6, HPyV7 and QPyV in the Urine and Plasma of HIV-1-Infected Patients. Viruses 2022; 14:v14112544. [PMID: 36423152 PMCID: PMC9698965 DOI: 10.3390/v14112544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Since it was clearly established that HIV/AIDS predisposes to the infection, persistence or reactivation of latent viruses, the prevalence of human polyomaviruses (HPyVs) among HIV-1-infected patients and a possible correlation between HPyVs and HIV sero-status were investigated. PCR was performed to detect and quantify JCPyV, BKPyV, MCPyV, HPyV6, HPyV7 and QPyV DNA in the urine and plasma samples of 103 HIV-1-infected patients. Subsequently, NCCR, VP1 and MCPyV LT sequences were examined. In addition, for MCPyV, the expression of transcripts for the LT gene was investigated. JCPyV, BKPyV and MCPyV's presence was reported, whereas HPyV6, HPyV7 and QPyV were not detected in any sample. Co-infection patterns of JCPyV, BKPyV and MCPyV were found. Archetype-like NCCRs were observed with some point mutations in plasma samples positive for JCPyV and BKPyV. The VP1 region was found to be highly conserved among these subjects. LT did not show mutations causing stop codons, and LT transcripts were expressed in MCPyV positive samples. A significant correlation between HPyVs' detection and a low level of CD4+ was reported. In conclusion, HPyV6, HPyV7 and QPyV seem to not have a clinical relevance in HIV-1 patients, whereas further studies are warranted to define the clinical importance of JCPyV, BKPyV and MCPyV DNA detection in these subjects.
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Affiliation(s)
- Sara Passerini
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Carla Prezioso
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy
- IRCSS San Raffaele Roma, Microbiology of Chronic Neuro-Degenerative Pathologies, 00163 Rome, Italy
| | - Annalisa Prota
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Giulia Babini
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Luigi Coppola
- Infectious Diseases Clinic, Polyclinic Tor Vergata, Viale Oxford 81, 00133 Rome, Italy
| | - Alessandra Lodi
- Infectious Diseases Clinic, Polyclinic Tor Vergata, Viale Oxford 81, 00133 Rome, Italy
| | - Anna Chiara Epifani
- Infectious Diseases Clinic, Polyclinic Tor Vergata, Viale Oxford 81, 00133 Rome, Italy
| | - Loredana Sarmati
- Infectious Diseases Clinic, Polyclinic Tor Vergata, Viale Oxford 81, 00133 Rome, Italy
| | - Massimo Andreoni
- Infectious Diseases Clinic, Polyclinic Tor Vergata, Viale Oxford 81, 00133 Rome, Italy
| | - Ugo Moens
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Marco Ciotti
- Virology Unit, Polyclinic Tor Vergata, Viale Oxford 81, 00133 Rome, Italy
- Correspondence:
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Liimatainen H, Weseslindtner L, Strassl R, Aberle SW, Bond G, Auvinen E. Next-generation sequencing shows marked rearrangements of BK polyomavirus that favor but are not required for polyomavirus-associated nephropathy. J Clin Virol 2019; 122:104215. [PMID: 31783265 DOI: 10.1016/j.jcv.2019.104215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/18/2019] [Accepted: 11/11/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND BKPyV is associated with polyomavirus-associated nephropathy (PVAN), a major cause of graft rejection in kidney transplant recipients (KTRs). Mutations occur in the transcriptional control region (TCR) of BKPyV, but whether they are required for the development of PVAN is not completely understood. To this end, we characterized BKPyV TCRs from KTRs to assess whether TCR mutations are associated with PVAN. STUDY DESIGN We analyzed urine and plasma samples of fifteen KTRs with biopsy-confirmed PVAN, presumptive PVAN, or probable PVAN in order to explore the contents of the BKPyV virome. BKPyV TCRs were amplified and deep sequenced to characterize the viral strains. Alterations in block structures and transcription factor binding sites were investigated. RESULTS The majority of sequences in both urine and plasma samples represented archetype BKPyV TCR. Minor populations harboring rearranged TCRs were detected in all patient groups. In one biopsy-confirmed PVAN patient rearranged TCRs predominated, and in another patient half of all reads represented rearranged sequences. CONCLUSIONS Although archetype BKPyV predominated in most patients, highest proportions and highest numbers of rearranged strains were detected in association with PVAN. TCR mutations seem not necessary for the development of PVAN, but immunosuppression may allow increased viral replication giving rise to TCR variants with enhanced replication efficiency.
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Affiliation(s)
- Hanna Liimatainen
- Department of Virology and Immunology, Helsinki University Hospital Laboratory, Helsinki, Finland; Department of Virology, University of Helsinki, Helsinki, Finland
| | - Lukas Weseslindtner
- Department of Virology, University of Helsinki, Helsinki, Finland; Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Robert Strassl
- Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Vienna, Austria
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Gregor Bond
- Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Vienna, Austria
| | - Eeva Auvinen
- Department of Virology and Immunology, Helsinki University Hospital Laboratory, Helsinki, Finland; Department of Virology, University of Helsinki, Helsinki, Finland.
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Polyomaviruses shedding in stool of patients with hematological disorders: detection analysis and study of the non-coding control region's genetic variability. Med Microbiol Immunol 2019; 208:845-854. [PMID: 31375897 PMCID: PMC6817764 DOI: 10.1007/s00430-019-00630-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/25/2019] [Indexed: 01/07/2023]
Abstract
Fragmented data are available on the human polyomaviruses (HPyVs) prevalence in the gastrointestinal tract. Rearrangements in the non-coding control region (NCCR) of JCPyV and BKPyV have been extensively studied and correlated to clinical outcome; instead, little information is available for KIPyV, WUPyV and MCPyV NCCRs. To get insights into the role of HPyVs in the gastrointestinal tract, we investigated JCPyV, BKPyV, KIPyV, WUPyV and MCPyV distribution among hematological patients in concomitance with gastrointestinal symptoms. In addition, NCCRs and VP1 sequences were examined to characterize the strains circulating among the enrolled patients. DNA was extracted from 62 stool samples and qPCR was carried out to detect and quantify JCPyV, BKPyV, KIPyV, WUPyV and MCPyV genomes. Positive samples were subsequently amplified and sequenced for NCCR and VP1 regions. A phylogenetic tree was constructed aligning the obtained VP1 sequences to a set of reference sequences. qPCR revealed low viral loads for all HPyVs searched. Mono and co-infections were detected. A significant correlation was found between gastrointestinal complications and KIPyV infection. Archetype-like NCCRs were found for JCPyV and BKPyV, and a high degree of NCCRs stability was observed for KIPyV, WUPyV and MCPyV. Analysis of the VP1 sequences revealed a 99% identity with the VP1 reference sequences. The study adds important information on HPyVs prevalence and persistence in the gastrointestinal tract. Gastrointestinal signs were correlated with the presence of KIPyV, although definitive conclusions cannot be drawn. HPyVs NCCRs showed a high degree of sequence stability, suggesting that sequence rearrangements are rare in this anatomical site.
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Anselmo A, Prezioso C, Saccà FA, Di Lella FM, Palmieri G, Tisone G, Pietropaolo V, Ciotti M. Kidney graft failure induced by BKPyV replication despite a strong reduction of the immunosuppressive therapy. J Med Virol 2019; 91:1698-1701. [PMID: 30866070 DOI: 10.1002/jmv.25458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 01/09/2023]
Abstract
BKPyV replication is a risk factor for the development of polyomavirus-associated nephropathy in kidney transplant recipients. Here, the case of a 42 years old Caucasian patient is described who developed a kidney allograft failure because of uncontrolled BKPyV replication 7 months after transplant despite a strong reduction of the immunosuppressive therapy. The genetic analysis of the noncoding control region did not show rearrangement but two point mutations at nucleotide positions 18 and 31 within P block. The mutation at position 31 involved the nuclear factor-1 site. Sequencing of the VP1 region revealed a subtype I/subgroup b-1.
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Affiliation(s)
- Alessandro Anselmo
- Department of Surgery Polyclinic Tor Vergata Foundation, Transplantation Surgery, Rome, Italy
| | - Carla Prezioso
- Department of Public Health and Infectious Diseases, "Sapienza" University, Rome, Italy
| | - Filippo Antonino Saccà
- Department of Surgery Polyclinic Tor Vergata Foundation, Transplantation Surgery, Rome, Italy
| | - Federica Maria Di Lella
- Department of Experimental Medicine, Section of Microbiology and Virology, University Hospital "Luigi Vanvitelli" of Naples, Naples, Italy
| | - Giampiero Palmieri
- Department of Experimental Medicine and Surgery, Tor Vergata University, Rome, Italy
| | - Giuseppe Tisone
- Department of Surgery Polyclinic Tor Vergata Foundation, Transplantation Surgery, Rome, Italy.,Department of Experimental Medicine and Surgery, Tor Vergata University, Rome, Italy
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, "Sapienza" University, Rome, Italy
| | - Marco Ciotti
- Department of Integrated Care Processes, Laboratory of Clinical Microbiology and Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
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Virtanen E, Seppälä H, Helanterä I, Laine P, Lautenschlager I, Paulin L, Mannonen L, Auvinen P, Auvinen E. BK polyomavirus microRNA expression and sequence variation in polyomavirus-associated nephropathy. J Clin Virol 2018. [DOI: 10.1016/j.jcv.2018.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Helle F, Brochot E, Handala L, Martin E, Castelain S, Francois C, Duverlie G. Biology of the BKPyV: An Update. Viruses 2017; 9:v9110327. [PMID: 29099746 PMCID: PMC5707534 DOI: 10.3390/v9110327] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 10/30/2017] [Accepted: 10/30/2017] [Indexed: 12/29/2022] Open
Abstract
The BK virus (BKPyV) is a member of the Polyomaviridae family first isolated in 1971. BKPyV causes frequent infections during childhood and establishes persistent infections with minimal clinical implications within renal tubular cells and the urothelium. However, reactivation of BKPyV in immunocompromised individuals may cause serious complications. In particular, with the implementation of more potent immunosuppressive drugs in the last decade, BKPyV has become an emerging pathogen in kidney and bone marrow transplant recipients where it often causes associated nephropathy and haemorrhagic cystitis, respectively. Unfortunately, no specific antiviral against BKPyV has been approved yet and the only therapeutic option is a modulation of the immunosuppressive drug regimen to improve immune control though it may increase the risk of rejection. A better understanding of the BKPyV life cycle is thus needed to develop efficient treatment against this virus. In this review, we provide an update on recent advances in understanding the biology of BKPyV.
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Affiliation(s)
- Francois Helle
- EA4294, Unité de Virologie Clinique et Fondamentale, Centre Universitaire de Recherche en Santé, Centre Hospitalier Universitaire et Université de Picardie Jules Verne, 80054 Amiens, France.
| | - Etienne Brochot
- EA4294, Unité de Virologie Clinique et Fondamentale, Centre Universitaire de Recherche en Santé, Centre Hospitalier Universitaire et Université de Picardie Jules Verne, 80054 Amiens, France.
| | - Lynda Handala
- EA4294, Unité de Virologie Clinique et Fondamentale, Centre Universitaire de Recherche en Santé, Centre Hospitalier Universitaire et Université de Picardie Jules Verne, 80054 Amiens, France.
| | - Elodie Martin
- EA4294, Unité de Virologie Clinique et Fondamentale, Centre Universitaire de Recherche en Santé, Centre Hospitalier Universitaire et Université de Picardie Jules Verne, 80054 Amiens, France.
| | - Sandrine Castelain
- EA4294, Unité de Virologie Clinique et Fondamentale, Centre Universitaire de Recherche en Santé, Centre Hospitalier Universitaire et Université de Picardie Jules Verne, 80054 Amiens, France.
| | - Catherine Francois
- EA4294, Unité de Virologie Clinique et Fondamentale, Centre Universitaire de Recherche en Santé, Centre Hospitalier Universitaire et Université de Picardie Jules Verne, 80054 Amiens, France.
| | - Gilles Duverlie
- EA4294, Unité de Virologie Clinique et Fondamentale, Centre Universitaire de Recherche en Santé, Centre Hospitalier Universitaire et Université de Picardie Jules Verne, 80054 Amiens, France.
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Anzivino E, Zingaropoli MA, Iannetta M, Pietropaolo VA, Oliva A, Iori F, Ciardi A, Rodio DM, Antonini F, Fedele CG, D'Abramo A, Mastroianni CM, Vullo V, Ciardi MR. Archetype and Rearranged Non-coding Control Regions in Urothelial Bladder Carcinoma of Immunocompetent Individuals. Cancer Genomics Proteomics 2017; 13:499-509. [PMID: 27807073 DOI: 10.21873/cgp.20013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 07/21/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Polyomaviruses (PyVs) are potential transforming viruses. Despite their involvement in human tumours still being debated, there is evidence to suggest a role for PyVs in bladder carcinoma (BC). Therefore, a possible association between PyVs and BC was investigated. MATERIALS AND METHODS Urine, blood and fresh bladder tissue specimens were collected from 29 patients with BC. PyV prevalence, non-coding control region (NCCR) organization and genotypic analysis were assessed. RESULTS Data showed a significant prevalence of John Cunningham (JC) PyV in BC tissues and in urine with respect to BKPyV, while simian virus 40 was not revealed. A BKPyV rearranged NCCR sequence was isolated, whereas a JCPyV archetypal structure was consistently retained. A prevalence of European genotypes was observed. CONCLUSION Our data would suggest a JCPyV involvement in cancer progression and a BKPyV association with BC pathogenesis in immunocompetent patients. However, further work is necessary to better understand the exact role of PyVs in urothelial carcinogenesis.
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Affiliation(s)
- Elena Anzivino
- Department of Health Sciences and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | | | - Marco Iannetta
- Department of Health Sciences and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | | | - Alessandra Oliva
- Department of Health Sciences and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Francesco Iori
- Department of Obstretics, Gynecology and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Antonio Ciardi
- Department of Radiological Sciences, Oncology and Pathology, Sapienza University of Rome, Rome, Italy
| | - Donatella Maria Rodio
- Department of Health Sciences and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Francesca Antonini
- Department of Obstretics, Gynecology and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Cesare Giovanni Fedele
- Diagnostic Microbiology Service National Center for Microbiology, Majadahonda, Madrid, Spain
| | - Alessandra D'Abramo
- Department of Health Sciences and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | | | - Vincenzo Vullo
- Department of Health Sciences and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Maria Rosa Ciardi
- Department of Health Sciences and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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The association between polyomavirus BK strains and BKV viruria in liver transplant recipients. Sci Rep 2016; 6:28491. [PMID: 27338010 PMCID: PMC4919687 DOI: 10.1038/srep28491] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/03/2016] [Indexed: 12/30/2022] Open
Abstract
BK virus (BKV) is a polyomavirus that cause of allograft dysfunction among kidney transplant recipients. The role of BKV infection in non-renal solid organ transplant recipients is not well understood neither for the relationship between various BKV strains with occurrence of BKV viral viruria. This study aimed to understand the prevalence of BKV infection and identified of BKV various strains in the urine of liver transplant recipients. There was not significant difference of renal outcome between high BKV viruria and low BKV viruria in the liver transplant recipients. The WW-non-coding control region (NCCR) BKV detected in urine was associated with higher urinary BKV load, whereas the Dunlop-NCCR BKV was detected in the urine of low urinary BKV load. An in vitro cultivation system demonstrated that WW-BKV strain exhibiting the higher viral DNA replication efficiency and higher BKV load. Altogether, this is the first study to demonstrate the impact of BKV strains on the occurrence of BK viruria in the liver transplant recipients.
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Wang ZY, Hong WL, Zhu ZH, Chen YH, Ye WLE, Chu GY, Li JL, Chen BC, Xia P. Phylogenetic reconstruction and polymorphism analysis of BK virus VP2 gene isolated from renal transplant recipients in China. Exp Ther Med 2015; 10:1759-1767. [PMID: 26640547 PMCID: PMC4665150 DOI: 10.3892/etm.2015.2723] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 08/13/2015] [Indexed: 01/31/2023] Open
Abstract
BK polyomavirus (BKV) is important pathogen for kidney transplant recipients, as it is frequently re-activated, leading to nephropathy. The aim of this study was to investigate the phylogenetic reconstruction and polymorphism of the VP2 gene in BKV isolated from Chinese kidney transplant recipients. Phylogenetic analysis was carried out in the VP2 region from 135 BKV-positive samples and 28 reference strains retrieved from GenBank. The unweighted pair-group method with arithmetic mean (UPGMA) grouped all strains into subtypes, but failed to subdivide strains into subgroups. Among the plasma and urine samples, all plasma (23/23) and 82 urine samples (82/95) were identified to contain subtype I; the other 10 urine samples contained subtype IV. A 86-bp fragment was identified as a highly conserved sequence. Following alignment with 36 published BKV sequences from China, 92 sites of polymorphism were identified, including 11 single nucleotide polymorphisms (SNPs) prevalent in Chinese individuals and 30 SNPs that were specific to the two predominant subtypes I and IV. The limitations of the VP2 gene segment in subgrouping were confirmed by phylogenetic analysis. The conserved sequence and polymorphism identified in this study may be helpful in the detection and genotyping of BKV.
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Affiliation(s)
- Zhang-Yang Wang
- Zhejiang Provincial Top Key Discipline in Surgery, Wenzhou Key Laboratory of Surgery, Department of Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Wei-Long Hong
- Zhejiang Provincial Top Key Discipline in Surgery, Wenzhou Key Laboratory of Surgery, Department of Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Zhe-Hui Zhu
- Zhejiang Provincial Top Key Discipline in Surgery, Wenzhou Key Laboratory of Surgery, Department of Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Yun-Hao Chen
- Zhejiang Provincial Top Key Discipline in Surgery, Wenzhou Key Laboratory of Surgery, Department of Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Wen-LE Ye
- Transplantation Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Guang-Yu Chu
- Transplantation Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Jia-Lin Li
- Transplantation Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Bi-Cheng Chen
- Zhejiang Provincial Top Key Discipline in Surgery, Wenzhou Key Laboratory of Surgery, Department of Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Peng Xia
- Transplantation Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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Umbro I, Anzivino E, Tinti F, Zavatto A, Bellizzi A, Rodio DM, Mancini C, Pietropaolo V, Mitterhofer AP. Possible antiviral effect of ciprofloxacin treatment on polyomavirus BK replication and analysis of non-coding control region sequences. Virol J 2013; 10:274. [PMID: 24004724 PMCID: PMC3766702 DOI: 10.1186/1743-422x-10-274] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/26/2013] [Indexed: 01/02/2023] Open
Abstract
Acute renal dysfunction (ARD) is a common complication in renal transplant recipients. Multiple factors contribute to ARD development, including acute rejection and microbial infections. Many viral infections after kidney transplantation result from reactivation of “latent” viruses in the host or from the graft, such as the human Polyomavirus BK (BKV). We report the case of a 39 year-old recipient of a 2nd kidney graft who experienced BKV reactivation after a second episode of acute humoral rejection. A 10-day treatment with the quinolone antibiotic ciprofloxacin was administered with an increase of immunosuppressive therapy despite the active BKV replication. Real Time PCR analysis performed after treatment with ciprofloxacin, unexpectedly showed clearance of BK viremia and regression of BK viruria. During the follow-up, BK viremia persisted undetectable while viruria decreased further and disappeared after 3 months. BKV non-coding control region sequence analysis from all positive samples always showed the presence of archetypal sequences, with two single-nucleotide substitutions and one nucleotide deletion that, interestingly, were all representative of the subtype/subgroup I/b-1 we identified by the viral protein 1 sequencing analysis. We report the potential effect of the quinolone antibiotic ciprofloxacin in the decrease of the BKV load in both blood and urine.
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Affiliation(s)
- Ilaria Umbro
- Department of Clinical Medicine, Nephrology and Dialysis Unit, "Sapienza" University of Rome, Viale dell'Università 37, Rome 00185, Italy.
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Zhong S, Suzuki M, Peng X, Shen ZJ, Wang XJ, Xu TY, Li T, Yogo Y, Homma Y. BK polyomavirus from patients with tissue-derived prostate adenocarcinoma. Future Virol 2013. [DOI: 10.2217/fvl.13.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Aim: To explore the potential role of BK polyomavirus (BKV) in prostate tumorigenesis. Materials & methods: A total of 82 patients (no immunosuppression history) were divided into two groups. Group 1 included 32 patients receiving radical prostatectomy due to prostate adenocarcinoma. Group 2 consisted of 50 patients receiving transurethral resection of prostate or incision of prostate (TUIP) due to benign prostatic hyperplasia. Prostate tissue specimens of group 1 were obtained from two regions of the prostate: one was from the peripheral section of the prostate or proximal to the region where adenocarcinoma was confirmed by the preoperative needle biopsies (mark A region), the other was from the central section of the prostate or distal from the region where adenocarcinoma was confirmed by the needle biopsies (mark B region). If BKV alone was detected in either of the two regions, that case was regarded as BKV-positive prostate cancer. Those of group 2 were obtained from transrectal prostate biopsy before transurethral resection of prostate or transurethral incision of the prostate. Total DNA was extracted from each of the tissues and subjected to single or nested PCR using the β-globin system to detect targeted sequences within: the LTag gene; the VP1 gene and the transcriptional control region (TCR). Results: In group 1, BKV DNA sequences were detected in six cases (18.8%, 6/32), which were all in the A regions. Among the six cases, there were four cases with all of LTag, VP1 and TCR amplified, one case with LTag and TCR amplified, and one case with only the LTag amplified. In group 2, there was only one case (2.0%, 1/50) in which BKV DNA sequences were detected, and the only amplified fragment was VP1. The difference between the two groups was statistically significant (p = 0.008). Conclusion: BKV is often detected in the prostate cancer tissue and may be associated with progression of prostate cancer.
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Affiliation(s)
- Shan Zhong
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No. 197, 2nd Ruijin Road, Shanghai 200025, China
| | - Makoto Suzuki
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Xu Peng
- Department of Systems Biology & Translational Medicine, College of Medicine, Texas A&M Healthy Science Center, Temple, TX, USA
| | - Zhou-Jun Shen
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No. 197, 2nd Ruijin Road, Shanghai 200025, China.
| | - Xian-Jin Wang
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No. 197, 2nd Ruijin Road, Shanghai 200025, China
| | - Tian-Yuan Xu
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No. 197, 2nd Ruijin Road, Shanghai 200025, China
| | - Tao Li
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, No. 197, 2nd Ruijin Road, Shanghai 200025, China
| | - Yoshiaki Yogo
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukio Homma
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Drew RJ, Walsh A, Laoi BN, Crowley B. Phylogenetic analysis of the complete genome of 11 BKV isolates obtained from allogenic stem cell transplant recipients in Ireland. J Med Virol 2012; 84:1037-48. [PMID: 22585720 DOI: 10.1002/jmv.23240] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BK polyomavirus (family Polyomaviridae) may cause hemorrhagic cystitis (BKV-HC) in hematopoietic stem cell transplant recipients. Eleven complete BKV genomes (GenBank accession numbers: JN192431-JN192441) were sequenced from urine samples of allogenic hematopoietic stem cell transplant recipients and compared to complete BKV genomes in the published literature. Of the 11 isolates, seven (64%) were subgroup Ib-1, three (27%) isolates belonged to subgroup Ib-2 and a single isolate belonged to subtype III. The analysis of single-nucleotide polymorphisms in this study showed that isolates could be subclassified into subtypes I-IV and subgroups Ib-1 and Ib-2 on the basis of VP1 of the first part of the Large T-antigen (LTag). The non-coding control region (NCCR) of the 11 isolates was also sequenced. These sequences showed that there was consistent sequence homology within subgroups Ib-1 and Ib-2. Two new mutations were described in the isolates, G→C at O(84) in isolate SJH-LG-310, and a deletion at R(2-7) in isolate SJH-LG-309. No known transcription factor is thought to be present at the site of either of these mutations. There were no rearrangements seen in isolates and this may be because the patients were not followed up over time. There were five nucleotide positions at which subgroup Ib-1 isolated differed from subgroup Ib-2 isolates in the NCCR sequence, O(41) , P(18) , P(31) , R(4) , and S(18) . The mutation O(41) is present in the promoter granulocyte/macrophage stimulating factor) gene and the P(31) mutation is present in the NF-1 gene.
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Affiliation(s)
- Richard John Drew
- Sir Patrick Dun Translational Research Laboratory, Trinity College Dublin, St James's Hospital Campus, Dublin, Ireland.
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Broekema NM, Imperiale MJ. Efficient propagation of archetype BK and JC polyomaviruses. Virology 2011; 422:235-41. [PMID: 22099377 DOI: 10.1016/j.virol.2011.10.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 09/27/2011] [Accepted: 10/28/2011] [Indexed: 01/29/2023]
Abstract
BKPyV and JCPyV are closely related, ubiquitous human pathogens that cause disease in immunocompromised patients. The DNA sequence of the regulatory regions distinguishes two forms of these viruses, designated archetype and rearranged. Although cell culture systems exist for rearranged BKPyV and JCPyV, currently there is no robust cell culture system to study the archetype viruses. Large T antigen (TAg) is a virally encoded protein required to initiate viral DNA synthesis. Because archetype virus produces undetectable levels of TAg, we hypothesized that TAg overexpression would stimulate archetype virus replication. Efficient propagation of the archetype forms of BKPyV and JCPyV was observed in 293TT cells, human embryonic kidney cells overexpressing SV40 TAg. Importantly, the archetypal structure of the regulatory region was maintained during viral growth. Significant replication was not observed for Merkel cell, KI, or WU polyomaviruses. 293TT cells provide a means of propagating archetype BKPyV and JCPyV for detailed study.
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Affiliation(s)
- Nicole M Broekema
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA.
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Anzivino E, Bellizzi A, Mitterhofer AP, Tinti F, Barile M, Colosimo MT, Fioriti D, Mischitelli M, Chiarini F, Ferretti G, Taliani G, Pietropaolo V. Early monitoring of the human polyomavirus BK replication and sequencing analysis in a cohort of adult kidney transplant patients treated with basiliximab. Virol J 2011; 8:407. [PMID: 21849069 PMCID: PMC3179958 DOI: 10.1186/1743-422x-8-407] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 08/17/2011] [Indexed: 01/08/2023] Open
Abstract
Background Nowadays, better immunosuppressors have decreased the rates of acute rejection in kidney transplantation, but have also led to the emergence of BKV-associated nephropathy (BKVAN). Therefore, we prospectively investigated BKV load in plasma and urine samples in a cohort of kidney transplants, receiving basiliximab combined with a mycophenolate mofetil-based triple immunotherapy, to evaluate the difference between BKV replication during the first 3 months post-transplantation, characterized by the non-depleting action of basiliximab, versus the second 3 months, in which the maintenance therapy acts alone. We also performed sequencing analysis to assess whether a particular BKV subtype/subgroup or transcriptional control region (TCR) variants were present. Methods We monitored BK viruria and viremia by quantitative polymerase chain reaction (Q-PCR) at 12 hours (Tx), 1 (T1), 3 (T2) and 6 (T3) months post-transplantation among 60 kidney transplant patients. Sequencing analysis was performed by nested-PCR with specific primers for TCR and VP1 regions. Data were statistically analyzed using χ2 test and Student's t-test. Results BKV was detected at Tx in 4/60 urine and in 16/60 plasma, with median viral loads of 3,70 log GEq/mL and 3,79 log GEq/mL, respectively, followed by a significant increase of both BKV-positive transplants (32/60) and median values of viruria (5,78 log GEq/mL) and viremia (4,52 log GEq/mL) at T2. Conversely, a significantly decrease of patients with viruria and viremia (17/60) was observed at T3, together with a reduction of the median urinary and plasma viral loads (4,09 log GEq/mL and 4,00 log GEq/mL, respectively). BKV TCR sequence analysis always showed the presence of archetypal sequences, with a few single-nucleotide substitutions and one nucleotide insertion that, interestingly, were all representative of the particular subtypes/subgroups we identified by VP1 sequencing analysis: I/b-2 and IV/c-2. Conclusions Our results confirm previous studies indicating that BKV replication may occur during the early hours after kidney transplantation, reaches the highest incidence in the third post-transplantation month and then decreases within the sixth month, maybe due to induction therapy. Moreover, it might become clinically useful whether specific BKV subtypes or rearrangements could be linked to a particular disease state in order to detect them before BKVAN onset.
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Affiliation(s)
- Elena Anzivino
- Department of Public Health and Infectious Diseases, "Sapienza" University of Rome, Rome, Italy
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Clinical polyomavirus BK variants with agnogene deletion are non-functional but rescued by trans-complementation. Virology 2010; 398:12-20. [DOI: 10.1016/j.virol.2009.11.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 08/13/2009] [Accepted: 11/17/2009] [Indexed: 11/24/2022]
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Yogo Y, Sugimoto C, Zhong S, Homma Y. Evolution of the BK polyomavirus: epidemiological, anthropological and clinical implications. Rev Med Virol 2009; 19:185-99. [PMID: 19530118 DOI: 10.1002/rmv.613] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BK polyomavirus (BKV) is essentially ubiquitous in all human populations worldwide. Asymptomatic infection with this virus occurs during early childhood, leading to life-long persistence in the kidney. BKV has four subtypes that can be identified using serological and genotyping methods. The evolutionary aspects of BKV have remained poorly understood due to the limited availability of BKV genomes, since urinary excretion of BKV DNA is detected primarily in immunocompromised individuals. However, we have found that BKV DNA sequences can often be amplified from non-immunocompromised elderly individuals, using a highly sensitive polymerase chain reaction (PCR) with highly concentrated urinary DNA as the source of viral DNA. Using this approach, we have PCR-amplified and sequenced a large number of partial and complete BKV genomes from various human populations worldwide and conducted a series of evolutionary studies using these sequences. We have shown that subtypes I and IV evolved into four and six subgroups, respectively, with each having a close relationship with a particular human population. In addition, we have provided evidence supporting the hypothesis that BKV strains with the archetypal transcriptional control region (TCR) circulate in the human population. In this review, we describe these findings and discuss their epidemiological, anthropological and clinical implications.
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Affiliation(s)
- Yoshiaki Yogo
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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Abstract
Polyomaviruses are a growing family of small DNA viruses with a narrow tropism for both the host species and the cell type in which they productively replicate. Species host range may be constrained by requirements for precise molecular interactions between the viral T antigen, host replication proteins, including DNA polymerase, and the viral origin of replication, which are required for viral DNA replication. Cell type specificity involves, at least in part, transcription factors that are necessary for viral gene expression and restricted in their tissue distribution. In the case of the human polyomaviruses, BK virus (BKV) replication occurs in the tubular epithelial cells of the kidney, causing nephropathy in kidney allograft recipients, while JC virus (JCV) replication occurs in the glial cells of the central nervous system, where it causes progressive multifocal leukoencephalopathy. Three new human polyomaviruses have recently been discovered: MCV was found in Merkel cell carcinoma samples, while Karolinska Institute Virus and Washington University Virus were isolated from the respiratory tract. We discuss control mechanisms for gene expression in primate polyomaviruses, including simian vacuolating virus 40, BKV, and JCV. These mechanisms include not only modulation of promoter activities by transcription factor binding but also enhancer rearrangements, restriction of DNA methylation, alternate early mRNA splicing, cis-acting elements in the late mRNA leader sequence, and the production of viral microRNA.
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Zhong S, Jeong BH, Ikegaya H, Kim YS, Xu Y, Zhu M, Chao Y, Suzuki M, Kitamura T, Homma Y, Yogo Y. Comparison of the distribution patterns of BK polyomavirus lineages among China, Korea and Japan: implications for human migrations in northeast Asia. Microbiol Immunol 2009; 53:266-76. [PMID: 19457167 DOI: 10.1111/j.1348-0421.2009.00121.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BKV is widespread among humans, infecting children asymptomatically and then persisting in renal tissue. Based on the serological or phylogenetic method, BKV isolates worldwide are classified into four subtypes (I-IV), with subtypes I and IV further divided into several genetically-distinct subgroups. Since, similarly to JCV, a close relationship exists between BKV lineages and human populations, BKV should be useful as a marker to trace human migrations. To elucidate ancient human migrations in northeast Asia, urine samples were collected from immunocompetent elderly patients in Shanghai, China; Anyang, South Korea; and various locations in Japan. Partial and complete BKV genomes from these samples were amplified and sequenced using PCR, and the determined sequences were classified into subtypes and subgroups by phylogenetic and SNP analyses. In addition, based on an SNP analysis, the major subtype I subgroup (I/c) was classified into two subdivisions, I/c/Ch and I/c/KJ. The distribution patterns of BKV subgroups and subdivisions among the three regions were compared. Some aspects of the subgroup and subdivision distribution were more similar between Korea and Japan, but others were more similar between China and Korea or between China and Japan. Based on these findings, we inferred various northeast Asian migrations. Most of the JCV-based inferences of northeastern Asian migrations were consistent with those based on BKV, but the previously suggested migration route from the Asian continent to the Japanese archipelago seemed to need revision.
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Affiliation(s)
- Shan Zhong
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
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