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Mes THM, van Doornum GJJ, Schutten M. Population genetic tests suggest that the epidemiologies of JCV and BKV are strikingly different. INFECTION GENETICS AND EVOLUTION 2009; 10:397-403. [PMID: 19379842 DOI: 10.1016/j.meegid.2009.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 02/18/2009] [Accepted: 04/06/2009] [Indexed: 11/30/2022]
Abstract
The JCV and BKV viruses have been used as markers for the study of human evolution by assuming that these viruses coevolved with their host. However, it is currently unclear whether the details of the population expansion of these viruses and humans agree. To study this in more detail, large numbers of complete genomes were used for population genetic tests to detect evidence for population expansion. Relative to the neutral expectation of no selective forces and no demographic changes, the JCV data set contained a striking excess of synonymous and non-synonymous mutations that occur only once in the data set. The same was found for non-synonymous mutations of BKV, but not at all for synonymous mutations of BKV. The different frequency spectra of mutations in JCV and BKV do not result from the inclusion of patients with clinical symptoms associated with BKV and JCV, such as nephropathy or progressive multifocal leucoencefalopathy, nor from the different numbers of genomes available for JCV and BKV. Instead, the distribution of unique mutations and population genetic models that use older mutation classes indicate a striking difference of the historical demographies of JCV and BKV with only the former virus exhibiting the evidence of demographic expansion. Our analyses expand on recent population genetic analyses that document a global population expansion of JCV by taking into account the impact of deleterious mutations and by comparing both human viruses. The striking difference between the demographics of BKV and JCV suggests that important aspects of their epidemiology remain to be discovered.
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Affiliation(s)
- Ted H M Mes
- Department of Virology, CA Rotterdam, The Netherlands.
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52
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Restriction of human polyomavirus BK virus DNA replication in murine cells and extracts. J Virol 2009; 83:5708-17. [PMID: 19297467 DOI: 10.1128/jvi.00300-09] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
BK virus (BKV) causes persistent and asymptomatic infections in most humans and is the etiologic agent of polyomavirus-associated nephropathy (PVAN) and other pathologies. Unfortunately, there are no animal models with which to study activation of BKV replication in the human kidney and the accompanying PVAN. Here we report studies of the restriction of BKV replication in murine cells and extracts and the cause(s) of this restriction. Upon infection of murine cells, BKV expressed large T antigen (TAg), but viral DNA replication and progeny were not detected. Transfection of murine cells with BKV TAg expression vectors also caused TAg expression without accompanying DNA replication. Analysis of the replication of DNAs containing chimeric BKV and murine polyomavirus origins revealed the importance of BKV core origin sequences and TAg for DNA replication. A sensitive assay was developed with purified BKV TAg that supported TAg-dependent BKV DNA replication with human but not with murine cell extracts. Addition of human replication proteins, DNA polymerase alpha-primase, replication protein A, or topoisomerase I to the murine extracts with BKV TAg did not rescue viral DNA replication. Notably, addition of murine extracts to human extracts inhibited BKV TAg-dependent DNA replication at a step prior to or during unwinding of the viral origin. These findings and differences in replication specificity between BKV TAg and the TAgs of simian virus 40 (SV40) and JC virus (JCV) and their respective origins implicate features of the BKV TAg and origin distinct from SV40 and JCV in restriction of BKV replication in murine cells.
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High frequency and diversity of rearrangements in polyomavirus bk noncoding regulatory regions cloned from urine and plasma of Israeli renal transplant patients and evidence for a new genetic subtype. J Clin Microbiol 2009; 47:1402-11. [PMID: 19261800 DOI: 10.1128/jcm.02065-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Polyomavirus BK (BKV) establishes latent infection in various human tissues, including the kidney. Reactivation following renal transplantation (RT) may cause BKV-associated nephropathy, leading to graft loss. BKV reactivation is often associated with extensive rearrangements in the BKV noncoding regulatory region (NCRR). We explored the formation and predominance of the rearrangements versus the diversity of the rearrangements by cloning and characterizing PCR-amplified NCRR sequences from six Israeli RT patients. We found a high frequency and a high degree of diversity of rearrangements: NCRRs that contained major rearrangements (mrNCRRs), including large insertions and deletions, were detected in 0 to 100% of the clones from individual samples (mean, 50% and 67% in plasma and urine, respectively). In addition, we found a high frequency of mrNCRRs that contained single-nucleotide variations (snvNCRRs) among identical mrNCRRs and archetype clones. mrNCRRs were present in plasma and in concomitantly collected urine samples, but for each patient, only a subset of the mrNCRRs and snvNCRRs were present in both compartments at the same time and/or in subsequent samples from the same compartment. Some mrNCRRs were observed over several months, indicating the continuous replication of the viral genomes carrying them. Phylogenetic analysis based on the snvNCRR in the archetype clones grouped isolates from four of the patients into a new subgroup of genotype IV. Genotypes Ib-1 and Ib-2 were also found. Isolates from two patients had NCRRs from two genotypes, one concurrently with a RT and one after a second RT. Our study prompts further investigation of the functional consequences of NCRR rearrangements to assess their biological significance and their putative role in disease progression and prognosis.
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Yogo Y, Zhong S, Xu Y, Zhu M, Chao Y, Sugimoto C, Ikegaya H, Shibuya A, Kitamura T. Conserved archetypal configuration of the transcriptional control region during the course of BK polyomavirus evolution. J Gen Virol 2008; 89:1849-1856. [PMID: 18632955 DOI: 10.1099/vir.0.2008/000836-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BK polyomavirus (BKV) is widespread among humans, asymptomatically infecting children and then persisting in renal tissue. The transcriptional control region (TCR) of the BKV genome is variable among clinical isolates. Thus, archetypal TCRs with a common basic configuration generally occur in BKV isolates from the urine of immunocompromised patients, but rearranged TCRs that possibly arise from the archetypal configuration have also been detected in clinical specimens. To examine the hypothesis that archetypal strains represent wild-type strains circulating in the human population (the archetype hypothesis), we analysed 145 complete viral genomes amplified directly from the urine of non-immunocompromised individuals worldwide. These genomes included 82, three, two and 58 sequences classified as belonging to subtypes I, II, III and IV, respectively. Rearranged TCRs with long duplications or deletions were detected from two subtype I and two subtype IV genomes, but not from the other 141 genomes (thus, the TCRs of these genomes were judged to be archetypal). The variations in the archetypal TCRs were nucleotide substitutions and single-nucleotide deletions, most of which were unique to particular subtypes or subgroups. We confirmed that the four complete BKV genomes with rearranged TCRs did not form a unique lineage on a phylogenetic tree. Collectively, the findings demonstrate that the archetypal TCR configuration has been conserved during the evolution of BKV, providing support for the archetype hypothesis. Additionally, we suggest that 'archetype' should be used as a conceptual term that denotes a prototypical structure that can generate various rearranged TCRs during viral growth in vivo and in vitro.
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Affiliation(s)
- Yoshiaki Yogo
- Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Shan Zhong
- Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yawei Xu
- Department of Cardiovascular Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yan Chang Road, Shanghai 200072, PR China
| | - Mengyun Zhu
- Department of Cardiovascular Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yan Chang Road, Shanghai 200072, PR China
| | - Yuegen Chao
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301 Yan Chang Road, Shanghai 200072, PR China
| | - Chie Sugimoto
- Tsukuba Primate Research Center, National Institute of Biomedical Innovation, 1 Hachimandai, Tsukuba, Ibaraki 305-0843, Japan
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Hiroshi Ikegaya
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ayako Shibuya
- Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Tadaichi Kitamura
- Department of Urology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
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Abend JR, Imperiale MJ. Transforming growth factor-beta-mediated regulation of BK virus gene expression. Virology 2008; 378:6-12. [PMID: 18559281 PMCID: PMC2569840 DOI: 10.1016/j.virol.2008.05.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Revised: 11/14/2007] [Accepted: 05/14/2008] [Indexed: 12/12/2022]
Abstract
The increasing prevalence of BK virus (BKV)-associated diseases in immunosuppressed patients has prompted an investigation of the immune response to BKV, especially the role of cytokines in regulating viral replication. We examined the effect of TGF-beta, a cytokine that is stimulated by certain immunosuppressive therapies, on BKV gene expression during lytic infection of renal proximal tubule epithelial cells. Viral gene expression, and specifically the activity of the BKV early promoter, is regulated by TGF-beta in a strain-dependent manner. Promoter activity is upregulated in the presence of TGF-beta for the TU strain of BKV, and not for the Dik, Dunlop, or Proto-2 strains. Using site-directed mutagenesis, we have identified a small segment of the TU promoter that is required for stimulation in response to TGF-beta. These results demonstrate that BKV strains can respond differently to cytokine treatment and suggest that TGF-beta may play a role in the reactivation of BKV.
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Affiliation(s)
- Johanna R. Abend
- Department of Microbiology and Immunology, and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael J. Imperiale
- Department of Microbiology and Immunology, and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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56
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Davidson I, Shulman LM. Unraveling the puzzle of human anellovirus infections by comparison with avian infections with the chicken anemia virus. Virus Res 2008; 137:1-15. [PMID: 18656506 DOI: 10.1016/j.virusres.2008.06.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 06/15/2008] [Accepted: 06/17/2008] [Indexed: 10/21/2022]
Abstract
Current clinical studies on human annelloviruses infections are directed towards finding an associated disease. In this review we have emphasized the many similarities between human anellovirus and avian circoviruses and the cell and tissue types infected by these pathogens. We have done this in order to explore whether knowledge acquired from natural and experimental avian infections could reflect and be extrapolated to the less well-characterized human annellovirus infections. The knowledge gained from the avian system may provide suggestions for decoding the enigmatic human anellovirus infections, and finding the specific disease or diseases caused by these human anellovirus infections. Each additional parallelism between chicken anemia virus (CAV) and Torque teno virus (TTV) further strengthens this premise. As we have seen information from human infections can also be used to better understand avian infections as well. Increased attention must be focused on the "hidden" or unrecognized, seemingly asymptomatic effects of circovirus and anellovirus infections. Understanding the facilitating effect of these infections on disease progression caused by other pathogens may help to explain differences in outcome of complicated poultry and human diseases. The final course of a pathogenic infection is determined by variations in the state of health of the host before, during and after contact with a pathogen, in addition to the phenotype of the pathogen and host. The health burden of circoviridae and anellovirus infections may be underestimated, due to lack of awareness of the need to search past the predominant clinical effect of identified pathogens and look for modulation of cellular-based immunity caused by co-infecting circoviruses, and by analogy, human anneloviruses.
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Affiliation(s)
- I Davidson
- Division of Avian Diseases, Kimron Veterinary Institute, Bet Dagan, Israel.
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57
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Lim L, Kay ID, Palladino S, Flexman J. Variability in patterns of BK viral load after renal transplantation. Diagn Microbiol Infect Dis 2008; 61:302-8. [DOI: 10.1016/j.diagmicrobio.2008.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Revised: 02/06/2008] [Accepted: 02/06/2008] [Indexed: 11/25/2022]
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58
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Gosert R, Rinaldo CH, Funk GA, Egli A, Ramos E, Drachenberg CB, Hirsch HH. Polyomavirus BK with rearranged noncoding control region emerge in vivo in renal transplant patients and increase viral replication and cytopathology. ACTA ACUST UNITED AC 2008; 205:841-52. [PMID: 18347101 PMCID: PMC2292223 DOI: 10.1084/jem.20072097] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Immunosuppression is required for BK viremia and polyomavirus BK–associated nephropathy (PVAN) in kidney transplants (KTs), but the role of viral determinants is unclear. We examined BKV noncoding control regions (NCCR), which coordinate viral gene expression and replication. In 286 day–matched plasma and urine samples from 129 KT patients with BKV viremia, including 70 with PVAN, the majority of viruses contained archetypal (ww-) NCCRs. However, rearranged (rr-) NCCRs were more frequent in plasma than in urine samples (22 vs. 4%; P < 0.001), and were associated with 20-fold higher plasma BKV loads (2.0 × 104/ml vs. 4.4 × 105/ml; P < 0.001). Emergence of rr-NCCR in plasma correlated with duration and peak BKV load (R2 = 0.64; P < 0.001). This was confirmed in a prospective cohort of 733 plasma samples from 227 patients. For 39 PVAN patients with available biopsies, rr-NCCRs were associated with more extensive viral replication and inflammation. Cloning of 10 rr-NCCRs revealed diverse duplications or deletions in different NCCR subregions, but all were sufficient to increase early gene expression, replication capacity, and cytopathology of recombinant BKV in vitro. Thus, rr-NCCR BKV emergence in plasma is linked to increased replication capacity and disease in KTs.
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Affiliation(s)
- Rainer Gosert
- Transplantation Virology and Molecular Diagnostic Laboratory, Institute for Medical Microbiology, Department of Biomedicine, University of Basel, CH-4003 Basel, Switzerland
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59
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Boldorini R, Veggiani C, Amoruso E, Allegrini S, Miglio U, Paganotti A, Ribaldone R, Monga G. Latent human polyomavirus infection in pregnancy: investigation of possible transplacental transmission. Pathology 2008; 40:72-7. [DOI: 10.1080/00313020701716458] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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60
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Influence of the viral regulatory region on tumor induction by simian virus 40 in hamsters. J Virol 2007; 82:871-9. [PMID: 17977966 DOI: 10.1128/jvi.01626-07] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Most of the simian virus 40 (SV40) genome is conserved among isolates, but the noncoding regulatory region and the genomic region encoding the large T-antigen C terminus (T-ag-C) may exhibit considerable variation. We demonstrate here that SV40 isolates differ in their oncogenic potentials in Syrian golden hamsters. Experimental animals were inoculated intraperitoneally with 10(7) PFU of parental or recombinant SV40 viruses and were observed for 12 months to identify genetic determinants of oncogenicity. The viral regulatory region was found to exert a statistically significant influence on tumor incidence, whereas the T-ag-C played a minor role. Viruses with a single enhancer (1E) were more oncogenic than those with a two-enhancer (2E) structure. Rearrangements in the 1E viral regulatory region were detected in 4 of 60 (6.7%) tumors. Viral loads in tumors varied, with a median of 5.4 SV40 genome copies per cell. Infectious SV40 was rescued from 15 of 37 (40%) cell lines established from tumors. Most hamsters with tumors and many without tumors produced antibodies to T antigen. All viruses displayed similar transforming frequencies in vitro, suggesting that differences in oncogenic potential in vivo were due to host responses to viral infection. This study shows that SV40 strains differ in their biological properties, suggests that SV40 replicates to some level in hamsters, and indicates that the outcome of an SV40 infection may depend on the viral strain present.
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61
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Sharma PM, Gupta G, Vats A, Shapiro R, Randhawa PS. Polyomavirus BK non-coding control region rearrangements in health and disease. J Med Virol 2007; 79:1199-207. [PMID: 17596823 DOI: 10.1002/jmv.20909] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND BK virus is an increasingly recognized pathogen in transplanted patients. DNA sequencing of this virus shows considerable genomic variability. METHODS To understand the clinical significance of rearrangements in the non-coding control region (NCCR) of BK virus (BKV), we report a meta-analysis of 507 sequences, including 40 sequences generated in our own laboratory, for associations between rearrangements and disease, tissue tropism, geographic origin, and viral genotype. RESULTS NCCR rearrangements were less frequent in (a) asymptomatic BKV viruria compared to patients viral nephropathy (1.7% vs. 22.5%), and (b) viral genotype 1 compared to other genotypes (2.4% vs. 11.2%). Rearrangements were commoner in malignancy (78.6%), and Norwegians (45.7%), and less common in East Indians (0%), and Japanese (4.3%). A surprising number of rearranged sequences were reported from mononuclear cells of healthy subjects, whereas most plasma sequences were archetypal. This difference could not be related to potential recombinase activity in lymphocytes, as consensus recombination signal sequences could not be found in the NCCR region. CONCLUSIONS NCCR rearrangements are neither required nor a sufficient condition to produce clinical disease. BKV nephropathy and hemorrhagic cystitis are not associated with any unique NCCR configuration or nucleotide sequence.
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Affiliation(s)
- Preety M Sharma
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
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62
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Sharma PM, Gupta G, Vats A, Shapiro R, Randhawa P. Phylogenetic analysis of polyomavirus BK sequences. J Virol 2006; 80:8869-79. [PMID: 16940499 PMCID: PMC1563921 DOI: 10.1128/jvi.00510-06] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Polyomavirus BK (BKV) has emerged as an important pathogen in kidney transplant patients. Existing taxonomic classifications of BKV come from conventional DNA sequence alignments based on limited data derived from the VP1 gene. We have used a phylogenetic whole-genome approach to examine the pattern of diversity and evolutionary relationships between 45 BKV strains isolated from multiple clinical settings. This analysis supports the classification of BKV into six genotypes, of which types V and VI have not been previously recognized. BKV strains hitherto classified as type I are, in fact, quite heterogeneous, and several cluster with our newly defined genotypes V and VI. The sequence information needed for assigning genotypes can be captured by VP1, VP2, VP3, or large T-gene sequencing. The most polymorphic coding region in the viral genome is VP1, but significant variation is also present in the large T-antigen gene, wherein polymorphisms are found in 11.39% of all nucleotide sites, 46.22% of which are cluster specific. Type-specific amino acid changes within the VP1 region are predicted to map to the BC and DE loops. The number of taxonomically informative amino acid changes in the large T antigen exceeds even that of the VP1 region. Viral strains isolated from healthy subjects and from patients with human immunodeficiency virus infection, Wiskott-Aldrich syndrome, and vasculopathy with capillary leak syndrome formed distinct subclusters. However, within the kidney transplant population, BKV strains derived from patients with asymptomatic viruria did not show complete separation from strains associated with allograft nephropathy.
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Affiliation(s)
- Preety M Sharma
- Division of Transplant Pathology, E737 UPMC-Montefiore Hospital, 3459 Fifth Ave., Pittsburgh, PA 15213, USA
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Gorrill T, Feliciano M, Mukerjee R, Sawaya BE, Khalili K, White MK. Activation of early gene transcription in polyomavirus BK by human immunodeficiency virus type 1 Tat. J Gen Virol 2006; 87:1557-1566. [PMID: 16690919 DOI: 10.1099/vir.0.81569-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyomavirus BK (BKV) is a serious problem for immunocompromised patients, where latent virus can enter into the lytic cycle causing cytolytic destruction of host cells. BKV infects >80% of the population worldwide during childhood and then remains in a latent state in the kidney. In the context of immunosuppression in kidney transplant patients, reactivation of the viral early promoter (BKV(E)) results in production of T antigen, enabling virus replication and transition from latency to the lytic phase, causing polyomavirus-associated nephropathy. Reactivation of BKV can also cause complications such as nephritis, atypical retinitis and haemorrhagic cystitis in AIDS patients. Here, the effects of human immunodeficiency virus type 1 (HIV-1) proteins Tat and Vpr on BKV transcription were investigated and it was demonstrated that Tat dramatically stimulated BKV(E). Site-directed mutagenesis analysis of potential Tat-responsive transcriptional motifs complemented by an electrophoretic mobility shift assay (EMSA) showed that Tat activated BKV(E) by inducing binding of the NF-kappaB p65 subunit to a kappaB motif near the 3' end of BKV(E). In addition, a sequence within the 5' UTR of BKV(E) transcripts (BKV(E)-TAR) was identified that is identical to the HIV-1 transactivation response (TAR) element. The BKV(E)-TAR sequence bound TAT in RNA EMSA assays and deletion of the BKV(E)-TAR sequence eliminated Tat transactivation of BKV(E) transcription. Thus, Tat positively affected BKV(E) transcription by a dual mechanism and this may be important in diseases involving BKV reactivation in AIDS patients.
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Affiliation(s)
- Timothy Gorrill
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, 1900 North 12th Street, 015-96, Room 203, Philadelphia, PA 19122, USA
| | - Mariha Feliciano
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, 1900 North 12th Street, 015-96, Room 203, Philadelphia, PA 19122, USA
| | - Ruma Mukerjee
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, 1900 North 12th Street, 015-96, Room 203, Philadelphia, PA 19122, USA
| | - Bassel E Sawaya
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, 1900 North 12th Street, 015-96, Room 203, Philadelphia, PA 19122, USA
| | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, 1900 North 12th Street, 015-96, Room 203, Philadelphia, PA 19122, USA
| | - Martyn K White
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, 1900 North 12th Street, 015-96, Room 203, Philadelphia, PA 19122, USA
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Pal A, Sirota L, Maudru T, Peden K, Lewis AM. Real-time, quantitative PCR assays for the detection of virus-specific DNA in samples with mixed populations of polyomaviruses. J Virol Methods 2006; 135:32-42. [PMID: 16527364 DOI: 10.1016/j.jviromet.2006.01.018] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 01/23/2006] [Accepted: 01/24/2006] [Indexed: 11/29/2022]
Abstract
Mixtures of polyomaviruses can be present in the central nervous system, the gastrointestinal tract, the genitourinary tract, blood, and urban sewage. We have developed 12 primer/probe sets (four per virus) for real-time, quantitative PCR assays (TaqMan) that can specifically detect BKV, JCV, and SV40 genomes present in mixtures of these viruses. The specificities of these primer/probe sets were determined by evaluating their level of interaction with the DNA from other polyomaviruses and their ability to estimate the number of copies of homologous viral DNA in blinded samples of defined mixtures of three polyomaviral DNAs. Three early region and three late region primer/probe sets determined, within a two-fold range, the number of copies of their respective DNAs. Four sets of SV40 primer/probes also detected 1.1-2.4 copies of SV40 DNA per COS-1 cell, cells estimated to contain a single copy of SV40 DNA. Three JCV primer/probe sets detected 3.7-4.2 copies per cell of JCV DNA in the JCV-transformed cell line M1-HR, cells estimated to contain between 0.5 and 1 copy of the JCV genome. We suggest that the virus-specific primer/probe sets in this study be considered sufficiently characterized to initiate the quantification of polyomavirus DNA in biological samples.
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Affiliation(s)
- Achintya Pal
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA
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