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Knowles WA. Discovery and epidemiology of the human polyomaviruses BK virus (BKV) and JC virus (JCV). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 577:19-45. [PMID: 16626025 DOI: 10.1007/0-387-32957-9_2] [Citation(s) in RCA: 211] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Although discovered over thirty years ago, many aspects of the epidemiology of BKV and JCV in the general population, such as the source of infectious virus and the mode of transmission, are still unknown. Primary infection with both BKV and JCV is usually asymptomatic, and so age seroprevalence studies have been used to indicate infection. BKV commonly infects young children in all parts of the world, with the exception of a few very isolated communities, adult seroprevalence rates of 65-90% being reached by the age of ten years. In contrast, the pattern of JCV infection appears to vary between populations; in some anti-JCV antibody is acquired early as for BKV, but in others anti-JCV antibody prevalence continues to rise throughout life. This indicates that the two viruses are probably transmitted independently and by different routes. Whilst BKV DNA is found infrequently in the urine of healthy adults, JCV viruria occurs universally, increasing with age, with adult prevalence rates often between 20% and 60%. Four antigenic subtypes have been described for BKV and eight genotypes are currently recognized for JCV. The latter have been used to trace population movements and to reconstruct the population history in various communities.
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Ravichandran V, Major EO. Viral proteomics: a promising approach for understanding JC virus tropism. Proteomics 2007; 6:5628-36. [PMID: 16991198 DOI: 10.1002/pmic.200600261] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The human polyomavirus JC virus (JCV) is responsible for the CNS demyelination observed in cases of progressive multifocal leukoencephalopathy. The JCV regulatory region (promoter) is a hypervariable, noncoding, nucleotide sequence positioned between the early and late protein-coding regions in the viral genome. Selective binding of cellular transcription factors to this promoter region participates in the control of viral tropism. Hence, further study of these proteins might provide new insights into JCV tropism and associated pathogenesis. This review gives an overview of viral proteomics - the study of all proteins expressed from the viral gene transcripts, and all the cellular proteins that play a role in JCV tropism. It also describes a new biochemical approach for studying relevant JCV promoter-binding proteins, which is an anchored-JCV transcriptional promoter (ATP) assay. An ATP assay utilizes the product of PCR-amplified JCV promoter sequences coupled with Sepharose beads in order to capture and isolate cellular nuclear proteins with specific promoter-binding affinity for analysis. Proteins that bind to JCV-ATPs can be eluted and subjected to proteomic analysis. Insights from this approach may improve the understanding of viral and cellular parameters that control JCV tropism.
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Affiliation(s)
- Veerasamy Ravichandran
- Laboratory of Molecular Medicine and Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892-1296, USA
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TAKASAKA TOMOKAZU, OHTA NOBUTAKA, ZHENG HUAIYING, IKEGAYA HIROSHI, SAKURADA KOICHI, KITAMURA TADAICHI, YOGO YOSHIAKI. JC polyomavirus lineages common among Kiribati Islanders: implications for human dispersal in the Pacific. ANTHROPOL SCI 2006. [DOI: 10.1537/ase.050719] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
| | | | - HUAI-YING ZHENG
- Department of Urology, Faculty of Medicine, The University of Tokyo
- Japanese Foundation for AIDS Prevention
| | | | | | | | - YOSHIAKI YOGO
- Department of Urology, Faculty of Medicine, The University of Tokyo
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Pavesi A. Detecting Traces of Prehistoric Human Migrations by Geographic Synthetic Maps of Polyomavirus JC. J Mol Evol 2004; 58:304-13. [PMID: 15045485 DOI: 10.1007/s00239-003-2552-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2003] [Accepted: 09/19/2003] [Indexed: 10/26/2022]
Abstract
The polyomavirus JC (JCV) is a double-stranded DNA virus that is ubiquitous in human populations and is excreted in urine by a large percentage of individuals (20-70%). The strong genetic stability, combined with a mechanism of transmission mainly within the family, makes JCV a good marker of human migrations. In this study, the coevolution of JCV with its human host is investigated by using over a thousand nucleotide sequences deposited in the EMBL database; they correspond to the IG region, which is the genomic region with the highest rate of variation. The pattern of genetic diversity in JCV is evaluated by the principal coordinates analysis and the construction of synthetic maps. The first principal coordinate supports the existence of two distinct virus lineages, both arising from the ancestral African type. The first synthetic map suggests a two-migration model of the human dispersal out of Africa, thus implying a more complex picture than that known from human genes. The second principal coordinate points out the distinctiveness of strains coming from Asian/Amerind populations. The picture yielded by the second synthetic map appears to be more consistent with that known from human genes. In fact, it provides evidence of a deep split of the Asian lineage of JCV into two main branches: one diffusing in Japan and Americas, the other in Southeast Asia. The view that JCV, with its peculiar feature of a dual early emergence from Africa, can provide new information about the evolutionary history of our ancestors is discussed.
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Affiliation(s)
- Angelo Pavesi
- Department of Genetics Anthropology Evolution, University of Parma, Parco Area delle Scienze 11/A, 1-43100 Parma, Italy.
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MIRANDA JASMINJIJI, TAKASAKA TOMOKAZU, ZHENG HUAIYING, KITAMURA TADAICHI, YOGO YOSHIAKI. JC virus genotype profile in the Mamanwa, a Philippine Negrito tribe, and implications for its population history. ANTHROPOL SCI 2004. [DOI: 10.1537/ase.03115] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- JASMIN JIJI MIRANDA
- National Institute of Molecular Biology and Biotechnology, University of the Philippines
| | | | - HUAI-YING ZHENG
- Department of Urology, Faculty of Medicine, The University of Tokyo
| | | | - YOSHIAKI YOGO
- Department of Urology, Faculty of Medicine, The University of Tokyo
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Ferrante P, Delbue S, Pagani E, Mancuso R, Marzocchetti A, Borghi E, Maserati R, Bestetti A, Cinque P. Analysis of JC virus genotype distribution and transcriptional control region rearrangements in human immunodeficiency virus-positive progressive multifocal leukoencephalopathy patients with and without highly active antiretroviral treatment. J Neurovirol 2003; 9 Suppl 1:42-6. [PMID: 12709871 DOI: 10.1080/13550280390195405] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Accepted: 01/24/2003] [Indexed: 10/20/2022]
Abstract
After the introduction of highly active antiretroviral therapy (HAART), the incidence of many acquired immunodeficiency syndrome (AIDS)-related opportunistic infections, but not of progressive multifocal leukoencephalopathy (PML), has been dramatically decreased. However, it has been shown that about 50% of the HAART-treated PML patients had a significantly prolonged (>6 months) survival time, in comparison to the short (<6 months) survival time of the classical form of PML. In order to verify if a particular genotype or genomic rearrangements of JC virus (JCV) could affect the clinical course of PML, the authors performed nucleotide sequencing of 25 virion protein (VP1) and 18 transcriptional control region (TCR) DNA amplified in the cerebrospinal fluid (CSF) of HAART-untreated PML patients, of 17 HAART-treated PML patients, and in the urine of 23 healthy individuals. In nontreated PML patients, 52% and 44% of amplified JCV were respectively type 1 and type 2, whereas in HAART-treated PML patients, 59% of the amplified JCV were type 1, 23% type 2, and 18% type 4, without differences between long and short survivors. In both groups, the amplified TCR had unique and extensive rearrangements, whereas archetype TCR without rearrangements was detected in all the healthy subjects and in the CSF of two long-survivor PML patients. The data obtained indicate that the introduction of HAART has induced changes in JCV genotype distribution and probably reduced the rate of rearrangements of TCR region among PML patients.
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Affiliation(s)
- Pasquale Ferrante
- Laboratory of Biology, Don C Gnocchi Foundation ONLUS, IRCCS, Milan, Italy.
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Miranda JJ, Sugimoto C, Paraguison R, Takasaka T, Zheng HY, Yogo Y. Genetic diversity of JC virus in the modern Filipino population: implications for the peopling of the Philippines. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2003; 120:125-32. [PMID: 12541330 DOI: 10.1002/ajpa.10155] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Philippines is generally believed to have been established by various peoples who migrated from neighboring areas. To gain new insights into the peopling of the Philippines, we used the JC virus (JCV) genotyping approach. We collected about 50 urine samples on each of two representative islands of the Philippines, Luzon and Cebu. DNA was extracted from the urine samples and used to amplify the 610-bp region (IG region) of the viral genome. For each island, we determined about 20 IG sequences, from which a neighbor-joining phylogenetic tree was constructed to classify the JCV isolates detected into distinct genotypes. The predominant genotype detected was SC, the Southeast Asian genotype. Minor JCV genotypes were SC/Phi, B1-a, and B3. SC/Phi was a subcluster of SC and has not been detected in areas other than the Philippines. B1-a was detected previously in mainland China, Pamalican Island (Palawan, Philippines), and Taiwan (an aboriginal tribe). B3 was classified in this study into two subgroups, one (B3-a) containing three Luzon isolates and several Chinese, Thai, and Uzbek isolates, the other (B3-b) containing two Luzon, one Cebu, and one Indonesian isolate. These findings suggest that the modern Filipino population was formed not only by Southeast Asians carrying SC but also by a few distinct ethnic groups carrying SC/Phi, B1-a, and B3-a or -b.
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Affiliation(s)
- Jasmin Jiji Miranda
- National Institute of Molecular Biology and Biotechnology, University of the Philippines, Quezon City 1101, Philippines
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Jeong BH, Lee KH, Choi EK, Kim K, Kim YS. Genotyping of the JC virus in urine samples of healthy Korean individuals. J Med Virol 2003; 72:281-9. [PMID: 14695671 DOI: 10.1002/jmv.10568] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A human polyomavirus, JC virus (JCV) is ubiquitous in humans and infects children asymptomatically. It persists in renal tissue and is excreted progeny in urine. DNAs from urine samples of 100 healthy Korean individuals were screened for the presence of JCV by polymerase chain reaction (PCR). Twenty of the samples were positive for JCV. JCV DNA was found in one individual (4%) in the 1-19-year group, two individuals (9%) in the 20-39-year group, ten individuals (38%) in the 40-59-year group, seven individuals (28%) in the over 60-year group. The prevalence of JC viral DNA was the highest in the 40-59-year-old Korean population. To investigate genotypes of JCV in Korea, the genotypes were determined by DNA sequence analysis of the regulatory region (333 bp) and the VT-intergenic region (656 bp) of DNA from the 20 JCV isolates. We have identified three distinctive JCV strains in the regulatory region and ten distinctive JCV strains in the VT-intergenic region of DNA from the 20 isolates. Based on restriction fragment length polymorphism (RFLP) analysis and phylogenetic analysis of the VT-intergenic region of JCV, two distinct subtypes, CY and type 2A (MY), were found to be prevalent in this Korean population. CY and type 2A of JCV were identified in 13 individuals (65%) and four individuals (20%), respectively. Interestingly, type 1, which was distributed mostly in Europe, was found in 3 (15%) isolates from healthy Korean individuals.
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Affiliation(s)
- Byung-Hoon Jeong
- Ilsong Institute of Life Science, The Hallym Academy of Sciences, Hallym University, Gwanyang-dong, Dongan-gu, Anyang, Kyonggi-do, Korea
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YOGO YOSHIAKI, ZHENG HUAIYING, HASEGAWA MASAMI, SUGIMOTO CHIE, TANAKA SHINTATU, HONJO TAKEO, KOBAYASHI NOBUYOSHI, OHTA NOBUTAKA, KITAMURA TADAICHI. Phylogenetic Analysis of JC Virus DNAs Detected in Ainus: An Attempt to Elucidate the Origin and Diversity of the Ainu. ACTA ACUST UNITED AC 2003. [DOI: 10.1537/asj.111.19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- YOSHIAKI YOGO
- Laboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
| | - HUAI-YING ZHENG
- Laboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
- Department of Urology, Faculty of Medicine, The University of Tokyo
| | - MASAMI HASEGAWA
- Department of Prediction and Control, The Institute of Statistical Mathematics
| | - CHIE SUGIMOTO
- Laboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
| | | | | | - NOBUYOSHI KOBAYASHI
- Laboratory of Viral Infection, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo
| | - NOBUTAKA OHTA
- Department of Urology, Faculty of Medicine, The University of Tokyo
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Suzuki M, Zheng HY, Takasaka T, Sugimoto C, Kitamura T, Beutler E, Yogo Y. Asian genotypes of JC virus in Japanese-Americans suggest familial transmission. J Virol 2002; 76:10074-8. [PMID: 12208989 PMCID: PMC136522 DOI: 10.1128/jvi.76.19.10074-10078.2002] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To examine the mode of JC virus (JCV) transmission, we collected urine samples from second- and third-generation Japanese-Americans in Los Angeles, Calif., whose parents and grandparents were all Japanese. From the urine samples of these Japanese-Americans, we mainly detected two subtypes (CY and MY) of JCV that are predominantly found among native Japanese. This finding provides support for the hypothesis that JCV is transmitted mainly within the family through long-term cohabitation.
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Affiliation(s)
- Makoto Suzuki
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA.
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Jensen PN, Major EO. A classification scheme for human polyomavirus JCV variants based on the nucleotide sequence of the noncoding regulatory region. J Neurovirol 2001; 7:280-7. [PMID: 11517403 DOI: 10.1080/13550280152537102] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The human polyomavirus JCV is responsible for the central nervous system (CNS) demyelination observed in cases of progressive multifocal leukoencephalopathy (PML). Lytic infection of oligodendrocytes, the cells that constitute the basis of myelin in the CNS, is established by JCV in conjunction with immunosuppressive conditions. Beyond this, however, many questions related to JCV pathogenesis remain unanswered. The JCV regulatory region is a hypervariable noncoding sequence positioned between the early and late protein-coding regions. The particular nucleotide sequence of a JCV regulatory region affects levels of viral transcription and replication. Modifications to this promoter/enhancer structure can alter the cellular host range and may be responsible for switching JCV between states of lytic and latent infection. The regulatory region structure has, therefore, been used to distinguish JCV variants. Nucleotide sequencing studies have uncovered numerous variations of regulatory region structure. Until now, however, no inclusive nomenclature existed that linked variants by regulatory region structure and/or activity. We have arranged all known variant JCV regulatory regions into quadrants according to the integration of particular sequence sections and repetition of sequence section groups. This arrangement of regulatory regions results in an updated nomenclature that is well-suited for describing the relationships between JCV variants. Four distinct structural forms (I-S, I-R, II-S, and II-R) are defined along with tissue tropisms. This design provides logical connections between the variant regulatory regions and may be useful for elucidating crucial steps in JCV pathogenesis.
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Affiliation(s)
- P N Jensen
- Laboratory of Molecular Medicine and Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
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Agostini HT, Deckhut A, Jobes DV, Girones R, Schlunck G, Prost MG, Frias C, Pérez-Trallero E, Ryschkewitsch CF, Stoner GL. Genotypes of JC virus in East, Central and Southwest Europe. J Gen Virol 2001; 82:1221-1331. [PMID: 11297697 DOI: 10.1099/0022-1317-82-5-1221] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Distinctive genotypes of JC virus have been described for the major continental landmasses. Studies on European-Americans and small cohorts in Europe showed predominantly Type 1. Types 2 and 7 are found in Asia, and Types 3 and 6 in Africa. These genotypes differ in sequence by about 1--3%. Each genotype may have several subtypes which differ from each other by about 0.5--1%. The genotypes can be defined by a distinctive pattern of nucleotides in a typing region of the VP1 gene. This genotyping approach has been confirmed by phylogenetic reconstruction using the entire genome exclusive of the rearranging regulatory region. In this first large European study, we report on the urinary excretion of JCV DNA of 350 individuals from Poland, Hungary, Germany and Spain. We included Gypsy cohorts in Hungary (Roma), Germany (Sinti), and Spain (Gitano), as well as Basques in Spain. We show that while Type 1 predominates in Europe, the proportions of Type 1A and 1B may differ from East to Southwest Europe. Type 4, closely related to the Type 1 sequence (only approximately 1% difference) was a minor genotype in Germany, Poland and Spain, but represented the majority in Basques. The Gitanos in Spain showed a variant Type 4 sequence termed 'Rom-1'. Interestingly, neither the Gitanos in Spain, nor Sinti or Roma in Germany or Hungary showed the Type 2 or Type 7 genotype that might be expected if their origins were in an Asian population.
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Affiliation(s)
- Hansjürgen T Agostini
- Department of Ophthalmology, University of Freiburg, Killianstr. 5, 79106 Freiburg, Germany1
| | - Alison Deckhut
- Neurotoxicology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 36 Convent Drive, Room 4A-27, MD 20892-4126, Bethesda, USA2
| | - David V Jobes
- Neurotoxicology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 36 Convent Drive, Room 4A-27, MD 20892-4126, Bethesda, USA2
| | - Rosina Girones
- Department of Microbiology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain3
| | - Günther Schlunck
- Department of Ophthalmology, University of Freiburg, Killianstr. 5, 79106 Freiburg, Germany1
| | - Marcin G Prost
- University Eye Clinic II, SPKSO, Sierakowskiego 13, 03709 Warsaw, Poland4
| | - Carolina Frias
- Department of Microbiology, Hospital Universitari Germans Trias i Pujol, E-08916 Badalona, Spain5
| | - E Pérez-Trallero
- Microbiology Department, Donostia Hospital, E-20014 San Sebastián, Spain6
| | - Caroline F Ryschkewitsch
- Neurotoxicology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 36 Convent Drive, Room 4A-27, MD 20892-4126, Bethesda, USA2
| | - Gerald L Stoner
- Neurotoxicology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 36 Convent Drive, Room 4A-27, MD 20892-4126, Bethesda, USA2
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