BK virus and a new type of JC virus excreted by HIV-1 positive patients in rural Tanzania

Molecular Characterization of BK Polyomavirus’ Large T Antigen Gene Sequences Detected in Prostate Cancer Tissues of Sudanese Patients

Background:

BK virus, which is associated with Prostate Cancer (PCa), have a global seroprevalence in humans. Based on the sequences of VP1 and the Large Antigen (LTAg) genes, there are four subtypes of BKV. Each subtype has its own subgroups.

Objective:

The aim of this study was to identify the BKV subtype that circulates among Sudanese patients with PCa.

Materials and Methods:

A total of 8 samples from our previous work on BKV were studied in this investigation. The LTAg gene was partially amplified (176nt) by a homemade PCR. All the amplicons were purified and subjected to sequencing. Bioedit version 7.0 and Mega X version 6.0 were used to analyze the sequence and compare the results with the BKV sequences and build a phylogenetic tree.

Results:

All the BKV LTAg gene sequences derived from Sudanese patients were classified with Subtype-1 BKV strains from Iran and Japan. Translated protein alignment showed that some isolates had identical amino acids with Iranian and Japanese strains, whereas others had a silent mutation. Interestingly, a point mutation was identified in the sequences of isolate 5 and 8 where adenine nucleotide (A) was replaced with Cytosine (C) at position 276, resulting in amino acid substitution.

Conclusion:

It was concluded that all the BKV isolates which circulated among Sudanese prostate tumor patients belonged to subtype 1. These findings only highlighted the need for the molecular detection and subtyping of BKV strains in Sudanese patients in order to better demonstrate the relationship between BKV infection and PCa.

Characterization of Jc Virus Dna Amplified from Urine of Chronic Progressive Multiple Sclerosis Patients

Thirty-seven chronic progressive multiple sclerosis (MS) patients, 20 of whom were taking cyclosporine, were examined for excretion of JC virus (JCV) in the urine. Polymerase chain reaction (PCR) amplification of DNA in urinary cell extracts detected JCV in 30% of the MS urines. In the cyclosporine treated group four of 20 (20%) excreted JCV, whereas in the untreated group seven of 17 (41%) excreted JCV. Thus, cyclosporine treatment did not enhance urinary excretion of the virus. A control group consisting of an unselected series of 89 patients donating urine in a general medical clinic and 16 healthy volunteers showed 41% with detectable urinary JCV. Thirty-three percent of the control females excreted JCV (18154), as did 49% of the control males (25151). Although the percentage of MS patients excreting detectable virus was not increased compared to the control group, the presence of JCV in the urine provides or convenient source of the virus for further characterization. Genotyping of DNA fragments amplified from the VPI region indicates mainly the presence of JCV Type 1 in these chronic progressive MS patients. This is also the type that predominates in the control group. An apparent recombinant between Type 1 and Type 3 (African) within the VPI region, tentatively designated Type 113 (or Type 4), was found in both the MS group and the controls. A larger series of MS patients that includes relapsing/remitting disease will be required to determine whether the genotype profile of JCV excreted in the urine of MS patients differs significantly from controls.

BK virus: microbiology, epidemiology, pathogenesis, clinical manifestations and treatment

Background: BK virus infection is common but is usually asymptomatic. However, it can become life threatening as severe hemorrhagic cystitis (HC) or the polyomavirus-associated nephropathy (PVAN) particularly in immune compromised and transplant recipients. Some investigators have studied the pathophysiology and there are anecdotal and uncontrolled studies of therapy with few conclusions allowing treatment guidelines. Objectives: Summarize literature review of current knowledge concerning the nature, epidemiology, pathophysiology, diagnosis and treatment of this common virus infection. Results: HC is a not uncommon and often misdiagnosed infection from BK virus. It is usually self limited but can become life threatening in immune compromised patients. PVAN threatens survival of transplanted kidneys and is difficult to differentiate from rejection without sophisticated molecular diagnostic technology. We have sufficient information for making a diagnosis of BK virus disease by using clinical, serological and molecular technology. Studies using manipulation of immunosuppression and a variety of antiviral agents, including cidofovir, leflunomide, intravenous immunoglobulin, vidarabine, fluroquinolones, have been published but most were uncontrolled reports of few cases. Cidofovir offers some promise but more must be learned before there is hope for evidence-based treatment guidelines.

The prevalence and isolated subtypes of BK polyomavirus reactivation among patients infected with human immunodeficiency virus-1 in southeastern China

BK polyomavirus (BKPyV) is an opportunistic infectious pathogen that is associated with hemorrhagic cystitis and nephropathy, mainly in transplant recipients and human immunodeficiency virus 1 (HIV-1) infected patients. However, molecular characterization studies of BKPyV in China are rare. This study was designed to elucidate the prevalence and to determine the main subtypes of BKPyV among HIV-1-infected patients in southeastern China. In addition, the increased incidences for BKPyV reactivation were analyzed. The isolated BKPyV DNA was amplified by polymerase chain reaction (PCR) and the specimen sequences were aligned with the reference sequences for phylogenetic analysis. In this study, BKPyV viruria was detected in 64.2% (88/137) of HIV-1-infected patients. Patients in the BKPyV-positive group were more diverse with respect to gender (P = 0.039) and age (P = 0.023) than their counterparts in the BKPyV-negative group, and they had a higher rate of co-infection with tuberculosis (TB) (P = 0.026). Viruria was more commonly found in patients with CD4 counts <200 cells/mm (72.7%) than in those with CD4 counts ≥200 cells/mm (58.5%) (not significant). All sequenced BKPyV isolates belonged to subtype I (13/32) and IV (19/32). A high prevalence of BKPyV reactivation was discovered in patients with HIV-1 infection. Females and elderly individuals, as well as those with a TB co-infection, appeared more susceptible to BKPyV reactivation in this study. BKPyV viruria was found more often and was associated with lower CD4 counts.

Detection and analysis of variants of JC polyomavirus in urine samples from HIV-1-infected patients in China's Zhejiang Province

Objectives Human JC polyomavirus (JCPyV) infection has an increased risk of developing progressive multifocal leukoencephalopathy (PML). Different JCPyV subtypes differ in the virulence with which they cause PML. Currently, the JCPyV infection status and subtype distribution in patients with human immunodeficiency virus-1 (HIV-1) in China are still unclear. This study aimed to investigate the epidemiology and subtype distribution of JCPyV in HIV-1-infected patients in China. Methods Urine samples from 137 HIV-1-infected patients in Zhejiang Province in China were tested for the presence of JCPyV DNA. The detected VP1 sequences were aligned and analysed using BioEdit and MEGA software. Results Among urine samples from HIV-1-infected patients, 67.2% were positive for JCPyV DNA (92/137). Primarily, the type 7 strains of JCPyV were detected, among which 45.5% (15/33) were subtype 7A, 30.3% (10/33) were 7B, and 24.2% (8/33) were 7C. Six nucleotide mutations, as well as one amino acid substitution, were isolated from the patients. Conclusions Urine samples from HIV-1-infected patients from Zhejiang Province show a high JCPyV infection rate. The most common JCPyV strains are subtypes 7A, 7B, and 7C.

BK nephropathy in the native kidneys of patients with organ transplants: Clinical spectrum of BK infection

Nephropathy secondary to BK virus, a member of the Papoviridae family of viruses, has been recognized for some time as an important cause of allograft dysfunction in renal transplant recipients. In recent times, BK nephropathy (BKN) of the native kidneys has being increasingly recognized as a cause of chronic kidney disease in patients with solid organ transplants, bone marrow transplants and in patients with other clinical entities associated with immunosuppression. In such patients renal dysfunction is often attributed to other factors including nephrotoxicity of medications used to prevent rejection of the transplanted organs. Renal biopsy is required for the diagnosis of BKN. Quantitation of the BK viral load in blood and urine are surrogate diagnostic methods. The treatment of BKN is based on reduction of the immunosuppressive medications. Several compounds have shown antiviral activity, but have not consistently shown to have beneficial effects in BKN. In addition to BKN, BK viral infection can cause severe urinary bladder cystitis, ureteritis and urinary tract obstruction as well as manifestations in other organ systems including the central nervous system, the respiratory system, the gastrointestinal system and the hematopoietic system. BK viral infection has also been implicated in tumorigenesis. The spectrum of clinical manifestations from BK infection and infection from other members of the Papoviridae family is widening. Prevention and treatment of BK infection and infections from other Papovaviruses are subjects of intense research.

Optimisation and analysis of polymerase chain reaction based DNA sequencing for genotyping polyoma virus in renal transplant patients: a report from South India

PURPOSE

To optimise a polymerase chain reaction (PCR) based DNA sequencing technique for genotyping polyoma virus in clinical specimens obtained from renal transplant patients.

MATERIALS AND METHODS

A hundred and thirty (106 peripheral blood and 24 urine) clinical specimens collected from renal transplant patients were included in the study for detecting the presence of  DNA of BK virus (BKV), JC virus (JCV) by PCR targeting the viral protein 1 (VP1) gene. PCR based DNA sequencing was performed to determine the genotypes of polyoma virus and subjected to bioinformatics analysis to determine the amino acid sequences and screen for mutations in the VP1 gene.

RESULTS

Polyoma virus was detected in 23 (17.69%) specimens of which 19 (82.60%) were positive for BK virus, 3 (13.04%) for JC virus and 1 for both BK and JC virus. PCR based DNA sequencing detected BK virus genotype I in 12 (50%), genotype IV in 8 (33.3%) and JC virus in 4 (16.6%) clinical specimens. BKV genotype I was the predominant genotype (64.2% in peripheral blood and 33.33% in urine) prevalent in south India. Six novel mutations were found--at position 29, 30 to 47 of BKV genotype I; at position 11 and 15 of BKV genotype IV and at position 2 and 30 of JCV.

CONCLUSION

BKV genotype I is the prominent genotype in India and novel mutations detected in the VP1 gene of BKV and JCV are being reported for the first time in literature.

Molecular biology, epidemiology, and pathogenesis of progressive multifocal leukoencephalopathy, the JC virus-induced demyelinating disease of the human brain

Progressive multifocal leukoencephalopathy (PML) is a debilitating and frequently fatal central nervous system (CNS) demyelinating disease caused by JC virus (JCV), for which there is currently no effective treatment. Lytic infection of oligodendrocytes in the brain leads to their eventual destruction and progressive demyelination, resulting in multiple foci of lesions in the white matter of the brain. Before the mid-1980s, PML was a relatively rare disease, reported to occur primarily in those with underlying neoplastic conditions affecting immune function and, more rarely, in allograft recipients receiving immunosuppressive drugs. However, with the onset of the AIDS pandemic, the incidence of PML has increased dramatically. Approximately 3 to 5% of HIV-infected individuals will develop PML, which is classified as an AIDS-defining illness. In addition, the recent advent of humanized monoclonal antibody therapy for the treatment of autoimmune inflammatory diseases such as multiple sclerosis (MS) and Crohn's disease has also led to an increased risk of PML as a side effect of immunotherapy. Thus, the study of JCV and the elucidation of the underlying causes of PML are important and active areas of research that may lead to new insights into immune function and host antiviral defense, as well as to potential new therapies.

Investigation of human JC and BK polyomaviruses in breast carcinomas

We have previously showed the presence of the simian virus 40 (SV40) and the mouse mammary tumor virus (MMTV)-like in a significant proportions of Tunisian breast carcinomas. However, to date there are no published studies concerning evaluation of the possible implication of the human polyomaviruses JC (JCV) and BK (BKV) in breast carcinomas. The presence of JCV and BKV DNA was investigated by PCR in a 123 primary breast carcinomas and matched adjacent non-tumor breast tissues. The results were correlated to clinicopathological and virological parameters. JCV T-antigen DNA was detected in 23% of breast carcinoma cases; however, all cases were negative for BKV. JCV T antigen PCR products were further confirmed as authentic JCV genome by direct sequencing. JCV was found in invasive ductal carcinomas (28/112 cases) but not in invasive lobular carcinomas (0/5) or medullary carcinomas (0/6). JCV DNA presence correlates inversely with the expression of estrogen (P = 0.022) and progesterone (P = 0.008) receptors. JCV DNA presence correlates also with "triple negative" phenotype (P = 0.021). With regard to virological data, a trend toward an inverse correlation was noted between the presence of JCV and SV40 (P = 0.06). Moreover, significant correlation was found between multiple viral infection (JCV, and/or SV40, and/or MMTV-like in the same tumor) and "triple negative" phenotype (P = 0.001) and also with p53 accumulation (P = 0.028). To the best of our knowledge, this is the first study demonstrating the presence of JCV in a subset of breast carcinomas. Also our results suggest that "triple negative" breast carcinomas are viral-related tumors.

Distribution of BK polyomavirus genotypes in Tunisian renal transplant recipients

BK polyomavirus (BKV) is a ubiquitous virus in humans that remains latent in the urogenital tract after a primary infection during childhood. The virus, which is reactivated frequently and excreted in urine, can cause nephropathy in renal transplant recipients. BKV sequences are classified into four subtypes (I-IV). Subtype I and IV are divided further into four and six subgroups, respectively. To characterize the subtypes of BKV prevalent in Tunisia, the presence of the virus was investigated by real-time PCR in urine samples from 77 renal transplant recipients. For subtype identification, a DNA fragment in the VP1 coding region, amplified by nested PCR from positive samples, was sequenced and a phylogenetic analysis was performed. In the studied population, subtype I (75.5%), II (14.5%), and IV (2.5%) were identified with a clear predominance of subtype Ib-2 (73%) as observed in European population. This study suggests that in North Africa, the BKV genotype distribution is similar to that of Europe and different from that of sub-Saharan Africa.

Evolution of the BK polyomavirus: epidemiological, anthropological and clinical implications

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.

Detection, distribution, and pathologic significance of BK virus strains isolated from patients with kidney transplants, with and without polyomavirus-associated nephropathy

CONTEXT

BK virus strains or regulatory region sequence variations may play a role in the pathogenesis of polyomavirus-associated nephropathy (PVAN), although no definite relationship has yet been demonstrated.

OBJECTIVE

To investigate the pathologic significance of BK virus strains and regulatory region sequence variations.

DESIGN

Eight (3.5%) of 226 patients with renal transplants developed PVAN; the remaining 218 cases were used as controls. From the patients who developed PVAN, 70 urine samples, 63 blood samples, and 17 renal biopsy samples were taken, and 682 urine samples, 677 blood samples, and 101 renal biopsy samples were taken from the control cases. Amplification and sequence analyses of regulatory region were obtained, and the sequences were analyzed using the Basic Local Alignment Search Tool program.

RESULTS

The WWT strain was more frequently detected in PVAN cases than in the control cases (urine: 88.5% vs 22.1%; blood: 85.2% vs 40%; renal biopsies: 77.8% vs 0%), and the AS and WW strains were only isolated from controls. Strain 128-1 was frequently associated with JC virus coinfection in both groups (PVAN: 78.3%; controls: 98%). Major WWT rearrangements were detected in 29.6% of the urine samples, 30.4% of the blood samples, and one renal biopsy from the PVAN cases, but in only one urine sample from the controls. Insertion of 8 base pairs (P block) was found in all 128-1 strains; WW and AS were archetypal in 78.9% and 57.7% of the samples, respectively.

CONCLUSIONS

Although the study included only 8 PVAN cases, regulatory region sequence variations seem to be frequent and independent of the development of the disease, and the WWT strain seems more frequently related to the development of nephropathy than other strains.

Polyomavirus BK non-coding control region rearrangements in health and disease

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.

Discovery and epidemiology of the human polyomaviruses BK virus (BKV) and JC virus (JCV)

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.

Presence, quantitation and characterization of JC virus in the urine of Italian immunocompetent subjects

Human polyomavirus JC (JCV) infects the worldwide population, remains latent in the kidney, and is excreted in the urine. A longitudinal study was performed in order to evaluate JCV excretion, to characterize molecularly the virus and to determine if its presence in urine is a consequence of viral reactivation or merely of epithelial squamous cell shedding. The presence of cellular sediment and the JCV genome were examined in 333 urine samples collected periodically for 3 months from 17 healthy subjects; molecular characterization, and quantitation of the virus were also undertaken. JCV DNA was detected in 40.2% of the samples, with a significant difference (P<0.001) observed between males and females. JCV shedding was independent of the presence of cellular sediment in every individual. JCV genotype 1 was the genome detected most frequently, while all of the amplified strains showed archetypal organization of the transcriptional control region (TCR). No clinical symptoms have been associated with JCV excretion and no microbial load was detected in the urine samples. The lack of correlation between JCV DNA detection and the presence of squamous cells in urine sediment indicates that viruria is regulated by the life cycle of JCV. Thus, the virus is eliminated as consequence of its reactivation.

Identification of a genomic subgroup of BK polyomavirus spread in European populations

BK polyomavirus (BKV) is highly prevalent in the human population, infecting children without obvious symptoms and persisting in the kidney in a latent state. In immunosuppressed patients, BKV is reactivated and excreted in urine. BKV isolates worldwide are classified into four serologically distinct subtypes, I-IV, with subtype I being the most frequently detected. Furthermore, subtype I is subdivided into subgroups based on genomic variations. In this study, the distribution patterns of the subtypes and subgroups of BKV were compared among four patient populations with various immunosuppressive states and of various ethnic backgrounds: (A) Finnish renal-transplant recipients; (B) Irish/English haematopoietic stem-cell transplant recipients with and without haemorrhagic cystitis; (C) Japanese renal-transplant recipients; and (D) Japanese bone-marrow transplant recipients. The typing sequences (287 bp) of BKV in population A were determined in this study; those in populations B-D have been reported previously. These sequences were subjected to phylogenetic and single nucleotide polymorphism analyses. Based on the results of these analyses, the BKV isolates in the four patient populations were classified into subtypes and subgroups. The incidence of subtype IV varied significantly among patient populations. Furthermore, the incidence of subgroup Ib-2 within subtype I was high in populations A and B, whereas that of Ic was high in populations C and D (P<0.01). These results suggest that subgroup Ib-2 is widespread among Europeans, whereas Ic is unique to north-east Asians. Furthermore, a phylogenetic analysis based on complete BKV DNA sequences supported the hypothesis that there is geographical separation of European and Asian BKV strains.

Subtype I BK polyomavirus strains grow more efficiently in human renal epithelial cells than subtype IV strains

BK polyomavirus (BKPyV) is ubiquitous in human populations, infecting children without obvious symptoms and persisting in the kidney. BKPyV isolates have been classified into four subtypes (I-IV) using either serological or genotyping methods. In general, subtype I occurs most frequently, followed by subtype IV, with subtypes II and III rarely detected. As differences in growth capacity in human cells possibly determine the proportion of the four subtypes of BKPyV in human populations, here the growth properties of representative BKPyV strains classified as subtype I or IV in renal proximal tubule epithelial cells (HPTE cells) of human origin were analysed. HPTE cells were transfected with four and three full-length BKPyV DNAs belonging to subtypes I and IV, respectively, and cultivated in growth medium. Virus replication, detected using the haemagglutination assay, was observed in all HPTE cells transfected with subtype I BKPyV DNAs, whereas it was markedly delayed or not detected in those transfected with subtype IV BKPyV DNAs. It was confirmed that the transfected viral DNAs induced virus replication in HPTE cells. Furthermore, it was found that BKPyVs with archetypal transcriptional control regions replicated in HPTE cells, with only the occasional emergence of variants carrying rearranged transcriptional control regions. Essentially the same results as described above were obtained with renal epithelial cells derived from whole kidney. Thus, it was concluded that subtype I BKPyV replicates more efficiently than subtype IV BKPyV in human renal epithelial cells, supporting the hypothesis that growth capacity in human cells is related to the proportion of BKPyV subtypes in human populations.

Evolution of BK virus based on complete genome data

The human polyomavirus BK virus (BKV) is ubiquitous in humans, infecting children asymptomatically. BKV is the only primate polyomavirus that has subtypes (I-IV) distinguishable by immunological reactivity. Nucleotide (nt) variations in a major capsid protein (VP1) gene region (designated the epitope region), probably responsible for antigenic diversity, have been used to classify BKV isolates into subtypes. Here, with all the protein-encoding gene sequences, we attempted to elucidate the evolutionary relationships among 28 BKV isolates belonging to subtypes I, III, and IV (no isolate belonging to subtype II, a minor one, was included). First, using the GTR + Gamma + I model, maximum likelihood trees were reconstructed for individual viral genes as well as for concatenated viral genes. On the resultant trees, the 28 BKV isolates were consistently divided into three clades corresponding to subtypes I, III, and IV, although bootstrap probabilities are not always high. Then we used more sophisticated likelihood models, one of which takes account of codon structure, to elucidate the phylogenetic relationships among BKV subtypes, but the phylogeny of the deep branchings remained ambiguous. Furthermore, the possibility of positive selection in the evolution of BKV was examined using the nonsynonymous/synonymous rate ratio as a measure of selection. An analysis based on entire genes could not detect any strong evidence for positive selection, but that based on the epitope region identified a few sites potentially under positive selection (these sites were among those showing subtype linked polymorphisms).

Subtype IV of the BK polyomavirus is prevalent in East Asia

BK polyomavirus (BKV) is ubiquitous in human populations, infecting children asymptomatically and then persisting in the kidney. Using either serological or genotyping methods, BKV isolates have been classified into four subtypes (I-IV), with subtype I mainly detected in all countries studied so far. To elucidate the subtype of BKV prevalent in East Asia, we examined BKV-positive urine samples collected from immunocompetent elderly patients in Mongolia, Northeast China, Northwest China, Southeast China, Southwest China, Vietnam and Japan. The 287-bp typing region of the viral genome in each of these samples was PCR-amplified and sequenced, and a phylogenetic tree was constructed. According to the tree, BKV isolates in East Asia were unambiguously classified into subtype I or IV (subtypes II and III were not detected). In Japan, subtype I was mainly detected and subtype IV was rare, whereas in the other regions subtype IV was detected frequently, at rates ranging from 24 to 100%. Thus, East Asia (excluding Japan) is a region in which subtype-IV BKV is prevalent, a finding that requires the view of the geographic distribution of BKV subtypes to be revised. Furthermore, we present evidence that the immunological states of urine donors do not affect the pattern of BKV subtypes.

Prevalence of BK virus subtype I in Germany

The primary infection with human polyomavirus BK (BKV) occurs in early childhood and leads to viral latency within the urogenital tract. Up to 90% of the adult population are seropositive. In immunosuppressed patients, the BKV may be reactivated resulting in typical disease patterns like hemorrhagic cystitis and tubulointerstitial nephritis. Based on serological and molecular methods, BKV isolates were classified into four subtypes previously. Sixty specimens obtained from German renal and bone marrow transplant recipients were analyzed to gain data on the prevalence of BKV subtypes in Germany. With 90.9%, BKV subtype I was found to be predominant in both patient groups. 6.1% of BKV strains were classified as subtype IV. This pattern of phylogenetic distribution is similar to that demonstrated previously in England, Tanzania, the United States and Japan. Remarkably, there was one German BKV virus with a sequence which clusters together with strain SB in subtype II. The BKV subtype I was found to consist of at least three subgroups designated as Ia, Ib, and Ic. While the majority of the German sequences represent subgroup Ic, most of the Japanese sequences are clearly distinct. These findings support the hypothesis of distinct geographical prevalence of BKV subgroups. For the genotyping region, a relationship of BKV subgroups to disease patterns like hemorrhagic cystitis or tubulointerstitial nephritis could not be demonstrated.

Genotypes of JC virus, DNA of cytomegalovirus, and proviral DNA of human immunodeficiency virus in eyes of acquired immunodeficiency syndrome patients

JC virus (JCV) is a human polyomavirus that exists in at least eight different genotypes as a result of coevolution with different human populations all over the world. Well adapted to its host, it usually persists in the kidneys and possibly the brain. If the host becomes immunodeficient, JCV can cause the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML). There is increasing evidence that JCV is transactivated by cytomegalovirus (CMV) and the human immunodeficiency virus (HIV). Both CMV and HIV can infect the retina of acquired immunodeficiency syndrome (AIDS) patients, causing severe necrosis in the case of CMV retinitis or a mild HIV-associated vasculopathy, with bleeding and cotton wool spots. The authors therefore investigated by polymerase chain reaction (PCR) whether DNA of these three viruses was detectable in paraffin-embedded eyes of AIDS patients with a clinical history of CMV retinitis. From a total of 65 eyes, JCV was detected in 21 (32%). Thirty-six (55%) were positive for CMV and 6 (9%) for proviral DNA of HIV. JCV and CMV were found in 13 eyes, JCV and HIV in 3 eyes, CMV and HIV in 1 eye, and DNA from all three viruses in 1 eye. The JCV genotypes were types 1A, 2A, 2E, 3, and 4. In 21 eyes of patients without AIDS, only one sample was JCV positive. In conclusion, JCV DNA can be detected in ocular tissue of AIDS patients at a significantly higher level than in eyes of nonimmunosuppressed patients. Further investigations will help to decide if JCV contributes to the retinopathy caused by CMV and HIV.

Polymorphism in the genome of non-passaged human polyomavirus BK: implications for cell tropism and the pathological role of the virus

Worldwide studies have demonstrated that the human polyomavirus BK resides ubiquitously in the human population. After primary infection, which occurs mainly during childhood, the virus seems to establish a life-long harmless infection in the host. However, impaired immune functions may lead to reactivation of BK virus. The recent findings that associate BK virus with an increasing number of clinical conditions, including renal, pulmonary, ophthalmologic, hepatic, neurological, and autoimmune diseases, has resuscitated the interest in this virus as a pathogenic agent. This review focuses on polymorphisms in the genomes of non-passaged BK virus isolates from nonneoplastic tissues, with special focus on the transcriptional control region, the regulatory proteins large T-antigen and agnoprotein, and the major capsid protein VP1. The possible implications of genome diversity with respect to cell tropism, pathogenicity, and therapeutic strategies are discussed.

Subtypes of BK virus prevalent in Japan and variation in their transcriptional control region

BK polyomavirus (BKV) is ubiquitous in the human population, infecting children without obvious symptoms, and persisting in the kidney in a latent state. In immunosuppressed patients, BKV is reactivated and excreted in urine. BKV isolates have been classified into four subtypes (I-IV) using either serological or genotyping methods. To elucidate the subtypes of BKV prevalent in Japan, the 287 bp typing region in the viral genome was PCR-amplified from urine samples of 45 renal transplant (RT) and 31 bone-marrow transplant (BMT) recipients. The amplified fragments were subjected to a phylogenetic or RFLP analysis to determine the subtypes of BKV isolates in urine samples. Subtypes I, II, III and IV were detected, respectively, in 70-80, 0, 2-3 and 10-20 % of the BKV-positive patients in both patient groups. This pattern of distribution was virtually identical to patterns previously demonstrated in England, Tanzania and the United States, suggesting that BKV subtypes are distributed similarly in various human populations. Furthermore, transcriptional control regions (TCRs) were PCR-amplified from the urine samples of 25 RT and 20 BMT recipients, and their nucleotide sequences were determined. The basic TCR structure (the so-called archetype configuration) was observed in most isolates belonging to subtypes I, III and IV (subtype II isolates were not available), albeit with several nucleotide substitutions and a few single-nucleotide deletions (or insertions). Only three TCRs carried extensive sequence rearrangements. Thus, it was concluded that the archetypal configuration of the BKV TCR has been conserved during the evolution of BKV.

Phylogenetic evidence of widespread distribution of genotype 3 JC virus in Africa and identification of a type 7 isolate in an African AIDS patient

JC virus (JCV) is the cause of progressive multifocal leukoencephalophathy (PML) in immunocompromised patients. The paucity of reports from Africa has led to the hypothesis that PML is rare because of an absence of virus genotypes associated with the condition. Genotypes 3 and 6 have been identified in East and West Africa but the distribution of types across the rest of Africa is unknown. Full-length sequences of five JCV cerebrospinal fluid samples from PML patients in South Africa are reported here. Three isolates from African AIDS patients grouped with type 3A or 3B, and one with type 7, while one from a Caucasian leukaemia patient grouped with type 2D. Widespread distribution of type 3 on the continent may reflect migration patterns in antiquity, but this is the first report of type 7 in an African individual. Type 2D has only been isolated previously in South Asia, although transmission of this genotype to Europeans who later settled in South Africa is not unlikely.

Detection and sequence analysis of human polyomaviruses DNA from autoptic samples of HIV-1 positive and negative subjects

The distribution of DNA of BK and JC human polyomaviruses (BKV and JCV) was investigated in samples from autopsies of different organs in 2 groups of patients: Human Immunodeficiency Virus -1 (HIV) positive and negative. Samples from various organs were analysed by a nested polymerase chain reaction (PCR) for the non-coding control and for the VP1 regions of both viruses. The results obtained showed that BKV DNA was present in both males and females with a higher prevalence in HIV-positive subject samples (spleen: 33%; kidney: 44%; brain: 22%, uterine cervix:100%; prostatic urethra: 50%). In prostatic urethra samples of HIV-positive subjects, the JCV DNA was revealed in a low percentage (33%), while it was not found at all in uterine cervix samples of both groups. The varying presence of BK and JC viral DNA in the different organs seems to reflect the different pathogenetic attitude of these viruses. JCV was mainly present in the brain (55%), confirming its typical neurotropism and its etiological role in neurological disorders found in immunodeficient patients. BKV, on the other hand, was mainly present in the kidney (44%) and in genital organs (uterine cervix: 100%; prostatic urethra: 50%) with the latter finding favouring the hypothesis of a possible sexual transmission of BKV. Furthermore, our results confirm the crucial role of the immune system in the persistence of human polyomaviruses in the host.

Analysis of the excreted JC virus strains and their potential oral transmission

JC virus (JCV) particles have been detected in urban sewage of divergent geographical areas. In this study, the authors evaluate the genetic characteristics and the infective capabilities of JCV strains in relation to the potential oral transmission of JCV in the population. JCV strains excreted in urine and detected in sewage have been described as presenting archetypal structure of the regulatory region of the viral genome. The regulatory region of JCV viral particles detected in two urban sewage samples have been cloned and characterized. From a total of 40 clones tested, 39 presented archetypal-like regulatory regions, whereas 1 of the clones analyzed presented a tandem repeated structure. Archetypal strains present in the urine of a pregnant woman were able to infect SVG cells, producing infectious virions, as demonstrated by confirmative cell culture, electron microscopy, and in situ DNA hybridization. This is the first description of archetypal JCV productive infection of SVG cells. SVG cells were also successfully infected with Mad-4 JCV viral particles subjected to pH 3 for 1 h at 37 degrees C and to 10 microg/ml of trypsin in the same conditions. A decrease in the viral progeny production was observed when Mad-4 was subjected to acidic pH. Mad-4 did not produce any detectable infection in the enteric cell line CaCo-2. The oral route could represent a significant route of transmission of JCV infections because JCV virions have demonstrated relative resistance in the environment and to some of the conditions present in the gastrointestinal tract. The archetypal strains commonly detected in the environment may be implicated in the transmission of JCV among the population. Sporadic infection with strains presenting tandem repeated structures may have implications in pathogenicity.

Autoimmunity to nucleosomes related to viral infection: a focus on hapten-carrier complex formation

Systemic lupus erythematosus (SLE) is an autoimmune disorder with unknown aetiology. The major hallmark of this disease is the presence of antibodies against nuclear components, including double-stranded (ds)DNA and histones. The disease affects different organs, particularly the skin, kidneys and the nervous system. Although the exact molecular mechanisms underlying the pathophysiological processes in SLE remain unknown, several inherent and environmental factors seem to be involved in the ethiopathogenesis of this disorder. Viruses may be one of the factors that induce the production of autoreactive antibodies although the involved mechanisms are still incompletely understood. One proposed mechanism for virus-induced production of autoantibodies is molecular mimicry. Another mechanism derives from studies with the human polyomavirus BK. In these studies, in vivo binding of the polyomaviruses large T-antigen to chromatin of infected cells may render chromatin immunogenic. The large T-antigen-chromatin complex may thus function as a hapten-carrier model with subsequent production of anti-chromatin antibodies, including anti-dsDNA and anti-histones antibodies. This review focuses on the recent findings suggesting that this model may be applicable for other human viruses associated with SLE.

Genotyping of the JC virus in urine samples of healthy Korean individuals

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.

Detection of human polyomaviruses and papillomaviruses in prostatic tissue reveals the prostate as a habitat for multiple viral infections

BACKGROUND

To determine whether human polyomavirus (hPy) genomes are present in prostate tissues, we have carried out a polymerase chain reaction (PCR) screening in two sets of prostate samples, archival and fresh frozen, as well as performing in situ hybridization (ISH). The frozen prostate samples as well as the urine from the same patients were also screened for human papillomavirus (HPV) sequences.

METHODS

Highly sensitive nested-PCR assays were used. The detection of subpopulations of JC virus (JCV) -transcriptional control regions (TCRs) was also evaluated by Southern analysis and by direct DNA sequencing. An in situ hybridization technique was also used to detect JCV DNA in prostatic tissue.

RESULTS

The paraffin-embedded archival samples gave variable, unsatisfactory results. Results from the fresh frozen samples, however, were consistent and were frequently positive for JCV and less frequent for BK virus DNA. ISH confirmed the presence of JCV DNA in prostatic glandular epithelium. The TCR region of JCV from prostate tissue and urine from prostate cancer patients showed the presence of both archetypal and rearranged TCRs, including several new sequence variants. HPV DNA was also frequently detected and in some cases also mixed with hPy DNA from frozen tissue and urine.

CONCLUSION

The use of fresh frozen samples proved to be essential for consistent and reproducible detection of HPV and hPy viral DNAs. The presence of JCV DNA by ISH and the occurrence of a subpopulation of JCV TCR regions suggests that the prostate is a site for virus replication. The prostate is a complex habitat where mixed infections with oncogenic DNA viruses frequently occur and opens the discussion to the potential role of these viruses in the cancer of the prostate.

Strains of JC virus in Amerind-speakers of North America (Salish) and South America (Guaraní), Na-Dene-speakers of New Mexico (Navajo), and modern Japanese suggest links through an ancestral Asian population

Previously we showed that strains of human polyoma virus JC among the Navajo in New Mexico, speakers of an Athapaskan language in the Na-Dene language phylum, and among the Salish people in Montana, speakers of a language of the Salishan group in the Amerind family, were mainly of a northeast Asian genotype found in Japan (type 2A). We now report partial VP1-gene, regulatory region, and complete genome sequences of JC virus (JCV) from the Guaraní Indians of Argentina. The Tupí-Guaraní language represents the Equatorial branch of the Amerind language family proposed by Greenberg ([1987] Language in the Americas, Stanford: Stanford University Press). The partial VP1 gene sequences of the Guaraní revealed several variants of strains found in northeast Asia (Japan), as did the Salish. In contrast, the strains in the Navajo largely conformed to the prototype type 2A sequence (MY). Phylogenetic reconstruction with both the neighbor-joining and maximum parsimony methods utilized three complete Guaraní JCV genome sequences, three genomes from the Salish people, and 27 other complete JCV genomes, including three from the Navajo and three from Japan. Both trees showed that all type 2A JCV strains from the North and South Americans are closely related phylogenetically to strains in present-day Japan. However, variant sites in the coding regions, the T-antigen intron, and the regulatory region link the type 2A strains in Amerind groups (Guaraní and Salish), but differentiate them from those in a Na-Dene-speaking (Navajo) population. The data suggest separation from a population ancestral to modern Japanese, followed by a second division within the ancestral group that led to Amerind- and Na-Dene-speaking groups. The data cannot, however, localize the latter split to the Asian mainland (two migrations) or to North America (one migration).

BK virus regulatory region rearrangements in brain and cerebrospinal fluid from a leukemia patient with tubulointerstitial nephritis and meningoencephalitis

BK virus (BKV) was recovered by polymerase chain reaction (PCR) from brain, kidney, lung, urine, and cerebrospinal fluid (CSF) of a fatal case of BKV tubulointerstitial nephritis with dissemination to lung and brain. Viral regulatory regions in PCR-amplified urine and the lung samples were identical to the archetypal structure, WWT. In the brain and CSF, a rearranged sequence predominated, however. A 94-bp deletion preceded a 71-bp tandem duplication because the same 94-bp segment was deleted from both copies. PCR-amplified regulatory region products were cloned and sequenced to define further the extent of the rearranged structures. Two kidney clones were archetypal, whereas two others were rearranged differently from the brain and from each other. In contrast to the brain clones, the kidney rearrangements seemed to involve deletion after duplication. Three of four brain clones sequenced were identical to the rearrangement found to dominate in the PCR product. A fourth clone showed two short deletions without any duplication. The four CSF clones all showed rearrangements identical to that which was amplified by PCR from CSF and brain. This represents the first molecular analysis of a BKV strain obtained from a central nervous system infection, and it reveals regulatory region rearrangements reminiscent of those described in JC virus from brains with progressive multifocal leukoencephalopathy. We suggest that the presence in the CSF of BKV with a dominant rearranged regulatory region may be useful in the diagnosis of BKV meningoencephalitis secondary to BKV nephritis.

Genotypes of JC virus in East, Central and Southwest Europe

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.

JC virus as a marker of human migration to the Americas

JC virus is a ubiquitous human polyomavirus present in populations worldwide. Seven genotypes differing in DNA sequence by approximately 1-3% characterize three Old World population groups (African, European and Asian) as well as Oceania. It is possible to follow Old World populations into the New World by the JC virus genotypes they carried. The first population to settle in the Americas, the Native Americans, brought with them type 2A from northeast Asia. European settlers arriving after Columbus carried primarily type 1 and type 4. Africans brought by the slave trade carried type 3 and type 6.

Human polyomavirus JC variants in Papua New Guinea and Guam reflect ancient population settlement and viral evolution

The peopling of the Pacific was a complex sequence of events that is best reconstructed by reconciling insights from various disciplines. Here we analyze the human polyomavirus JC (JCV) in Highlanders of Papua New Guinea (PNG), in Austronesian-speaking Tolai people on the island of New Britain, and in nearby non-Austronesian-speaking Baining people. We also characterize JCV from the Chamorro of Guam, a Micronesian population. All JCV strains from PNG and Guam fall within the broad Asian group previously defined in the VP1 gene as Type 2 or Type 7, but the PNG strains were distinct from both genotypes. Among the Chamorro JCV samples, 8 strains (Guam-1) were like the Type 7 strains found in Southeast Asia, while nine strains (Guam-2) were distinct from both the mainland strains and most PNG strains. We identified three JCV variants within Papua New Guinea (PNG-1, PNG-2 and PNG-3), but none of the Southeast Asian (Type 7) strains. PNG-1 strains were present in all three populations (Highlanders and the Baining and Tolai of New Britain), but PNG-2 strains were restricted to the Highlanders. Their relative lack of DNA sequence variation suggests that they arose comparatively recently. The single PNG-3 strain, identified in an Austronesian-speaking Tolai individual, was closely related to the Chamorro variants (Guam-2), consistent with a common Austronesian ancestor. In PNG-2 variants a complex regulatory region mutation inserts a duplication into a nearby deletion, a change reminiscent of those seen in the brains of progressive multifocal leukoencephalopathy patients. This is the first instance of a complex JCV rearrangement circulating in a human population.

Use of denaturing gradient gel electrophoresis for human polyomavirus JC sequence analysis

Five genotypes of human polyomavirus JC (JCV) have been detected so far by nucleotide sequencing and by restriction fragment length polymorphism analysis. These genotypes are the result of geographically based virus evolution. However, interesting aspects of genotyping could involve both pathogenetic and diagnostic aspects. The product from amplification of JCV sequences, found in urine from 12 healthy individuals from different countries, have been analysed by denaturing gradient gel electrophoresis (DGGE) and by nucleotide sequencing. The aim of this study was to assess if the DGGE analysis could be used to study the variability of the JCV genome. The target sequence of this study was 233 bp long, within the gene coding for the VP1, known to contain several type-determining sites. Four DGGE patterns have been observed among our strains. Five strains, from African individuals, were of type 3 and exhibited the same electrophoretic pattern, clearly distinguishable from that of the type 1 strains detected in the urine from 6 European individuals. Five type 1 strains shared a similar DGGE pattern, slightly different from that of the sixth. A different pattern characterised as a type 2 strain was detected in the urine from a Peruvian individual. These results suggest that DGGE analysis could be used as a screening assay for choosing strains for nucleotide sequencing. The analysis of a fragment larger than the one used in this study could allow the identification of more types and subtypes.

Progressive multifocal leukoencephalopathy and JC virus genotypes in West African patients with acquired immunodeficiency syndrome: a pathologic and DNA sequence analysis of 4 cases

OBJECTIVE

Progressive multifocal leukoencephalopathy is caused by polyomavirus JC in immunosuppressed patients. JC virus genotypes are identified by sequence analysis of the viral genome. Despite the prevalence of acquired immunodeficiency syndrome in sub-Saharan Africa, few cases of progressive multifocal leukoencephalopathy have been reported from this region. Here we describe 4 African cases and provide an analysis of viral genotypes.

METHODS

Immunohistochemical staining by labeled streptavidin-biotin for capsid protein antigen was performed on all cases. Polymerase chain reaction amplification of viral genomic DNA was followed by direct cycle sequencing.

RESULTS

JC virus type 3 was identified in 2 cases, and type 6 was isolated in 1 case. The viral regulatory region from 1 case showed an uncommon rearrangement pattern.

CONCLUSIONS

Progressive multifocal leukoencephalopathy in West African patients with acquired immunodeficiency syndrome is caused by African genotypes of JC virus (types 3 and 6). The prevalence of disease in this autopsy series from sub-Saharan Africa (1.5%) was less than has been reported from Europe and the United States (4% to 10%) and may be partly due to biological differences in JC virus genotypes. Further studies will be needed to confirm this observation.

Molecular epidemiology of human polyomavirus JC in the Biaka Pygmies and Bantu of Central Africa

Polyomavirus JC (JCV) is ubiquitous in humans and causes a chronic demyelinating disease of the central nervous system, progressive multifocal leukoencephalopathy which is common in AIDS. JCV is excreted in urine of 30-70% of adults worldwide. Based on sequence analysis of JCV complete genomes or fragments thereof, JCV can be classified into geographically derived genotypes. Types 1 and 2 are of European and Asian origin respectively while Types 3 and 6 are African in origin. Type 4, a possible recombinant of European and African genotypes (1 and 3) is common in the USA. To delineate the JCV genotypes in an aboriginal African population, random urine samples were collected from the Biaka Pygmies and Bantu from the Central African Republic. There were 43 males and 25 females aged 4-55 years, with an average age of 26 years. After PCR amplification of JCV in urine, products were directly cycle sequenced. Five of 23 Pygmy adults (22%) and four of 20 Bantu adults (20%) were positive for JC viruria. DNA sequence analysis revealed JCV Type 3 (two), Type 6 (two) and one Type 1 variant in Biaka Pygmies. All the Bantu strains were Type 6. Type 3 and 6 strains of JCV are the predominant strains in central Africa. The presence of multiple subtypes of JCV in Biaka Pygmies may be a result of extensive interactions of Pygmies with their African tribal neighbors during their itinerant movements in the equatorial forest.

Archetype JC virus efficiently replicates in COS-7 cells, simian cells constitutively expressing simian virus 40 T antigen

JC polyomavirus (JCV), the causative agent of progressive multifocal leukoencephalopathy (PML), is ubiquitous in humans, infecting children asymptomatically and then persisting in the kidney. Renal JCV is not latent but replicates to excrete progeny in the urine. The renal-urinary JCV DNAs carry the archetype regulatory region that generates various rearranged regulatory regions occurring in JCVs derived from the brains of PML patients. Tissue cultures that support the efficient growth of archetype JCV have not been reported. We studied whether archetype JCV could replicate in COS-7 cells, simian cells transformed with an origin-defective mutant of simian virus 40 (SV40). Efficient JCV replication, as detected by a hemagglutination assay, was observed in cultures transfected with five of the six archetype DNAs. The progeny JCVs could be passaged to fresh COS-7 cells. However, when the parental cells of COS-7 not expressing T antigen were transfected with archetype JCV DNAs, no viral replication was detected, indicating that SV40 T antigen is essential for the growth of JCV in COS-7 cells. The archetype regulatory region was conserved during viral growth in COS-7 cells, although a small proportion of JCV DNAs underwent rearrangements outside the regulatory region. We then attempted to recover archetype JCV from urine by viral culture in COS-7 cells. Efficient JCV production was observed in COS-7 cells infected with five of the six JCV-positive urine samples examined. Thus, COS-7 cells should be of use not only for the production of archetype JCV on a large scale but also for the isolation of archetype JCV from urine.

Tubulointerstitial nephritis due to a mutant polyomavirus BK virus strain, BKV(Cin), causing end-stage renal disease

A renal biopsy from a 36-year-old man with AIDS showed a severe tubulointerstitial nephritis with intranuclear inclusions in epithelial cells. Electron microscopy revealed the characteristic findings of a polyomavirus (PyV) infection, and immunofluorescence indicated the presence of BK virus (BKV) antigen. Inoculation of rhesus monkey kidney cell cultures both with urine and with buffy coat blood cells resulted in a cytopathic response which was subsequently confirmed to be due to BKV. Further characterization of the viral DNA from the kidney by PCR amplification and Southern blot analysis with PyV and strain-specific primers and probes indicated that the virus was closely related to the BK(Dun) strain but different in its apparent sequence arrangement. Subsequent cycle sequencing showed a dinucleotide mutation of TG-->AA which substitutes hydrophilic Gln for hydrophobic Leu in a sequence homologous to an origin DNA-binding domain of simian virus 40 T antigen. It is suggested that the mutation and a coding region rearrangement of this strain of BKV designated BKV(Cin) has the potential to alter viral DNA replication and enhance pathogenicity.

Rearrangements of archetypal regulatory regions in JC virus genomes from urine

The regulatory region of progressive multifocal leukoencephalopathy-type JC virus (JCV) is rearranged in each host by a process of deletion and duplication. Of the more than 40 that have been examined, no two regulatory regions have been rearranged identically in the brain. The substrate for this rearrangement appears to be a highly stable archetypal regulatory region excreted in the urine. Its role as the transmissible form of the virus, although inferred, has never been proven. We have now amplified by PCR and cycle-sequenced the regulatory regions from 48 urinary strains of the virus. We find that the urinary form of the regulatory region is not entirely stable. Short deletions and duplications in the range of 2-16 bp were observed in seven of these strains. One of these, an inverted repeat, is a pattern of rearrangement not yet found in the brain. Two others (#208 and 230) showed a 2-bp deletion at position nos. 221 and 222, and an unusual mutation at position no. 219. These two urines were collected in different states of the USA at different times and analysed months apart. It is very unlikely that these unusual changes represent sample contamination or that they arose independently. This finding indicates that archetypal forms of the JCV regulatory region are infectious, despite their relative inactivity in tissue culture. While changes in the archetypal structure can be found, it is clear that rearrangements in the kidney are rare or rarely infectious.

JC virus excreted by multiple sclerosis patients and paired controls from Hungary

JC virus (JCV), a human polyomavirus, is the agent of the demyelinating disease progressive multifocal leukoencephalopathy (PML). JCV exists in four main genotypes in the USA. Type 1, including subtypes Type 1A and Type 1B, makes up about 64% of strains in the USA and is thought to be of European origin. Type 2 is found in Asia, and Type 3 in Africa. A fourth type is found only in the USA. In general, these genotypes differ in 1-2.5% of their DNA sequence. Thirty MS patients and 30 paired controls from Budapest were studied. The clinical course of MS was mainly secondary progressive, and patients were stable at the time of testing. Most of the controls were relatives of the probands: a spouse, parent, or child. Overall, 25 of 60 (42%) of the urines tested positive for JCV by PCR. These included 13 of 30 MS patients, and 12 of 30 controls. Genotyping in the VPI gene showed all 25 JCV strains to be Type 1. Among the MS patients, seven were Type 1A and six were Type 1B. Among the controls, nine were Type 1A and three were Type 1B. In five pairs of MS patients and controls, both were positive for JCV by PCR. Two of these were husband/wife pairs of which one pair was matched for subtype (both Type 1A), and the other was not. Two of them were mother/daughter pairs, and both were matched for subtype (both Type 1B). These findings demonstrate that JCV Type 1 predominates among Hungarians, and suggest that parent/child pairs can be used to trace JCV transmission within the MS family.

Asian genotypes of JC virus in Native Americans and in a Pacific Island population: markers of viral evolution and human migration

The human polyomavirus JC (JCV) causes the central nervous system demyelinating disease progressive multifocal leukoencephalopathy. Previously, we showed that 40% of Caucasians in the United States excrete JCV in the urine as detected by PCR. We have now studied 68 Navaho from New Mexico, 25 Flathead from Montana, and 29 Chamorro from Guam. By using PCR amplification of a fragment of the VP1 gene, JCV DNA was detected in the urine of 45 (66%) Navaho, 14 (56%) Flathead, and 20 (69%) Chamorro. Genotyping of viral DNAs in these cohorts by cycle sequencing showed predominantly type 2 (Asian), rather than type 1 (European). Type 1 is the major type in the United States and Hungary. Type 2 can be further subdivided into 2A, 2B, and 2C. Type 2A is found in China and Japan. Type 2B is a subtype related to the East Asian type, and is now found in Europe and the United States. The large majority (56-89%) of strains excreted by Native Americans and Pacific Islanders were the type 2A subtype, consistent with the origin of these strains in Asia. These findings indicate that JCV infection of Native Americans predates contact with Europeans, and likely predates migration of Amerind ancestors across the Bering land bridge around 12,000-30,000 years ago. If JCV had already differentiated into stable modern genotypes and subtypes prior to first settlement, the origin of JCV in humans may date from 50,000 to 100,000 years ago or more. We conclude that JCV may have coevolved with the human species, and that it provides a convenient marker for human migrations in both prehistoric and modern times.

Typing of urinary JC virus DNA offers a novel means of tracing human migrations

Although polyomavirus JC (JCV) is the proven pathogen of progressive multifocal leukoencephalopathy, the fatal demyelinating disease, this virus is ubiquitous as a usually harmless symbiote among human beings. JCV propagates in the adult kidney and excretes its progeny in urine, from which JCV DNA can readily be recovered. The main mode of transmission of JCV is from parents to children through long cohabitation. In this study, we collected a substantial number of urine samples from native inhabitants of 34 countries in Europe, Africa, and Asia. A 610-bp segment of JCV DNA was amplified from each urine sample, and its DNA sequence was determined. A worldwide phylogenetic tree subsequently constructed revealed the presence of nine subtypes including minor ones. Five subtypes (EU, Af2, B1, SC, and CY) occupied rather large territories that overlapped with each other at their boundaries. The entire Europe, northern Africa, and western Asia were the domain of EU, whereas the domain of Af2 included nearly all of Africa and southwestern Asia all the way to the northeastern edge of India. Partially overlapping domains in Asia were occupied by subtypes B1, SC, and CY. Of particular interest was the recovery of JCV subtypes in a pocket or pockets that were separated by great geographic distances from the main domains of those subtypes. Certain of these pockets can readily be explained by recent migrations of human populations carrying these subtypes. Overall, it appears that JCV genotyping promises to reveal previously unknown human migration routes: ancient as well as recent.

Detection of archetype and rearranged variants of JC virus in multiple tissues from a pediatric PML patient

JC virus (JCV) establishes persistent infections in its human host, and in some immunocompromised individuals, the virus causes the fatal brain disease progressive multifocal leukoencephalopathy (PML). Two forms of the virus, archetype and rearranged, have been isolated, with the latter being derived from the archetype form by deletion and duplication of sequences within the viral transcriptional control region (TCR). We have used the PCR technique to amplify JCV TCR sequences present within multiple tissues of a pediatric PML patient and have cloned and sequenced the PCR products. Archetype JCV was readily detected in kidney tissue; this form of JCV was also identified for the first time in brain and lymph node tissue by employing archetype-specific PCR primers. In addition, several archetype-like variants containing small deletions within their regulatory regions were isolated from cardiac muscle and lung. Different, but related rearranged forms were detected in most of the tissue examined. Each of the rearranged TCRs lacked portions of a 66 base pair (bp) region found within the archetype promoter-enhancer but retained a 23 bp region that is deleted in the prototype (Mad 1) rearranged form of JCV. Although several rearranged forms of JCV were identified in this patient, the TCRs could be assigned to one of two groups based upon the deletion boundaries generated during the adaptation from archetype to rearranged JCV. This study is the first to characterize multiple JCV variants present in different tissues from a patient likely to have succumbed to PML during a primary infection.

Persistent JC virus (JCV) infection is demonstrated by continuous shedding of the same JCV strains

The polyomavirus JC virus (JCV), the causative agent of progressive multifocal leukoencephalopathy, is ubiquitous in the human population, infecting children asymptomatically. JCV is often detected in normal renal tissue and in the urine of healthy individuals. We demonstrate that renal JCV represents that which persists after primary infection.