Multiple origins of the complementary defective genomes of RF and origin proximal sequences of GS, two human papovavirus isolates

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.

Conserved archetypal configuration of the transcriptional control region during the course of BK polyomavirus evolution

BK polyomavirus (BKV) is widespread among humans, asymptomatically infecting children and then persisting in renal tissue. The transcriptional control region (TCR) of the BKV genome is variable among clinical isolates. Thus, archetypal TCRs with a common basic configuration generally occur in BKV isolates from the urine of immunocompromised patients, but rearranged TCRs that possibly arise from the archetypal configuration have also been detected in clinical specimens. To examine the hypothesis that archetypal strains represent wild-type strains circulating in the human population (the archetype hypothesis), we analysed 145 complete viral genomes amplified directly from the urine of non-immunocompromised individuals worldwide. These genomes included 82, three, two and 58 sequences classified as belonging to subtypes I, II, III and IV, respectively. Rearranged TCRs with long duplications or deletions were detected from two subtype I and two subtype IV genomes, but not from the other 141 genomes (thus, the TCRs of these genomes were judged to be archetypal). The variations in the archetypal TCRs were nucleotide substitutions and single-nucleotide deletions, most of which were unique to particular subtypes or subgroups. We confirmed that the four complete BKV genomes with rearranged TCRs did not form a unique lineage on a phylogenetic tree. Collectively, the findings demonstrate that the archetypal TCR configuration has been conserved during the evolution of BKV, providing support for the archetype hypothesis. Additionally, we suggest that 'archetype' should be used as a conceptual term that denotes a prototypical structure that can generate various rearranged TCRs during viral growth in vivo and in vitro.

Noncoding control region of naturally occurring BK virus variants: sequence comparison and functional analysis

The human polyomavirus BK (BKV) has a proven oncogenic potential, but its contribution to tumorigenesis under natural conditions remains undetermined. As for other primate polyomaviruses, the approximately 5.2 kbp double-stranded circular genome of BKV has three functional regions: the coding regions for the two early (T, t antigens) and four late (agno, capsid proteins; VP1-3) genes separated by a noncoding control region (NCCR). The NCCR contains the origin of replication as well as a promoter/enhancer with a mosaic of cis-acting elements involved in the regulation of both early and late transcription. Since the original isolation of BKV in 1971, a number of other strains have been identified. Most strains reveal a strong sequence conservation in the protein coding regions of the genome, while the NCCR exhibits considerable variation between different BKV isolates. This variation is due to deletions, duplications, and rearrangements of a basic set of sequence blocks. Comparative studies have proven that the anatomy of the NCCR may determine the transcriptional activities governed by the promoter/enhancer, the host cell tropism and permissivity, as well as the oncogenic potential of a given BKV strain. In most cases, however, the NCCR sequence of new isolates was determined after the virus had been passaged several times in more or less arbitrarily chosen cell cultures, a process known to predispose for NCCR rearrangements. Following the development of the polymerase chain reaction (PCR), it has become feasible to obtain naturally occurring BKV NCCRs, and their sequences, in samples taken directly from infected human individuals. Hence, the biological significance of BKV NCCR variation may be studied without prior propagation of the virus in cell culture. Such variation has general interest, because the BKV NCCRs represent typical mammalian promoter/enhancers, with a large number of binding motifs for cellular transacting factors, which can be conveniently handled for experimental purposes. This communication reviews the naturally occurring BKV NCCR variants, isolated and sequenced directly from human samples, that have been reported so far. The sequences of the different NCCRs are compared and analyzed for the presence of proven and putative cellular transcription factor binding sites. Differences in biological properties between BKV variants are discussed in light of their aberrant NCCR anatomies and the potentially modifying influence of transacting factors.

Persistence of the SV40 early region without expression in permissive simian cells

SV40 containing recombinant vectors were introduced into permissive simian, non-permissive rodent and semi-permissive human cell lines, and assayed for transformation. All mouse and human cell clones expressed T-antigen (T-Ag) and were morphologically transformed when they contained only the wt T-Ag gene (E-SV40) or the entire wt viral genome with an interrupted late region. However, of 63 simian clones with these recombinant vectors, none became morphologically transformed and T-Ag containing cells were rare or absent. Nearly all simian cell lines made either no detectable early SV40 RNA or only small amounts of viral RNA but contained viral DNA restriction fragments similar to those in the original recombinant vectors. Functional T-Ag genes were recoverable from several cell clones and used to regenerate infectious virus. Hence, T-Ag gene expression had been suppressed. We found two conditions where T-Ag expression was activated. In a BSC-1 cell line containing E-SV40 DNA, subsequent introduction of a vector with a functional viral late coding region (L-SV40) resulted in the appearance of T-Ag and transformation. These findings suggest that L-SV40 sequences activate or enhance T-Ag expression and that this activation requires a functional Vpl gene. We found also, that vectors with E-SV40 DNA from the bipartite variant EL-SV40 consistently transformed simian CV-1 cells. Transformation was shown to be effected by the multiple alterations present in the regulatory region of this variant.

Reconstitution of wild type viral DNA in simian cells transfected with early and late SV40 defective genomes

The DNAs of polyomaviruses ordinarily exist as a single circular molecule of approximately 5000 base pairs. Variants of SV40, BKV and JCV have been described which contain two complementing defective DNA molecules. These defectives, which form a bipartite genome structure, contain either the viral early region or the late region. The defectives have the unique property of being able to tolerate variable sized reiterations of regulatory and terminus region sequences, and portions of the coding region. They can also exchange coding region sequences with other polyomaviruses. It has been suggested that the bipartite genome structure might be a stage in the evolution of polyomaviruses which can uniquely sustain genome and sequence diversity. However, it is not known if the regulatory and terminus region sequences are highly mutable. Also, it is not known if the bipartite genome structure is reversible and what the conditions might be which would favor restoration of the monomolecular genome structure. We addressed the first question by sequencing the reiterated regulatory and terminus regions of E- and L-SV40 DNAs. This revealed a large number of mutations in the regulatory regions of the defective genomes, including deletions, insertions, rearrangements and base substitutions. We also detected insertions and base substitutions in the T-antigen gene. We addressed the second question by introducing into permissive simian cells, E- and L-SV40 genomes which had been engineered to contain only a single regulatory region. Analysis of viral DNA from transfected cells demonstrated recombined genomes containing a wild type monomolecular DNA structure. However, the complete defectives, containing reiterated regulatory regions, could often compete away the wild type genomes. The recombinant monomolecular genomes were isolated, cloned and found to be infectious. All of the DNA alterations identified in one of the regulatory regions of E-SV40 DNA were present in the recombinant monomolecular genomes. These and other findings indicate that the bipartite genome state can sustain many mutations which wtSV40 cannot directly sustain. However, the mutations can later be introduced into the wild type genomes when the E- and L-SV40 DNAs recombine to generate a new monomolecular genome structure.

Genomic typing of BK virus in clinical specimens by direct sequencing of polymerase chain reaction products

Two hundred and twelve urine specimens, from several clinical groups, were examined for BK virus (BKV) using the polymerase chain reaction (PCR) to detect the VP1 region of BKV DNA. Positive results were obtained on 14 specimens from 44 post-transplant patients (31.8%), 10 specimens from 39 pregnant women (25.6%), and 5 specimens from 100 children (5%) but not on any specimens from 29 laboratory staff. Twenty-eight of the amplified BKV genomes, 19 from urine specimens, eight from culture fluid of inoculated tissue, and also one from a throat washing were directly sequenced from single-stranded templates immobilized via a biotinylated primer; it was possible to assign all to one of the four subtypes of BKV which had previously been identified on the basis of variation in nucleotide sequence of the VP1 region. Serological subgroup classification correlated with the genomic subtyping results in 21 of the isolates. The distribution of the BKV subtypes and the clinical status of the infected individuals are discussed.

Host range analysis of a chimeric simian virus 40 genome containing the BKV capsid genes

Simian virus 40 (SV40) propagates poorly in cells from human embryonic kidney (HEK) and human fetal fibroblasts (HFF) while BK virus grows well in many human cell types. It has been suggested that sequences within the SV40 late region but not within the BKV late region may act to inhibit growth of virus in HEK and HFF cells. In order to test this and to identify a late region host range function, we have replaced the late region of wtSV40 DNA with the late region of RFV (a variant of BKV) to produce an intermolecular hybrid or chimera. The constructed SV40/RFV chimeric genome contained approx. 5900 base pairs, more than 650 base pairs greater than wtSV40. Nevertheless, when introduced by transfection the chimera appeared to be infectious. Three chimeric genomes were recovered from infected cells and all contained deletions of nearly 600 base pairs, exclusively at the region of the 3' terminal junction. Since all three chimeras propagated in human HFF and HEK cells, the RFV late region and not the RFV regulatory region possesses a host range function required for growth in human cells. Analysis of T-antigen gene expression suggests that the replacement of the SV40 late region with the BKV late region leads to full expression of the SV40 early region in human cells. Two chimeras exhibited a BKV-like host range and the third exhibited both a BKV and an SV40-like host range. We determined precisely which sequences were deleted in each chimera and we exchanged 3' terminal junction fragments containing these deletions, between two chimeras with different host ranges. From these experiments we demonstrated that: (1) The 3' terminus of the SV40 large T-antigen gene is required for growth of SV40/RFV in TC-7 and CV-1 simian cells but not for growth in human cells; (2) while the SV40 late region is refractory for growth in human cells, the RFV late region is not refractory for growth in simian cells; (3) the 3' terminus of the RFV T-antigen gene is not required for growth in human cells. The results of the 3' terminal junction exchanges and studies of early gene expression also demonstrate that BKV and SV40 can penetrate human and simian cells, even when they failed to grow in one cell type.

Prevalence of the archetypal regulatory region and sequence polymorphisms in nonpassaged BK virus variants

Since the first isolation and characterization of BK virus (BKV), a number of BKV variants which differ in genomic structure or antigenic determinants have been described. The regulatory region, in particular, the enhancer elements, show the most divergent sequences among different isolates. The structural organization of a putative ancestral prototype or archetype, from which all of the variants are probably derived, has been proposed. By sequencing the regulatory regions of 13 different isolates from the urine of bone marrow transplant recipients, we determined the structures and sequences of BKV variants diffused in the human population. The enhancer region was amplified by polymerase chain reaction to avoid passage in culture, and the product was directly sequenced. The structure most frequently observed is in agreement with the postulated archetype, containing a single enhancer element with no repeats. By sequence analysis we identified four hot spots of nucleotide variation. These variations are consistent with the existence of two consensus sequences. One sequence motif, observed in about 85% of the isolates, is referred to as the archetypal BKV, while a second motif, observed in the remaining 15% of the variants, is highly reminiscent of the AS strain.

Recurring theme of changes in the transcriptional control region of BK virus during adaptation to cell culture

BK virus, when cloned directly from human urine, shows no amplification in the transcriptional control region, unlike cell culture-passaged strains, but possesses an additional sequence element. To confirm our proposal that this represents the archetypal in vivo form of the virus, we passaged this BK virus through cell culture. Changes in the transcriptional control region occurred as early as the first passage and were characterized in all cases by a deletion followed by amplification events.

Regulatory DNA sequence conserved in the course of BK virus evolution

Within the genome of human polyomavirus BK (BKV), there exists a noncoding regulatory region toward the late region side of the origin of DNA replication. In most BKV strains isolated by viral culture, this regulatory region contains tandem repeats varying in size. Recently, however, several laboratories isolated new BKV strains (designated as archetypal strains) lacking such repeat sequences. To examine the genetic relationship between archetypal strains, a phylogenetic tree was constructed for seven BKV strains, including three archetypal strains, from DNA sequence data on the late genes, those for leader protein (agnoprotein), and those for structural proteins (VP1, VP2, and VP3). For three strains data previously reported were used, whereas for the others sequences were determined in this study. From total numbers of nucleotide substitutions in each pair of strains, a phylogenetic tree was constructed by the unweighted pair-group method. The phylogenetic tree obtained reveals that BKV strains containing the archetypal regulatory region do not constitute a cluster of closely related strains and that these strains, together with those carrying the major part of the archetypal regulatory region, are widespread in the BKV population. This finding suggests that the basic structure of the archetypal regulatory region has been conserved in the course of BKV evolution.

Antigenic and transforming properties of the DB strain of the human polyomavirus BK virus

The analysis of the antigenic and transforming properties of the DB strain of the human polyomavirus BK Virus [BKV(DB)] is presented. Two genomes were molecularly cloned from a single virus preparation and were shown to represent viable virus; one clone [pBKV(DB)dl82] contained an 82 nucleotide deletion in the regulatory region relative to the second clone [pBKV(DB)]; pBKV(DB)dl82 demonstrated enhanced lytic and transforming activities relative to pBKV(DB). BKV(DB) is antigenically distinct from the prototype Gardner strain of BK Virus, and 50 to 60% of the population display serological evidence of BKV(DB) infection. Implications of the existence of antigenic variants on estimation of BK virus prevalence in the population are discussed.

Identification of HeLa cell nuclear factors that bind to and activate the early promoter of human polyomavirus BK in vitro

Human polyomavirus BK (BKV), an oncogenic DNA virus, differs from other papovaviruses in the organization of the regulatory region and in tissue tropism for kidney cells. The noncoding regulatory region of the viral genome in prototype strains includes three 68-base-pair (bp) repeats, each containing a number of potential regulatory elements. Some of these signals are unique to human papovaviruses, and others are homologous to those identified in many viral and cellular genes. We evaluated the contribution of individual 68-bp repeats to the initiation of transcription from the early promoter in a HeLa cell extract and identified cis-acting elements to which human cellular factors bind to activate transcription. The early promoter with only one copy of the 68-bp repeat could accurately initiate transcription in vitro, but additional copies were required for its stimulation. DNA-binding assays and DNase I protection experiments identified six domains in the regulatory region protected by human cellular factors. Two of these footprints were located within the proximal and distal 68-bp repeats, and one was located at the late side of the repeats. These footprints were centered over a TGGA(N)5-6GCCA core and were produced by a protein of the nuclear factor 1 (NF-1) family. This protein is either identical or similar to that which binds to the high-affinity site at the origin of adenovirus DNA replication. Three other domains, two at the junctions of the 68-bp repeats and one in the late side of the repeats, were partially protected by proteins with AP-1- and Sp-1-like activities. Transcription initiation from the early promoter was drastically reduced when a complete 68-bp repeat or the NF-1 binding site was used as a competitor in the in vitro assay. However, a point mutation within the NF-1 binding site, which reduced NF-1 binding in vitro to a level comparable to that of nonspecific DNA, also eliminated its ability to compete with early transcription. The murine homolog of the AP-1 binding site had a modest effect on in vitro transcription. Our results suggest that, among the multiple HeLa cell nuclear factors, NF-1 acts as a major activator of the early promoter in vitro.

Identification of HeLa cell nuclear factors that bind to and activate the early promoter of human polyomavirus BK in vitro

Human polyomavirus BK (BKV), an oncogenic DNA virus, differs from other papovaviruses in the organization of the regulatory region and in tissue tropism for kidney cells. The noncoding regulatory region of the viral genome in prototype strains includes three 68-base-pair (bp) repeats, each containing a number of potential regulatory elements. Some of these signals are unique to human papovaviruses, and others are homologous to those identified in many viral and cellular genes. We evaluated the contribution of individual 68-bp repeats to the initiation of transcription from the early promoter in a HeLa cell extract and identified cis-acting elements to which human cellular factors bind to activate transcription. The early promoter with only one copy of the 68-bp repeat could accurately initiate transcription in vitro, but additional copies were required for its stimulation. DNA-binding assays and DNase I protection experiments identified six domains in the regulatory region protected by human cellular factors. Two of these footprints were located within the proximal and distal 68-bp repeats, and one was located at the late side of the repeats. These footprints were centered over a TGGA(N)5-6GCCA core and were produced by a protein of the nuclear factor 1 (NF-1) family. This protein is either identical or similar to that which binds to the high-affinity site at the origin of adenovirus DNA replication. Three other domains, two at the junctions of the 68-bp repeats and one in the late side of the repeats, were partially protected by proteins with AP-1- and Sp-1-like activities. Transcription initiation from the early promoter was drastically reduced when a complete 68-bp repeat or the NF-1 binding site was used as a competitor in the in vitro assay. However, a point mutation within the NF-1 binding site, which reduced NF-1 binding in vitro to a level comparable to that of nonspecific DNA, also eliminated its ability to compete with early transcription. The murine homolog of the AP-1 binding site had a modest effect on in vitro transcription. Our results suggest that, among the multiple HeLa cell nuclear factors, NF-1 acts as a major activator of the early promoter in vitro.

Growth efficiency of naturally occurring BK virus variants in vivo and in vitro

We molecularly cloned a number of BK virus (BKV) DNAs from urine samples collected from a patient with systemic lupus erythematosus undergoing immunosuppressive therapy. On the basis of the structure of the noncoding regulatory region, cloned viral DNAs were classified into a major group and several minor groups. The major group contained a single 68-base-pair (bp) promoter-enhancer element and a 63-bp sequence identified in the genomes of many BKV strains. Most of the minor groups retained a variety of duplications within the transcriptional control region and the origin of DNA replication. We assayed various cloned viral DNAs for the capacity to induce viral growth in transfected human embryonic kidney cells. While major viral DNAs induced slow viral replication, a minor viral DNA retaining partial duplication of the 68-bp element induced rapid viral growth. We concluded that reiteration of the promoter-enhancer element, which is required for efficient growth of BKV in cell culture, is not advantageous for replication of BKV in natural hosts.

Absence of BK virus sequences in transformed hamster cells transfected by human tumor DNA

In an attempt to gain insight into the mechanism of oncogenic transformation by BK virus (BKV), a human papovavirus, we have probed for BKV sequences in transformed hamster cells in which oncogenic transformation had occurred as a result of transfection by human tumor DNA positive for BKV sequences. Even though the sources of the transfecting DNA contained BKV sequences, the transformed hamster cells which arose from the transfection for the most part did not retain BKV sequences. In only one barely detectable case was BKV-specific DNA found associated with chromosomal DNA, and in only a small minority of the transformed cells was BKV DNA detected in the Hirt supernatant, indicating an episomal configuration. Even in these few cases where BKV sequences were present in an episomal form, altered migration on gels of some BKV-positive bands (compared to bands derived from cloned viral DNA) suggested deletions and rearrangements of BKV DNA. We employed several different probe methodologies for these studies, including nick-translation, random primer and a non-isotopic biotinylated probe which gave a sensitivity that could detect better than 0.01 copy of viral genome per diploid cell. We conclude that transformation by transfection with human tumor DNA does not require persistence of the BKV viral genome, suggesting that either BKV virus was irrelevant to original oncogenesis, in analogy with models proposed by others for herpesvirus oncogenesis.

Nucleotide sequence of the human polyomavirus AS virus, an antigenic variant of BK virus

The complete DNA sequence of the human polyomavirus AS virus (ASV) is presented. Although ASV can be differentiated antigenically from the other human polyomaviruses (BK and JC viruses), it shares 94.9% homology at the nucleotide level with the Dunlop strain of BK virus. Differences found in ASV relative to BK virus include the absence of tandem repeats in its regulatory region, the deletion of 32 nucleotides in the late mRNA leader region (altering the initiation codon for the agnoprotein), the presence of a cluster of base pair substitutions within the coding region of the major capsid protein, VP1, and the absence of 4 amino acids in the carboxy-terminal region of the early protein, T antigen. The 43 nucleotides deleted in the Dunlop strain of BK virus relative to the Gardner prototype strain of BK virus are present in ASV. Possible reasons for the distinct antigenicity of the ASV capsid, given the high degree of nucleotide homology with BK virus, are discussed. To reflect the high degree of sequence homology between ASV and BK virus, we suggest ASV be renamed BKV(AS).

Transformation of human cells by a polyomavirus containing complementing JCV and RFV genomes

Molecularly cloned viral DNA from late RFV (L-RFV) and early JCV (E-JCV) were transfected into human fetal brain (HFB) cells and complementation was demonstrated. A new infectious virus (E-JCV/L-RFV) was produced. Infection resulted in partial transformation of HFB and human embryonic kidney cells. No transformation was observed with EL-JCV or wtJCV. The transformants contained T-antigen and had a lifespan similar to SV40-transformed human cells but failed to express some phenotypes of transformation. All transformants contained E-JCV viral DNA, usually both integrated and episomal. Although no L-RFV DNA was present in the transformants, L-RFV appears to play a role in the initiation of transformation.

Isolation and characterization of a variant of human papillomavirus type 11 from a nasal inverting (Schneiderian) papilloma

We have previously reported the presence of a variant of human papillomavirus (HPV) type 11 in a nasal inverting papilloma [Respler et al., 1987]. In the present study, we have cloned molecularly the DNA of this variant at its unique restriction enzyme Bam HI site into lambda BF101 phage. Restriction enzyme mapping and DNA sequencing revealed that the genome of this virus contained an extra 531 base pair (bp) which was the repeat of most of the noncoding region (ncr) of HPV 11. Insertion of transcriptional control elements, including the repeated sequence, in front of the chloramphenicol acetyltransferase (CAT) gene resulted in a 5- to 30-fold increase in expression in transfected cells, as compared to the constructs containing a single ncr of HPV 11. This increased expression was due to enhanced levels of CAT RNA the synthesis of which is initiated by the viral promoter element.

Structure and function of the transcriptional control region of nonpassaged BK virus

We compared the nucleotide sequence in the transcriptional control region of BK virus isolates cloned directly from human urine (BK-WW) with that of prototype BK virus. BK-WW was found to have a 63-base-pair insertion and only one of the 68-base-pair enhancer repeat elements. In transient expression assays, BK-WW enhancer showed approximately one-half the activity given by the prototype enhancer.

Analysis of the early regulatory region of the human papovavirus BK

BKV is a human papovavirus which latently infects a majority of the world population and whose DNA has been found in human tumor tissue. Along with simian virus 40 (SV40) and JCV, it is one of several highly homologous polyomaviruses which display distinct host ranges, tissue tropisms, and transformation potentials. Determination of these properties is thought to reside, in part, in the noncoding regulatory region of these viruses. We have studied the regulation of gene expression by the early promoter and enhancer of BKV. Our results show that the early promoter of BKV consists of elements found both to the early side of and within the proximal 18 bp of the first enhancer element itself. At least one BKV regulatory element appears to be downstream of the mRNA start sites. The BKV enhancer consists of two different types of elements, three direct repeats, and an element (denoted "c") found in the 30 bp to the late side of the distal repeat. When used with the BKV promoter the enhancer repeat elements were found to be redundant, optimal promoter activity requiring only two of the three repeats plus the c element. Using the heterologous SV40 promoter the optimal BKV enhancer consisted of either three repeats or two repeats plus the c element. Subfragments of the enhancer region were capable of partial activation of homologous and heterologous promoters. We conclude that the regulation of BKV early gene expression involves novel elements arranged in ways not previously described in other papovaviruses.

Complementation between SV40 and RFV defectives and acquisition of SV40 origins by late RFV genomes

EL SV40 and RFV are variants of SV40 and BKV which contain bipartite or dual genomes. One molecule contains all the early viral sequences (E-SV40, E-RFV) and the other all the late viral sequences (L-SV40, L-RFV). Early and late genomes complement one another during productive infection. Experiments were designed to determine if E-genomes of one virus could complement L-genomes of another virus. If complementation did occur, intermolecular recombination events which lead to a more efficient infection or an altered host range might occur, and the sequences involved could than be identified. Two combinations were generated by direct transfection of BSC-1 green monkey cells. E-RFV and L-SV40 DNA complementation resulted in hybrid virus growth and cell killing. The hybrid demonstrated a narrow host range. Following serial passage, some E-RFV genomes contained SV40 origin region sequences but these recombinants did not overgrow prototype E-RFV genomes, even after many virus passages. In addition, no significant alterations in host range could be detected. Complementation between E-SV40 and L-RFV yielded a virus with a relatively wider host range. Virus growth and cell killing appeared very slowly at first. However, with each passage of E-SV40/L-RFV, cell killing occurred progressively more rapidly, until passage 7 when it became extensive in 7 days rather than 6-8 weeks. Infected cells contained 10-20 times more E-SV40 than L-RFV DNA during the first passage. However, by passage 7, both genomes were equally represented. During serial passage, L-RFV DNA acquired SV40 sequences from around the origin and the terminus of replication, such that recombinant (r) L-RFV genomes contained three SV40 origins [corrected] (including the 72-bp repeat) and 2 termini, and prototype L-RFV DNA was lost. E-SV40/rL-RFV demonstrated an altered host range propagating in some cell lines which did not support E-SV40/L-RFV growth. Both the host range change and the increased growth of rL-RFV genomes were shown to be at least partly caused by the acquisition of the SV40 sequences.

Evolutionary changes of transcriptional control region in a minute-plaque viable deletion mutant of BK virus

Two plaque morphology BK virus (BKV) mutants (pm526 and pm527) rescued from a hamster pineocytoma cell line Pc13 were characterized and compared with a similarly rescued and previously characterized mutant (pm522), its derivatives (tr530, tr531, and tr532), and the wild type (501) for their biological activities and for the structures of their transcriptional control regions. The two mutants grew somewhat more slowly in human embryonic kidney cells but transformed rat 3Y1 cells more efficiently than did the wild-type BKV. BKV pm526 formed minute plaques and had the shortest transcriptional control region, having only one 68-base-pair element, which is triplicated in the wild-type BKV. BKV pm526 was unstable during repeated replication in human embryonic kidney cells and yielded large-plaque viruses with longer HindIII C segments encompassing the BKV DNA replication origin. Comparison of nucleotide sequences of the transcriptional control regions among the mutants and the wild type showed that pm526 is a parent virus, from which all the other mutants had evolved, and that the evolutionary changes of the plaque size, from minute to small to large, were due to duplications of a certain segment containing the adenovirus E1A enhancer core or the simian virus 40 enhancer core found in the BKV 68-base-pair element. The activities to enhance early transcription, as measured by the ability to direct the synthesis of chloramphenicol acetyltransferase, approximately paralleled the plaque size. The duplication containing the adenovirus E1A enhancer core did not affect the transforming capacity of the parent virus, but the duplication including the simian virus 40 enhancer core significantly lowered the transforming capacity for rat cells.

Transformation of primary human embryonic kidney cells to anchorage independence by a combination of BK virus DNA and the Harvey-ras oncogene

Primary human embryonic kidney (HEK) cells were transformed by a focus assay with BK virus (BKV) DNA molecularly cloned at its unique EcoRI site. Both viral DNA sequences and viral tumor antigens were present and expressed in all the foci that we examined. However, cells isolated from foci were incapable of growth in soft agar. We then examined the transformation of HEK cells after their transfection with a combination of BKV DNA and either the normal or the activated form of the human Ha-ras oncogene (EJ c-Ha-ras-1). Only the cells transfected with a combination of BKV DNA and the activated form of Ha-ras were capable of growth in soft agar. Both BKV and Ha-ras DNAs were present in the transformed colonies. BKV tumor antigens and the Ha-ras p21 protein were also expressed.

DNA rearrangement in the control region for early transcription in a human polyomavirus JC host range mutant capable of growing in human embryonic kidney cells

A human polyomavirus JC virus (JCV) host range mutant (JC-HEK) can grow in human embryonic kidney cells, whereas the brain cell-tropic wild-type JCV strain (Mad-1) cannot; JC-HEK contains two complementing defective DNAs, JC-HEK-A and JC-HEK-B. We determined the nucleotide sequence of the putative transcriptional control region of JC-HEK-A DNA that can induce T-antigen synthesis in human embryonic kidney cells and compared it with the sequence of JCV Mad-1 DNA. The JC-HEK-A control region was found to have a complex DNA rearrangement, namely, a partial local duplication of a noncoding region generating two extra replication origins and translocation of segments from the large-T-antigen gene (415 base pairs) and the VP-1 gene (78 base pairs). In the rearranged segment, JC-HEK-A had seven sets of the sequence 5'TGGA(T)A(T)A(T)3', which is found in the simian virus 40 enhancer core, whereas JCV Mad-1 had only one set in its control region. JC-HEK-A also had a 5'TGGAAGTGTAA3' sequence resembling the adenovirus early region 1A enhancer core sequence 5'AGGAAGTGAA3'. Because the viral enhancer is host discriminatory and because another human polyomavirus, BK virus, that grows well in human embryonic kidney cells has these signals in its control region, it is likely that some of the newly acquired signals in JC-HEK play an important role in the altered host range of JCV.

Isolation of a papovavirus with a bipartite genome containing unlinked SV40 and BKV sequences

Wild-type (wt) BK virus was introduced into permissive BSC-1 cells along with either early or late defective SV40 genomes. The defectives contained all of the late (L-SV40) or all of the early (E-SV40) coding sequences. Persistently infected (PI) BSC-1 cultures were established and contained wt BKV DNA and E- or L-SV40 DNA in Hirt supernatants. Each of the BKV/SV40 combinations could be serially passed in BSC-1 cells. Also, DNase I digestion of virus stocks from BKV/E-SV40 infections did not eliminate E-SV40. This suggested that (1) E-SV40 genomes could be packaged in BKV capsids and (2) BKV T antigen acted to stimulate the growth of L-SV40 genomes. During continuous culture of PI BSC-1 cells containing BKV and L-SV40, wt BKV genomes were lost and replaced by a BKV defective. The BKV defective (E-BKV) contained a deletion in the late region, an intact early region, and a duplication of the origin. This combination represents a new papovavirus with a bipartite genome in which the early region is derived from BKV and the late region from SV40, and both are present in separate molecules. The BKV and SV40 defectives complement each other for infectivity. Infectious virus is formed with the E-BKV genomes packaged in SV40 capsids. It is hypothesized that this kind of recombination (reassortment) is a way in which papovaviruses may generate variation. The host range for the new BKV/SV40 is narrow. It propagates well in BSC-1 cells, relatively poorly in fetal human brain cells, and not at all in green monkey TC-7 or human embryonic kidney cells. However, it transforms fetal human brain cells at a frequency 25-50 times greater than wt BKV does.

Naturally occurring BK virus variants (JL and Dik) with deletions in the putative early enhancer-promoter sequences

The genomes of two independently isolated BK virus (BKV) variants (JL and Dik) were compared with prototype BKV DNA by restriction endonuclease mapping and sequence analysis. Differences were mainly detected in two regions: the BKV (JL) and BKV (Dik) putative early enhancer-promoter regions and the middle of the T-antigen-coding regions. Base sequence analysis of these two regions showed the following. (i) The putative enhancer-promoter regions of BKV (Dik) and BKV (JL) contained only one 68-base-pair (bp) unit of the 68-bp triplication (the central copy of which is missing 18 bp) present in prototype BKV. (ii) In the same region, BKV (JL) and BKV (Dik) contained unique stretches of DNA 33 and 63 bp long, respectively. In these 63 bp, a sequence which was very similar to the proposed simian virus 40 enhancer core sequence (GGAGTGGAAAG) was present. (iii) The altered restriction endonuclease recognition sites in the sequenced part of the T-antigen-coding region of BKV (JL) and BKV (Dik) were due to base sequence changes, leaving the amino acid sequence unchanged.

Differences in regulatory sequences of naturally occurring JC virus variants

The regulatory region was sequenced for DNAs representative of seven independent isolates of JC virus, the probable agent of progressive multifocal leukoencephalopathy. The isolates included an oncogenic variant (MAD-4), an antigenic variant (MAD-11), and two different isolates derived from the urine (MAD-7) and from the brain (MAD-8) of the same patient. The representative DNAs were molecularly cloned directly from diseased brain tissue and from human fetal glial cells infected with the corresponding isolated viruses. The regulatory sequences of these DNAs were compared with those of the prototype isolate, MAD-1, sequenced previously (R. J. Frisque, J. Virol. 46:170-176, 1983). We found that the regulatory region of JC viral DNA is highly variable due to complex alterations of the previously described 98-base-pair repeat of MAD-1 DNA. On the basis of these alterations, there are two general types of JC virus. There were no consistent alterations in regulatory sequences which could distinguish brain tissue DNAs from tissue culture DNAs. Furthermore, for each isolate except MAD-1 (R. J. Frisque, J. Virol. 46:170-176, 1983), the regulatory regions of brain tissue and tissue culture DNAs were not identical. The arrangement, sequence, or both of potential regulatory elements (TATA sequence, GGGXGGPuPu, tandem repeats) of JC viral DNAs are sufficiently different from those in other viral and eucaryotic systems that they may effect the unique properties of this slow virus.