Collection, particle sizing and detection of airborne viruses.

Viruses that affect humans, animals and plants are often dispersed and transmitted through airborne routes of infection. Due to current technological deficiencies, accurate determination of the presence of airborne viruses is challenging. This shortcoming limits our ability to evaluate the actual threat arising from inhalation or other relevant contact with aerosolized viruses. To improve our understanding of the mechanisms of airborne transmission of viruses, air sampling technologies that can detect the presence of aerosolized viruses, effectively collect them and maintain their viability, and determine their distribution in aerosol particles, are needed. The latest developments in sampling and detection methodologies for airborne viruses, their limitations, factors that can affect their performance and current research needs, are discussed in this review. Much more work is needed on the establishment of standard air sampling methods and their performance requirements. Sampling devices that can collect a wide size range of virus-containing aerosols and maintain the viability of the collected viruses are needed. Ideally, the devices would be portable and technology-enabled for on-the-spot detection and rapid identification of the viruses. Broad understanding of the airborne transmission of viruses is of seminal importance for the establishment of better infection control strategies.

Simian virus 40 regulatory region structural diversity and the association of viral archetypal regulatory regions with human brain tumors.

The regulatory region (RR) of simian virus 40 (SV40) contains enhancer/promoter elements and an origin of DNA replication. Natural SV40 isolates from simian brain or kidney tissues typically have an archetypal RR arrangement with a single 72-basepair enhancer element. A rare simpler, shorter SV40 RR exists that lacks a duplicated sequence in the G/C-rich region and is termed protoarchetypal. Occasionally, SV40 strain variants arise de novo that have complex RRs, which typically contain sequence reiterations, rearrangements, and/or deletions. These variants replicate faster and to higher titers in tissue culture; we speculate that such faster-growing variants were selected when laboratory strains of SV40 were initially recovered. SV40 strains with archetypal RRs have been found in some human brain tumors. The possible implications of these findings and a brief review of the SV40 RR structure are presented.

Molecular characterization of SV40 DNA in multiple samples from a human mesothelioma.

BACKGROUND: Prolonged exposure to asbestos, a potent carcinogen, has been the generally accepted factor responsible for the development of human mesotheliomas. Recent reports documenting the detection of SV40 DNA in human mesotheliomas suggest the possibility that this known tumor virus may be an additional factor involved in the development of some tumors. METHODS: A detailed analysis was performed by polymerase chain reaction and DNA sequencing of the genetic characteristics of SV40 viral DNA detected in samples taken from multiple sites of a human mesothelioma. RESULTS: A single virus variant was detected within the tumor that encoded a novel variable region at the C-terminus of the large T-antigen oncoprotein. The viral regulatory region was predominantly archetypal in sequence (lacking duplications of the enhancer), typical of natural isolates. CONCLUSIONS: These data confirm previous reports from several laboratories showing an association of SV40 DNA with human mesotheliomas and provide the first evidence of a novel virus variant present in separated regions of a mesothelioma.

Molecular evidence of simian virus 40 infections in children.

Recent studies have detected simian virus 40 (SV40) DNA in certain human tumors and normal tissues. The significance of human infections by SV40, which was first discovered as a contaminant of poliovirus vaccines used between 1955 and 1963, remains unknown. The occurrence of SV40 infections in unselected hospitalized children was evaluated. Polymerase chain reaction and DNA sequence analyses were done on archival tissue specimens from patients positive for SV40 neutralizing antibody. SV40 DNA was identified in samples from 4 of 20 children (1 Wilms' tumor, 3 transplanted kidney samples). Sequence variation among SV40 regulatory regions ruled out laboratory contamination of specimens. This study shows the presence of SV40 infections in pediatric patients born after 1982.

Polyomaviruses and human tumors: a brief review of current concepts and interpretations.

Polyomaviruses are small DNA viruses that typically establish persistent but inapparent infections of their natural hosts, although cytolytic disease may develop if the host becomes immunocompromised. Most polyomaviruses have the ability to induce tumor formation when introduced into certain foreign hosts and are considered oncoviruses. Some polyomaviruses, including those that infect humans, have occasionally been detected in cancerous tissue of their natural hosts. This article briefly reviews the biology of polyomaviruses and explores issues pertaining to the significance of association of polyomaviruses with human tumors.

Cell and molecular biology of simian virus 40: implications for human infections and disease.

Simian virus 40 (SV40), a polyomavirus of rhesus macaque origin, was discovered in 1960 as a contaminant of polio vaccines that were distributed to millions of people from 1955 through early 1963. SV40 is a potent DNA tumor virus that induces tumors in rodents and transforms many types of cells in culture, including those of human origin. This virus has been a favored laboratory model for mechanistic studies of molecular processes in eukaryotic cells and of cellular transformation. The viral replication protein, named large T antigen (T-ag), is also the viral oncoprotein. There is a single serotype of SV40, but multiple strains of virus exist that are distinguishable by nucleotide differences in the regulatory region of the viral genome and in the part of the T-ag gene that encodes the protein's carboxyl terminus. Natural infections in monkeys by SV40 are usually benign but may become pathogenic in immunocompromised animals, and multiple tissues can be infected. SV40 can replicate in certain types of simian and human cells. SV40-neutralizing antibodies have been detected in individuals not exposed to contaminated polio vaccines. SV40 DNA has been identified in some normal human tissues, and there are accumulating reports of detection of SV40 DNA and/or T-ag in a variety of human tumors. This review presents aspects of replication and cell transformation by SV40 and considers their implications for human infections and disease pathogenesis by the virus. Critical assessment of virologic and epidemiologic data suggests a probable causative role for SV40 in certain human cancers, but additional studies are necessary to prove etiology.

Detection of authentic SV40 DNA sequences in human brain and bone tumours.

This report summarizes our follow-up studies of SV40 DNA sequences in human brain tumors of early childhood and our confirmation of the presence of SV40 DNA in human osteosarcomas. We examined brain tumors and osteosarcoma samples by the polymerase chain reaction (PCR) using primers from four separated regions of the SV40 genome. Sequence analysis confirmed that authentic SV40 DNA was present. The regulatory region of each tumor-associated viral DNA was of archetypal length (non-duplicated enhancer); sequence variation was noted at the extreme C-terminus of the large T-antigen (T-ag) genes. Infectious SV40 was recovered from one brain tumor. We sequenced the entire early genomic region from three human isolates of SV40 and two laboratory strains originally recovered from monkeys. The predicted amino acid sequence of the large T-ags showed remarkable sequence conservation among isolates, except for a small variable region identified at the C-terminus of the protein. There were no human-isolate-specific changes detected that could serve to distinguish a human variant of SV40 nor were any tumor-type-specific viral markers observed. Based on these data, we conclude that authentic SV40 is associated with some human brain and bone tumors and that multiple SV40 strains can infect humans.

Consideration of PCR methods for the detection of SV40 in tissue and DNA specimens.

SV40 is capable of infecting humans, although its association with human diseases remains controversial. Recently, a subgenomic SV40 DNA sequence was detected by polymerase chain reaction (PCR) in certain types of human tumour tissue as well as in normal pituitary tissue. However, due to the limited DNA sequence information that was obtained in those experiments, SV40 could not be authenticated, and it was uncertain whether a related or hybrid virus (or endogenous DNA) accounted for the PCR-amplified DNA. To gain more insight into these observations, we are experimenting with PCR primers directed at various sites of the SV40 genome, as well as with various parameters of the PCR assay. In this communication, we describe methodology we currently use in our studies and discuss problems associated with the PCR detection of SV40 in various types of samples.

Cytotoxic T lymphocyte recognition sequences as markers for distinguishing among tumour antigens encoded by SV40, BKV and JCV.

Simian virus 40 (SV40) has been shown to be associated with a number of human tumours. Two other human papova viruses, BKV and JCV, infect humans at a relatively high frequency and are activated upon immune suppression. The T antigens of both of these viruses share considerable homologies with the transforming protein T antigen of SV40. We have used SV40 T antigen specific cytotoxic T lymphocyte (CTL) clones to discriminate among the T antigens of SV40, BKV and JCV. These CTL clones directed to four distinct CTL epitopes serve as specific probes and can differentiate subtle alterations or deletions in the CTL epitopes relative to SV40 T antigen. Using this strategy, we have been able to authenticate three SV40 viruses isolated from humans as all four distinct CTL epitopes in the T antigens encoded by these three SV40 human isolates (SVCPC, SVMEN, and SVPML-1) were found to be identical to prototype SV40. We have further identified a 198 amino acid deletion T antigen variant of SVCPC. The finding of a deletion mutant in the SVCPC virus population suggests that the cellular immune response may play a role in the selection of antigenic loss variants.

Sequence analyses of human tumor-associated SV40 DNAs and SV40 viral isolates from monkeys and humans.

SV40 DNA has been found associated with several types of human tumors. We now report a sequence comparison of SV40 DNAs from pediatric brain tumors and from osteosarcomas with viral isolates from monkeys and from humans. We analyzed the entire genomic sequences of five isolates, Baylor and VA45-54 strains from monkeys and SVCPC, SVMEN, and SVPML-1 recovered from humans, and compared them to the reference virus SV40-776. The viral sequences were highly conserved, but isolates could be distinguished by variations in the structure of the viral regulatory region and in the nucleotide sequence of the variable domain at the C-terminus of the large T-antigen gene. We conclude that multiple strains of SV40 exist that can be identified on the basis of sequences in these regions of the viral genome. The isolates were more similar to each other and to the Baylor strain than to the reference strain SV40-776. Human isolates SVCPC and SVMEN were found to be identical. The DNAs present in some human brain and bone tumors were authentic SV40 sequences. Many of the C-terminal T-ag sequences associated with human tumors were unique, but some sequences were shared by independent sources. There was no compelling evidence for human-specific strains of SV40 or for tumor type-specific associations, suggesting that SV40 has a relatively broad host range. The source of the viral DNA found in human tumors remains unknown.

Natural isolates of simian virus 40 from immunocompromised monkeys display extensive genetic heterogeneity: new implications for polyomavirus disease.

Simian virus 40 (SV40) DNAs in brain tissue and peripheral blood mononuclear cells (PBMCs) of eight simian immunodeficiency virus-infected rhesus monkeys with SV40 brain disease were analyzed. We report the detection, cloning, and identification of five new SV40 strains following a quadruple testing-verification strategy. SV40 genomes with archetypal regulatory regions (containing a duplication within the G/C-rich regulatory region segment and a single 72-bp enhancer element) were recovered from seven animal brains, two tissues of which also contained viral genomes with nonarchetypal regulatory regions (containing a duplication within the G/C-rich regulatory region segment as well as a variable duplication within the enhancer region). In contrast, PBMC DNAs from five of six animals had viral genomes with both regulatory region types. It appeared, based on T-antigen variable-region sequences, that nonarchetypal virus variants arose de novo within each animal. The eighth animal exclusively yielded a new type of SV40 strain (SV40-K661), containing a protoarchetypal regulatory region (lacking a duplication within the G/C-rich segment of the regulatory region and containing one 72-bp element in the enhancer region), from both brain tissue and PBMCs. The presence of SV40 in PBMCs suggests that hematogenous spread of viral infection may occur. An archetypal version of a virus similar to SV40 reference strain 776 (a kidney isolate) was recovered from one brain, substantiating the idea that SV40 is neurotropic as well as kidney-tropic. Indirect evidence suggests that maternal-infant transmission of SV40 may have occurred in one animal. These findings provide new insights for human polyomavirus disease.

SV40 DNA in human osteosarcomas shows sequence variation among T-antigen genes.

Authentic simian virus 40 (SV40) has been detected in association with human choroid plexus and ependymoma tumors, and SV40-like DNA sequences have been found in some human osteosarcomas. We report here an analysis of human osteosarcoma samples for the presence of SV40 DNA using PCR and primers directed at 4 distinct sites of the SV40 genome, coupled with sequence analysis. Authentic SV40 DNA sequences were detected in 5 of 10 osteosarcoma tumor samples. The SV40 regulatory region in each case was identical and of archetypal length (non-duplicated enhancer), as is usually found in natural isolates of SV40 from monkeys and in human brain tumors. A section of the gene that encodes a viral late gene product (VP1) was detected in 5 of 10 tumors and had an exact match with the known sequence of SV40. Two separated segments of the large T-antigen (T-ag) gene were found in the same 5 tumors. Analysis of the DNA sequences encoding the T-ag carboxy terminus revealed sequence variation among the tumors, as observed previously in viral DNA associated with human brain tumors. There does not appear to be a preferential association of a T-ag variable domain sequence with a given tumor type. No sequences from the regulatory region of human polyomaviruses JCV and BKV were detected in the bone tumors. We also noted less efficient recovery of SV40 DNA from tumor samples fixed in paraffin as compared to frozen tumors. Our results confirm the presence of SV40 DNA in human bone tumors and, based on the sequence variation observed for the carboxy terminus of the T-ag gene, suggest that there is not a specific SV40 strain associated with human osteosarcomas.

Tissue culture adaptation of natural isolates of simian virus 40: changes occur in viral regulatory region but not in carboxy-terminal domain of large T-antigen.

The regulatory region of natural isolates of simian virus 40 (SV40) is different from that of laboratory-adapted strains of the virus. The latter have a nucleotide sequence duplication within the enhancer region which varies slightly with each strain, whereas the duplication is lacking in fresh isolates of SV40, which contain an 'archetypal' regulatory region. Many isolates also display nucleotide differences in the DNA encoding the carboxy terminus of large tumour antigen (T-ag). To determine whether genetic changes in these two regions of the SV40 genome were detectable during laboratory adaptation and long-term passage, low-passage virus stocks of two laboratory strains which had detailed passage histories spanning more than 25 years (Baylor strain and VA45-54) were analysed using PCR, cloning and sequencing assays. Both laboratory and archetypal regulatory regions were present in low-passage stocks. Following duplication in the regulatory region, no additional changes were detectable. The variable region at the T-ag carboxy terminus did not undergo any change with tissue culture passage and may serve as a useful site for taxonomic classification of different strains of SV40. Cloned genomes containing single or duplicated enhancers derived from both SV40 strains were viable in CV-1 cells. Attempts to induce regulatory region duplications by 14 serial passages of SV40 archetypal strains in monkey cells were not successful. The results are compatible with tissue culture adaptation of SV40, reflecting either selection of a rare variant pre-existing in the original sample or generation of a rare regulatory region duplication in infected cells.

A coupled PCR and restriction digest method for the detection and analysis of the SV40 regulatory region in infected-cell lysates and clinical samples.

The polymerase chain reaction (PCR) is an increasingly popular analytical tool for the detection of virus sequences in laboratory preparations as well as in human clinical samples. In studies involving papovaviruses SV40, BK virus (BKV), and JC virus (JCV), one of the primary targets for analysis is the viral regulatory region, as that section of the papovavirus genome is distinct. A primary concern with PCR-based studies is whether amplified DNA sequences may be derived from laboratory contaminants. Recognizing that common sources of PCR contamination are the positive control templates, we devised a facile method to distinguish between real and false-positive PCR-amplified SV40 regulatory region DNAs. SV40 constructs that had been engineered to contain different combinations of 72-basepair (bp) enhancer elements and 21-bp repeats, as well as two introduced unique restriction enzyme sites, were used as positive control templates for PCR amplification. Cleavage of PCR-amplified DNA identifies products from the engineered control plasmids. The procedure is rapid, simple and cost-effective. We also report that primer sets predicted to be specific for the SV40 regulatory region can be used to amplify BKV and JCV regulatory region sequences under conditions of reduced stringency.

High-fidelity PCR amplification of infectious copies of the complete simian virus 40 genome from plasmids and virus-infected cell lysates.

We describe here a long-polymerase chain reaction (PCR) method that can be used to amplify complete simian virus 40 (SV40) DNA with high fidelity, and we show that authentic, viable virus can be produced from molecular clones of the PCR-amplified viral DNAs. A commercial long-PCR kit that employed a combination of Taq and GB-D polymerases was used, together with a pair of overlapping primers that recognized a unique EcoRI site in the SV40 genome. Efficient amplification required linearization of the circular SV40 genomic DNAs with EcoRI. Entire SV40 genomes were successfully PCR-amplified from an SV40 plasmid and from two different SV40-infected cell lysates and were cloned into pUC-19. Three separate segments of the cloned viral genomes were DNA sequenced, and no nucleotide changes relative to the parental virus were detected, suggesting that the viral DNAs had been amplified with high fidelity. Each PCR clone was infectious, and no differences were detected in the growth characteristics of viruses derived from these clones as compared to the original viral strain. The procedure we utilized shortens and simplifies the molecular cloning of small double-stranded DNA viruses and will be useful for viral diagnostic tests and for recovery of virus from clinical samples. The results of these experiments have broad implications, as the methodology is applicable to many systems.

Identification of a variable region at the carboxy terminus of SV40 large T-antigen.

The entire early regions of three human isolates of simian virus 40 (SV40), as well as two laboratory strains recovered from monkeys, were sequenced. The early coding region of each isolate contains a number of nucleotide differences when compared to the reference strain SV40-776. These differences result in some changes in the predicted amino acid sequence of the unique region of small t-antigen and in the carboxy (C) terminus of large T-antigen. The amino acid sequence of the remainder of large T-antigen was absolutely conserved among all isolates. Thus, SV40 large T-antigen contains a variable domain at the C-terminal end of the molecule.

Natural simian virus 40 strains are present in human choroid plexus and ependymoma tumors.

Simian virus 40 (SV40) sequences for large tumor antigen (T-ag) were recently detected in a significant fraction of certain human brain tumors of early childhood (Bergsagel et al., N. Engl. J. Med. 326, 988-993, 1992). In the current study, we sought to determine whether authentic SV40 was present in the choroid plexus and ependymoma tumors previously examined. Polymerase chain reaction and DNA sequence analysis revealed authentic SV40 regulatory region and major capsid (VP1) sequences in 14 of 17 tumors tested. Only one 72-basepair element was detected in the SV40 enhancer region of positive tumor samples, an arrangement designated as "archetypal." The C terminus of the T-ag gene was detected in the same 14 tumors and was sequenced from 5 tumors; some nucleotide changes were found that would result in amino acid changes in T-ag. Infectious SV40 was isolated from one sample after lipofection of tumor DNA into monkey kidney cells. Sequence analysis of the rescued virus SVCPC revealed (i) an archetypal regulatory region, (ii) nucleotide changes in the C terminus of the T-ag gene that distinguished it from SV40 laboratory strains 776 and SV40-B2 and from human isolate SVPML-1, and (iii) identity with previous human brain tumor isolate SVMEN in the three genomic regions sequenced. No human-isolate-specific distinguishing features were detected among the viral sequences analyzed. Thus, authentic SV40 is present in humans and associated with two tumor types known to be induced experimentally by the virus.