Genetic relatedness studies with adenovirus-associated viruses

Cloning of adeno-associated virus type 4 (AAV4) and generation of recombinant AAV4 particles

We have cloned and characterized the full-length genome of adeno-associated virus type 4 (AAV4). The genome of AAV4 is 4,767 nucleotides in length and contains an expanded p5 promoter region compared to AAV2 and AAV3. Within the inverted terminal repeat (ITR), several base changes were identified with respect to AAV2. However, these changes did not affect the ability of this region to fold into a hairpin structure. Within the ITR, the terminal resolution site and Rep binding sites were conserved; however, the Rep binding site was expanded from three GAGC repeats to four. The Rep gene product of AAV4 shows greater than 90% homology to the Rep products of serotypes 2 and 3, with none of the changes occurring in regions which had previously been shown to affect the known functions of Rep68 or Rep78. Most of the differences in the capsid proteins lie in regions which are thought to be on the exterior surface of the viral capsid. It is these unique regions which are most likely to be responsible for the lack of cross-reacting antibodies and the altered tissue tropism compared to AAV2. The results of our studies, performed with a recombinant version of AAV4 carrying a lacZ reporter gene, suggest that AAV4 can transduce human, monkey, and rat cells. Furthermore, comparison of transduction efficiencies in a number of cell lines, competition cotransduction experiments, and the effect of trypsin on transduction efficiency all suggest that the cellular receptor for AAV4 is distinct from that of AAV2.

Restriction enzyme analysis of faecal adenoviruses in Newcastle upon Tyne

Adenovirus DNA was isolated directly from virus-containing stools and digested with restriction endonucleases. The resulting fragments were separated by polyacrylamide gel electrophoresis (PAGE) and visualized by silver staining. This enabled us to assign most of the viruses detected to subgenus, serotype and, sometimes, unique strains. Although less sensitive than electron microscopy, the method allowed more information about the infecting virus to be obtained and no cultivation was necessary. Comparison with culture also allowed dual infections to be recognized. A 2-year survey of faecal adenoviruses in Newcastle upon Tyne showed that type 41 (strain 41a) was the predominant type and strain 41p was not recorded. Heterogeneity in strain 41a was also noted as found elsewhere. Adenovirus type 40 was common prior to 1985 but was absent during the last 2 years.

Characterization and molecular cloning of a human parvovirus genome

The genome of the small human virus serologically associated with erythrocyte aplasia and erythema infectiosum (fifth disease) is shown to be a linear, nonpermuted, single-stranded DNA molecule with self-priming hairpin termini, properties which are characteristic of the genomes of the family Parvoviridae. This human parvovirus chromosome was molecularly cloned into bacterial plasmid vectors and the cloned DNA was used to explore its relatedness to other mammalian parvovirus serotypes by DNA:DNA hybridization. It is not related to the human adeno-associated viruses but does show a distant evolutionary relationship to genomes of the helper-independent parvoviruses of rodents. This strongly suggests that it is an autonomous parvovirus, and as such is the first example of a member of this group of common animal pathogens to cause disease in man.

Electron microscopic comparison of the sequences of single-stranded genomes of mammalian parvoviruses by heteroduplex mapping

The sequence homologies among the linear single-stranded genomes of several mammalian parvoviruses have been studied by electron microscopic analysis of the heteroduplexes produced by reannealing the complementary strands of their DNAs. The genomes of Kilham rat virus, H-1, minute virus of mice and LuIII, which are antigenically distinct non-defective parvoviruses, have considerable homology: about 70% of their sequences are conserved. The homologous regions map at similar locations in the left halves (from the 3' ends) of the genomes. No sequence homology, however, is observed between the DNAs of these nondefective parvoviruses and that of bovine parvovirus, another non-defective virus, or that of defective adenoassociated virus, nor between the genomes of bovine parvovirus and adenoassociated virus. This suggests that only very short, if any, homologous regions are present. From our results, we predict an evolutionary relationship among Kilham rat virus, H-1, minute virus of mice and LuIII. It is interesting to note that, although LuIII was originally isolated from a human cell line and is specific for human cells in vitro, its genome has sequences in common only with the rodent viruses Kilham rat virus, minute virus of mice and H-1, and not with the other two mammalian parvoviruses tested.

DNA-minus temperature-sensitive mutants of adenovirus type 5 help adenovirus-associated virus replication

Efficient potentiation of adenovirus-associated viruses (AAV) replication occurs in coinfections with either of two DNA-minus temperature-sensitive mutants of adenovirus type 5 (Ad5), ts125 and ts149. The helper activity of these mutants does not result from leakiness. At the nonpermissive termperature (39.5 C) there was little or no detectable adenovirus DNA synthesis, and only a relatively low level of adenovirus transcription was observed. However, the synthesis of AAV DNA and RNA and the yield of infectious AAV were comparable in amounts to those found when wild-type Ad5 was the helper. Furthermore, an apparent lag in the initiation of AAV transcription after the onset of AAV DNA synthesis was seen in coinfections with both wild type or ts125. These findings strongly suggest that the adenovirus factor(s) required for AAV multiplication is produced early in the adenovirus DNA replication, this requirement does not include all factors directly needed for adenovirus DNA synthesis.

Adenovirus-associated virus multiplication. VII. Helper requirement for viral deoxyribonucleic acid and ribonucleic acid synthesis

The adsorption of adenovirus-associated virus (AAV) type 2 by KB cells and the subsequent penetration of the AAV genome to the cell nucleus was measured with and without helper adenovirus type 2 (Ad2). It was found that the helper virus did not enhance either process. On the other hand, a synthesis of AAV deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) was not detected by nucleic acid hybridization after KB cells were infected with AAV type 2 alone, whereas both AAV DNA and RNA synthesis were readily detected when cells were additionally infected with Ad2 or herpes simplex virus type 1, a partial helper of AAV replication. AAV RNA synthesis was initially observed 10 to 11 hr after simultaneous infection with Ad2, but the interval between AAV infection and AAV transcription could be reduced to 4 to 5 hr when cells were first infected with Ad2 for 10 hr. It was estimated that AAV DNA synthesis accounted for 3% of the total DNA in cells after a simultaneous infection with Ad2. These findings, together with the previous observation that adenovirus provides a helper function(s) after AAV uncoating, suggest that AAV are defective only subsequent to the uncoating process, and that helper viruses may provide a factor(s) needed for initiating synthesis of AAV DNA, RNA, or both.

Immunological reactivity of antisera prepared against the sodium dodecyl sulfate-treated structural polypeptides of adenovirus-associated virus

The preparation of antisera to the three purified sodium dodecyl sulfate (SDS)-treated polypeptide components (VP1, VP2, VP3) of adenovirus-associated virus (AAV) type 3H is described. In immunofluorescence tests (FA), these antisera stained heat-stable antigens with distinct morphologies in cells co-infected with either adenovirus or herpes simplex virus. Kinetic studies of antigen formation showed that VP1 antiserum first stained the cytoplasm (14 hr) and later (by 18 hr) stained both cytoplasmic and intranuclear areas. VP2 antiserum stained only discrete intranuclear areas, and VP3 antiserum stained nearly the entire nucleus. All three VP antigens appeared at about the 14th hr postinfection, about 2 hr prior to the appearance of whole virion antigen. The VP antisera cross-reacted in FA with AAV types 1 and 2 (all at one-eighth of the homologous titer), but did not react with other parvoviruses, i.e., rat virus, hemadsorbing enteric virus of calves, minute virus of mice, or H-1 virus. These non-neutralizing antisera reacted specifically with SDS-treated AAV virion antigens in complement fixation and immunodiffusion tests, and antiserum prepared against SDS-treated helper adenovirus structural polypeptides reacted with adenovirus polypeptide antigens. All antisera to SDS-treated polypeptides were specific for new antigens revealed on the dissociated peptides and did not react with whole virions, whereas whole-virion antisera did not cross-react with the polypeptide antigens. These findings suggest that antigens unique to the polypeptides of AAV are revealed by SDS treatment and that these antigens can be detected in cells prior to the folding of the polypeptides into the molecular configuration they possess as virion subunits. These results also indicate that at least one AAV polypeptide component is synthesized in the cell cytoplasm.

Adenovirus-associated virus multiplication. VI. Base compostion of the deoxyribonucleic acid strand species and strand-specific in vivo transcription

The two complementary strand species of 5-bromodeoxyuridine-substituted, adenovirus-associated virus type 2 (AAV-2) deoxyribonucleic acid were preparatively separated in CsCl density gradients and further purified by sedimentation through 5 to 20% sucrose. The base composition of each strand species was determined, and it was found that the species banding at a greater density in CsCl (heavy strands) had an expected higher thymidine content (26.5%) than that 21.7%) of the less dense species (light strands). Furthermore, the base composition of in vivo-synthesized, AAV-specific ribonucleic acid was similar to that of light-strand deoxyribonucleic acid, and this ribonucleic acid apparently hybridized only with heavy strands. These observations indicate that the heavy-strand species alone serves as the transcriptional template in vivo. This study represents the first instance in which the base composition and specificity of in vivo transcription have been determined for each of the complementary strands of an animal virus deoxyribonucleic acid.

Structural proteins of adenovirus-associated viruses

The structural proteins of adenovirus-associated virus (AAV) types 1, 2, and 3 were analyzed by acrylamide gel electrophoresis. In each case, one major protein (C) and two minor proteins (A and B) were identified. Component C had an estimated molecular weight of 62,000 daltons, and the molecular weights of components A and B were found to be 87,000 and 73,000 daltons, respectively. Coelectrophoresis of adenovirus and AAV proteins revealed an overlap only between the adenovirus fiber-penton component and the AAV C polypeptide. Among AAV serotypes, homologous components were electrophoretically identical, except that the C component of AAV-2 was of slightly lower molecular weight than the C components of AAV-1 and AAV-3. The relative incorporation of (14)C-arginine and (14)C-mixed amino acids into the three polypeptides of AAV-2 was similar, indicating an absence of an arginine-rich component. In addition, AAV-2 was found to have a substantially lower arginine content than helper adenoviruses.

Remarks on the Classification of Viruses

This chapter presents remarks on viruses, phanerogram, cryptogram, and gymnogram. It discusses various characteristics of the families of viruses. Viruses are defined by the sum of the distinctive traits of the virion. These distinctive traits are as follows: (1) presence of a single nucleic acid; (2) incapacity to grow and to divide; (3) reproduction from the genetic material only; (4) absence of enzymes for energy metabolism; (5) absence of ribosomes; (6) absence of information for the production of enzymes in the energy cycle; (7) absence of information for the synthesis of the ribosomal proteins; and (8) absence of information for the synthesis of ribosomal RNA and transfer RNA. The viral infectious particle presents a great diversity in composition and structure. Order could be achieved only through a classification, which is a system of order. The goal of biological classification is to group together organisms presenting certain analogies and certain affinities and, if possible, to also bring out phylogenic relationships. The conceptions relative to the methodology of taxonomy, which is the science of classification, are diverse. A virus may have evolved from a given sector of DNA within the host cell. It could also very well have derived from the corresponding RNA messenger that contains the same information, both qualitatively and quantitatively. Therefore, theoretically, different viruses could have originated from nucleic acids of different but complementary nature. The nucleic acid of viruses is either single- or double-stranded. Viruses, as is generally accepted, derive from the nucleic acid of their host. Thus, RNA viruses could possibly have their origin in the RNA messenger.

Evidence for a single-stranded adenovirus-associated virus genome: isolation and separation of complementary single strands

Single-stranded adenovirus-associated virus type 2 deoxyribonucleic acid (AAV-2 DNA) has been isolated from the virion after enzymatic pretreatment of the particles by heating at 53 C for 1 hr in 0.015 m NaCl plus 0.0015 m sodium citrate in the presence of 1% sodium dodecyl sulfate. Double-stranded AAV-2 DNA present as a marker is not denatured by this treatment. AAV-2 single-stranded DNA is composed of two complementary species which can be separated in neutral CsCl when 5-bromodeoxyuridine has been substituted for thymidine in the DNA. The present report is the first documented instance of the separation of complementary strands of an animal virus DNA.

Evidence for a single-stranded adenovirus-associated virus genome: formation of a DNA density hybrid on release of viral DNA

Extracted adenovirus-associated virus DNA is known to be double-stranded, and, therefore, it has been assumed that these virus particles contain a double-stranded genome. Recent findings, however, have suggested that the DNA in virus particles is equivalent to only half the molecular weight of extracted molecules. A density analysis of DNA extracted from a mixture of virus particles containing either bromodeoxyuridine-substituted or unsubstituted DNA shows that virions contain single-stranded DNA which, when released, forms duplex structures. A similar circumstance is as yet unknown among other viruses.