Isolation and characterization of an endogenous type C virus of rhesus monkeys

Chemical induction of endogenous retrovirus particles from the vero cell line of African green monkeys

Endogenous retroviral sequences are present in high copy numbers in the genomes of all species and may be expressed as RNAs; however, the majority are defective for virus production. Although virus has been isolated from various Old World monkey and New World monkey species, there has been no report of endogenous retroviruses produced from African green monkey (AGM) tissues or cell lines. We have recently developed a stepwise approach for evaluating the presence of latent viruses by chemical induction (Khan et al., Biologicals 37:196-201, 2009). Based upon this strategy, optimum conditions were determined for investigating the presence of inducible, endogenous retroviruses in the AGM-derived Vero cell line. Low-level reverse transcriptase activity was produced with 5-azacytidine (AzaC) and with 5'-iodo-2'-deoxyuridine (IUdR); none was detected with sodium butyrate. Nucleotide sequence analysis of PCR-amplified fragments from the gag, pol, and env regions of RNAs, prepared from ultracentrifuged pellets of filtered supernatants, indicated that endogenous retrovirus particles related to simian endogenous type D betaretrovirus (SERV) sequences and baboon endogenous virus type C gammaretrovirus (BaEV) sequences were induced by AzaC, whereas SERV sequences were also induced by IUdR. Additionally, sequence heterogeneity was seen in the RNAs of SERV- and BaEV-related particles. Infectivity analysis of drug-treated AGM Vero cells showed no virus replication in cell lines known to be susceptible to type D simian retroviruses (SRVs) and to BaEV. The results indicated that multiple, inducible endogenous retrovirus loci are present in the AGM genome that can encode noninfectious, viruslike particles.

Novel endogenous type D retroviral particles expressed at high levels in a SCID mouse thymic lymphoma

A xenograft model of the human disease Langerhans cell histiocytosis (LCH) was investigated with severe combined immunodeficiency (SCID) mice. Transplantation of human LCH biopsy material into SCID mice resulted in the generation of mouse tumors resembling lymphomas. A thymoma cell line (ThyE1M6) was generated from one of these mice and found to display significant levels of Mg2+-dependent reverse transcriptase activity. Electron microscopy revealed particles with type D retroviral morphology budding from ThyE1M6 cells at a high frequency, whereas control cultures were negative. Reverse transcription-PCR of virion RNA with degenerate primers for conserved regions of various mouse, human, and primate retroviruses amplified novel sequences related to primate type D retroviruses, murine intracisternal A particles, Jaagsiekte sheep retrovirus, and murine long interspersed nuclear elements but not other retroviral classes. We demonstrate that these sequences represent a novel group of endogenous retroviruses expressed at low levels in mice but expressed at high levels in the ThyE1M6 cell line. Furthermore, we propose that the activation of endogenous retroviral elements may be associated with a high incidence of thymomas in SCID mice.

Characterization of antigens expressed in normal baboon trophoblast and cross-reactive with HIV/SIV antibodies

Electron microscopic studies have revealed the presence of endogenous retroviral (ERV) particles in normal primate placental tissues. These particles have ultrastructural similarities to type C retroviral particles and are mainly associated with the trophoblast. In normal human placental tissues, they have antigenic similarity with exogenous retroviruses, such as the human immunodeficiency virus (HIV), and may have a role to play in the regulation of cellular gene expression, syncytiotrophoblast formation or pregnancy-related immunosuppression. In this study, a panel of antibodies (polyclonal and monoclonal antibodies) against viral proteins (anti-HIV and anti-SIV) and endogenous retroviral (ERV) proteins were assessed by immunohistochemistry and immunoblotting, for their cross-reactivity with ERV particles isolated from normal baboon placental tissues. The antibodies (anti-HERV-K RT, anti-ERV3 env, anti-HIV-1 p17, anti-HIV-2 gp120) reacted positively with the syncytiotrophoblast and each antibody recognized one or two proteins of molecular weights (MW) 38, 58 or 64 kDa present in the baboon placental villous tissues and SIV-infected molt-4 Cl8 cells, but not in uninfected cells. The results of this study confirm the specific expression of retroviral cross-reactive antigens in normal baboon placental tissues and suggest placental cellular proteins may have antigenic similarity with those recognized by anti-HIV/SIV antibodies. The role of these retroviral-related proteins expressed at the maternal-fetal interface remain unclear.

Complete nucleotide sequence of simian endogenous type D retrovirus with intact genome organization: evidence for ancestry to simian retrovirus and baboon endogenous virus

A complete endogenous type D viral genome has been isolated from a baboon genomic library. The provirus, simian endogenous retrovirus (SERV), is 8,393 nucleotides long and contains two long terminal repeats and complete genes for gag, pro, pol, and env. The primer binding site is complementary to tRNA(Lys)3, like in lentiviruses. The env GP70 protein is highly homologous to that of baboon endogenous virus (BaEV). PCR analysis of primate DNA showed that related proviral sequences are present in Old World monkeys of the subfamily Cercopithecinae but not in apes and humans. Analysis of virus and host sequences indicated that the proviral genomes were inherited from a common ancestor. Comparison of the evolution of BaEV, exogenous simian retrovirus types 1 to 3 (SRV1 to SRV3), and SERV suggests that SERV is ancestral to both BaEV and the SRVs.

An array of murine leukemia virus-related elements is transmitted and expressed in a primate recipient of retroviral gene transfer

Direct RNA-PCR analyses of T-cell lymphomas that developed in rhesus macaques during a gene transfer experiment revealed the presence of several different recombinant murine leukemia viruses (MuLV). Most prominent was the expected MuLV recombinant, designated MoLTRAmphoenv in which the amphotropic env of the helper packaging virus was joined to the long terminal repeat (LTR) of the Moloney MuLV-derived vector. This retrovirus does not exist in nature. An additional copy of the core enhancer acquired from the vector LTR may have augmented the replicative properties of MoLTRAmphoenv MuLV in several different rhesus cell types compared with the prototype amphotropic MuLV4070A. Unexpectedly, at least two types of mink cell focus-forming MuLV elements, arising from endogenous retroviral sequences expressed in the murine packaging cell line, were also transmitted and highly expressed in one of the macaques. Furthermore, murine virus-like VL-30 sequences were detected in the rhesus lymphomas, but these were not transcribed into RNA. The unanticipated presence of an array of MuLV-related structures in a primate gene transfer recipient demands ever-vigilant scrutiny for the existence of transmissible retroviral elements and replication-competent viruses possessing altered tropic or growth properties in packaging cells producing retroviral vectors.

Distribution of baboon endogenous virus among species of African monkeys suggests multiple ancient cross-species transmissions in shared habitats

PCR amplification of baboon endogenous virus (BaEV) long terminal repeat, reverse transcriptase gene, and env fragments from 24 different species of African monkeys indicates that BaEV is less widespread than was formerly thought. Instead of being present in every species of African primates, BaEV can be found only in baboons, geladas, and mangabeys (all belonging to the Papionini tribe) and in African green monkey (Cercopithecus aethiops)subspecies. BaEV, which can be activated from baboon and gelada tissues, was most likely introduced in the germ line only recently (less than a few million years ago) and has not been inherited from a common ancestor of all extant African monkeys. Neighbor-joining and maximum-likelihood analyses of the sequences obtained showed that two distinct virus clusters can be distinguished: the first containing baboon, gelada, and African green monkey BaEV sequences and the second consisting of mandrill and mangabey BaEV sequences. This viral evolutionary tree does not follow host phylogeny, indicating the cross-species transmissions and multiple germ line fixations of the virus must have occurred in the past. BaEV sequences are found in monkeys inhabiting savannas (baboons, geladas, and African green monkeys) as well as forests (managabeys and mandrills) and cluster according to the habitats of their hosts, providing evidence for cross-species transmission in shared habitats.

Full-length proviruses of baboon endogenous virus (BaEV) and dispersed BaEV reverse transcriptase retroelements in the genome of baboon species

Baboon endogenous virus (BaEV) is present in multiple copies in many Old World monkey species. BaEV proviruses may contain open reading frames for all major genes, as is indicated by the rescue of infectious virus particles from baboon and gelada tissues after cocultivation with permissive cells. We have analyzed full-length BaEV proviral structures in a baboon (Papio cynocephalus) genomic library and found no evidence for the rearrangements or large deletions commonly observed in endogenous virus genomes from other mammalian species. The two proviruses studied were integrated next to or nearby long interspersed repeat sequence (LINE) transposable elements. Additionally, isolated dispersed fragments with 100% and approximately 77% homology, respectively, to part of the BaEV reverse transcriptase gene were detected. These presumed retroelements were present in an approximately 10-fold excess compared with the full-length proviral genomes. PCR amplification and sequencing of BaEV reverse transcriptase and env fragments from the lambda clones and from the genomic DNA of other baboon species showed that there is little sequence variation present in BaEV DNA in the baboon genome.

Biology of retroviruses: detection, molecular biology, and treatment of retroviral infection

The general physical characteristics and replication of retroviruses are considered, along with assays for viral products. The specific agent for acquired immunodeficiency syndrome, the human immunodeficiency virus (HIV), is characterized as a lentivirus causing persistent, lifelong infection. While human immunodeficiency virus retroviruses share many of the same properties as other replication-competent viruses, genetic variability occurs among HIV isolates, and this variability may have a considerable effect on the virus' virulence, cell type specificity, viral susceptibility to antiviral compounds, clinical presentation, and disease progression. The most notable difference between HIV replication and other retroviruses is the intricate control of HIV gene expression by viral and cellular factors. Possible mechanisms by which HIV kills infected cells include the formulation of multinucleate syncytia; cytopathic components within the virions themselves; and interaction between viral envelope proteins and the CD4 molecule on the cell surface. Agents shown to inhibit viral replication at the level of the reverse transcriptase are phosphonoformate, sulfated polysaccharides, rifabutin, and nucleoside analogs, as well as purine and pyrimidine analogs. To date, only one nucleoside analog, zidovudine, has demonstrated clear clinical benefit and anti-HIV activity.

Detection and immunochemical characterization of a primate type C retrovirus-related p30 protein in normal human placentas

We find that 12 of 14 specimens of normal human term placentas analyzed by one- or two-dimensional electrophoresis and immunoblotting contain a protein or polypeptide of approximately equal to 30,000 daltons that is antigenically cross-reactive with p30 core protein of the simian sarcoma-associated virus/gibbon ape leukemia virus primate retrovirus group and is physicochemically similar to reference murine and primate type C retrovirus p30s. This finding may lead to an understanding of endogenous type C retrovirus gene expression in humans.

Efficient isolation of endogenous rhesus retrovirus from trophoblast

An examination of various rhesus monkey (Macaca mulatta) organs has shown a preference for type C viral antigen expression in the placenta. Separate cocultivations of isolated trophoblasts from 10 rhesus monkey placentas with cell lines from heterologous mammalian species led to rapid isolation of type C rhesus retrovirus in 4 of 10 cases. These four retrovirus isolates have been designated MMC-2 through MMC-5. Five of the remaining six sets of cocultivations grew simian foamy virus and were discontinued. Distinction of these viral isolates from the initial rhesus isolate (MMC-1) and the previous isolate from the stumptail monkey, Macaca arctoides (MAC-1), could be made by liquid DNA hybridization, although not by limited restriction endonuclease digestion. Both MAC-1 and MMC-1 were obtained in single long-term cocultivation experiments (over 7 months). The present isolates MMC-2 through MMC-5 were detected in 2 to 5 weeks. Consequently, primary trophoblast cells represent a useful differentiated cell type for isolation of infectious retrovirus from this primate species.

Isolation of a unique retrovirus, MNV-1, from Macaca nemestrina

Cell cultures established from the spleen of a Macaca nemestrina with enzootic retroperitoneal fibromatosis (ERF) spontaneously released a unique retrovirus. Throughout 14 serial passages, the spleen cell cultures remained fibroblastic and no cytopathic effect was evident. The virus incorporates [3H]uridine, contains an RNA-dependent DNA polymerase (RDDP), has a buoyant density of 1.15 g/cm3 in sucrose, and was designated MNV-1. Virion-associated reverse transcriptase showed no preference for either Mg2+ or Mn2+ in standard RDDP assays. Complementary DNA (cDNA) transcribed from polyadenylated MNV-1 RNA hybridized to genomic DNA and RNA extracted from diseased tissues but not to nucleic acids from normal tissues of a healthy Macaca nemestrina or a Macaca mulatta. MNV-1 is therefore exogenous to these species. MNV-1 had no detectable homology to the endogenous macaque virus isolates MAC-1 and MMC-1. Liquid hybridization of MNV-1 cDNA to viral RNA derived from exogenous and endogenous subhuman primate retroviruses (SiSV(SSAV), GALV-SF, BaEV-M7, and BILN) did not reveal any significant sequence homologies. In addition, MNV-1 does not share homology with bovine leukemia virus or Mason-Pfizer monkey virus as determined by Southern blot hybridization. We conclude that MNV-1 is a unique retrovirus which has not previously been described. As the ultrastructure of virions in in vitro cell cultures, as well as disease involved tissue, show some particles with type C morphology and others with type D morphology, MNV-1 may be comprised of more than one component.

In vivo modification of retroviral gag gene-encoded polyproteins by myristic acid

It has recently been shown by mass spectral analysis (Henderson et al., Proc. Natl. Acad. Sci. U.S.A. 80:339-343, 1983) that the p15gag protein of murine leukemia viruses contains a novel post-translational modification, an amino-terminal myristyl (tetradecanoyl) amide. In this report we show that p15gag is the only structural protein to contain this fatty acid. In addition, the gag precursor polyproteins of type B, C, and D retroviruses have been examined for the presence of myristic acid by metabolic labeling and immunoprecipitation studies. In a panel of mammalian type C retroviruses we found that the precursor polyprotein Pr65gag homologs, but not the glycosylated forms (gPr80gag homologs), were specifically labeled after a 5-min incubation of infected cells with [3H]myristic acid. The gag precursor polyprotein was also labeled in mouse mammary tumor virus and in Mason-Pfizer monkey virus, but Pr76gag of Rous sarcoma virus failed to incorporate [3H]myristate. Under similar conditions, [3H]palmitate was not found to be incorporated into any viral gag proteins. Thus, myristylation appears to be a common feature of mammalian type B, C, and D retroviruses but not of avian retroviruses.

Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites

We find that both human and rat U3 snRNA can function as self-priming templates for AMV reverse transcriptase in vitro. The 74 base cDNA is primed by the 3' end of intact U3 snRNA, and spans the characteristically truncated 69 or 70 base U3 sequence found in four different human U3 pseudogenes. The ability of human and rat U3 snRNA to self-prime is consistent with a U3 secondary structure model derived by a comparison between rat U3 snRNA and the homologous D2 snRNA from Dictyostelium discoideum. We propose that U3 pseudogenes are generated in vivo by integration of a self-primed cDNA copy of U3 snRNA at new chromosomal sites. We also consider the possibility that the same cDNA mediates gene conversion at the 5' end of bona fide U3 genes where, over the entire region spanned by the U3 cDNA, the two rat U3 sequence variants U3A and U3B are identical.

Molecular cloning of a family of retroviral sequences found in chimpanzee but not human DNA

A number of retrovirus-like sequences have been cloned from chimpanzee DNA which constitute the chimpanzee homologs of the endogenous colobus type C virus CPC-1. One of the clones contains a nearly complete viral genome, but others have sustained deletions of 1 to 2 kilobases in the polymerase gene. The pattern of related sequences detected in other primate species is consistent with the genetic transmission of these sequences for millions of years. However, the appropriately related sequences have not been detected in human, gibbon, or orangutan DNAs. These results suggest either that this family of sequences has been deleted from humans, gibbons, and orangutans, or that the genes were recently acquired in the chimpanzee and gorilla lineages.

Colobus type C virus: molecular cloning of unintegrated viral DNA and characterization of the endogenous viral genomes of Colobus

The unintegrated viral DNA intermediates of colobus type C virus (CPC-1) were isolated from infected human cells that were permissive for viral growth. There were two major species of DNA, linear molecules with two copies of the long terminal repeat and relaxed circles containing only a single long terminal repeat. In addition, there was a minor species (approximately 10%) composed of relaxed circles with two copies of the long terminal repeat. A restriction endonuclease map of the unintegrated DNA was constructed. The three EcoRI fragments of circular CPC-1 DNA were cloned in the EcoRI site of lambda gtWES . lambda B and then subcloned in the EcoRI site of pBR322. Using these subgenomic fragments as probes, we have characterized the endogenous viral sequences found in colobus cellular DNA. They are not organized in tandem arrays, as is the case in some other gene families. The majority of sequences detected in cellular DNA have the same map as the CPC-1 unintegrated DNA at 17 of 18 restriction endonuclease sites. There are, however, other sequences that are present in multiple copies and do not correspond to the CPC-1 map. They do not contain CPC-1 sequences either in an altered form or fused to common nonviral sequences. Instead, they appear to be derived from a distinct family of sequences that is substantially diverged from the CPC-1 family. This second family of sequences, CPC-2, is also different from the sequences related to baboon endogenous type C virus that forms a third family of virus-related sequences in the colobus genome.

Chemical and Immunological characterization of the major structural protein (p28) of MMC-1, a rhesus monkey endogenous type C virus: homology with the major structural protein of avian reticuloendotheliosis virus

The major core protein (p28) of MMC-1, an endogenous type C virus of the rhesus monkey (Macaca mulatta), was purified and subjected to structural and immunological analyses. The NH2-terminal amino acid sequence of MMC-1 p28 showed extensive homology to the sequences of the major structural proteins (p30) of known mammalian type C viruses. Similarly, interspecies antigenic determinants shared by all the above viral proteins were detected in MMC-1 p28. Competition radioimmunoassays together with the results of statistical analysis of the primary structure data provided evidence that MMC-1 p28 is not more closely related to primate type C viruses of the Papio genus than to those isolated from rodents, cats, or New World monkeys. MMC-1 p28 was found to be closely related structurally to the p30 protein of the avian reticuloendotheliosis virus (REV-A), a horizontally transmitted type C virus of putative mammalian origin. In addition, MMC-1 p28 and REV-A p30 shared a specific subset of antigenic determinants not present in any of the other avian or mammalian type C viruses studied. These findings suggest that MMC-1 and REV may have a common evolutionary origin.

Detection and cloning of murine leukemia virus-related sequences from African green monkey liver DNA

By using low-stringency nucleic acid hybridization conditions and specific subgenomic segments of the AKR ecotropic provirus as probes, murine leukemia virus (MuLV)-related sequences were detected in African green monkey (AGM) liver DNA. The MuLV-reactive segments present in restricted AGM DNA ranged from 1.9 kilobases (kb) to greater than 10 kb in size. On the basis of this finding, a 17-kb segment was cloned from a partial EcoRI AGM library in lambda Charon 4A which shared nearly 5 kb of homology with AKR ecotropic MuLV DNA. The MuLV-related sequences detected in restricted preparations of AGM DNA or present in the cloned monkey DNA reacted with probes mapping 2.0 to 7.0 kb from the 5' terminus of the AKR ecotropic provirus. The AGM clone also contained repeated sequences that flanked the MuLV-related segment. Labeled, subgenomic, MuLV-reactive segments of the monkey clone hybridized to multiple restriction fragments of AGM liver DNA, indicating the presence of several copies of the MuLV-related sequences.

Identification and cloning of endogenous retroviral sequences present in human DNA

Using nonstringent annealing conditions and a 2.75-kilobase segment of cloned African green monkey DNA that specifically hybridizes to the proviruses of AKR ecotropic murine leukemia virus (MuLV) and baboon endogenous virus (BaEV) as a probe, we detected related sequences in three different preparations of human brain DNA fragments. The blot-hybridization pattern obtained with cleaved human DNA was similar to that previously reported for the interaction of MuLV cDNA and cleaved mouse DNA and suggested the presence of numerous copies of retrovirus-related sequences in the human genome. The labeled 2.75-kilobase fragment derived from cloned monkey DNA was used to screen a human DNA library in Charon 4A. One clone obtained hybridized to three contiguous MuLV-and BaEV-reactive fragments of the cloned monkey DNA and to multiple fragments of human DNA including a prominent 1.0-kilobase EcoRI fragment also present in the clone.

5'-terminal nucleotide noncoding sequences of retroviruses: relatedness of two old world primate type C viruses and avian spleen necrosis virus

Computer-assisted comparison of the 5'-terminal regions of mammalian type C viruses serves as a useful model of evolutionary divergence of noncoding nucleic acid sequences. It has led to the concept that regions of conserved nucleic acid sequences, the slowly divergent sequences, contain signals of translational, transcriptional, or integrative significance. Interspersed among the conserved regions are rapidly divergent sequences in which base changes, insertions, and deletions are especially prevalent. In the present study, CPC-1, a type C virus isolated from Colobus polykomos, was shown to be related to another Old World type C monkey virus, endogenous stump-tailed monkey virus, MAC-1, by analysis of their 5'-terminal nucleotide sequences. The 5'-terminal regions of CPC-1 and MAC-1 showed a 76% nucleotide correspondence and were of similar lengths, 132 and 127 nucleotides, respectively. Previous strong-stop analyses of other type C viruses have defined two subgroups: (i) Rauscher murine leukemia virus and gibbon ape leukemia virus and (ii) baboon endogenous virus and endogenous cat virus RD114. Based on the present sequence analysis of their 5'-terminal sequences, CPC-1 and MAC-1 formed a third subgroup. Computer-assisted comparison of the 5'-terminal sequences of CPC-1 and MAC-1 to the previously reported sequence of avian spleen necrosis virus (SNV) (Shimotohno et al., Nature [London] 285:550-554, 1980) showed SNV to be a member of that subgroup of mammalian type C viruses. Consistent with the inclusion of SNV in this subgroup of mammalian type C viruses, SNV was distantly related to other mammalian type C viruses. Interestingly, the SNV 5'-terminal sequences showed no significant evolutionary relationship by these criteria to the avian leukemia and sarcoma viruses. CPC-1, MAC-1, and SNV contained conserved regulatory signals in similar positions in their 5'-terminal RNA sequences analogous to those observed in other mammalian type C retroviruses. These sequences included the canonical AAUAAA sequence, a palindrome, a putative ribosome binding site, and an integration site. Some of these highly conserved subsequences were common to 3'- and 5'-terminal noncoding sequences of nonviral eucaryotic mRNA's (Efstratiadis et al., Cell 21:653-668, 1980). Thus, analysis and comparison of 5'-terminal nucleotide sequences have been useful in defining common functional signals and in extending the matrix of relationships among retroviruses.

Analysis of the virogenes related to the rhesus monkey endogenous type C retrovirus in monkeys and apes

Molecular hybridization studies were carried out by using a [3H]complementary DNA (cDNA) probe to compare the endogenous type C retrovirus of rhesus monkeys (MMC-1) with other known retroviruses and related sequences in various primate DNAs. The genomic RNA of the endogenous type C retrovirus of stumptail monkeys (MAC-1) was found to be highly related to the MMC-1 cDNA probe, whereas the other retroviral RNAs tested showed no homology. Related sequences were found in Old World monkey DNAs and to a lesser extent in gorilla dn chimpanzee DNAs. No homology was detected between MMC-1 cDNA and DNA of gibbon, orangutan, or human origin. Restriction endonuclease analysis of genomic DNA indicated that many of the several hundred sequences related to MMC-1 in rhesus monkey DNA differed from that integrated into DNA of infected canine cells. Gorilla and chimpanzee DNAs contained a specific restriction endonuclease fragment of the MMC-1 genome.

The baboon endogenous virus genome. II. Provirus sequence variations in baboon cell DNA

Restriction analysis of the approximately 100 integrated baboon endogenous virus (BaEV) proviruses in baboon cells and tissues has revealed two major sequence variations, both in the gag gene region of the genome. One, a 150 nucleotide pair insert, is present in a small proportion of the proviral DNAs and some baboons, but is present in the majority of the proviral DNAs of other baboons. The second, a Bam HI recognition sequence located 2.25 kb from the proviral 5' end, is missing or modified in approximately one-half of the integrated genomes. We consider the possibility that accumulation of proviruses not containing the 0.15 kb insert is correlated with viral activation and expression since it is this form that is a replication intermediate in freshly infected permissive cells. It is evident from these initial studies that the organization of the multiple BaEV proviruses in baboon DNA has undergone modification during evolution.