Sequence analysis of the simian foamy virus type 1 genome

Spumaretroviruses: Updated taxonomy and nomenclature

Spumaretroviruses, commonly referred to as foamy viruses, are complex retroviruses belonging to the subfamily Spumaretrovirinae, family Retroviridae, which naturally infect a variety of animals including nonhuman primates (NHPs). Additionally, cross-species transmissions of simian foamy viruses (SFVs) to humans have occurred following exposure to tissues of infected NHPs. Recent research has led to the identification of previously unknown exogenous foamy viruses, and to the discovery of endogenous spumaretrovirus sequences in a variety of host genomes. Here, we describe an updated spumaretrovirus taxonomy that has been recently accepted by the International Committee on Taxonomy of Viruses (ICTV) Executive Committee, and describe a virus nomenclature that is generally consistent with that used for other retroviruses, such as lentiviruses and deltaretroviruses. This taxonomy can be applied to distinguish different, but closely related, primate (e.g., human, ape, simian) foamy viruses as well as those from other hosts. This proposal accounts for host-virus co-speciation and cross-species transmission.

Complete Genome Sequence of a Naturally Occurring Simian Foamy Virus Isolate from Rhesus Macaque (SFVmmu_K3T)

The full-length genome sequence of a simian foamy virus (SFVmmu_K3T), isolated from a rhesus macaque (Macaca mulatta), was obtained using high-throughput sequencing. SFVmmu_K3T consisted of 12,983 bp and had a genomic organization similar to that of other SFVs, with long terminal repeats (LTRs) and open reading frames for Gag, Pol, Env, Tas, and Bet.

Foamy-like endogenous retroviruses are extensive and abundant in teleosts

Recent discoveries indicate that the foamy virus (FV) (Spumavirus) ancestor may have been among the first retroviruses to appear during the evolution of vertebrates, demonstrated by foamy endogenous retroviruses present within deeply divergent hosts including mammals, coelacanth, and ray-finned fish. If they indeed existed in ancient marine environments hundreds of millions of years ago, significant undiscovered diversity of foamy-like endogenous retroviruses might be present in fish genomes. By screening published genomes and by applying PCR-based assays of preserved tissues, we discovered 23 novel foamy-like elements in teleost hosts. These viruses form a robust, reciprocally monophyletic sister clade with sarcopterygian host FV, with class III mammal endogenous retroviruses being the sister group to both clades. Some of these foamy-like retroviruses have larger genomes than any known retrovirus, exogenous or endogenous, due to unusually long gag-like genes and numerous accessory genes. The presence of genetic features conserved between mammalian FV and these novel retroviruses attests to a foamy-like replication biology conserved for hundreds of millions of years. We estimate that some of these viruses integrated recently into host genomes; exogenous forms of these viruses may still circulate.

An expanded search for simian foamy viruses (SFV) in Brazilian New World primates identifies novel SFV lineages and host age-related infections

Background

While simian foamy viruses have co-evolved with their primate hosts for millennia, most scientific studies have focused on understanding infection in Old World primates with little knowledge available on the epidemiology and natural history of SFV infection in New World primates (NWPs). To better understand the geographic and species distribution and evolutionary history of SFV in NWPs we extend our previous studies in Brazil by screening 15 genera consisting of 29 NWP species (140 monkeys total), including five genera (Brachyteles, Cacajao, Callimico, Mico, and Pithecia) not previously analyzed. Monkey blood specimens were tested using a combination of both serology and PCR to more accurately estimate prevalence and investigate transmission patterns. Sequences were phylogenetically analyzed to infer SFV and host evolutionary histories.

Results

The overall serologic and molecular prevalences were 42.8 and 33.6 %, respectively, with a combined assay prevalence of 55.8 %. Discordant serology and PCR results were observed for 28.5 % of the samples, indicating that both methods are currently necessary for estimating NWP SFV prevalence. SFV prevalence in sexually mature NWPs with a positive result in any of the WB or PCR assays was 51/107 (47.7 %) compared to 20/33 (61 %) for immature animals. Epidemiological analyses revealed an increase in SFV prevalence with age in captive Cebus monkeys. Phylogenetic analysis identified novel SFVs in Cacajao,Leontopithecus, and Chiropotes species that had 6–37 % nucleotide divergence to other NWP SFV. Comparison of host and SFV phylogenies showed an overall cospeciation evolutionary history with rare ancient and contemporaneous host-switching for Saimiri and Leontopithecus and Cebus xanthosternos, respectively.

Conclusions

We identified novel SFV in four neotropical monkey genera in Brazil and demonstrate that SFV prevalence increases with age in Cebus monkeys. Importantly, our test results suggest that both molecular and serological screening are currently required to accurately determine infection with NWP SFV. Our study significantly expands knowledge of the epidemiology and natural history of NWP SFVs. The tools and information provided in our study will facilitate further investigation of SFV in NWPs and the potential for zoonotic infection with these viruses.

Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution

Background

Foamy viruses (FVs) are a unique subfamily of retroviruses that are widely distributed in mammals. Owing to the availability of sequences from diverse mammals coupled with their pattern of codivergence with their hosts, FVs have one of the best-understood viral evolutionary histories ever documented, estimated to have an ancient origin. Nonetheless, our knowledge of some parts of FV evolution, notably that of prosimian and afrotherian FVs, is far from complete due to the lack of sequence data.

Results

Here, we report the complete genome of the first extant prosimian FV (PSFV) isolated from a lorisiforme galago (PSFVgal), and a novel partial endogenous viral element with high sequence similarity to FVs, present in the afrotherian Cape golden mole genome (ChrEFV). We also further characterize a previously discovered endogenous PSFV present in the aye-aye genome (PSFVaye). Using phylogenetic methods and available FV sequence data, we show a deep divergence and stable co-evolution of FVs in eutherian mammals over 100 million years. Nonetheless, we found that the evolutionary histories of bat, aye-aye, and New World monkey FVs conflict with the evolutionary histories of their hosts. By combining sequence analysis and biogeographical knowledge, we propose explanations for these mismatches in FV-host evolutionary history.

Conclusion

Our discovery of ChrEFV has expanded the FV host range to cover the whole eutherian clade, and our evolutionary analyses suggest a stable mammalian FV-host co-speciation pattern which extends as deep as the exafroplacentalian basal diversification. Nonetheless, two possible cases of host switching were observed. One was among New World monkey FVs, and the other involves PSFVaye and a bat FV which may involve cross-species transmission at the level of mammalian orders. Our results highlight the value of integrating multiple sources of information to elucidate the evolutionary history of viruses, including continental and geographical histories, ancestral host locations, in addition to the natural history of host and virus.

Electronic supplementary material

The online version of this article (doi:10.1186/1742-4690-11-61) contains supplementary material, which is available to authorized users.

Identification and characterization of highly divergent simian foamy viruses in a wide range of new world primates from Brazil

Foamy viruses naturally infect a wide range of mammals, including Old World (OWP) and New World primates (NWP), which are collectively called simian foamy viruses (SFV). While NWP species in Central and South America are highly diverse, only SFV from captive marmoset, spider monkey, and squirrel monkey have been genetically characterized and the molecular epidemiology of SFV infection in NWPs remains unknown. We tested a large collection of genomic DNA (n = 332) comprising 14 genera of NWP species for the presence of SFV polymerase (pol) sequences using generic PCR primers. Further molecular characterization of positive samples was carried out by LTR-gag and larger pol sequence analysis. We identified novel SFVs infecting nine NWP genera. Prevalence rates varied between 14-30% in different species for which at least 10 specimens were tested. High SFV genetic diversity among NWP up to 50% in LTR-gag and 40% in pol was revealed by intragenus and intrafamilial comparisons. Two different SFV strains infecting two captive yellow-breasted capuchins did not group in species-specific lineages but rather clustered with SFVs from marmoset and spider monkeys, indicating independent cross-species transmission events. We describe the first SFV epidemiology study of NWP, and the first evidence of SFV infection in wild NWPs. We also document a wide distribution of distinct SFVs in 14 NWP genera, including two novel co-speciating SFVs in capuchins and howler monkeys, suggestive of an ancient evolutionary history in NWPs for at least 28 million years. A high SFV genetic diversity was seen among NWP, yet these viruses seem able to jump between NWP species and even genera. Our results raise concerns for the risk of zoonotic transmission of NWP SFV to humans as these primates are regularly hunted for food or kept as pets in forest regions of South America.

Identification of recombination in the envelope gene of simian foamy virus serotype 2 isolated from Macaca cyclopis

The full-length sequence of simian foamy virus serotype 2 (SFVmcy-2), isolated from a Taiwanese macaque, was determined. SFVmcy-2 was highly related to SFV serotype 1 (SFVmcy-1), an isolate from the same species, except in the putative receptor binding domain (RBD) in env, which contained novel sequences related to SFV serotype 3 (SFVagm-3), isolated from an African green monkey. The results identify a potential region of neutralization in SFVs and demonstrate recombination between genetically divergent foamy viruses.

Regulation of foamy viral transcription and RNA export

Foamy viruses (FVs) are distinct members of the retrovirus (RV) family. In this chapter, the molecular regulation of foamy viral transcription, splicing, polyadenylation, and RNA export will be compared in detail to the orthoretroviruses. Foamy viral transcription is regulated in early and late phases, which are separated by the usage of two promoters. The viral transactivator protein Tas activates both promoters. The nature of this early-late switch and the molecular mechanism used by Tas are unique among RVs. RVs duplicate the long terminal repeats (LTRs) during reverse transcription. These LTRs carry both a promoter region and functional poly(A) sites. In order to express full-length transcripts, RVs have to silence the poly(A) signal in the 5' LTR and to activate it in the 3' LTR. FVs have a unique R-region within these LTRs with a major splice donor (MSD) at +51 followed by a poly(A) signal. FVs use a MSD-dependent mechanism to inactivate the polyadenylation. Most RVs express all their genes from a single primary transcript. In order to allow expression of more than one gene from this RNA, differential splicing is extensively used in complex RVs. The splicing pattern of FV is highly complex. In contrast to orthoretroviruses, FVs synthesize the Pol precursor protein from a specific and spliced transcript. The LTR and IP-derived primary transcripts are spliced into more than 15 different mRNA species. Since the RNA ratios have to be balanced, a tight regulation of splicing is required. Cellular quality control mechanisms retain and degrade unspliced or partially spliced RNAs in the nucleus. In this review, I compare the RNA export pathways used by orthoretroviruses with the distinct RNA export pathway used by FV. All these steps are highly regulated by host and viral factors and set FVs apart from all other RVs.

AZT-resistant foamy virus

Azidothymidine (AZT) is a reverse transcriptase (RT) inhibitor that efficiently blocks the replication of spumaretroviruses or foamy viruses (FVs). To more precisely elucidate the mechanism of action of the FV RT enzyme, we generated an AZT-resistant FV in cell culture. Biologically resistant virus was obtained for simian foamy virus from macaque (SFVmac), which was insensitive to AZT concentrations of 1 mM, but not for FVs derived from chimpanzees. Nucleotide sequencing revealed four non-silent mutations in the pol gene. Introduction of these mutations into an infectious molecular clone identified all changes to be required for the fully AZT-resistant phenotype of SFVmac. The alteration of individual sites showed that AZT resistance in SFVmac was likely acquired by consecutive acquisition of pol mutations in a defined order, because some alterations on their own did not result in an efficiently replicating virus, neither in the presence nor in the absence of AZT. The introduction of the mutations into the RT of the closely related prototypic FV (PFV) did not yield an AZT-resistant virus, instead they significantly impaired the viral fitness.

Isolation and characterization of a new simian retrovirus type D subtype from monkeys at the Tsukuba Primate Center, Japan

Exogenous type D simian retroviruses (SRV/D) are prevalent in captive and feral populations of various macaque monkeys. Thus far, five subtypes of SRV/Ds have been reported, three of which (SRV-1, -2 and -3) have been molecularly characterized. Two SRV/D strains (N27 and T150) were isolated from seropositive cynomolgus macaques at the Tsukuba Primate Center (TPC) in Japan, showing clinical signs of SRV/D infection, including anemia and persistent unresponsive diarrhea. Electron microscopy demonstrated that both SRV/D isolates have a virion morphology typical of type D retrovirus. The SRV/D N27 and T150 isolates were essentially the same based on sequence analysis. From homology analysis of the entire gag sequence, the N27 isolate is closely related to the other known SRV/Ds but is distinct from the three molecularly characterized SRV/Ds. Thus, we have tentatively designated the N27 and T150 viruses isolated from TPC cynomolgus macaques as SRV/D-Tsukuba (SRV/D-T).

Foamy virus vectors

Gene therapy is a promising novel treatment for a variety of human diseases. Successful application of gene therapy requires the availability of vehicles with the ability to efficiently deliver and express genes. Viral vectors are efficient means of transferring a gene of interest into target cells. Current available vehicles for gene transfer are either inefficient or potentially unsafe for human gene therapy applications. Foamy viruses offer a fresh alternative vector system for gene transfer with the potential to overcome the concerns of the current vectors. Foamy viruses are nonpathogenic and have a broad host range with the ability to infect various types of cells from different species. Foamy virus replication is distinct and may provide an edge for foamy virus vector usage over other retroviral vectors. These features offer the foamy vectors unique opportunities to deliver several genes into a number of different cell types in vivo safely and efficiently. The principal problems for the design of foamy virus vectors have been solved, and several foamy virus vectors that efficiently transduce a variety of cell types are available. This chapter reviews specific features of foamy virus vector systems and recent advances in the development and use of these vectors.

Structural and evolutionary analysis of an orangutan foamy virus

The full-length proviral genome of a foamy virus infecting a Bornean orangutan was amplified, and its sequence was analyzed. Although the genome showed a clear resemblance to other published foamy virus genomes from apes and monkeys, phylogenetic analysis revealed that simian foamy virus SFVora was evolutionarily equidistant from foamy viruses from other hominoids and from those from Old World monkeys. This finding suggests an independent evolution within its host over a long period of time.

Low-level expression of functional foamy virus receptor on hematopoietic progenitor cells

Foamy viruses have several qualities favorable for vector development: they are not known to cause disease; they can transduce stationary cells; and the foamy virus receptor is expressed on a wide variety of cells. Here, we analyzed the level of virus receptor expression on hematopoietic progenitor cells. Foamy virus binding was measured by a flow cytometric assay and was found to be considerably reduced in hematopoietic progenitors cell lines as well as in primary CD34(+) cells when compared to fibroblasts. Retroviral vectors based on murine leukemia virus (MLV) pseudotyped with a foamy virus envelope transduced hematopoietic cell lines with a more than 10-fold lower efficiency than fibroblasts. Moreover, less than 1% of primary CD34(+) hematopoietic progenitor cells were transduced with the foamy virus pseudotypes, while gene transfer efficiencies of 8-40% were achieved using pseudotypes with amphotropic envelope or the G protein of vesicular stomatitis virus. In conclusion, the expression of functional foamy virus receptors on hematopoietic progenitors cells was found to be insufficient to achieve high levels of gene transfer into CD34(+) hematopoietic progenitor cells with cell-free vector supernatants using current transduction protocols.

Double-stranded RNA as a not-self alarm signal: to evade, most viruses purine-load their RNAs, but some (HTLV-1, Epstein-Barr) pyrimidine-load

For double-stranded RNA (dsRNA) to signal the presence of foreign (non-self) nucleic acid, self-RNA-self-RNA interactions should be minimized. Indeed, self-RNAs appear to have been fine-tuned over evolutionary time by the introduction of purines in clusters in the loop regions of stem-loop structures. This adaptation should militate against the "kissing" interactions which initiate formation of dsRNA. Our analyses of virus base compositions suggest that, to avoid triggering the host cell's dsRNA surveillance mechanism, most viruses purine-load their RNAs to resemble host RNAs ("stealth" strategy). However, some GC-rich latent viruses (HTLV-1, EBV) pyrimidine-load their RNAs. It is suggested that when virus production begins, these RNAs suddenly increase in concentration and impair host mRNA function by virtue of an excess of complementary "kissing" interactions ("surprise" strategy). Remarkably, the only mRNA expressed in the most fundamental form of EBV latency (the "EBNA-1 program") is purine-loaded. This apparent stealth strategy is reinforced by a simple sequence repeat which prefers purine-rich codons. During latent infection the EBNA-1 protein may evade recognition by cytotoxic T-cells, not by virtue of containing a simple sequence amino acid repeat as has been proposed, but by virtue of the encoding mRNA being purine-loaded to prevent interactions with host RNAs of either genic or non-genic origin.

Simian foamy virus infections in a baboon breeding colony

The prevalence, transmission, and variation of simian foamy viruses (SFVs) in baboons was investigated. Over 95% of adult baboons in the breeding colony as well as recently imported adult animals had high titers of anti-SFV serum IgG. Maternal antibody was detectable in infants' serum up to 6 months of age. Approximately 30% of infants in breeding harems experienced SFV infections by 1 year of age. Shedding of SFV in oral secretions was common, with 13% of samples from normal adult animals and 35% from immunosuppressed animals containing infectious SFV. SFV was isolated from three baboon subspecies (olive, yellow, and chacma baboons) and sequences from both the pol and the LTR regions of the provirus were amplified by PCR and sequenced. Phylogenetic analysis indicated that all baboon isolates formed a single lineage distinct from SFVs of other African monkey species. Within the baboon SFV lineage, two distinct clades were apparent, which consisted of isolates from yellow and olive baboons and isolates from chacma baboons. Competition ELISAs indicated that, while SFV isolates of these two groups were very closely related, antigenic differences do exist between them. SFV isolates from a drill and a mandrill were distinct from baboon SFV isolates, both genetically and antigenically.

Mutational analysis of the 5' leader region of simian foamy virus type 1

The sequence within the 5' untranslated region of the retroviral genome contains important cis elements for many steps in viral replication. There is limited information available on the role of this region in foamy virus replication. Similar to other retroviruses, the 5' untranslated region of foamy viruses predicts extensive RNA secondary structure. Serial mutations that could change parts of the predicted secondary structure were introduced in the 5' leader sequence including the R-U5 region of simian foamy virus type 1 (SFV-1) to investigate their role in virus genome packaging and virus replication. Point mutations in the R-U5 regions at nucleotide positions 7-12 (I), 241-243 (B), and 256-257 (D) had no effect on virus replication. Base substitution mutation at positions 193-195 (C), however, severely impaired virus replication. Deletion of sequences in the leader region, between the primer-binding site and the gag gene, at positions 364-399 (d1), 397-435 (d2), or 364-435 (d3), which included sequences for RNA genome dimerization, also blocked SFV-1 replication. Interestingly, none of these mutations affected genome packaging or the synthesis of viral transcripts, suggesting that a step(s) of virus replication following packaging is affected. The region between the primer-binding site and the gag gene, therefore, is not essential for foamy virus genome packaging. Furthermore, the cis-acting elements for genome dimerization and packaging appear to be localized in separate regions for foamy viruses.

Genetic stability of foamy viruses: long-term study in an African green monkey population

The genetic variability of the envelope surface domain (SU) of simian foamy virus (FV) of African green monkeys was studied. To assess the interindividual diversity of FV, isolates were obtained from 19 animals living together in a monkey house. The monkeys had been imported from Kenya prior to being placed in long-term housing in the research institute. In addition, a simian FV isolate and proviral DNA were obtained from an animal caretaker infected in this setting. DNA of the complete SU (1779 to 1793 bp) was analyzed by PCR and sequencing. The sequences revealed four clusters with high homologies (>95%). Between the clusters, divergencies ranged from 3 to 25%. Obviously, the clusters reflect four different strains or subtypes of simian FV type 3 that were prevalent in the colony. In contrast to lentiviruses, hypervariable regions could not be detected in the FV SU. Furthermore, to analyze the intraindividual diversity of FV, we investigated the virus population within an individual monkey at a given time point and its evolution over 13 years. For this purpose, 22 proviral SU clones generated by PCR from one oral swab and seven isolates obtained from the same animal between 1982 and 1995 were examined. These sequences revealed exceptionally high homology rates (99.5 to 100%), and only a minimal genetic drift was recognized within the series of isolates. In conclusion, the low in vivo divergency of FV SU suggests that genetic variability is not important for the maintenance of FV persistence.

Sensitive assays for isolation and detection of simian foamy retroviruses

Simian foamy viruses (SFVs) are highly prevalent in a variety of nonhuman primate species ranging from prosimians to apes. SFVs possess a broad host range, and human infections can occur by cross-species transfer (W. Heneine et al., Nat. Med. 4:403-407, 1998). Retrovirus screening of potential sources of infection, such as laboratory research animals and simian-derived biological products, could minimize human exposure to SFVs by reducing the risk of potential retrovirus infection in humans. We describe a variety of sensitive assays for SFV isolation and detection which were developed with a prototype strain of SFV serotype 2. The Mus dunni cell line (M. R. Lander and S. K. Chattopadhyay, J. Virol. 52:695-698, 1984) was found to be highly sensitive for SFV production on the basis of various general and specific retrovirus detection assays such as reverse transcriptase assay, transmission electron microscopy, immunofluorescence assay, and Western blotting. A highly sensitive PCR assay was developed on the basis of the sequences in primary SFV isolates obtained from pig-tailed macaques (Macaca nemestrina) and rhesus macaques (Macaca mulatta). Analysis of naturally occurring SFV infection in macaques indicated that analysis by a combination of assays, including both highly sensitive, specific assays and less sensitive, broadly reactive assays, is important for evaluation of retrovirus infection.

Detection and molecular characterisation of feline foamy virus serotypes in naturally infected cats

The characterisation of two distinct feline foamy virus sequence groupings in the external surface portion of the viral env gene are reported. Although amino acid identities in the Gag nucleocapsid, Pol protease, and Env transmembrane domains were greater than 92% in the 12 proviral sequences examined, two distinct sequence groups were observed in the Env surface (SU) protein. Only 57% amino acid identity was observed in the Env SU between the two groups designated FUV7-like or 951-like, while within these groups > 97% identity was found. Isolates FUV7 and 951 represent two serogroups previously characterised by Flower et al. (1985). A 100% correlation was found among FeFV seroreactivity, virus isolation, and detection of viral DNA in feline leucocytes using a single round of PCR amplification. Serum neutralisation assay using autologous virus, as well as isolates 951 and FUV7, revealed that viruses with FUV7-like sequences were in a single neutralisation group and viruses with 951-like sequences were in a single neutralisation group. Based on these results, group-specific PCRs were developed, using the same sense primer with an antisense primer specific for each group. Using he PCR, no evidence of superinfection of any cat with virus from both serogroups was detected.

An evolutionarily conserved splice generates a secreted env-Bet fusion protein during human foamy virus infection

Foamy viruses (spumaretroviruses) represent a retroviral genus which exhibits unusual features relating it to pararetroviruses. Previously, we reported the existence of a protein species harboring Env, Bel, and Bet epitopes in human foamy virus (HFV)-infected cells (M. L. Giron, F. Rozain, M. C. Debons-Guillemin, M. Canivet, J. Périès, and R. Emanoil-Ravier, J. Virol. 67:3596-3600, 1993). Here, we identify this protein as a 160-kDa Env-Bet fusion glycoprotein (gp160) translated from an mRNA species harboring a highly conserved splice site which deletes the membrane anchor domain of Env and fuses the env open reading frame with that of bel1/bet. While gp160 and Bet proteins were both secreted into the supernatant, only Bet was taken up by recipient cells. Since Bet plays a key role in the switch from lytic to chronic infection, secretion of Bet and gp160, together with cellular uptake of Bet, could be highly relevant for both immune response and development of HFV infection in vivo.

cis-Acting sequences required for simian foamy virus type 1 vectors

We have constructed a series of vectors based on simian foamy virus type 1 (SFV-1) to define the minimum cis-acting elements required for gene transfer. To characterize these vectors, we inserted the coding sequence of the bacterial lacZ gene linked to the cytomegalovirus immediate-early gene promoter. Introduction of a deletion mutation in the leader region between the 5' long terminal repeat and the start of the gag gene at position 1659 to 1694 completely abrogated gene transfer by the SFV-1 vector. Deletion of 39 nucleotides from position 1692 to 1731 in the leader region resulted in a significant reduction in the transducing-particle titer. Furthermore, we have identified a second cis-acting element located at the 3' end of the pol gene between position 6486 and 6975 to be critical for SFV-1 vector transduction. These results identify the two important cis-acting elements required for SFV-1 vector construction, and the finding of a cis-acting element in the pol gene is unique among retroviruses.

The nucleotide sequence and spliced pol mRNA levels of the nonprimate spumavirus bovine foamy virus

We have determined the complete nucleotide sequence of a replication-competent clone of bovine foamy virus (BFV) and have quantitated the amount of splice pol mRNA processed early in infection. The 544-amino-acid Gag protein precursor has little sequence similarity with its primate foamy virus homologs, but the putative nucleocapsid (NC) protein, like the primate NCs, contains the three glycine-arginine-rich regions that are postulated to bind genomic RNA during virion assembly. The BFV gag and pol open reading frames overlap, with pro and pol in the same translational frame. As with the human foamy virus (HFV) and feline foamy virus, we have detected a spliced pol mRNA by PCR. Quantitatively, this mRNA approximates the level of full-length genomic RNA early in infection. The integrase (IN) domain of reverse transcriptase does not contain the canonical HH-CC zinc finger motif present in all characterized retroviral INs, but it does contain a nearby histidine residue that could conceivably participate as a member of the zinc finger. The env gene encodes a protein that is over 40% identical in sequence to the HFV Env. By comparison, the Gag precursor of BFV is predicted to be only 28% identical to the HFV protein.

Characterization of provirus clones of simian foamy virus type 1

We have cloned proviral DNA of simian foamy virus type 1 (SFV-1) from linear unintegrated DNA (pSFV-1). Transfection of pSFV-1 induces cytopathology in several cell lines with supernatants from the transfected cell culture containing infectious viral particles. Electron microscopy of the transfected cells revealed foamy virus particles. Deletion analysis of pSFV-1 indicated that the transcriptional transactivator (tas) gene located between env and the long terminal repeat is critical for virus replication, whereas the second open reading frame (ORF-2) in this region is dispensable. Although the tas and ORF-2 regions of foamy viruses have significantly diverged, the results presented here suggested that the gene products have similar functions. Recombinant pSFV-1 containing the cat gene was able to transduce the heterologous gene, indicating the utility of SFV-1 as a vector. An infectious clone of SFV-1 which is distantly related to the human foamy virus will provide a means to understand the biology of this unique group of viruses.

Characterization of the genome of feline foamy virus and its proteins shows distinct features different from those of primate spumaviruses

The genome of the feline foamy virus (FeFV) isolate FUV was characterized by molecular cloning and nucleotide sequence analysis of subgenomic proviral DNA. The overall genetic organization of FeFV and protein sequence comparisons of different FeFV genes with their counterparts from other known foamy viruses confirm that FeFV is a complex foamy virus. However, significant differences exist when FeFV is compared with primate foamy viruses. The FeFV Gag protein is smaller than that of the primate spumaviruses, mainly due to additional MA/CA sequences characteristic of the primate viruses only. Gag protein sequence motifs of the NC domain of primate foamy viruses assumed to be involved in genome encapsidation are not conserved in FeFV. FeFV Gag and Pol proteins were detected with monospecific antisera directed against Gag and Pol domains of the human foamy virus and with antisera from naturally infected cats. Proteolytic processing of the FeFV Gag precursor was incomplete, whereas more efficient proteolytic cleavage of the pre125Pro-Pol protein was observed. The active center of the FeFV protease contains a Gln that replaces an invariant Gly residue at this position in other retroviral proteases. Functional studies on FeFV gene expression directed by the promoter of the long terminal repeat showed that FeFV gene expression was strongly activated by the Bell/Tas transactivator protein. The FeFV Bell/Tas transactivator is about one-third smaller than its counterpart of primate spumaviruses. This difference is also reflected by a limited sequence similarity and only a moderate conservation of structural motifs of the different foamy virus transactivators analyzed.

Expression and molecular characterization of an enzymatically active recombinant human spumaretrovirus protease

The human foamy virus (HFV) protease (PR) was cloned into a modified thioredoxin fusion vector that carried a His-tag in the centrally located surface loop of the E. coli trxA protein, bacterially expressed as a soluble fusion protein, and subsequently purified by affinity chromatography. By using HFV Gag protein substrates, the purified recombinant HFV PR was enzymatically active whereas the corresponding active site PR mutant Asp/Ala was inactive. Incubation of synthetic peptides containing residues that flank the putative cleavage site with the recombinant HFV PR and subsequent matrix-assisted laser desorption ionization mass spectrometry of the cleavage products identified the proteolytic processing site of the HFV Gag precursor p74 and revealed that the peptide sequence RAVNTVTQ was cleaved between the Asn and Thr bond.

Gene transfer using replication-defective human foamy virus vectors

Replication-defective vectors based on an infectious molecular clone of human foamy virus (HFV) were constructed by deletion and replacement of the accessory genes with expression cassettes for puromycin-resistance and beta-glucouronidase. Cell lines which produced in excess of 10(5) helper virus-free transducing units/ml were generated by trans-complementation of the replication defect using a BHK-21-derived cell line expressing the Bel-1 transactivator. Vectors based on the HFV genome may provide useful alternatives to existing retroviral vectors.

Long terminal repeat U3 length polymorphism of human foamy virus

Size determination of the long terminal repeat (LTR) of an early (1985) and a more recent (1993) passage of wild-type human foamy virus (HFV) revealed that the virus has undergone substantial deletions in the U3 region upon replication in tissue culture. Two LTR deletion variants (HSRV1 and 2) have been characterized in the past and used to construct molecular clones which are replication competent in cell culture. We now report the molecular cloning, sequencing, and biological characterization of an HFV genome with full-length LTR (pHFV2). Sequence analysis revealed that the deletions in HSRV1 and 2 are nonrandom and probably occurred by misalignment during reverse transcription. The comparative analysis of HFV2 and the variant with the largest U3 deletion, HSRV2, revealed a differential ability to replicate in human cell cultures. While HSRV2 replicated faster in diploid human fibroblasts, cells which have been used extensively for amplification of HFV in the past, replication of HFV2 was faster in a lymphoblastoid cell line. Reporter gene assays indicated that the cell-type specific ability of the LTRs to respond to the viral transcriptional transactivator may be a likely, reason for the different growth properties of both viruses and for the occurrence of the HFV U3 deletions. In foamy virus-infected chimpanzees only the full-length type of LTR was observed; however, the HSRV1 deletion variant was detected as the dominating virus in an accidentally HFV-infected human.

Identification of sites that act together to direct dimerization of human foamy virus RNA in vitro

Retroviral particles contain two molecules of genomic RNA, which are noncovalently linked near their 5' ends in a region called the dimer linkage structure (DLS). By using complementary DNA oligonucleotides and deletion mutants to impair RNA dimerization of the human foamy virus (HFV), three sites, designated SI, SII, and SIII, were found within a 159-nucleotide RNA fragment of HFV that are involved in dimerization in vitro. SI overlaps the primer-binding site; and SII contains the palindromic sequence, UCCCUAGGGA, the disruption of which impairs dimer formation; and SIII extends into the gag gene. The first two sites are highly conserved in the other primate foamy viruses, SFV-1, SFV-3, and SFVcpz, whereas the third appears to be shared only by HFV and SFVcpz. RNA of HFV and SFV-3 could form heterodimers, indicating that both viruses dimerize by similar mechanisms. On testing thermal stability, dimers of the 159-nucleotide fragment dissociated between 40 and 70 degrees, with half of the dimers dissociating at 55 degrees. Since the splice donor site of HFV is located at position 51 of viral RNA, the DLS is part of the genomic RNA exclusively.

Three retroviral sequences in amphibians are distinct from those in mammals and birds

We isolated and characterized three endogenous retroviral fragments from the dart-poison frog Dendrobates ventrimaculatus. These are the first retroviral sequences to be identified in amphibians, and consequently retroviruses have now been found in each of the five major vertebrate classes. Comparison of the amphibian retroviral fragments, termed DevI, DevII, and DevIII, with mammalian and avian isolates revealed significant differences between their nucleotide sequences. This suggested that they were only distantly related to the seven currently recognized retroviral genera. Additional analysis by phylogeny reconstruction showed that the amphibian retroviral fragments were approximately equally related to the Moloney leukemia-related viruses, the spumaviruses, and walleye dermal sarcoma virus. Hybridization experiments revealed that viruses closely related to DevI, DevII, and DevIII do not appear to be widespread in other vertebrates and that DevI, DevII, and DevIII are all present at high copy numbers within their amphibian hosts, typically at over 250 copies per genome. The viruses described here, along with two others which have recently been found in a fish and a reptile, indicate that there may be some major differences in the retroviruses harbored by different vertebrate classes. This suggests that further characterization of retroviruses of fish, reptiles, and amphibians will help in understanding the evolution of the whole retroviral family and may well lead to the discovery of retroviruses with novel biological properties.

Foamy virus reverse transcriptase is expressed independently from the Gag protein

In the foamy virus (FV) subgroup of retroviruses the pol genes are located in the +1 reading frame relative to the gag genes and possess potential ATG initiation codons in their 5' regions. This genome organization suggests either a + 1 ribosomal frameshift to generate a Gag-Pol fusion protein, similar to all other retroviruses studied so far, or new initiation of Pol translation, as used by pararetroviruses, to express the Pol protein. By using a genetic approach we have ruled out the former possibility and provide evidence for the latter. Two down-mutations (M53 and M54) of the pol ATG codon were found to abolish replication and Pol protein expression of the human FV isolate. The introduction of a new ATG in mutation M55, 3' to the down-mutated ATG of mutation M53, restored replication competence, indicating that the pol ATG functions as a translational initiation codon. Two nonsense mutants (M56 and M57), which functionally separated gag and pol with respect to potential frame-shifting sites, were also replication-competent, providing further genetic evidence that FVs express the Pol protein independently from Gag. Our results show that during a particular step of the replication cycle, FVs differ fundamentally from all other retroviruses.

Isolation and characterization of infectious full-length DNA clones of chimpanzee foamy viruses SFV6 and SFV7: evidence for a Taf-dependent internal promoter

We have cloned complete viral genomes directly from Hirt supernatant DNAs of simian foamy virus types 6 and 7 (SFV6 and SFV7) -infected cells. These clones were shown to be infectious by transfection into cells and subsequent infection of susceptible cells either by cocultivation or by passage of cell-free supernatants. The presence of virus particles, suggested by a typical cytopathic effect, was confirmed by electron microscopy. These viruses were characterized at different levels of the replication cycle. The proviral genomes revealed a taf deletion comparable to that previously described in the human foamy virus (HFV) bel1 gene. Analysis of viral RNAs revealed similar patterns of transcripts for SFV6- and SFV7-infected cells, with predominant expression of accessory genes. Characteristic major viral polypeptides were identified by radioimmunoprecipitation for both isolates. Sequences homologous to the gene encoding Taf and to a potential internal promoter were identified in the infectious clones and subcloned into expression vectors. Their functional properties were tested by transfection assays, which provided evidence for the presence of a Taf-dependent internal promoter in both SFV6 and SFV7 isolates.

Isolation of novel human endogenous retrovirus-like elements with foamy virus-related pol sequence

A new class of reverse transcriptase coding sequences was detected in reverse-transcribed RNAs from human placenta by polymerase chain amplification with primers in highly conserved regions of the pol gene of mammalian retroviruses and retrotransposons. Using one of these novel sequences as a probe to screen a human genomic library, we isolated retrovirus-like elements bordered by long terminal repeats and having a potential leucine tRNA primer-binding site. Determination of the complete nucleotide sequence (6,591 bp) of one of these elements, termed HERV-L (for human endogenous retrovirus with leucine tRNA primer), revealed domains of amino acid similarities to retroviral reverse transcriptase and integrase proteins. In addition, a region with homologies to dUTPase proteins was found unexpectedly downstream from the integrase domain. Amino acid sequence and phylogenetic analysis indicate that the HERV-L pol gene is related to that of foamy retroviruses. HERV-L-related sequences are detected in several mammalian species and have expanded in primate and mouse genomes up to 100 to 200 copies.

Functional analysis of human spuma retrovirus genome

Human spuma retrovirus (HSRV) belongs to retroviruses that possess a complex genome organization. HSRV carries at least three extra genes in the region between env and the 3' long terminal repeat, which are not found in simple retroviruses. Via alternative splicing, these HSRV genes can encode several proteins. To genetically study the requirements of these viral proteins for viral replication in tissue cultures, a number of mutant viruses were constructed from an infectious molecular clone of HSRV. All mutants grew normally in the cell lines tested, except for those lacking transcriptional transactivator activity. By reporter-based transient assay systems, no Rev/Rex equivalent was detected in the HSRV proteins.

Markers of foamy virus infections in monkeys, apes, and accidentally infected humans: appropriate testing fails to confirm suspected foamy virus prevalence in humans

Foamy viruses (FVs) persist in healthy individuals of various mammalian species, including nonhuman primates. Laboratory markers of FV infection are (1) virus in throat epithelium or peripheral blood lymphocytes (PBLs), (2) proviral DNA sequences in PBLs and various solid organs, and (3) antibodies reactive to viral antigens on Western blots, in radioimmunoprecipitation tests, and in immunofluorescence assays. Using PCR and serological tests, we readily detected FV markers in naturally infected African green monkeys, rhesus monkeys, and chimpanzees, as well as in accidentally infected humans. Transmission of simian foamy viruses to humans (by bite or inadvertent laboratory infection) leads to viral markers, without affecting the recipient. Reports on FV-associated clinical disorders (e.g., thyroid or neurological) have remained controversial. In this study we failed to detect, by PCR, viral sequences in the samples from 223 patients, including 16 HIV-infected Africans, 46 Graves' disease patients, and 28 patients with the de Quervain's thyroiditis. Evaluation of 2688 sera from suspected high-risk areas (e.g., Central and East Africa, or high-risk groups such as HIV-infected individuals and patients with AIDS, thyroid, and neurological disorders) did not reveal FV-specific antibodies in a single case. Previously reported FV seroprevalence in various populations has never been verified by appropriate confirmatory tests. The strain of "human foamy virus" has remained a unique isolate. In conclusion, FVs are unlikely--at present--to circulate in human populations.

Isolation of a new foamy retrovirus from orangutans

We have isolated a new foamy virus from blood samples taken from two apparently healthy orangutans (Pongo pygmaeus). The older orangutan has since died with encephalopathy after a brief acute illness, while the younger one, his grandson, remains well. These animals and 12 other orangutans had specific antibodies to foamy virus as measured by immunofluorescence. The new foamy virus and the antisera showed strong and specific neutralization, with only weak cross-reaction with other simian foamy virus strains. Southern blotting with gag and env probes of human foamy virus and PCR amplification showed that the new foamy virus, designated SFV-11, is related to, yet distinct from, previously characterized strains from humans, chimpanzees, and monkeys.

Structure and function of the long terminal repeat of the chimpanzee foamy virus isolates (SFV-6)

The complete long terminal repeat (LTR) nucleotide sequence of the chimpanzee foamy virus isolate SFV-6 was determined. Its 1761-bp size makes it the longest LTR reported to date among all retroviruses. Since the length of its LTR is similar to that of other simian isolates while its sequence homology is closer to that of HFV, SFV-6 genetic structure appears to be intermediate between simian and human foamy viruses. Transient expression assays demonstrate that SFV-6 encodes a transactivator of viral gene expression directed either by its own LTR or by heterologous promoters like HFV and HIV-1 LTRs. Our data also provide evidence for cross-transactivation between SFV-6 and HFV.

Nuclear localization of foamy virus Gag precursor protein

All foamy viruses give rise to a strong nuclear staining when infected cells are reacted with sera from infected hosts. This nuclear fluorescence distinguishes foamy viruses from all other retroviruses. The experiments reported here indicate that the foamy virus Gag precursor protein is transiently located in the nuclei of infected cells and this is the likely reason for the typical foamy virus nuclear fluorescence. By using the vaccinia virus expression system, a conserved basic sequence motif in the nucleocapsid domain of foamy virus Gag proteins was identified to be responsible for the nuclear transport of the gag precursor molecule. This motif was also found to be able to direct a heterologous protein, the Gag protein of human immunodeficiency virus, into the nucleus.

Absence of foamy virus DNA in Graves' disease

A report on the high prevalence of foamy virus DNA in lymphocytes from French patients with Graves' disease prompted us to investigate a similar cohort of 41 German patients. Using PCR amplification and Southern blot hybridization, we detected foamy virus DNA only in lymphocytes of two accidentally infected humans and five naturally infected monkeys, as well as in DNA samples from four Graves' disease patients investigated in the French study. However, we failed to detect foamy virus DNA in peripheral blood lymphocytes from any of the 41 Graves' disease patients of the German cohort. Thus, a causative role of foamy viruses in this thyroid disease is highly improbable.

Analysis of the 5' long terminal repeat of bovine syncytial virus

Four molecular clones of the bovine syncytial virus (BSV) were determined to be replication competent by the initiation of cytopathic infections and production of viable virus following transfection of viral DNA into permissive cells. The nucleotide (nt) sequence of the 5' long terminal repeat (LTR) of the infectious clone, BSV-11, was determined and analyzed to identify regions common to retroviral LTRs and elements with the potential for involvement in transcriptional regulation.

Expression of the human foamy virus bel-1 transactivator in insect cells

The human foamy virus (HFV) bel-1 transactivator protein was expressed in insect cells by a recombinant baculovirus. For the generation of the recombinant baculovirus, Acbel-1, the bel-1 gene of an HFV mutant was used, that bears truncations in the bel-1 overlapping bel-2 open reading frame. Acbel-1 infected Sf9 cells produced high amounts of recombinant protein of the same electrophoretic mobility (36 kD) as bel-1 expressed in mammalian cells. The baculovirus expressed bel-1 protein was readily identified by a polyclonal rabbit serum directed against bel-1 in immunoblot assay. As in mammalian cells, bel-1 was predominantly localized to the nucleus of Acbel-1 infected insect cells. The baculovirus expressed bel-1 protein will be of use to determine the action of this novel viral transactivator more precisely.

Endonucleolytic cleavages and DNA-joining activities of the integration protein of human foamy virus

The bacterial expression plasmids, pET3b and pET16b, that contain the integrase domain of the human foamy virus (HFV) reverse transcriptase were constructed and expressed in Escherichia coli. The histidine-tagged HFV IN protein was purified to near homogeneity by single-step Ni2+ chelate affinity chromatography. HFV-specific proteins of 39 and 120 kDa from virus-infected cells reacted with antisera raised against the recombinant IN protein. Purified recombinant HFV IN protein was active as an endonuclease specifically cleaving two nucleotides from a 20-bp oligodeoxynucleotide substrate that mimics the authentic 5' ends of HFV DNA. Substrates with mutations relatively close to the cleavage site were less efficiently cleaved or not cleaved at all compared with the HFV U5 DNA end. The purified recombinant protein was active as integrase with double-stranded oligodeoxynucleotide substrates. The reverse reaction of DNA strand transfer, the disintegration activity, was shown by efficient cleavage of an intermediate Y-shaped oligodeoxynucleotide. In the presence of Mn2+ as the preferred divalent cation, oligodeoxynucleotides were specifically and efficiently cleaved. In contrast, endonucleolytic cleavages in the presence of Mg2+ ions led to a broad range of reaction products with the His-tagged HFV IN protein. After further purification of the HFV IN by cation-exchange chromatography, the unspecific degradation of oligonucleotide substrate in the presence of Mg2+ was not detectable.

Human foamy virus genome possesses an internal, Bel-1-dependent and functional promoter

The human foamy or spumaretrovirus (HSRV) is a complex retrovirus that encodes the three retroviral genes gag, pol, and env and, in addition, at least three bel genes. The HSRV Bel-1 protein was identified as a transcriptional trans-activator. HSRV transcription starts in the 5' long terminal repeat at a defined guanine residue. We report here that a second efficiently utilized start site of transcription is contained within a HSRV env DNA sequence upstream of the bel genes. Bel-specific transcripts that initiate at the internal transcriptional start site at nt 9196 were identified in HSRV-infected cells by primer extension and S1 nuclease analysis, and the intragenic promoter was shown to be constitutively activated by Bel-1 in the HSRV provirus. In transient expression assays with indicator gene constructs, expression by the HSRV intragenic promoter/enhancer is Bel-1 dependent. The data provide evidence for an intragenic start site of transcription in the genome of a complex, exogenous human retrovirus and are discussed in terms of a model for regulating spumaretroviral gene expression.

Human foamy virus polypeptides: identification of env and bel gene products

Human foamy virus (HFV) proteins were identified in human cells cultured in vitro by immunoprecipitation and immunoblotting with specific antisera. Among several viral polypeptides, four glycoproteins of approximately 160, 130, 70, and 48 kDa were identified in HFV-infected cells. gp130 was shown to represent the intracellular env precursor, and gp70 and gp48 were shown to represent the external and transmembrane env proteins, respectively. The nature of gp160, which shares sequences with the env, bel1, and bel2 proteins, is not yet resolved. In addition, a p62 identified with bel1- and bel2-specific antisera likely corresponds to the bet gene product.

The foamy virus family: molecular biology, epidemiology and neuropathology

The family of foamy viruses designates a group of retroviruses which share a specific morphology and provoke characteristic cytopathic effects in cultured cells. Like HTLV and HIV, foamy viruses are complex viruses encoding a number of ancillary genes in addition to gag, pol and env, including a transcriptional transactivator. Foamy viruses are endemic in various primate species, and human foamy viruses (HFV) have been isolated from patients with various neoplastic and degenerative diseases. Despite a growing body of knowledge on the biology of foamy viruses, it has not yet been possible to identify a disease specifically caused by foamy virus infection. After reviewing the epidemiology and molecular biology of the various animal foamy viruses, this article focuses on the pathogenic properties of HFV in transgenic mouse systems. HFV transgenes exhibit a striking neurotropism and elicit a progressive degenerative disease of the central nervous system and striated muscle. Similarly to patients with HIV-associated encephalopathy, HFV transgenic mice develop accumulations of syncytial giant cells in their brains. The relevance of these findings for human neuropathology is discussed.

Human spumaretrovirus-related sequences in the DNA of leukocytes from patients with Graves disease

Viruses, and more particularly retroviruses, have been postulated to play a role in the pathogenesis of autoimmune diseases. In a search for spumaretrovirus infection markers, we screened a group of 29 patients with Graves disease and a representative healthy population (23 subjects) as a control. Southern blot hybridization under stringent conditions, of patients' DNA extracted from peripheral blood lymphocytes, with a spumaretrovirus-specific genomic probe derived from the human spumaretrovirus (HSRV) prototype, gave a positive signal in 10 cases. Moreover, by PCR, HSRV-related sequences were detected in the DNA of 19 patients (66%). Positive DNA samples in Southern blots were also positive in PCR for all regions tested (gag, bel1, bel2, long terminal repeat). Amplified (gag and bel2) products were cloned and sequenced; they showed high homology with HSRV. On the other hand, all 23 control subjects were negative by both procedures. Sera from both populations were examined for the presence of antibodies reactive with antigens of the spumaretrovirus family. These sera were negative by several immunodetection techniques: ELISA, indirect immunofluorescence, serum neutralization, and Western blotting. These results strongly suggest the existence of an association between Graves disease and the presence of HSRV-related infection markers.

Bacterial expression of the capsid antigen domain and identification of native gag proteins in spumavirus-infected cells

A bacterial expression plasmid containing the central part of the gag gene of the human spumaretrovirus (HSRV) was constructed and expressed in E. coli. The expected protein product consisting of the complete region of the HSRV capsid antigen and part of the matrix protein was expressed in relatively large amounts. Polyclonal antisera raised against this recombinant protein were used to identify authentic gag precursors of 78 and 74 kDa and processed gag proteins of 60, 58, and 33 kDa in HSRV-infected human embryonal fibroblast cells by radioimmunoprecipitation. The recombinant antigen will be useful for the detection of antibodies against HSRV gag proteins in human sera.