Taxonomic features of seven serotypes of simian and ape foamy viruses

Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

Wide distribution and ancient evolutionary history of simian foamy viruses in New World primates

BACKGROUND

Although simian foamy viruses (SFV) are the only exogenous retroviruses to infect New World monkeys (NWMs), little is known about their evolutionary history and epidemiology. Previous reports show distinct SFVs among NWMs but were limited to small numbers of captive or wild monkeys from five (Cebus, Saimiri, Ateles, Alouatta, and Callithrix) of the 15 NWM genera. Other studies also used only PCR testing or serological assays with limited validation and may have missed infection in some species. We developed and validated new serological and PCR assays to determine the prevalence of SFV in blood specimens from a large number of captive NWMs in the US (n = 274) and in captive and wild-caught NWMs (n = 236) in Peruvian zoos, rescue centers, and illegal trade markets. Phylogenetic and co-speciation reconciliation analyses of new SFV polymerase (pol) and host mitochondrial cytochrome B sequences, were performed to infer SFV and host co-evolutionary histories.

RESULTS

124/274 (45.2 %) of NWMs captive in the US and 59/157 (37.5 %) of captive and wild-caught NWMs in Peru were SFV WB-positive representing 11 different genera (Alouatta, Aotus, Ateles, Cacajao, Callithrix, Cebus, Lagothrix, Leontopithecus, Pithecia, Saguinus and Saimiri). Seroprevalences were lower at rescue centers (10/53, 18.9 %) compared to zoos (46/97, 47.4 %) and illegal trade markets (3/7, 8/19, 42.9 %) in Peru. Analyses showed that the trees of NWM hosts and SFVs have remarkably similar topologies at the level of species and sub-populations suggestive of co-speciation. Phylogenetic reconciliation confirmed 12 co-speciation events (p < 0.002) which was further supported by obtaining highly similar divergence dates for SFV and host genera and correlated SFV-host branch times. However, four ancient cross-genus transmission events were also inferred for Pitheciinae to Atelidae, Cacajao to ancestral Callithrix or Cebus monkeys, between Callithrix and Cebus monkeys, and Lagothrix to Alouatta.

CONCLUSIONS

We demonstrate a broad distribution and stable co-speciation history of SFV in NWMs at the species level. Additional studies are necessary to further explore the epidemiology and natural history of SFV infection of NWMs and to determine the zoonotic potential for persons exposed to infected monkeys in captivity and in the wild.

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.

An endogenous foamy virus in the aye-aye (Daubentonia madagascariensis)

We report the discovery and analysis of an endogenous foamy virus (PSFVaye) within the genome of the aye-aye (Daubentonia madagascariensis), a strepsirrhine primate from Madagascar. Phylogenetic analyses indicate that PSFVaye is divergent from all known simian foamy viruses, suggesting an association between foamy viruses and primates since the haplorrhine-strepsirrhine split. The discovery of PSFVaye indicates that primate foamy virus might be more broadly distributed than previously thought.

Species-specific inhibition of foamy viruses from South American monkeys by New World Monkey TRIM5{alpha} proteins

Foamy virus evolution closely parallels that of the host species, indicating virus-host coadaptation. We studied simian foamy viruses (SFVs) from common marmosets, spider monkeys, and squirrel monkeys, New World monkey (NWM) species that share geographic ranges. The TRIM5alpha protein from each of these NWM species inhibited the replication of at least one of the SFVs associated with the other two species but did not affect the replication of its own SFV. Thus, TRIM5alpha has potentially shaped the evolution of SFVs in NWM hosts. Conversely, SFVs may have influenced the evolution of TRIM5 variants in New World primates.

Foamy virus infection in primates

Foamy viruses (FV), the oldest known genus of Retroviridae, are unique among the retroviruses in having no disease association. It is not known why FV are non-pathogenic while infection by their closest relatives can be deadly. This may be related to the estimated 60 million years of coevolution of FV and their primate hosts. We review the current state of knowledge of FV infection, including information about the sites of viral replication and host immune responses, and discuss the role these may play in establishing persistent yet non-pathogenic infections. Whether FV has pathologic consequences in immunosuppressed hosts has not been thoroughly investigated. As most primates in HIV/SIV research are coinfected with FV, investigation into possible interactions between these viruses is of interest. The use of FV as a vector for gene therapy is also discussed.

Replication of primate foamy viruses in natural and experimental hosts

Foamy viruses (FVs) are common apathogenic retroviruses readily spread by horizontal transmission in nonhuman primate and some other mammalian host populations. Primate FV infections have been known for half a century, i.e., 15 years before the definition of retroviruses and another 15 years before the detection of primate immune deficiency viruses. The emerging interest in human retroviruses included primate FV, and although the role of human hosts for FV was greatly overestimated temporarily, enthusiastic researchers compiled invaluable data on molecular biology and classic as well as molecular epidemiology of these viruses. It has been shown that lytic FV infection in a wide range of cell cultures is in great contrast to the silent state of the infection in animals. Once transmitted by saliva via biting, FVs reside in all tissues as DNA copies, but their replication is untraceable except in oral submucosal cells, which are thought to supply the virus for transmission. FVs have not definitely been associated with any disease, regardless of viral phylogenetic differences. Various primate and nonprimate species have been used for studies on the natural carrier state and primary infection. Experimental infections have mostly proven to be inefficient in primates as well as lower laboratory animals. However, investigation of the immune response in FV-infected animals has only partly explained the control of FV replication in the animal host. Thus, the biological role of FV remains an enigma to be resolved in the future.

Historical perspective of foamy virus epidemiology and infection

Foamy viruses (FV) are complex retroviruses which are widespread in many species. Despite being discovered over 40 years ago, FV are among the least well characterized retroviruses. The replication of these viruses is different in many interesting respects from that of all other retroviruses. Infection of natural hosts by FV leads to a lifelong persistent infection, without any evidence of pathology. A large number of studies have looked at the prevalence of primate foamy viruses in the human population. Many of these studies have suggested that FV infections are prevalent in some human populations and are associated with specific diseases. More recent data, using more rigorous criteria for the presence of viruses, have not confirmed these studies. Thus, while FV are ubiquitous in all nonhuman primates, they are only acquired as rare zoonotic infections in humans. In this communication, we briefly discuss the current status of FV research and review the history of FV epidemiology, as well as the lack of pathogenicity in natural, experimental, and zoonotic infections.

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.

Absence of serological evidence for foamy virus infection in patients with amyotrophic lateral sclerosis

Foamy virus (FV) infection has been implicated in the pathogenesis of sporadic motor neuron disease (MND) by means of serological assays. To confirm these results we tested serum and cerebrospinal fluid (CSF) samples from 23 cases of clinically verified non-familial MND and 11 cases of suspected non-familial MND for the presence of FV infection as determined by Western blot (WB) and indirect immunofluorescence assay (IFA). Using the same tests we also screened sera from 87 healthy chimpanzees for the presence of FV antibodies. None of the human samples in question tested positive. However, the testing revealed that 84 of 87 chimpanzees (96.6%) were seropositive for FV, indicating that combined WB and IFA are suitable methods for the serodiagnosis of FV infection. Given these results an association of FV infection and sporadic MND is highly improbable. Furthermore a suggested therapeutic trial with anti-retroviral drugs appears unjustified.

Cell tropism of the simian foamy virus type 1 (SFV-1)

Several cell lines representing different species and cell types were tested for simian foamy virus type 1 (SFV-1) infection. SFV-1 infections were monitored by polymerase chain reaction, reverse transcriptase, cytopathology, and immunofluorescent assays. All cells tested were permissive for SFV-1, demonstrating that SFV-1 has a broad host range with respect to species and cell types. Infected fibroblasts, epithelial cells, and neural cells all showed extensive cytopathology that is characteristic of foamy virus infection. No cytopathology was induced in T cell-derived Jurkats and Hut-78 cell lines. The cytopathic effects in B and macrophage originated cells were delayed by several days. Cytopathology in these cell lines was not as dramatic as seen in the infected fibroblast and epithelial cells. The reverse transcriptase values in the SFV-1 infected lymphoid and macrophage cell lines were severalfold lower than that of the fibroblasts and epithelial cells. Therefore, SFV-1 appears to establish a low level persistent infection in lymphoid and macrophage cell lines.

Effects of human recombinant alpha and gamma and of highly purified natural beta interferons on simian Spumavirinae prototype (simian foamy virus 1) multiplication in human cells

The present study demonstrates the inhibitory effect of human recombinant interferons (r-Hu-IFN) alpha and gamma, and that of highly purified natural human interferon beta on the replication of simian foamy virus type 1 (SFV1) in human AV3-cell cultures. All IFN led to strong inhibition of the SFV1 cytopathic effect. Electron microscopy showed a 70 to 95% decrease in viral particles. Significant inhibition of virus-associated reverse transcriptase activity was found in supernatant fluids of infected IFN-treated cultures. Metabolic labelling of the virus confirmed the inhibition of extracellular release of SFV1. PAGE analysis of immunoprecipitates indicated a reduction in viral-specific protein bands. Altogether, these results indicate that the mechanism of inhibition of Spumavirinae infection by interferon differs from that described for the other Retroviridae, and particularly for types B, C and D viruses. Our data is of therapeutic interest since Spumavirinae have been linked to pathological processes such as de Quervain thyroiditis.

Purification and characterization of simian foamy virus type I structural core polypeptides

The present study concerns the purification and partial characterization of simian foamy virus type 1 (SFV 1) structural core polypeptides. The obtention of SFV 1 cores separated from envelope components after viral disrupture was verified by electron microscopy (EM), density gradient, and polyacrylamide gel electrophoresis (PAGE). Multistep purification by column chromatography, verified by PAGE, enabled us to separate the structural core polypeptides from the 80,000 molecular weight reverse transcriptase. Two species of structural core polypeptides were identified with apparent molecular weights of 51 and 15 kd. By affinity chromatography on a double-stranded DNA-cellulose column, the main internal protein, p51, was shown to be composed of a major 30 kd protein and a minor 19 kd polypeptide, which binds to double stranded DNA. The p15 internal protein was shown to have a ribonucleotide binding nature.

Syncytium-forming virus of common marmosets (Callithrix jacchus jacchus)

This communication describes the isolation and characterization of a new syncytium-forming virus of common marmosets (Callithrix jacchus jacchus). The virus, isolated from skin explants and peripheral leukocytes of healthy animals, induced syncytia and subsequent cytolysis of several human, simian, and rodent fibroblastic cultures and induced a carrier state in mixed fibroblastic-epithelial or epithelial cell lines. Cytoplasmic and nuclear viral antigen was demonstrated in infected cells by indirect immunofluorescence tests using serum obtained from persistently infected common marmosets. Abundant virus particles were detected within cisternae of endoplasmic reticulum of lytically infected cells by electron microscopy. The virus incorporated [3H]uridine, banded at a density of 1.14 to 1.16 g/cm3 in sucrose, and possessed ribonucleic acid-dependent deoxyribonucleic acid polymerase. No antigenic cross-reactivity was detected between the marmoset virus and simian foamy virus serotypes 1 to 8 in neutralization and immunofluorescence assays. A seroepidemiological survey of a marmoset colony revealed that 53.5% of common marmosets contained antibodies against the virus, whereas other species of marmosets maintained in the same colony remained free of antibodies.

The foamy viruses

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Pathogenesis of simian foamy virus infection in natural and experimental hosts

Inoculation of simian foamy virus type 1 into New Zealand white rabits resulted in an infection which was very similar to that observed in naturally infected nonhuman primates. Both intraperitoneal and intranasal inculations were found to be efficient procedures for the establishment of the infection in rabbits. Infection by the nasal route was found to be the best method, whereas no infection could be established by feeding virus in the drinking water. Once infection was established, virus persisted in the tissues and organs for as long as 264 days after inoculation, during which time the animals maintained significant levels of neutralizing antibody. Infectious virus was recovered from spleen, liver, lung, salivary gland, kidney, and, to a lesser extent, the brain. Virus was isolated from the blood only during early infection and never from the urine. A comparison of the distribution of foamy virus in naturally infected monkeys and baboon with experimentally infected rabbits showed that both groups harbored infectious virus in the same internal tissues and organs. Recovery of infectious virus from both groups of animals was accomplished by cultivation and/or co-cultivation of infected cells onto Vero cells.

Isolation of a new simian foamy virus from a spider monkey brain culture

A syncytium-forming (foamy) virus was isolated from a spider monkey brain cell culture. Cytopathic effect was observed both in the brain culture and in human embryonic kidney cells. Neutralizing antibody was present in the sera of the spider monkey from whom the isolation was made. The virus was inhibited by 5-bromo-2-deoxyuridine (20 mug/ml), contained a ribonucleic acid-dependent deoxyribonucleic acid polymerase, and had an infectivity peak at 1.15 g/cm(3) in a sucrose density gradient. The virus passed through a 220-nm but not a 100-nm membrane filter, was chloroform sensitive, and was inactivated at 56 C in 30 min. Hemagglutinating and hemadsorption activity was not noted with a variety of erythrocytes. The virion was spherical, formed in the cytoplasm, and was 105 to 115 nm in diameter. Ring-shaped nucleoids, 45 to 50 nm in diameter, were associated with tubular profiles. The virus was not neutralized by sera prepared against known viruses, including simian foamy virus types 1 through 7, Mason-Pfizer monkey virus, and bovine syncytial and measles viruses. Sera from a rabbit hyperimmunized with the isolate and sera from 19 spider monkeys had neutralizing antibody to the isolate; however, these sera did not cross-react with simian foamy virus types 1 through 7. Neutralizing antibody to the isolate was not detected in sera from 16 humans, 9 rhesus monkeys, and 10 chimpanzees.

Reverse transcriptases of primate viruses as immunological markers

Antibodies were prepared against the DNA polymerases (reverse transcriptases) of three potentially oncogenic RNA viruses of primates. Two type C viruses, isolated from a woolly monkey fibrosarcoma and from a gibbon ape lymphosarcoma, have polymerases that are immunologically related to each other and are distinct from the type C viruses isolated from other mammals.