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Dynesen LT, Fernandez I, Coquin Y, Delaplace M, Montange T, Njouom R, Bilounga-Ndongo C, Rey FA, Gessain A, Backovic M, Buseyne F. Neutralization of zoonotic retroviruses by human antibodies: Genotype-specific epitopes within the receptor-binding domain from simian foamy virus. PLoS Pathog 2023; 19:e1011339. [PMID: 37093892 PMCID: PMC10159361 DOI: 10.1371/journal.ppat.1011339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/04/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Infection with viruses of animal origin pose a significant threat to human populations. Simian foamy viruses (SFVs) are frequently transmitted to humans, in which they establish a life-long infection, with the persistence of replication-competent virus. However, zoonotic SFVs do not induce severe disease nor are they transmitted between humans. Thus, SFVs represent a model of zoonotic retroviruses that lead to a chronic infection successfully controlled by the human immune system. We previously showed that infected humans develop potent neutralizing antibodies (nAbs). Within the viral envelope (Env), the surface protein (SU) carries a variable region that defines two genotypes, overlaps with the receptor binding domain (RBD), and is the exclusive target of nAbs. However, its antigenic determinants are not understood. Here, we characterized nAbs present in plasma samples from SFV-infected individuals living in Central Africa. Neutralization assays were carried out in the presence of recombinant SU that compete with SU at the surface of viral vector particles. We defined the regions targeted by the nAbs using mutant SU proteins modified at the glycosylation sites, RBD functional subregions, and genotype-specific sequences that present properties of B-cell epitopes. We observed that nAbs target conformational epitopes. We identified three major epitopic regions: the loops at the apex of the RBD, which likely mediate interactions between Env protomers to form Env trimers, a loop located in the vicinity of the heparan binding site, and a region proximal to the highly conserved glycosylation site N8. We provide information on how nAbs specific for each of the two viral genotypes target different epitopes. Two common immune escape mechanisms, sequence variation and glycan shielding, were not observed. We propose a model according to which the neutralization mechanisms rely on the nAbs to block the Env conformational change and/or interfere with binding to susceptible cells. As the SFV RBD is structurally different from known retroviral RBDs, our data provide fundamental knowledge on the structural basis for the inhibition of viruses by nAbs. Trial registration: The study was registered at www.clinicaltrials.gov: https://clinicaltrials.gov/ct2/show/NCT03225794/.
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Affiliation(s)
- Lasse Toftdal Dynesen
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Ignacio Fernandez
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Youna Coquin
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Manon Delaplace
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Thomas Montange
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | | | | | - Félix A Rey
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Antoine Gessain
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
| | - Marija Backovic
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, Paris, France
| | - Florence Buseyne
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d'épidémiologie et Physiopathologie des Virus Oncogènes, Paris, France
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Sumiyoshi A, Kitao K, Miyazawa T. Genetic and biological characterization of feline foamy virus isolated from a leopard cat (Prionailurus bengalensis) in Vietnam. J Vet Med Sci 2021; 84:157-165. [PMID: 34880191 PMCID: PMC8810315 DOI: 10.1292/jvms.21-0550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Foamy viruses have been isolated from various mammals and show long-term co-speciation with their hosts. However, the frequent inter-species transmission of feline foamy viruses (FFVs) from
domestic cats to wild cats across genera has been reported. Because infectious molecular clones of FFVs derived from wild cats have not been available, whether there are specific
characteristics enabling FFVs to adapt to the new host species is still unknown. Here, we obtained the complete genome sequences of two FFV isolates (strains NV138 and SV201) from leopard
cats (Prionailurus bengalensis) in Vietnam and constructed an infectious molecular clone, named pLC960, from strain NV138. The growth kinetics of the virus derived from
pLC960 were comparable to those of other FFVs derived from domestic cats. Phylogenetic analysis revealed that these two FFVs from leopard cats are clustered in the same clade as FFVs from
domestic cats in Vietnam. Comparisons of the amino acid sequences of Env and Bet proteins showed more than 97% identity among samples and no specific amino acid substitutions between FFVs
from domestic cats and ones from leopard cats. These results indicate the absence of genetic constraint of FFVs for interspecies transmission from domestic cats to leopard cats.
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Affiliation(s)
- Aoi Sumiyoshi
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University
| | - Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University
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3
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Genome Analysis and Replication Studies of the African Green Monkey Simian Foamy Virus Serotype 3 Strain FV2014. Viruses 2020; 12:v12040403. [PMID: 32268512 PMCID: PMC7232438 DOI: 10.3390/v12040403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/27/2020] [Accepted: 04/01/2020] [Indexed: 01/23/2023] Open
Abstract
African green monkey (AGM) spumaretroviruses have been less well-studied than other simian foamy viruses (SFVs). We report the biological and genomic characterization of SFVcae_FV2014, which was the first foamy virus isolated from an African green monkey (AGM) and was found to be serotype 3. Infectivity studies in various cell lines from different species (mouse, dog, rhesus monkey, AGM, and human) indicated that like other SFVs, SFVcae_FV2014 had broad species and cell tropism, and in vitro cell culture infection resulted in cytopathic effect (CPE). In Mus dunni (a wild mouse fibroblast cell line), MDCK (Madin-Darby canine kidney cell line), FRhK-4 (a fetal rhesus kidney cell line), and MRC-5 (a human fetal lung cell line), SFVcae_FV2014 infection was productive resulting in CPE, and had delayed or similar replication kinetics compared with SFVmcy_FV21 and SFVmcy_FV34[RF], which are two Taiwanese macaque isolates, designated as serotypes 1 and 2, respectively. However, in Vero (AGM kidney cell line) and A549 (a human lung carcinoma cell line), the replication kinetics of SFVcae_FV2014 and the SFVmcy viruses were discordant: In Vero, SFVcae_FV2014 showed rapid replication kinetics and extensive CPE, and a persistent infection was seen in A549, with delayed, low CPE, which did not progress even upon extended culture (day 55). Nucleotide sequence analysis of the assembled SFVcae_FV2014 genome, obtained by high-throughput sequencing, indicated an overall 80–90% nucleotide sequence identity with SFVcae_LK3, the only available full-length genome sequence of an AGM SFV, and was distinct phylogenetically from other AGM spumaretroviruses, corroborating previous results based on analysis of partial env sequences. Our study confirmed that SFVcae_FV2014 and SFVcae_LK3 are genetically distinct AGM foamy virus (FV) isolates. Furthermore, comparative infectivity studies of SFVcae_FV2014 and SFVmcy isolates showed that although SFVs have a wide host range and cell tropism, regulation of virus replication is complex and depends on the virus strain and cell-specific factors.
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4
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Hashimoto-Gotoh A, Yoshikawa R, Nakagawa S, Okamoto M, Miyazawa T. Phylogenetic analyses reveal that simian foamy virus isolated from Japanese Yakushima macaques (Macaca fuscata yakui) is distinct from most of Japanese Hondo macaques (Macaca fuscata fuscata). Gene 2020; 734:144382. [PMID: 31978513 DOI: 10.1016/j.gene.2020.144382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 11/25/2022]
Abstract
Japanese macaque (Macaca fuscata) is an indigenous Old World monkey (OWM) species that inhabits the Japanese archipelago. There are two subspecies of Japanese macaque: Yakushima macaque (M. f. yakui) which inhabits Yakushima Island exclusively, and Hondo macaque (M. f. fuscata) which inhabits the mainland of Japan. Yakushima macaque is considered to be branched off from a certain parental macaque group that had inhabited the mainland of Japan. However, the process of sub-speciation of the Yakushima macaque is still unclear at present. In this study, to gain new insight into the process of sub-speciation of Japanese macaque, we utilized the simian foamy virus (SFV) as a marker. SFVs are found in virtually all primates except humans and undergo species-specific cospeciation with the hosts. The phylogenetic analysis of conserved regions of the env gene in SFVs remarkably resembled that of the OWMs with high statistical confidence. The phylogenetic analyses also indicated that there are four (1-4) genotypes among Asian OWMs investigated. SFVs derived from Asian OWMs except Yakushima macaque were classified as genotypes 1-3, whereas SFVs isolated from all Yakushima macaques and one Hondo macaque were classified as genotype 4. Interestingly, genotype 4 was firstly branched off from the rest of the genotypes, which might indicate that the macaques infected with genotype 4 SFV were derived from the "older" population of Japanese macaques. The high prevalence of genotype 4 SFVs among Yakushima macaque might reflect the possibility that they are a descendant of the population settled earlier, which has been geographically isolated in Yakushima Island.
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Affiliation(s)
- Akira Hashimoto-Gotoh
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Rokusuke Yoshikawa
- National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan
| | - Munehiro Okamoto
- Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Aichi 484-8506, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; International Research Unit of Advanced Future Studies, Kyoto University, Kyoto 606-8502, Japan.
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5
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Aiewsakun P. Avian and serpentine endogenous foamy viruses, and new insights into the macroevolutionary history of foamy viruses. Virus Evol 2020; 6:vez057. [PMID: 31942244 PMCID: PMC6955096 DOI: 10.1093/ve/vez057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This study reports and characterises two novel distinct lineages of foamy viruses (FVs) in the forms of endogenous retroviruses (ERVs). Several closely related elements were found in the genome of oriental stork (Ciconia boyciana) and other was found in the genome of spine-bellied sea snake (Hydrophis hardwickii), designated ERV-Spuma.N-Cbo (where 'N' runs from one to thirteen) and ERV-Spuma.1-Hha, respectively. This discovery of avian and serpentine endogenous FVs adds snakes, and perhaps more crucially, birds to the list of currently known hosts of FVs, in addition to mammals, reptiles, amphibians, and fish. This indicates that FVs are, or at least were, capable of infecting all major lineages of vertebrates. Moreover, together with other FVs, phylogenetic analyses showed that both of them are most closely related to mammalian FVs. Further examination revealed that reptilian FVs form a deep paraphyletic group that is basal to mammalian and avian FVs, suggesting that there were multiple ancient FV cross-class transmissions among their hosts. Evolutionary timescales of various FV lineages were estimated in this study, in particular, the timescales of reptilian FVs and that of the clade of mammalian, avian, and serpentine FVs. This was accomplished by using the recently established time-dependent rate phenomenon models, inferred using mainly the knowledge of the co-speciation history between FVs and mammals. It was found that the estimated timescales matched very well with those of reptiles. Combined with the observed phylogenetic patterns, these results suggested that FVs likely co-speciated with ancient reptilian animals, but later jumped to a protomammal and/or a bird, which ultimately gave rise to mammalian and avian FVs. These results contribute to our understanding of FV emergence, specifically the emergence of mammalian and avian FVs, and provide new insights into how FVs co-evolved with their non-mammalian vertebrate hosts in the distant past.
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Affiliation(s)
- Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, 272, Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand.,Center of Microbial Genomics (CENMIG), Faculty of Science, Mahidol University, 272, Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
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6
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Kraberger S, Fountain-Jones NM, Gagne RB, Malmberg J, Dannemiller NG, Logan K, Alldredge M, Varsani A, Crooks KR, Craft M, Carver S, VandeWoude S. Frequent cross-species transmissions of foamy virus between domestic and wild felids. Virus Evol 2020; 6:vez058. [PMID: 31942245 PMCID: PMC6955097 DOI: 10.1093/ve/vez058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Emerging viral outbreaks resulting from host switching is an area of continued scientific interest. Such events can result in disease epidemics or in some cases, clinically silent outcomes. These occurrences are likely relatively common and can serve as tools to better understand disease dynamics, and may result in changes in behavior, fecundity, and, ultimately survival of the host. Feline foamy virus (FFV) is a common retrovirus infecting domestic cats globally, which has also been documented in the North American puma (Puma concolor). The prevalent nature of FFV in domestic cats and its ability to infect wild felids, including puma, provides an ideal system to study cross-species transmission across trophic levels (positions in the food chain), and evolution of pathogens transmitted between individuals following direct contact. Here we present findings from an extensive molecular analysis of FFV in pumas, focused on two locations in Colorado, and in relation to FFV recovered from domestic cats in this and previous studies. Prevalence of FFV in puma was high across the two regions, ∼77 per cent (urban interface site) and ∼48 per cent (rural site). Comparison of FFV from pumas living across three states; Colorado, Florida, and California, indicates FFV is widely distributed across North America. FFV isolated from domestic cats and pumas was not distinguishable at the host level, with FFV sequences sharing >93 per cent nucleotide similarity. Phylogenetic, Bayesian, and recombination analyses of FFV across the two species supports frequent cross-species spillover from domestic cat to puma during the last century, as well as frequent puma-to-puma intraspecific transmission in Colorado, USA. Two FFV variants, distinguished by significant difference in the surface unit of the envelope protein, were commonly found in both hosts. This trait is also shared by simian foamy virus and may represent variation in cell tropism or a unique immune evasion mechanism. This study elucidates evolutionary and cross-species transmission dynamics of a highly prevalent multi-host adapted virus, a system which can further be applied to model spillover and transmission of pathogenic viruses resulting in widespread infection in the new host.
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Affiliation(s)
- Simona Kraberger
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA
| | - Nicholas M Fountain-Jones
- Department of Veterinary Population Medicine, University of Minnesota, 1365 Gortner Ave, Falcon Heights, St Paul, MN 55108, USA
| | - Roderick B Gagne
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer Malmberg
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Nicholas G Dannemiller
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Ken Logan
- Colorado Parks and Wildlife, 317 W Prospect Rd, Fort Collins, CO 80526, USA
| | - Mat Alldredge
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery Fort Collins, CO 80523, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Kevin R Crooks
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery Fort Collins, CO 80523, USA
| | - Meggan Craft
- Department of Veterinary Population Medicine, University of Minnesota, 1365 Gortner Ave, Falcon Heights, St Paul, MN 55108, USA
| | - Scott Carver
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Sue VandeWoude
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
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7
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Hashimoto-Gotoh A, Kitao K, Miyazawa T. Persistent Infection of Simian Foamy Virus Derived from the Japanese Macaque Leads to the High-Level Expression of microRNA that Resembles the miR-1 microRNA Precursor Family. Microbes Environ 2020; 35:ME19130. [PMID: 31969530 PMCID: PMC7104284 DOI: 10.1264/jsme2.me19130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are a group of small non-coding RNAs that suppress the expression of target mRNAs. The seed sequence of miRNA plays a crucial role in recognizing the 3'-untranslated region of the target mRNA. Cells infected with a simian foamy virus (SFV) isolated from an African green monkey (Chlorocebus aethiops) (SFVcae) showed high expression levels of viral miRNAs encoded in the long terminal repeat of SFVcae. In the present study, we investigated the roles and expression of miRNAs derived from an SFV isolated from a Japanese macaque (Macaca fuscata) (SFVmfu) using next-generation sequencing technologies. The results obtained showed that SFVmfu also expressed viral miRNAs; however, the seed sequences of most miRNAs derived from SFVmfu differed from those reported previously from SFVcae. Cells persistently infected with SFVmfu strongly expressed an miRNA with the same seed sequence as the miR-1 microRNA precursor family. Luciferase reporter assays indicated that this miRNA down-regulates the expression of adenylyl cyclase-associated protein 1, which is up-regulated in several solid tumors. The present results suggest that SFVmfu utilizes viral miRNAs to establish long-term co-existence with the Japanese macaque.
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Affiliation(s)
- Akira Hashimoto-Gotoh
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606–8507, Japan
| | - Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606–8507, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606–8507, Japan
- International Research Unit of Advanced Future Studies, Kyoto University, Kyoto 606–8502, Japan
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8
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Aiewsakun P, Richard L, Gessain A, Mouinga-Ondémé A, Vicente Afonso P, Katzourakis A. Modular nature of simian foamy virus genomes and their evolutionary history. Virus Evol 2019; 5:vez032. [PMID: 31636999 PMCID: PMC6795992 DOI: 10.1093/ve/vez032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Among all known retroviruses, foamy viruses (FVs) have the most stable virus–host co-speciation history, co-diverging in concert with their vertebrate hosts for hundreds of millions of years. However, detailed molecular analyses indicate that different parts of their genome might have different evolutionary histories. While their polymerase gene displays a robust and straightforward virus–host co-speciation pattern, the evolutionary history of their envelope (env) gene, is much more complicated. Here, we report eleven new FV env sequences in two mandrill populations in Central Africa, geographically separated by the Ogooué River into the North and the South populations. Phylogenetic reconstruction of the polymerase gene shows that the two virus populations are distinct, and each contains two variants of env genes co-existing with one another. The distinction between the two env variants can be mapped to the surface domain, flanked by two recombination hotspots, as previously reported for chimpanzee and gorilla FVs. Our analyses suggest that the two env variants originated during the diversification of Old World monkeys and apes, ∼30 million years ago. We also show that this env gene region forms two phylogenetically distinct clades, each displaying a host co-divergence and geographical separation pattern, while the rest of the genome of the two strains is phylogenetically indistinguishable in each of the host-specific groups. We propose possible evolutionary mechanisms to explain the modular nature of the FV genome.
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Affiliation(s)
- Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Léa Richard
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Paris, France.,Université Paris Diderot - Paris7, Sorbonne Paris Cité, Paris, France
| | - Antoine Gessain
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Paris, France
| | - Augustin Mouinga-Ondémé
- Unité des Infections Rétrovirales et Pathologies Associées, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Philippe Vicente Afonso
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur, UMR3569 CNRS, Paris, France
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
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9
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Aiewsakun P, Simmonds P, Katzourakis A. The First Co-Opted Endogenous Foamy Viruses and the Evolutionary History of Reptilian Foamy Viruses. Viruses 2019; 11:v11070641. [PMID: 31336856 PMCID: PMC6669660 DOI: 10.3390/v11070641] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/17/2022] Open
Abstract
A recent study reported the discovery of an endogenous reptilian foamy virus (FV), termed ERV-Spuma-Spu, found in the genome of tuatara. Here, we report two novel reptilian foamy viruses also identified as endogenous FVs (EFVs) in the genomes of panther gecko (ERV-Spuma-Ppi) and Schlegel’s Japanese gecko (ERV-Spuma-Gja). Their presence indicates that FVs are capable of infecting reptiles in addition to mammals, amphibians, and fish. Numerous copies of full length ERV-Spuma-Spu elements were found in the tuatara genome littered with in-frame stop codons and transposable elements, suggesting that they are indeed endogenous and are not functional. ERV-Spuma-Ppi and ERV-Spuma-Gja, on the other hand, consist solely of a foamy virus-like env gene. Examination of host flanking sequences revealed that they are orthologous, and despite being more than 96 million years old, their env reading frames are fully coding competent with evidence for strong purifying selection to maintain expression and for them likely being transcriptionally active. These make them the oldest EFVs discovered thus far and the first documented EFVs that may have been co-opted for potential cellular functions. Phylogenetic analyses revealed a complex virus–host co-evolutionary history and cross-species transmission routes of ancient FVs.
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Affiliation(s)
- Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK.
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10
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Shankar A, Sibley SD, Goldberg TL, Switzer WM. Molecular Analysis of the Complete Genome of a Simian Foamy Virus Infecting Hylobates pileatus (pileated gibbon) Reveals Ancient Co-Evolution with Lesser Apes. Viruses 2019; 11:E605. [PMID: 31277268 PMCID: PMC6669568 DOI: 10.3390/v11070605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/27/2019] [Accepted: 06/30/2019] [Indexed: 02/07/2023] Open
Abstract
Foamy viruses (FVs) are complex retroviruses present in many mammals, including nonhuman primates, where they are called simian foamy viruses (SFVs). SFVs can zoonotically infect humans, but very few complete SFV genomes are available, hampering the design of diagnostic assays. Gibbons are lesser apes widespread across Southeast Asia that can be infected with SFV, but only two partial SFV sequences are currently available. We used a metagenomics approach with next-generation sequencing of nucleic acid extracted from the cell culture of a blood specimen from a lesser ape, the pileated gibbon (Hylobates pileatus), to obtain the complete SFVhpi_SAM106 genome. We used Bayesian analysis to co-infer phylogenetic relationships and divergence dates. SFVhpi_SAM106 is ancestral to other ape SFVs with a divergence date of ~20.6 million years ago, reflecting ancient co-evolution of the host and SFVhpi_SAM106. Analysis of the complete SFVhpi_SAM106 genome shows that it has the same genetic architecture as other SFVs but has the longest recorded genome (13,885-nt) due to a longer long terminal repeat region (2,071 bp). The complete sequence of the SFVhpi_SAM106 genome fills an important knowledge gap in SFV genetics and will facilitate future studies of FV infection, transmission, and evolutionary history.
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Affiliation(s)
- Anupama Shankar
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Samuel D Sibley
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA.
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11
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Ensser A, Großkopf AK, Mätz-Rensing K, Roos C, Hahn AS. Isolation and sequence analysis of a novel rhesus macaque foamy virus isolate with a serotype-1-like env. Arch Virol 2018; 163:2507-2512. [PMID: 29860676 DOI: 10.1007/s00705-018-3892-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/20/2018] [Indexed: 11/28/2022]
Abstract
SFVmmu-DPZ9524 represents the third completely sequenced rhesus macaque simian foamy virus (SFV) isolate, alongside SFVmmu_K3T with a similar SFV-1-type env, and R289HybAGM with a SFV-2-like env. Sequence analysis demonstrates that, in gag and pol, SFVmmu-DPZ9524 is more closely related to R289HybAGM than to SFVmmu_K3T, which, outside of env, is more similar to a Japanese macaque isolate than to the other two rhesus macaque isolates SFVmmu-DPZ9524 and R289HybAGM. Further, we identify bel as another recombinant locus in R289HybAGM, confirming that recombination contributes to sequence diversity in SFV.
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Affiliation(s)
- Armin Ensser
- Virologisches Institut, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany
| | - Anna K Großkopf
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Kellnerweg 4, 37077, Göttingen, Germany
| | - Kerstin Mätz-Rensing
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Kellnerweg 4, 37077, Göttingen, Germany
| | - Christian Roos
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alexander S Hahn
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Kellnerweg 4, 37077, Göttingen, Germany.
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12
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Khan AS, Bodem J, Buseyne F, Gessain A, Johnson W, Kuhn JH, Kuzmak J, Lindemann D, Linial ML, Löchelt M, Materniak-Kornas M, Soares MA, Switzer WM. Spumaretroviruses: Updated taxonomy and nomenclature. Virology 2018; 516:158-164. [PMID: 29407373 PMCID: PMC11318574 DOI: 10.1016/j.virol.2017.12.035] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 12/29/2017] [Accepted: 12/29/2017] [Indexed: 01/28/2023]
Abstract
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.
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Affiliation(s)
- Arifa S Khan
- Laboratory of Retroviruses, US Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Jochen Bodem
- Institut für Virologie und Immunbiologie, Universität Würzburg, Würzburg, Germany
| | - Florence Buseyne
- Unit of Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, Paris, France; Centre National de la Recherche Scientifique, CNRS UMR3569, Paris, France
| | - Antoine Gessain
- Unit of Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, Paris, France; Centre National de la Recherche Scientifique, CNRS UMR3569, Paris, France
| | - Welkin Johnson
- Biology Department, Boston College, Chestnut Hill, MA 02467, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Jacek Kuzmak
- Department of Biochemistry, National Veterinary Research Institute, Puławy, Poland
| | - Dirk Lindemann
- Institute of Virology, Technische Universität Dresden, Dresden, Germany
| | - Maxine L Linial
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Martin Löchelt
- Research Program Infection, Inflammation and Cancer, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | | | - Marcelo A Soares
- Instituto Nacional de Câncer and Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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13
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Complete Genome Sequence of a Naturally Occurring Simian Foamy Virus Isolate from Rhesus Macaque (SFVmmu_K3T). GENOME ANNOUNCEMENTS 2017; 5:5/33/e00827-17. [PMID: 28818911 PMCID: PMC5604784 DOI: 10.1128/genomea.00827-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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.
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14
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Reid MJC, Switzer WM, Schillaci MA, Klegarth AR, Campbell E, Ragonnet-Cronin M, Joanisse I, Caminiti K, Lowenberger CA, Galdikas BMF, Hollocher H, Sandstrom PA, Brooks JI. Bayesian inference reveals ancient origin of simian foamy virus in orangutans. INFECTION GENETICS AND EVOLUTION 2017; 51:54-66. [PMID: 28274887 DOI: 10.1016/j.meegid.2017.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 02/25/2017] [Accepted: 03/03/2017] [Indexed: 02/08/2023]
Abstract
Simian foamy viruses (SFVs) infect most nonhuman primate species and appears to co-evolve with its hosts. This co-evolutionary signal is particularly strong among great apes, including orangutans (genus Pongo). Previous studies have identified three distinct orangutan SFV clades. The first of these three clades is composed of SFV from P. abelii from Sumatra, the second consists of SFV from P. pygmaeus from Borneo, while the third clade is mixed, comprising an SFV strain found in both species of orangutan. The existence of the mixed clade has been attributed to an expansion of P. pygmaeus into Sumatra following the Mount Toba super-volcanic eruption about 73,000years ago. Divergence dating, however, has yet to be performed to establish a temporal association with the Toba eruption. Here, we use a Bayesian framework and a relaxed molecular clock model with fossil calibrations to test the Toba hypothesis and to gain a more complete understanding of the evolutionary history of orangutan SFV. As with previous studies, our results show a similar three-clade orangutan SFV phylogeny, along with strong statistical support for SFV-host co-evolution in orangutans. Using Bayesian inference, we date the origin of orangutan SFV to >4.7 million years ago (mya), while the mixed species clade dates to approximately 1.7mya, >1.6 million years older than the Toba super-eruption. These results, combined with fossil and paleogeographic evidence, suggest that the origin of SFV in Sumatran and Bornean orangutans, including the mixed species clade, likely occurred on the mainland of Indo-China during the Late Pliocene and Calabrian stage of the Pleistocene, respectively.
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Affiliation(s)
- Michael J C Reid
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada; Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada.
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA.
| | - Michael A Schillaci
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada.
| | - Amy R Klegarth
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA; Department of Anthropology, University of Washington, Seattle, WA 98105, USA.
| | - Ellsworth Campbell
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA.
| | - Manon Ragonnet-Cronin
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, United Kingdom
| | - Isabelle Joanisse
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kyna Caminiti
- Centre for Biosecurity, Public Health Agency of Canada, 100 Colonnade Road, Ottawa, Ontario, Canada.
| | - Carl A Lowenberger
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Birute Mary F Galdikas
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada; Orangutan Foundation International, 824 S. Wellesley Ave., Los Angeles, CA 90049, USA
| | - Hope Hollocher
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Paul A Sandstrom
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Ontario, Canada.
| | - James I Brooks
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; The Ottawa Hospital, Division of Infectious Diseases, Department of Medicine, University of Ottawa, 1053 Carling Ave., Ottawa, ONK1Y 4E9, Canada
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15
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Cocirculation of Two env Molecular Variants, of Possible Recombinant Origin, in Gorilla and Chimpanzee Simian Foamy Virus Strains from Central Africa. J Virol 2015; 89:12480-91. [PMID: 26446599 DOI: 10.1128/jvi.01798-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/28/2015] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Simian foamy virus (SFV) is a ubiquitous retrovirus in nonhuman primates (NHPs) that can be transmitted to humans, mostly through severe bites. In the past few years, our laboratory has identified more than 50 hunters from central Africa infected with zoonotic SFVs. Analysis of the complete sequences of five SFVs obtained from these individuals revealed that env was the most variable gene. Furthermore, recombinant SFV strains, some of which involve sequences in the env gene, were recently identified. Here, we investigated the variability of the env genes of zoonotic SFV strains and searched for possible recombinants. We sequenced the complete env gene or its surface glycoprotein region (SU) from DNA amplified from the blood of (i) a series of 40 individuals from Cameroon or Gabon infected with a gorilla or chimpanzee foamy virus (FV) strain and (ii) 1 gorilla and 3 infected chimpanzees living in the same areas as these hunters. Phylogenetic analyses revealed the existence of two env variants among both the gorilla and chimpanzee FV strains that were present in zoonotic and NHP strains. These variants differ greatly (>30% variability) in a 753-bp-long region located in the receptor-binding domain of SU, whereas the rest of the gene is very conserved. Although the organizations of the Env protein sequences are similar, the potential glycosylation patterns differ between variants. Analysis of recombination suggests that the variants emerged through recombination between different strains, although all parental strains could not be identified. IMPORTANCE SFV infection in humans is a great example of a zoonotic retroviral infection that has not spread among human populations, in contrast to human immunodeficiency viruses (HIVs) and human T-lymphotropic viruses (HTLVs). Recombination was a major mechanism leading to the emergence of HIV. Here, we show that two SFV molecular envelope gene variants circulate among ape populations in Central Africa and that both can be transmitted to humans. These variants differ greatly in the SU region that corresponds to the part of the Env protein in contact with the environment. These variants may have emerged through recombination between SFV strains infecting different NHP species.
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16
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Rua R, Gessain A. Origin, evolution and innate immune control of simian foamy viruses in humans. Curr Opin Virol 2015; 10:47-55. [PMID: 25698621 PMCID: PMC7185842 DOI: 10.1016/j.coviro.2014.12.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/04/2014] [Accepted: 12/10/2014] [Indexed: 12/23/2022]
Abstract
Simian foamy viruses (SFV) are transmitted to humans after contact, mainly bites, with infected monkeys and apes. Contexts of transmission include mainly hunting activities and monkeys’ sympatry. In humans, active immune response probably explains SFV latency in blood and saliva. It is a model of restriction of retroviral emergence after cross-species transmission.
Most viral pathogens that have emerged in humans have originated from various animal species. Emergence is a multistep process involving an initial spill-over of the infectious agent into single individuals and its subsequent dissemination into the human population. Similar to simian immunodeficiency viruses and simian T lymphotropic viruses, simian foamy viruses (SFV) are retroviruses that are widespread among non-human primates and can be transmitted to humans, giving rise to a persistent infection, which seems to be controlled in the case of SFV. In this review, we present current data on the discovery, cross-species transmission, and molecular evolution of SFV in human populations initially infected and thus at risk for zoonotic emergence.
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Affiliation(s)
- Rejane Rua
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, 28 Rue du Dr. Roux, 75015 Paris, France; Département de Virologie, Institut Pasteur, 25-28 rue du Dr Roux, 75724 Paris, Cedex 15, France; CNRS, UMR369, 28 Rue du Dr. Roux, F-75015 Paris, France; Université Paris Diderot, Cellule Pasteur, Paris, France.
| | - Antoine Gessain
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, 28 Rue du Dr. Roux, 75015 Paris, France; Département de Virologie, Institut Pasteur, 25-28 rue du Dr Roux, 75724 Paris, Cedex 15, France; CNRS, UMR369, 28 Rue du Dr. Roux, F-75015 Paris, France
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17
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Yoshikawa R, Nakagawa S, Okamoto M, Miyazawa T. Construction of an infectious clone of simian foamy virus of Japanese macaque (SFVjm) and phylogenetic analyses of SFVjm isolates. Gene 2014; 548:149-54. [PMID: 25017058 DOI: 10.1016/j.gene.2014.07.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/30/2014] [Accepted: 07/10/2014] [Indexed: 01/08/2023]
Abstract
Foamy viruses belong to the genus Spumavirus of the family Retroviridae and have been isolated from many mammalian species. It was reported that simian foamy viruses (SFVs) have co-evolved with host species. In this study, we isolated four strains (WK1, WK2, AR1 and AR2) of SFV (named SFVjm) from Japanese macaques (Macaca fuscata) in main island Honshu of Japan. We constructed an infectious molecular clone of SFVjm strain WK1, termed pJM356. The virus derived from the clone replicated and induced syncytia in human (human embryonic kidney 293T cells), African green monkey (Vero cells) and mouse cell lines (Mus dunni tail fibroblast cells). Phylogenetic analysis also revealed that these four SFVjm strains formed two distinct SFVjm clusters. SFVjm strains WK1 and WK2 and SFV isolated from Taiwanese macaques (Macaca cyclopis) formed one cluster, whereas strains AR1 and AR2 formed the other cluster with SFV isolated from a rhesus macaque (Macaca mulatta).
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Affiliation(s)
- Rokusuke Yoshikawa
- Laboratory of Signal Transduction, Department of Cell Biology, Institute for Virus Research, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, Kyoto 606-8507, Japan; Laboratory of Virolution, Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, Kyoto 606-8507, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
| | - Munehiro Okamoto
- Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Takayuki Miyazawa
- Laboratory of Signal Transduction, Department of Cell Biology, Institute for Virus Research, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, Kyoto 606-8507, Japan; Laboratory of Signal Transduction, Department of Cell Biology, Institute for Virus Research, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, Kyoto 606-8507, Japan.
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18
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Evaluation of the broad-range PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) system and virus microarrays for virus detection. Viruses 2014; 6:1876-96. [PMID: 24777034 PMCID: PMC4036539 DOI: 10.3390/v6051876] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/04/2014] [Accepted: 04/15/2014] [Indexed: 12/31/2022] Open
Abstract
Advanced nucleic acid-based technologies are powerful research tools for novel virus discovery but need to be standardized for broader applications such as virus detection in biological products and clinical samples. We have used well-characterized retrovirus stocks to evaluate the limit of detection (LOD) for broad-range PCR with electrospray ionization mass spectrometry (PCR/ESI-MS or PLEX-ID), RT-PCR assays, and virus microarrays. The results indicated that in the absence of background cellular nucleic acids, PLEX-ID and RT-PCR had a similar LOD for xenotropic murine retrovirus-related virus (XMRV; 3.12 particles per µL) whereas sensitivity of virus detection was 10-fold greater using virus microarrays. When virus was spiked into a background of cellular nucleic acids, the LOD using PLEX-ID remained the same, whereas virus detection by RT-PCR was 10-fold less sensitive, and no virus could be detected by microarrays. Expected endogenous retrovirus (ERV) sequences were detected in cell lines tested and known species-specific viral sequences were detected in bovine serum and porcine trypsin. A follow-up strategy was developed using PCR amplification, nucleotide sequencing, and bioinformatics to demonstrate that an RD114-like retrovirus sequence that was detected by PLEX-ID in canine cell lines (Madin-Darby canine kidney (MDCK) and Cf2Th canine thymus) was due to defective, endogenous gammaretrovirus-related sequences.
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19
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Blochmann R, Curths C, Coulibaly C, Cichutek K, Kurth R, Norley S, Bannert N, Fiebig U. A novel small animal model to study the replication of simian foamy virus in vivo. Virology 2014; 448:65-73. [DOI: 10.1016/j.virol.2013.09.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 06/09/2013] [Accepted: 09/29/2013] [Indexed: 10/26/2022]
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20
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Simian foamy virus infection of rhesus macaques in Bangladesh: relationship of latent proviruses and transcriptionally active viruses. J Virol 2013; 87:13628-39. [PMID: 24109214 DOI: 10.1128/jvi.01989-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Simian foamy viruses (SFV) are complex retroviruses that are ubiquitous in nonhuman primates (NHP) and are zoonotically transmitted to humans, presumably through NHP saliva, by licking, biting, and other behaviors. We have studied SFV in free-ranging rhesus macaques in Bangladesh. It has been previously shown that SFV in immunocompetent animals replicates to detectable levels only in superficial epithelial cells of the oral mucosa, although latent proviruses are found in most, if not all, tissues. In this study, we compare DNA sequences from latent SFV proviruses found in blood cells of 30 Bangladesh rhesus macaques to RNA sequences of transcriptionally active SFV from buccal swabs obtained from the same animals. Viral strains, defined by differences in SFV gag sequences, from buccal mucosal specimens overlapped with those from blood samples in 90% of animals. Thus, latent proviruses in peripheral blood mononuclear cells (PBMC) are, to a great extent, representative of viruses likely to be transmitted to other hosts. The level of SFV RNA in buccal swabs varied greatly between macaques, with increasing amounts of viral RNA in older animals. Evidence of APOBEC3-induced mutations was found in gag sequences derived from the blood and oral mucosa.
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21
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Rethwilm A, Bodem J. Evolution of foamy viruses: the most ancient of all retroviruses. Viruses 2013; 5:2349-74. [PMID: 24072062 PMCID: PMC3814592 DOI: 10.3390/v5102349] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 08/27/2013] [Accepted: 09/18/2013] [Indexed: 12/24/2022] Open
Abstract
Recent evidence indicates that foamy viruses (FVs) are the oldest retroviruses (RVs) that we know and coevolved with their hosts for several hundred million years. This coevolution may have contributed to the non-pathogenicity of FVs, an important factor in development of foamy viral vectors in gene therapy. However, various questions on the molecular evolution of FVs remain still unanswered. The analysis of the spectrum of animal species infected by exogenous FVs or harboring endogenous FV elements in their genome is pivotal. Furthermore, animal studies might reveal important issues, such as the identification of the FV in vivo target cells, which than require a detailed characterization, to resolve the molecular basis of the accuracy with which FVs copy their genome. The issues of the extent of FV viremia and of the nature of the virion genome (RNA vs. DNA) also need to be experimentally addressed.
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Affiliation(s)
- Axel Rethwilm
- Universität Würzburg, Institut für Virologie und Immunbiologie, Versbacher Str.7, Würzburg 97078, Germany.
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22
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Kehl T, Tan J, Materniak M. Non-simian foamy viruses: molecular virology, tropism and prevalence and zoonotic/interspecies transmission. Viruses 2013; 5:2169-209. [PMID: 24064793 PMCID: PMC3798896 DOI: 10.3390/v5092169] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 12/27/2022] Open
Abstract
Within the field of retrovirus, our knowledge of foamy viruses (FV) is still limited. Their unique replication strategy and mechanism of viral persistency needs further research to gain understanding of the virus-host interactions, especially in the light of the recent findings suggesting their ancient origin and long co-evolution with their nonhuman hosts. Unquestionably, the most studied member is the primate/prototype foamy virus (PFV) which was originally isolated from a human (designated as human foamy virus, HFV), but later identified as chimpanzee origin; phylogenetic analysis clearly places it among other Old World primates. Additionally, the study of non-simian animal FVs can contribute to a deeper understanding of FV-host interactions and development of other animal models. The review aims at highlighting areas of special interest regarding the structure, biology, virus-host interactions and interspecies transmission potential of primate as well as non-primate foamy viruses for gaining new insights into FV biology.
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Affiliation(s)
- Timo Kehl
- German Cancer Research Center, INF242, Heidelberg 69120, Germany
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49-6221-42-4935; Fax: +49-6221-42-4932
| | - Juan Tan
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; E-Mail:
| | - Magdalena Materniak
- Department of Biochemistry, National Veterinary Research Institute, Partyzantow Ave. 57, Pulawy 24-100, Poland; E-Mail:
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