Porcine endogenous retroviruses infect cells lacking cognate receptors by an alternative pathway: implications for retrovirus evolution and xenotransplantation

Insight into the epigenetic landscape of a currently endogenizing gammaretrovirus in mule deer (Odocoileus hemionus)

Endogenous retroviruses (ERVs) constitute a significant part of vertebrate genomes. They originated from past retroviral infections and some of them retain transcriptional activity. The key mechanism avoiding uncontrolled ERV transcription is DNA methylation-mediated epigenetic silencing. Despite numerous studies describing the involvement of ERV activity in cellular processes, epigenetic regulation of ERVs is still poorly understood. We previously described a cervid endogenous retrovirus (CrERV) in the mule deer genome. This virus exhibits massive insertional polymorphism, suggesting recent activity. Here we employed NGS-based strategy to determine the methylation pattern of CrERV integrations in four mule deer. Besides the vast majority of methylated integrations, we identified a tiny fraction of demethylated proviral copies. These copies represent evolutionary older integrations located near gene promoters. In general, our work is a first attempt to characterize the epigenetic landscape of insertionally polymorphic ERV on a whole-genome scale and offers insight into its interactions with a host.

Porcine Endogenous Retrovirus (PERV) - Molecular Structure and Replication Strategy in the Context of Retroviral Infection Risk of Human Cells

The xenotransplantation of porcine tissues may help overcome the shortage of human organs for transplantation. However, there are some concerns about recipient safety because the risk of porcine endogenous retrovirus (PERV) transmission to human cells remains unknown. Although, to date, no PERV infections have been noted in vivo, the possibility of such infections has been confirmed in vitro. Better understanding of the structure and replication cycle of PERVs is a prerequisite for determining the risk of infection and planning PERV-detection strategies. This review presents the current state of knowledge about the structure and replication cycle of PERVs in the context of retroviral infection risk.

Genome-Wide Screening of Retroviral Envelope Genes in the Nine-Banded Armadillo (Dasypus novemcinctus, Xenarthra) Reveals an Unfixed Chimeric Endogenous Betaretrovirus Using the ASCT2 Receptor

Retroviruses enter host cells through the interaction of their envelope (Env) protein with a cell surface receptor, which triggers the fusion of viral and cellular membranes. The sodium-dependent neutral amino acid transporter ASCT2 is the common receptor of the large RD114 retrovirus interference group, whose members display frequent env recombination events. Germ line retrovirus infections have led to numerous inherited endogenous retroviruses (ERVs) in vertebrate genomes, which provide useful insights into the coevolutionary history of retroviruses and their hosts. Rare ERV-derived genes display conserved viral functions, as illustrated by the fusogenic syncytin env genes involved in placentation. Here, we searched for functional env genes in the nine-banded armadillo (Dasypus novemcinctus) genome and identified dasy-env1.1, which clusters with RD114 interference group env genes and with two syncytin genes sharing ASCT2 receptor usage. Using ex vivo pseudotyping and cell-cell fusion assays, we demonstrated that the Dasy-Env1.1 protein is fusogenic and can use both human and armadillo ASCT2s as receptors. This gammaretroviral env gene belongs to a provirus with betaretrovirus-like features, suggesting acquisition through recombination. Provirus insertion was found in several Dasypus species, where it has not reached fixation, whereas related family members integrated before diversification of the genus Dasypus >12 million years ago (Mya). This newly described ERV lineage is potentially useful as a population genetic marker. Our results extend the usage of ASCT2 as a retrovirus receptor to the mammalian clade Xenarthra and suggest that the acquisition of an ASCT2-interacting env gene is a major selective force driving the emergence of numerous chimeric viruses in vertebrates.

IMPORTANCE

Retroviral infection is initiated by the binding of the viral envelope glycoprotein to a host cell receptor(s), triggering membrane fusion. Ancient germ line infections have generated numerous endogenous retroviruses (ERVs) in nearly all vertebrate genomes. Here, we report a previously uncharacterized ERV lineage from the genome of a xenarthran species, the nine-banded armadillo (Dasypus novemcinctus). It entered the Dasypus genus >12 Mya, with one element being inserted more recently in some Dasypus species, where it could serve as a useful marker for population genetics. This element exhibits an env gene, acquired by recombination events, with conserved viral fusogenic properties through binding to ASCT2, a receptor used by a wide range of recombinant retroviruses infecting other vertebrate orders. This specifies the ASCT2 transporter as a successful receptor for ERV endogenization and suggests that ASCT2-binding env acquisition events have favored the emergence of numerous chimeric viruses in a wide range of species.

Induction and characterization of a replication competent cervid endogenous gammaretrovirus (CrERV) from mule deer cells

Endogenous retroviruses (ERVs) were acquired during evolution of their host organisms after infection and mendelian inheritance in the germline by their exogenous counterparts. The ERVs can spread in the host genome and in some cases they affect the host phenotype. The cervid endogenous gammaretrovirus (CrERV) is one of only a few well-defined examples of evolutionarily recent invasion of mammalian genome by retroviruses. Thousands of insertionally polymorphic CrERV integration sites have been detected in wild ranging mule deer (Odocoileus hemionus) host populations. Here, we describe for the first time induction of replication competent CrERV by cocultivation of deer and human cells. We characterize the physical properties and tropism of the induced virus. The genomic sequence of the induced virus is phylogenetically related to the evolutionarily young endogenous CrERVs described so far. We also describe the level of replication block of CrERV on deer cells and its capacity to establish superinfection interference.

A soluble envelope protein of endogenous retrovirus (FeLIX) present in serum of domestic cats mediates infection of a pathogenic variant of feline leukemia virus

T-lymphotropic feline leukemia virus (FeLV-T), a highly pathogenic variant of FeLV, induces severe immunosuppression in cats. FeLV-T is fusion defective because in its PHQ motif, a gammaretroviral consensus motif in the N terminus of an envelope protein, histidine is replaced with aspartate. Infection by FeLV-T requires FeLIX, a truncated envelope protein encoded by an endogenous FeLV, for transactivation of infectivity and Pit1 for binding FeLIX. Although Pit1 is present in most tissues in cats, the expression of FeLIX is limited to certain cells in lymphoid organs. Therefore, the host cell range of FeLV-T was thought to be restricted to cells expressing FeLIX. However, because FeLIX is a soluble factor and is expressed constitutively in lymphoid organs, we presumed it to be present in blood and evaluated its activities in sera of various mammalian species using a pseudotype assay. We demonstrated that cat serum has FeLIX activity at a functional level, suggesting that FeLIX is present in the blood and that FeLV-T may be able to infect cells expressing Pit1 regardless of the expression of FeLIX in vivo. In addition, FeLIX activities in sera were detected only in domestic cats and not in other feline species tested. To our knowledge, this is the first report to prove that a large amount of truncated envelope protein of endogenous retrovirus is circulating in the blood to facilitate the infection of a pathogenic exogenous retrovirus.

Detection of porcine endogenous retrovirus in xenotransplantation

Xenotransplantation can provide a virtually limitless supply of cells, tissues and organs for a variety of therapeutic procedures. Cells and tissues for use in human transplantation procedures could be supplied using material taken from pigs. However, there is a potential risk of transmission of porcine infectious agents, including porcine endogenous retroviruses (PERVs), to a novel human host, with as yet unknown consequences. Three subtypes of PERV have been identified, of which both PERV-A and PERV-B have the ability to infect human cells in vitro. The third subtype, PERV-C, does not show this ability. Recombinant PERV-A/C forms have demonstrated infectivity in human cell culture. Monitoring in xenotransplantation should comprise screening of the source pig herd (PERV-A and PERV-B level expression assessment, PERV-C detection) and screening of recipients (differentiation between PERV transmission and chimerism). The detection of PERVs includes analyses of both DNA and RNA (PCR and RT-PCR), quantitative determination of the level of PERV nucleic acids (real-time PCR and real-time RT-PCR), assessment of reverse transcriptase (RT) activity (RT assays) and viral and recipient protein detection (immunological methods). In summary, all available methods should be used in monitoring of PERVs in xenotransplantation, and caution should be exercised at all stages of monitoring. Such monitoring has enormous significance for eliminating the possibility of transmission of PERV infection, thus contributing to higher levels of safety in xenotransplantation.

Role of DNA methylation in expression and transmission of porcine endogenous retroviruses

Porcine endogenous retroviruses (PERV) represent a major safety concern in pig-to-human xenotransplantation. To date, no PERV infection of a xenograft recipient has been recorded; however, PERVs are transmissible to human cells in vitro. Some recombinants of the A and C PERV subgroups are particularly efficient in infection and replication in human cells. Transcription of PERVs has been described in most pig cells, but their sequence and insertion polymorphism in the pig genome impede identification of transcriptionally active or silenced proviral copies. Furthermore, little is known about the epigenetic regulation of PERV transcription. Here, we report on the transcriptional suppression of PERV by DNA methylation in vitro and describe heavy methylation in the majority of PERV 5' long terminal repeats (LTR) in porcine tissues. In contrast, we have detected sparsely methylated or nonmethylated proviruses in the porcine PK15 cells, which express human cell-tropic PERVs. We also demonstrate the resistance of PERV DNA methylation to inhibitors of methylation and deacetylation. Finally, we show that the high permissiveness of various human cell lines to PERV infection coincides with the inability to efficiently silence the PERV proviruses by 5'LTR methylation. In conclusion, we suggest that DNA methylation is involved in PERV regulation, and that only a minor fraction of proviruses are responsible for the PERV RNA expression and porcine cell infectivity.

Identification of a novel subgroup of Koala retrovirus from Koalas in Japanese zoos

We identified a new subgroup of koala retrovirus (KoRV), named KoRV-J, which utilizes thiamine transport protein 1 as a receptor instead of the Pit-1 receptor used by KoRV (KoRV-A). By subgroup-specific PCR, KoRV-J and KoRV-A were detected in 67.5 and 100% of koalas originating from koalas from northern Australia, respectively. Altogether, our results indicate that the invasion of the koala population by KoRV-J may have occurred more recently than invasion by KoRV-A.

Infection barriers to successful xenotransplantation focusing on porcine endogenous retroviruses

Xenotransplantation may be a solution to overcome the shortage of organs for the treatment of patients with organ failure, but it may be associated with the transmission of porcine microorganisms and the development of xenozoonoses. Whereas most microorganisms may be eliminated by pathogen-free breeding of the donor animals, porcine endogenous retroviruses (PERVs) cannot be eliminated, since these are integrated into the genomes of all pigs. Human-tropic PERV-A and -B are present in all pigs and are able to infect human cells. Infection of ecotropic PERV-C is limited to pig cells. PERVs may adapt to host cells by varying the number of LTR-binding transcription factor binding sites. Like all retroviruses, they may induce tumors and/or immunodeficiencies. To date, all experimental, preclinical, and clinical xenotransplantations using pig cells, tissues, and organs have not shown transmission of PERV. Highly sensitive and specific methods have been developed to analyze the PERV status of donor pigs and to monitor recipients for PERV infection. Strategies have been developed to prevent PERV transmission, including selection of PERV-C-negative, low-producer pigs, generation of an effective vaccine, selection of effective antiretrovirals, and generation of animals transgenic for a PERV-specific short hairpin RNA inhibiting PERV expression by RNA interference.

Development of sensitive methods for detection of porcine endogenous retrovirus-C (PERV-C) in the genome of pigs

Porcine endogenous retroviruses (PERV) represent a risk for xenotransplantation using pig cells, tissues or organs. PERV-A and PERV-B are present in the genome of all pigs and both infect human cells in vitro. PERV-C infects only pig cells and it is integrated in the genome of most, but not all pigs. Recombinants between PERV-A and PERV-C were described that infect human cells and replicate at high titres. To avoid such recombinations, PERV-C positive animals should not be used for breeding animals suited for xenotransplantation. In order to detect PERV-C positive pigs, different methods were developed such as specific PCRs using different primers, a highly sensitive nested PCR and a real-time PCR allowing measurement of proviral copy numbers. The real-time PCR was found to be useful to discriminate between contamination and actual provirus copies. The PCRs were optimized and their sensitivity was determined. Screening can be started with PCR1, if the result is negative, PCR2 to PCR5 or the nested PCR should be used, if the result is positive, the real-time PCR should be used to exclude contaminations. All methods were used to evaluate the prevalence of PERV-C and to identify PERV-C free animals. Due to the risk of contamination with cells from other animals testing should be performed with blood cells, not with ear biopsies.

Focus assay on FeLIX-dependent feline leukemia virus

T-lymphotropic feline leukemia virus (FeLV-T) induces immunodeficiency in cats. FeLV-T is fusion-defective and requires a cofactor, termed FeLIX, for infection. FeLIX is a truncated envelope glycoprotein of an endogenous FeLV and mediates infection by binding a phosphate transporter Pit-1. In this study, we established a feline sarcoma-positive leukemia-negative cell line expressing FeLIX, named QN/FeLIX cells. Upon infection, FeLV-T induced prominent foci with syncytia in QN/FeLIX cells and could be titrated by the focus assay. In addition, we established a FeLIX-expressing feline fibroblast cell line, named AH/FeLIX cells. FeLV-T productively infected AH/FeLIX cells and induced severe CPE with syncytia. QN/FeLIX and AH/FeLIX cells will be useful for the study of FeLIX-dependent mutants in FeLV-infected cats.

Recombinant porcine endogenous retroviruses (PERV-A/C): a new risk for xenotransplantation?

PERVs are integrated in the genome of all pigs. Some of them infect human cells and represent therefore a potential risk for xenotransplantation using pig cells or organs. Three replication-competent subtypes have been described, PERV-A, PERV-B and PERV-C. Whereas PERV-A and PERV-B are polytropic viruses and infect, among others, human cells, PERV-C is an ecotropic virus, infecting only pig cells. Recombinant PERV-A/C are able to infect human cells, they are characterised by high-titre replication and their proviruses have been found de novo integrated in the genome of somatic pig cells, but not in the germ line. This review compares recombinant PERVs with other recombinant retroviruses in order to evaluate their potential pathogenicity.

Reappraisal of biosafety risks posed by PERVs in xenotransplantation

Donor materials of porcine origin could potentially provide an alternative source of cells, tissues or whole organs for transplantation to humans, but is hampered by the health risk posed by infection with porcine viruses. Although pigs can be bred in such a way that all known exogenous microorganisms are eliminated, this is not feasible for all endogenous pathogens, such as the porcine endogenous retroviruses (PERVs) which are present in the germline of pigs as proviruses. Upon transplantation, PERV proviruses would be transferred to the human recipient along with the xenograft. If xenotransplantation stimulates or facilitates replication of PERVs in the new hosts, a risk exists for adaptation of the virus to humans and subsequent spread of these viruses. In a worst-case scenario, this might result in the emergence of a new viral disease. Although the concerns for disease potential of PERVs are easing, only limited pre-clinical and clinical data are available. Small-scale, well-designed and carefully controlled clinical trials would provide more evidence on the safety of this approach and allow a better appreciation of the risks involved. It is therefore important to have a framework of protective measures and monitoring protocols in place to facilitate such initially small scale clinical trials. This framework will raise ethical and social considerations regarding acceptability.

Functional epitopes on porcine endogenous retrovirus envelope protein interacting with neutralizing antibody combining sites

Porcine cell and organ transplantation provides promise for maintaining normal physiological conditions in patients with end-stage organ failure. The approach however poses serious risk of transmitting pig pathogens to humans. Among many potential pathogens, porcine endogenous retroviruses (PERV) are of particular concern due to their ubiquitous nature in pigs and capability of infecting human cells. Major antigenic determinants and receptor binding domains on PERV remain unclear until now. Two monoclonal antibodies (mAb), named 8E10 and 7C4 capable of neutralizing PERV infection in HEK293 cells are isolated at an IC(50) of 3.0 and 2.7 microg/ml, respectively, in this work. Epitope location for mAb 8E10 was mapped to amino acids 427-434, residing at the C-terminal region of the gp70 component of type A PERV Env protein. The mAb 8E10 bound directly to the PERV indicating that the epitope is exposed on the virion surface. The mAb 7C4 epitope was assigned to the region comprising amino acids 517-537 on the p15E component of PERV. In contrast to mAb 8E10, the 7C4 mAb bound native PERV inefficiently suggesting that its epitope is accessible only after the virus interacts with its receptor. Finally, both mAbs variable regions were cloned and nucleotide sequence determined. All together, these results reveal that both mAbs 8E10 and 7C4 effectively neutralize PERV infection and may be used as a mean to prevent PERV infection in patients receiving xenotransplantation.

Feline leukemia virus T entry is dependent on both expression levels and specific interactions between cofactor and receptor

Feline leukemia virus (FeLV) subgroup T uses both a multiple membrane-spanning receptor, FePit1, and a soluble cofactor, FeLIX, to enter feline cells. FeLIX is expressed from endogenous FeLV-related sequence and resembles the receptor binding domain (RBD) of the viral envelope protein. It remains unclear whether FeLV-T receptor activity requires specific residues within FePit1 and FeLIX and/or a threshold level of receptor/cofactor expression. To address this, we examined FeLV-T infection of cells expressing variable levels of FePit1 and other gammaretroviral receptors in the presence of variable amounts of soluble cofactor, either RBD or the envelope surface subunit (SU). Cofactor-receptor pairs fall into three groups with regard to mediating FeLV-T infection: those that are efficient at all concentrations tested, such as FePit1 and FeLIX; those requiring high expression of both cofactor and receptor; and those that are non-functional as receptors even at high expression. This suggests that both expression levels and specific interactions with receptor and cofactor are critical for mediating entry of FeLV-T.

Host cell range of T-lymphotropic feline leukemia virus in vitro

We compared the host cell range of T-lymphotropic feline leukemia virus (FeLV-T) with that of FeLV subgroup B (FeLV-B) by pseudotype assay in the presence of FeLIX, a truncated envelope glycoprotein of endogenous FeLV. Although both viruses use Pit1 as a receptor and FeLIX does not hamper FeLV-B infection by receptor interference, the host ranges of FeLV-T and -B were not exactly the same, suggesting a different Pit1 usage at the post-binding level. A comparison of Pit1 sequences of various mammalian species indicated that extracellular loop 1 in a topology model deduced with the PHD PredictProtein algorism may be one of the regions responsible for efficient infection by FeLV-T.

Envelope determinants for dual-receptor specificity in feline leukemia virus subgroup A and T variants

Gammaretroviruses, including the subgroups A, B, and C of feline leukemia virus (FeLV), use a multiple-membrane-spanning transport protein as a receptor. In some cases, such as FeLV-T, a nonclassical receptor that includes both a transport protein (Pit1) and a soluble cofactor (FeLIX) is required for entry. To define which regions confer specificity to classical versus nonclassical receptor pathways, we engineered mutations found in either FeLV-A/T or FeLV-T, individually and in combination, into the backbone of the transmissible form of the virus, FeLV-A. The receptor specificities of these viruses were tested by measuring infection and binding to cells expressing the FeLV-A receptor or the FeLV-T receptors. FeLV-A receptor specificity was maintained when changes at amino acid position 6, 7, or 8 of the mature envelope glycoprotein were introduced, although differences in infection efficiency were observed. When these N-terminal mutations were introduced together with a C-terminal 4-amino-acid insertion and an adjacent amino acid change, the resulting viruses acquired FeLV-T receptor specificity. Additionally, a W-->L change at amino acid position 378, although not required, enhanced infectivity for some viruses. Thus, we have found that determinants in the N and C termini of the envelope surface unit can direct entry via the nonclassical FeLV-T receptor pathway. The region that has been defined as the receptor binding domain of gammaretroviral envelope proteins determined entry via the FeLV-A receptor independently of the presence of the N- and C-terminal FeLV-T receptor determinants.

[Evolution of lentiviruses and receptor specificity]

Lentiviruses consist of primate lentiviruses, ungulate lentiviruses and feline immunodeficiency virus (FIV). The primate lentiviruses utilize CD4 and chemokine receptors as a primary receptor and coreceptors, respectively. Recently we found that FIV utilizes CD134 and CXCR4 as a primary receptor and a coreceptor, respectively. FIV utilizes feline CD134 but not human CD134, whereas it can utilize both feline and human CXCR4. Exceptionally an FIV laboratory strain can infect human cells via CXCR4 only by the CD134-independent manner. Similarly several strains of primate lentiviruses also infect cells by the CD4-independent manner. In this review, the evolution of the lentiviruses and possible mechanism for lentiviral cross-species transmission is discussed.

Cell-binding properties of the envelope proteins of porcine endogenous retroviruses

To examine the binding properties of the envelope glycoproteins of porcine endogenous retrovirus subgroups A and B (PERV-A and PERV-B), we produced two forms of soluble envelope proteins, termed Env-ST and Env-SU, using a baculovirus expression system. Env-ST and Env-SU encompass one-third of the N-terminal and the entire surface unit (SU) of the envelope protein, respectively. Using these proteins, binding assays were performed in various mammalian cell lines. The binding properties of the Env-STs that contain the putative receptor binding domain (RBD) did not correlate with the susceptibility to the pseudotype viruses having PERV envelopes, whereas those of the Env-SUs correlated fairly well. These results suggested that the Env-SUs but not Env-STs interacted with their receptors in various cell lines. Interestingly, PERV-A Env-SU did not bind to a mink cell line (Mv1-Lu cells) that is highly susceptible to the PERV-A pseudotype virus. In addition, PERV-B Env-SU did not interfere with the PERV-B pseudotype virus on Mv1-Lu cells. These results suggest the existence of a cognate receptor-independent entry pathway as demonstrated in an immunodeficiency-inducing variant of feline leukemia virus FeLV.