Genomically intact endogenous feline leukemia viruses of recent origin

Copy number polymorphism of endogenous feline leukemia virus-like sequences

In the cat genome, endogenous feline leukemia virus (enFeLV) exists as multiple, nearly full-length proviral sequences. Even though no infectious virus is produced from enFeLV sequences, transcription and translation have been demonstrated in tissues of healthy cats and in feline cell lines. To test the hypothesis that the enFeLV loads play a role in exogenous FeLV-A infection and pathogenesis, we designed three real-time PCR assays to quantify U3 and env enFeLV loads (two within U3 amplifying different sequences; one within env). Applying these assays, we investigated the loads in blood samples derived from Swiss privately owned domestic cats, specific pathogen-free (SPF) cats and European wildcats (Felis silvestris silvestris). Significant differences in enFeLV loads were observed between privately owned cats and SPF cats as well as among SPF cats originating from different catteries and among domestic cats of different breeds. Within privately owned cats, FeLV-infected cats had higher loads than uninfected cats. In addition, higher enFeLV loads were found in wildcats compared to domestic cats. The assays described herein are important prerequisites to quantify enFeLV loads and thus to investigate the influence of enFeLV loads on the course of FeLV infection.

New Simian β Retroviruses from Rhesus Monkeys (Macaca Mulatta) and Langurs (Semnopithecus Entellus) from Rajasthan, India

Natural infection of feral Indian rhesus monkeys (Macaca mulatta) by a new simian beta retrovirus, provisionally called simian retrovirus-7 (SRV-7) is described. The virus is capable of in vitro replication in primary human peripheral blood lymphocytes (PBL) and B and T cell lines. We have earlier reported a novel SRV, SRV-6 from Indian langurs (Semnopithecus entellus). Additional sequence analyses from gp20 transmembrane (TM) env genes of SRV-6 and SRV-7 place them in a separate cluster, related to but distinct from known exogenous SRVs and also close to the simian endogenous beta retrovirus, (SERV) from African baboon. Phylogenetic analyses of pol gene of SRV-7 place it closer to SERV when the stop codons of the SERV genes are removed. On the other hand, additional sequence data from gp70, surface glycoprotein (SU) region of the env gene of SRV-6 suggest it is more closely related to known exogenous SRVs, (SRV-1 to 3). It is also related to the endogenous langur virus, Po-1-Lu. We hypothesize that SRV-6 and SRV-7 probably originated from a progenitor exogenous SRV which recombined with an endogenous SERV in the TM env and pol genes during evolution, based on the phylogenetic analyses.

Quantitation of feline leukaemia virus viral and proviral loads by TaqMan real-time polymerase chain reaction

Feline leukaemia virus (FeLV) infection in cats is not only of veterinary importance but also a well-acknowledged animal model for studying the pathogenesis of retroviral disease. After virus exposure, different courses and outcomes of FeLV infection may prevail; they have been associated with cellular and humoral immune responses and the FeLV proviral load in peripheral blood. We hypothesized that the plasma viral RNA load might be an additional relevant indicator for the infection outcome. To quantify these loads, a real-time reverse transcriptase (RT) polymerase chain reaction (PCR) assay was developed. The assay amplifies FeLV-A, -B, and -C as some naturally infected cats could not be identified with a FeLV-A-based assay previously. The assay was applied to determine plasma FeLV RNA loads in cats infected both naturally and experimentally with FeLV. In addition, an improved real-time PCR assay for quantitation of FeLV proviral loads is described. The assays developed were more sensitive than ELISA and virus isolation in the early phase of infection. In addition, PCR allows the identification of provirus carriers that have overcome antigenaemia. Thus, for most effective detection of FeLV exposure and characterization of the infection in a cat, PCR assays are recommended as diagnostic tools.

Insertional polymorphisms of endogenous feline leukemia viruses

The number, chromosomal distribution, and insertional polymorphisms of endogenous feline leukemia viruses (enFeLVs) were determined in four domestic cats (Burmese, Egyptian Mau, Persian, and nonbreed) using fluorescent in situ hybridization and radiation hybrid mapping. Twenty-nine distinct enFeLV loci were detected across 12 of the 18 autosomes. Each cat carried enFeLV at only 9 to 16 of the loci, and many loci were heterozygous for presence of the provirus. Thus, an average of 19 autosomal copies of enFeLV were present per cat diploid genome. Only five of the autosomal enFeLV sites were present in all four cats, and at only one autosomal locus, B4q15, was enFeLV present in both homologues of all four cats. A single enFeLV occurred in the X chromosome of the Burmese cat, while three to five enFeLV proviruses occurred in each Y chromosome. The X chromosome and nine autosomal enFeLV loci were telomeric, suggesting that ectopic recombination between nonhomologous subtelomeres may contribute to enFeLV distribution. Since endogenous FeLVs may affect the infectiousness or pathogenicity of exogenous FeLVs, genomic variation in enFeLVs represents a candidate for genetic influences on FeLV leukemogenesis in cats.

Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans

Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been proposed, but little evidence exists for such events in the human/great ape lineage of evolution. Based on analysis of finished BAC chimpanzee genome sequence, we characterize a retroviral element (Pan troglodytes endogenous retrovirus 1 [PTERV1]) that has become integrated in the germline of African great ape and Old World monkey species but is absent from humans and Asian ape genomes. We unambiguously map 287 retroviral integration sites and determine that approximately 95.8% of the insertions occur at non-orthologous regions between closely related species. Phylogenetic analysis of the endogenous retrovirus reveals that the gorilla and chimpanzee elements share a monophyletic origin with a subset of the Old World monkey retroviral elements, but that the average sequence divergence exceeds neutral expectation for a strictly nuclear inherited DNA molecule. Within the chimpanzee, there is a significant integration bias against genes, with only 14 of these insertions mapping within intronic regions. Six out of ten of these genes, for which there are expression data, show significant differences in transcript expression between human and chimpanzee. Our data are consistent with a retroviral infection that bombarded the genomes of chimpanzees and gorillas independently and concurrently, 3–4 million years ago. We speculate on the potential impact of such recent events on the evolution of humans and great apes.

Comparison of human and other primate genomes provides evidence for a retroviral infection that bombarded the genomes of chimpanzees and gorillas 3-4 million years ago