The Evolution, Distribution and Diversity of Endogenous Retroviruses (original) (raw)
References
Boeke J.D. and Stoye J.P., Retrotransposons, endogenous retroviruses, and the evolution of retroelements, in Coffin J.M., Hughes S.H., and Varmus H.E. (eds.), Retroviruses, CSHL Press, New York, 1997, pp. 343-435. Google Scholar
Coffin J.M., Hughes S.H., Varmus H.E., The interactions of retroviruses and their hosts, in Coffin J.M., Hughes S.H., and Varmus H.E. (eds.), Retroviruses, CSHL Press, New York, 1997, pp. 335-341. Google Scholar
Vogt P.K., Historical introduction to the general properties of retroviruses, in Coffin J.M., Hughes S.H., and Varmus H.E., (eds.), Retroviruses, CSHL Press, New York, 1997, pp. 1-25. Google Scholar
van Regenmortel M.H.V. et al., Academic Press, San Diego, 2000, p. 1167.
Stoye J.P., Endogenous retroviruses: Still active after all these years? Burr Biol 11, R914-R916, 2001. Google Scholar
Maynard Smith J., Haigh J., The hitchhiking effect of a favourable gene. Genet Res 23, 23-35, 1974. Google Scholar
Tristem M., Identification and characterisation of novel human endogenous retrovirus families by phylogenetic screening of the human genome mapping project database. J Virol 74, 3715-3730, 2000. Google Scholar
Yoder J.A., Walsh C.P., Bestro T.H., Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13, 335-340, 1997. Google Scholar
Waugh O'Neill R.J., Waugh O'Neill M.J., Graves J.A., Undermethylation associated with chromosome remodelling in an interspecific mammalian hybrid. Nature 393, 68-72, 1998. Google Scholar
Barbulescu M., Turner G., and Su M., Kim R., Jensen-Seaman M.L., Deinhard A.S., Kidd K.K., Lenz J., A HERV-K provirus in chimpanzees, bonobos and gorillas, but not humans. Curr Biol 11, 779-783, 2001. Google Scholar
Reus K., and Mayer J., Sauter M., Zischler H., Müller-Lantzsch N., Meese E., HERV-K(OLD): Ancestor sequences of the human endogenous retrovirus family HERV-K(HML-2). J Virol 75, 8917-8926, 2001. Google Scholar
Best S., and LeTissier G., Towers G., Stoye J.P., Positional cloning of the mouse retrovirus restriction gene Fvl. Nature 382, 826-829, 1996. Google Scholar
Stoye J., An intracellular block to private lentivirus replication. Proc Natl Acad Sci 99, 11549-11551.
Venables P.J.W., Brookes S.M., Griffiths D., Weiss R.A., and Boyd M.T., Abundance of an endogenous retroviral envelope protein in placental trophoblasts suggests a biological function. Virology 211, 589-592, 1995. Google Scholar
Andersson A.-C., Venables P.J.W., Tönjes R.R., Scherer J., Eriksson L., and Larsson E., Developmental expression of HERV.R (ERV.3) and HERV.K in human tissue. Virology 297, 220-225, 2002. Google Scholar
Mi S., et al. Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 403, 785-789, 2000. Google Scholar
Ting C.N., Rosenburg M.P., Snow C.M., Samuelson L.C., and Meisler M.H., Endogenous retroviral sequences are required for tissue-specific expression of a human salivary amylase gene. Gen Dev 6, 1457-1465, 1992. Google Scholar
Samuelson L.C., Phillips R.S., and Swanberg L.J., Amylase gene structures in primates: Retroposon insertions and promotor evolution. Mol Biol Evol 13, 767-779, 1996. Google Scholar
Swanstrom R., and Wills J.W., Synthesis, assembly, and processing of viral proteins, in Coffin J.M., Hughes S.H., and Varmus H.E. (eds.), Retroviruses, CSHL Press, New York, 1997, pp. 263-334. Google Scholar
Muriaux D., Mirro J., Nagashima K., Harvin D., and Rein A., Murine leukaemia virus nucleocapsid mutant particles lacking viral RNA encapsidate ribosomes. J Virol 76, 11405-11413, 2002. Google Scholar
Muriaux D., Mirro J., Harvin D., and Rein A., RNA is a structrual element in retrovirus particles. Proc Natl Acad Sci USA 98, 5246-5251, 2001. Google Scholar
Browing M.T., Schmidt R.D., Lew K.A., and Rizvi T.A., Primate and feline lentivirus vector RNA packaging and propagation by heterologous lentivirus virions. J Virol 75, 5129-5140, 2001. Google Scholar
Beasley B.E., and Hu W.-S., cis-acting elements important for retroviral RNA packaging specificity. J Virol 76, 4950-4960, 2002. Google Scholar
Certo J.L., Kabdulov T.O., Paulson M.L., Anderson J.A., and Hu W.-S., The nucleocapsid domain is responsible for the ability of spleen necrosis virus (SNV) gag polyprotein to package both SNV and murine leuaemia virus RNA. J Virol 73, 9170-9177, 1999. Google Scholar
Kato S., Matsuo K., Nishimura N., Takahashi N., and Takano T., The entire nucleotide sequence of baboon endogenous virus DNA: A chimeric genome structure of murine type C and simian type D retroviruses. Jpn J Genet 62, 127-137, 1987. Google Scholar
Van der Kuyl A.C., Mang R., Decker J.C., and Goudsmit J., Complete nucleotide sequence of simian endogenous type D retrovirus with intact genome organisation: Evidence for ancestry to simian retrovirus and baboon endogenous virus. J Virol 71, 3666-3676, 1997. Google Scholar
Mang R., Goudsmit J., and Van der Kuyl A.C., Novel endogenous type C retrovirus in baboons: complete sequence, providing evidence for baboon endogenous virus gag-pol ancestry. J Virol 73, 1999.
Van der Kuyl A.C., Dekker J.T., and Goudsmit J., Distribution of baboon endogenous virus among species of African monkeys suggests multiple ancient cross-species transmissions in shared habitats. J Virol 69, 7877-7887, 1995. Google Scholar
Doolittle R.F., Feng D.F., McClure M.A., and Johnson M.S., Retrovirus phylogeny and evolution. Curr Top Microbiol Immunol 157, 1-18, 1990. Google Scholar
Weiss R.A., Friis R.R., Katz E., and Vogt P.K., Induction of avian tumor viruses in normal cells by physical and chemical carcinogens. Virology 46, 920-938, 1971. Google Scholar
Benveniste R.E., and Todaro G.J., Homology between type C viruses of various species as determined by molecular hybridisation. Proc Natl Acad Sci USA 70, 3316-3320, 1973. Google Scholar
Benveniste R.E., and Todaro G.J., Evolution of C-type viral genes: inheritance of exogenously acquired viral genes. Nature 252, 456-459, 1974. Google Scholar
Bonner T.I., and Todaro G.J., The evolution of baboon endogenous type C virus: related sequences in the genomes of distant species. Virology 103, 217-227, 1980. Google Scholar
Cohen J.C., and Varmus H.E., Endogenous mammery tumour virus DNA varies among wild mice and segregates during inbreeding. Nature 278, 418-423, 1979. Google Scholar
Frisby D.P., Weiss R.A., Rousell M., and Stehelin D., The distribution of endogenous retroviral sequences in the DNA of galliforme birds does not coincide with avian phylogenetic relationships. Cell 17, 1979.
Kröger B., and Horde I., Isolation of novel human retrovirus-related sequences by hybridization to synthetic oligonucleotides complementary to the tRNAPro primer binding site. J Virol 69, 2071-2075, 1987. Google Scholar
Lueders K.K., and Kuff E.L., Intracisternal A particle genes: Identification in the genome of Mus musculus and comparison of multiple isolates from a mouse gene library. Proc Natl Acad Sci USA 77, 3571-3575, 1980. Google Scholar
Dunwiddie C.T., Resnick R., Boyce-Jacino M., Alegre J.N., and Faras A.J., Molecular cloning and characterisation of _gag_-, pol, and _env_-related sequences in _ev_-chicken. J Virol 59, 669-675, 1986. Google Scholar
Ono M., Toh H., and Miyata T.A.T., Nucleotide sequence of the Syrian hamster intracisternal A—particle gene: close evolutionary relationship of type A particle gene to types B and D oncovirus genes. J Virol 55, 387-394, 1985. Google Scholar
Medstrand P., and Blomberg J., Characterization of novel reverse transcriptase encoding humanendogenous retroviral sequences similar to type A and type B retroviruses: differential transcription in normal human tissues. J Virol 67, 6778-6787, 1993. Google Scholar
Shih R.M., and Rush M.G., Detection of multiple, novel reverse transcriptase coding sequences in human nucleic acids; Relation to primate retroviruses. J Virol 63, 64-75, 1989. Google Scholar
Tristem M., Amplification of divergent retroelements by PCR. Biotechniques 20, 608-612, 1996. Google Scholar
Herniou E., Martin J., Miller K., Cook J., Wilkinson M., and Tristem M., Retroviral diversity and distribution in vertebrates. J Virol 72, 5955-5966, 1998. Google Scholar
Baillie G.J., and Wilkins R.J., Endogenous type D retrovirus in a marsupial, the common brushtail possum (Trichosurus vulpecula). J Virol 75, 2499-2507, 2001. Google Scholar
Consortium I.h.g.s., Initial sequencing and analysis of the human genome. Nature 409, 860-921, 2001. Google Scholar
Consortium M.g.s., Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562, 2002. Google Scholar
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.L., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25, 3389-3402, 1997. Google Scholar
Smit A.F.A., Identification of a New, Abundant Superfamily of Mammalian LTR-Transposons. Nucl Acids Res 21, 1863-1872, 1993. Google Scholar
Griffiths D.J., Endogenous retroviruses and the human genome sequence. Gen Biol 2, 1017.1-1017.5, 2001. Google Scholar
Mayer J., and Meese E.U., The human endogenous retrovirus family HERV.K (HML-3). Genomics 80, 331-343, 2002. Google Scholar
Greenwood A.D., Lee F., Capelli C., DeSalle R., Tikhonov A., Marx P.A., and MacPhee R.D., Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives. Mol Biol Evol 18, 840-847, 2001. Google Scholar
Coffin J.M., Structure and classification of retroviruses, in Levy J.A. (ed.), The Retroviridae, Plenum Press, New York, 1992, pp. 19-49. Google Scholar
Williams K.J., and Loeb L.A., Retroviral reverse transcriptases: Error frequencies and mutagenesis. Curr Top Microbiol Immunol 176, 165-180, 1992. Google Scholar
Sala M., and Wain-Hobson S., Are RNA viruses adapting or merely changing?. J Mol Evol 51, 12-20, 2000. Google Scholar
Xiong Y., and Eickbush T.H., Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9, 3353-3362, 1990. Google Scholar
Doolittle R.F., Feng D.F., Johnson M.S., and McClure M.A., Origins and evolutionary relationships of retroviruses. Q Rev Biol 64, 1-30, 1989. Google Scholar
McClure M.A., Johnson M.S., Feng D.-F., and Doolittle R.F., Sequence comparisons of retroviral proteins: Relative rates of change and general phylogeny. Proc Natl Acad Sci USA 85, 2469-2473, 1988. Google Scholar
Bénit L., Dessen P., and Heidmann T., Identification, phylogeny, and evolution of retroviral elements based on their envelope genes. J Virol 75, 11709-11719, 2001. Google Scholar
Nandi S., and McGrath C.M., Mammary neoplasia in mice. Adv Cancer Res 17, 353-414, 1973. Google Scholar
Palmarini M., Cousens C., Dalziel R.G., Bai J., Stedman K., DeMartini J.C., and Sharp J.M., The exogenous form of jaagsiekte retrovirus is specifically associated with a contagious lung cancer of sheep. J Virol 70, 1618-1623, 1996. Google Scholar
Bock M., and Stoye J.P., Endogenous retroviruses and the human germline. Curr Opin Genet Dev 10, 2000.
Kim A., Terzian C., Santamaria P., Pelisson A., Prudhomme N., and Bucheton A., Retroviruses in Invertebrates—the Gypsy Retrotransposon Is Apparently an Infectious Retrovirus of Drosophila-Melanogaster. Proceedings of the National Academy of Sciences of the United States of America 91, 1285-1289, 1994. Google Scholar
Song S.U., Gerasimonva T., Kurkulos M., Boeke J.D., and Corces V.G., An env-like protein encoded by a Drosphila retroelement: Evidence that gypsy is an infectious retrovirus. Genes Dev 8, 2046-2057, 1994. Google Scholar
Peterson-Burch B.D., Wright D.A., Laten H.M., and Voystas D.F., Retroviruses in plants?. TIG 16, 151-152, 2000. Google Scholar
Martin J., Herniou E., Cook J., Waugh O'Neill R., and Tristem M., Human endogenous retrovirus type I-related viruses have an apparently widespread distribution within vertebrates. J Virol 71, 437-443, 1997. Google Scholar
Kambol R., in Biological Sciences, Imperial College, London, 2002, p. 191. Google Scholar
Miller K., Lynch C., Martin J., Herniou E., and Tristem M., Identification of multiple gypsy LTR-retrotransposon lineages in vertebrate genomes. J Mol Evol 49, 358-366, 1999. Google Scholar
Flavell A.J., Pearce S.R., Heslop-Harrison P., and Kumar A., The evolution of Tyl-copia retrotransposons in eukaryote genomes. Genetica 100, 185-195, 1997. Google Scholar
Beck G., and Habicht G.S., Immunity and the invertebrates. Sci Amer 275, 60-66, 1996. Google Scholar
Litman G.W., Sharks and the origins of vertebrate immunity. Sci Amer 275, 67-71, 1996. Google Scholar
Marchalonis J.J., Kaveri S., Lacroix-Desmazes S., and Kazatchkine M.D., Natural recoginition repertoire and the evolutionary emergence of the combinatorial immune system. FASAB J 16, 842-848, 2002. Google Scholar
Litman G.W., and Rast J.P., The organisation and structure of immunoglobulin and T-cell receptor genes in the most phylogenetically distant jawed vertebrates: evolutionary implications. Res Immunol 147, 226-233, 1996. Google Scholar
Ellerman R.N., and Bang O., Experimentalle Lekamie bei Huhnern. Zentrabl Bakeriol Parasitenkd Infectionskr Hyg Abt Orig 46, 595-609, 1908. Google Scholar
Petropoulos C., Retroviral taxonomy, protein structures, sequences, and genetic maps, in Coffin J.M. Hughes S.H., and Varmus H.E. (eds.), Retroviruses, CSHL Press, New York, 1997, pp. 757-805. Google Scholar
Schwartz D.E., Tizard R., and Gilbert W., Nucleotide Sequence of Rous Sarcoma Virus. Cell 32, 853-869, 1983. Google Scholar
Boyce-Jacino M.T., Odonoghue K., and Faras A.J., Multiple Complex Families of Endogenous Retroviruses Are Highly Conserved in the Genus Gallus. J Virol 66, 4919-4929, 1992. Google Scholar
Vogt P.K., and Friis R.R., An avian leukosis related to RSV(0). Properties and evidence for helper activity. Virology 43, 223-234, 1971. Google Scholar
Hughes S.H., Mutschler A., Bishop J.M., and Varmus H.E., Rous sarcoma virus provirus is flanked by short direct repeats of cellular DNA sequence present in only one copy prior to integration. Proc Natl Acad Sci USA 78, 4299-4305, 1981. Google Scholar
Payne L.N., Brown S.R., Bumstead N., Howes K., Frazier J.A., and Thouless M.E., A novel subgroup of exogenous avian leukosis virus in chickens. J Gen Virol 72, 801-807, 1991. Google Scholar
Boyce-Jacino M.T., Resnick R., and Faras A.J., Structural and functional characterization of the unusually short long terminal repeats and their adjacent regions of a novel endogenous avian retrovirus. Virology 173, 157-166, 1989. Google Scholar
Sacco M.A., Howes K., and Venugopal K., Intact EAV-HP endogenous retrovirus in Sonnerat's jungle fowl. J Virol 75, 2029-2032, 2001. Google Scholar
Resnick R.M., Boycejacino M.T., Fu Q., and Faras A.J., Phylogenetic Distribution of the Novel Avian Endogenous Provirus Family EAV-0. J Virol 64, 4640-4653, 1990. Google Scholar
Hanafusa T., Hanafusa H., Metroka C.E., Hayward W.S., Rettenmier C.W., Sawyer R.C., Dougherty R.M., and Di Stefano H.S., Pheasant virus: New class of ribodeoxyvirus. Proc Natl Acad Sci USA 73, 1333-1337, 1976. Google Scholar
Dimcheff D.E., Drovetski S.V., Krishnan M., and Mindell D.P., Cospeciation and horizontal transmission of avian sarcoma and leukosis virus gag genes in galliform birds. J Virol 74, 3984-3995, 2000. Google Scholar
Dimcheff D.E., Krishnan M., and Mindell D.P., Evolution and characterization of tetraonine endogenous retrovirus: A new virus related to avian sarcoma and leukosis viruses. J Virol 75, 2002-2009, 2001. Google Scholar
Vogt V.M., Retroviral virions and genomes, in Coffin J.M., Hughes S.H., and Varmus H.E. (eds.), Retroviruses, CSHL Press, New York, 1997. pp. 27-69. Google Scholar
Chopra H.C., and Mason M.M., A new virus in a spontaneous mammary tumour of a rhesus monkey. Cancer Res 30, 2081, 1970. Google Scholar
Nandi J.S., Bhavalkar-Potdar V., Tikute S., and Raut C.G., A novel type D simian retrovirus naturally infecting the Indian Hanuman Langur (Semnopithecus entellus). Virology 277, 6-13, 2000. Google Scholar
A.Rosenblum L., and McClure M., Non-lentiviral primate lentiviruses in HIV and the new viruses, in Dalgleish A.G., and Weiss K.A. (eds.), Academic Press, London, 1999, pp. 252-279. Google Scholar
Jones T.W.H., Sheep pulmonary adenomatosis (Jaagsiekte). Veterinary Record 117, 210, 1985. Google Scholar
Mager D.L., and Freeman J.D., Novel mouse type D endogenous proviruses and ETn elements share long terminal repeat and internal sequences. J Virol 74, 7221-7229, 2000. Google Scholar
Benveniste R.E., and Todaro G.J., Evolution of primate oncornaviruses: An endogenous virus from langue (Presbytis spp.) with related virogene sequence in other Old World monkeys. Pro Natl Acad Sci USA 74, 4557, 1977. Google Scholar
Todaro G.J., Beneveniste R.E., Sherr C.J., Schlon J., Schidlovsky G., and Stephenson J.R., Isolation and characterisation of a new type D retrovirus from the Asian primate Presbytis obscura (spectacled langur). Virology 84, 189-194, 1978. Google Scholar
Heberling R.L., Barker S.T., Kalter S.S., Smith G.C., and Helmke R.J., Oncornavirus: isolation from a squirrel monkey (Saimiri sciureus) lung culture. Science 195, 289-292, 1977. Google Scholar
Hecht S.J., Stedman K.E., Carlson J.O., and DeMartini J.C., Distribution of endogenous type B and type D sheep retrovirus sequences in ungulates and other mammals. Proc Natl Acad Sci USA 93, 3297-3302, 1996. Google Scholar
Dalton A.J., Potter M., and Merwin R.M., Some ultrastructural characteristics of a series of primary and transplanted plasma-cell tumours of the mouse. J Natl Cancer Inst 26, 1221-1267, 1961. Google Scholar
Kuff E.L., and Leuders K.K., The intracisternal A-particle family: Structure and functional aspects. Ad Cancer Res 51, 184-276, 1988. Google Scholar
Grassi M., Girault J.M., Wang W.P., Thiery J.P., and Jouanneau J., Metastatic rat carcinoma cells express a new retrotransposon. Gene 233, 59-66, 1999. Google Scholar
Mietz J.A., Grossman Z., Lueders K.K., and Kuff E.L., Nucleotide sequence of a complete mouse intracisternal A-particle genome: relationship to known aspects of particle assembly and function. J Virol 61, 3020-3029, 1987. Google Scholar
Reuss F.U., and Schaller H.C., Cdna Sequence and Genomic Characterization of Intracisternal a-particle-related retroviral elements containing an envelope gene. J Virol 65, 5702-5709, 1991. Google Scholar
Fennelly J., Harper K., Laval S., Wright E., and Plumb M., Co-amplification of tail-to-tail copies of MuRVY and IAPE retrovial genomes on the Mus musculus Y chromosome. Mammalian Genome 7, 31-36, 1996. Google Scholar
Gross L., “Spontaneous” leukemia developing in C3H mice following inoculation in infancy, with A-K leukemic extracts, or A-K embryos. Proc Soc Exp Biol Med 76, 27-32, 1951. Google Scholar
Levy J.A., Xenotropic viruses: murine leukaemia viruses associated with NIH Swiss, NZB, and other mouse strains. Science 182, 1151-1153, 1973. Google Scholar
Shinnick T.M., Lerner R.A., and Sutcliffe J.G., Nucleotide sequence of Moloney murine leukaemia virus. Nature 293, 543-548, 1981. Google Scholar
Delassus S., Sonigo P., and Wain-Hobson S., Genetic organization of gibbon ape leukemia virus. Virology 173, 205-213, 1989. Google Scholar
Donahue P.R., Hoover E.A., Beltz G.A., Riedel N., Hirsch V.M., Overbaugh J., and Mullins J.I., Strong sequence conservation among horizontally transmissible, minimally pathogenic feline leukaemia viruses. J Virol 62, 722-731, 1988. Google Scholar
Patience C., Switzer W.M., Takeuchi Y., Griffiths D.J., Goward M.E., Heneine W., Stoye J.P., and Weiss R.A., Multiple groups of novel retroviral genomes in pigs and related species. J Virol 75, 2771-2775, 2001. Google Scholar
Purchase H.G., Ludford C., Nazerian K., and W C.H., A new group of oncogenic viruses: reticuloendotheliosis, chick syncytial, duck infectious anemia, and spleen necrosis viruses. J Natl Cancer Inst 51, 489-499, 1973. Google Scholar
Payne L.N., Biology of avian retroviruses, in Levy J.A. (ed.), The Retroviridae, Plenum Press, New York, 1992, pp. 299-389. Google Scholar
Lunger P.D., Hardy W.D., and Clark H.F., C-type particles in a reptilian tumor. J Natl Cancer Inst 52, 1231-1235, 1974. Google Scholar
Tristem M., Kabat P., Lieberman L., Linde S., Karpas A., and Hill F., Characterization of a novel murine leukemia virus-related subgroup within mammals. J Virol 70, 8241-8246, 1996. Google Scholar
Martin J., Herniou E., Cook J., Waugh O'Neill R., and Tristem M., Interclass transmission and phyletic host tracking in murine leukaemia virus related retroviruses. J Virol 73, 2442-2449, 1999. Google Scholar
Hart D., Frerichs N., Rambaut A., and Onions D.E., Complete nucleotide sequence and transcriptional analysis of the snakehead fish retrovirus. J Virol 70, 3606-3616, 1996. Google Scholar
Holzschu D.L., Martineau D., Fodor S.K., Vogt V.M., Bowser P.R., and Casey J.W., Nucleotide sequence and protein analysis of a complex piscine retrovirus, walleye dermal sarcoma virus. J Virol 69, 5320-5331, 1995. Google Scholar
LaPierre L.A., Casey J.W., and Holzschu D.L., Walleye retroviruses associated with skin tumors and hyperplasias encode cyclin D homologs. J Virol 72, 8765-8771, 1998. Google Scholar
LaPierre L.A., Holzschu D.L., Bowser P.R., and Casey J.W., Sequence and transcriptional analyses of the fish retroviruses walleye epidermal hyperplasia virus types 1 and 2: evidence for a gene duplication. J Virol 73, 9393-9403, 1999. Google Scholar
Kambol R., Kabat P., and Tristem M., Complete nucleotide sequence of an endogenous retrovirus from the amphibian, Xenopus laevis. Virology (In the Press).
Helps C.R., and Harbour D.A., Comparison of the complete sequence of feline spumavirus with those of the primate spumaviruses reveals a shorter gag gene. J Gen Virol 78, 2549-2564, 1997. Google Scholar
Renshaw R.W., and Casey J.W., Transcriptional mapping of the 3′ end of the bovine syncytial virus genome. J Virol 68, 1021-1028, 1994. Google Scholar
Flügel R.M., Rethwilm A., Maurer B., and Darai G., Nucleotide sequence analysis of the env gene and its flanking regions of the human spumaretrovirus reveals two novel genes. EMBO J 6, 2077-2084, 1987. Google Scholar
Cordonnier A., Casella J.-P., and Heidmann T., Isolation of novel human endogenous retroviral-like elements with foamy virus-related pol sequence. J Virol 69, 5890-5897, 1995. Google Scholar
Bénit L., deParseval N., Casella J.-F., Callebaut I., Cordonnier A., and Heidmann T., Cloning of a new murine endogenous retrovirus, MuERV.L, with strong similarity to the human HERV.L element and with a gag coding sequence closely related to the Fvl restriction gene. J Virol 71, 1997.
Perl A., Rosenblatt J.D., Chen I.S., DiVincenzo J.P., Bever R., Poiesz B.J., and Abraham G.N., Detection and cloning of new HTLV-relaterd endogenous sequence in man. Nucleic Acids Res 17, 6841-6854, 1989. Google Scholar
Löwer R., Löwer J., and Kurth R., The viruses in all of us: Characteristics and biological significance of human endogenous retrovirus sequences, PNAS 93, 5177-5184, 1996. Google Scholar
Martin J., Kabat P., Herniou E., and Tristem M., Characterization and complete nucleotide sequence of an unusual reptilian retrovirus recovered from the order Crocodylia. J Virol 76, 4651-4654, 2002. Google Scholar
Huder J.B., Böni J., Hatt J.-P., Soldati G., Lutz H., and Schüpbach J., Identification and characterization of two closely related unclassifiable endogenous retroviruses in pythons (Python molurus and Python curtus). J Virol 76, 7607-7615, 2002. Google Scholar
Beck S., and Sterk P., Genome scale DNA sequencing: where are we?. Curr Opin Biotechnol 9, 116-120, 1998. Google Scholar
Smit A.F., Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 9, 657-663, 1999. Google Scholar
Prak E.T., and Kazazian H.H.J., Mobile elements and the human genome. Nature Rev Genet 1, 134-144, 2000. Google Scholar
Hughes J.F., and Coffin J.M., Evidence for genomic rearrangements mediated by human endogenous retroviruses during primate evolution. Natl Genet 29, 487-489, 2001. Google Scholar
Andersson M.L., Lindeskog M., Medstrand P., Westley B., May F., and Blomberg J., Diversity of human endogenous retrovirus class II-like sequences. J Gen Virol 80, 255-260, 1999. Google Scholar
Wilkinson D.A., Mager D.L., and Leong J.C., Endogenous human retroviruses, in Levy J.A. (ed.), The Retroviridae, Plenum Press, New York, 1994, pp. 465-535. Google Scholar
Mager D.L., and Henthorn P.S., Identification of a retrovirus-like repetitive element in human DNA. Proc Natl Acad Sci USA 81, 7510-7514, 1984. Google Scholar
Hirose Y., Takamatsu M., and Harada F., Presence of env genes in members of the RTLVH family of human endogenous retrovirus-like elements. Virology 192, 52-61, 1993. Google Scholar
Andersson M.L., Sjottem E., Svineng G., and Johansen T., Comparative analyses of LTRs of the ERV-H family of primate-specific retrovirus-like elements isolated from marmoset, African green monkey, and man. Virology 234, 14-30, 1997. Google Scholar
Mager D.L., and Freeman J.D., HERV.H endogenous retroviruses-presence in the new-world branch but amplification in the old-world primate lineage. Virology 213, 395-404, 1995. Google Scholar
Shih A., Couvavas E.E., and Rush M.G., Evolutionary implications of primate endogenous retroviruses. Virology 182, 495-501, 1991. Google Scholar
Kim H.S., Takenaka O., and Crow T.J., Isolation and phylogeny of endogenous retrovirus sequences belonging to the HERV-W family in primates. J Gen Virol 80, 2613-2619, 1999. Google Scholar
Mayer J., Meese E., and Müeller-Lantzsch N., Human endogenous retrovirus K homologous sequences and their coding capacity in old world primates. J Virol 72, 1870-1875, 1998. Google Scholar
Barbulescu M., Turner G., Seaman M.L., Deinard A.S., Kidd K.K., and Lenz J., Many human endogenous retrovirus K (HERV.K) proviruses are unique to humans. Curr Biol 9, 861-868, 1999. Google Scholar
Mayer J., Sauter M., Racz A., Scherer D., Müller-Lantzsch N., and Meese E., An almost-intact human endogenous retrovirus K on human chromosome 7. Nat Genet 21, 257-258, 1999. Google Scholar
Turner G., Barbulescu M., Su M., Jensen-Seaman M.L., Kidd K.K., and Lenz J., Insertional polymorphisms of full-length endogenous retroviruses in humans. Curr Biol 11, 1531-1535, 2001. Google Scholar
Reus K., Meyer J., Sauter M., Scherer D., Müller-Lantzsch N., and Meese E., Genome organisation of the human endogenous retrovirus HERV.K (HML-2HOM) (ERVK6) on chromosome 7. Genomics 72, 314-320, 2001. Google Scholar
Paces J., Pavlicek A., and Paces V., HERVd: database of human endogenous retroviruses. Nucleic Acids Res 30, 205-206, 2002. Google Scholar
Kjellman C., Sjogren H.O., Salford L.G., and Widegren B., HERV.F(XA-34) is a full-length human endogenous retrovirus expressed in placental and fetal tissues. Gene 239, 99-107, 1999. Google Scholar
Lindeskog M., Mager D.L., and Blomberg J., Isolation of a human endogenous retroviral HERV.H element with an open env reading frame. Virology 258, 441-450, 1999. Google Scholar
Blond J.L., Beseme F., Duret L., Bouton O., Bedin F., Perron H., Mandrand B., and Mallet F., Molecular characterisation and placental expression of HERV.W, a new human endogenous retrovirus family. J Virol 73, 1175-1185, 1999. Google Scholar
Wilkinson D.A., Goodchild N.L., Saxton T.M., Wood S., and Mager D.L., Evidence for a functional subclass of the RTLV-H family of human endogenous retrovirus-like sequences. J Virol 67, 2981-2989, 1993. Google Scholar
Lindeskog M., Medstrand P., Cunningham A.A., and Blomberg J., Coamplification and dispersion of adjacent human endogenous retroviral HERV.H and HERV.E elements; presence of spliced hybrid transcripts in normal leukocytes. Virology 244, 219-229, 1998. Google Scholar
Franklin G.C., Chretien S., Hanson I.M., Rochefort H., May F.E., and Westley B.R., Expression of human sequences related to those of mouse mammary tumor virus. J Virol 62, 1203-1210, 1988. Google Scholar
Tönjes R.R., Boller K., Limbach C., Lugert R., and Kurth R., Characterization of human endogenous retrovirus type K virus-like particles generated from recombinant baculoviruses. Virology 233, 280-291, 1997. Google Scholar
Berhout B., Jebbink M., and Zsiros J., Identification of an active reverse transcriptase enzyme encoded by a human endogenous HERV.K retrovirus. J Virol 73, 2365-2375, 1999. Google Scholar
Mueller-Lantzsch N., Sauter M., Weiskircher A., Kramer K., Best B., Buck M., and Grässer F., Human endogenous retroviral element K10 (HERV-K10) encodes a full-length gag homologous 73-kDA protein and a functional protease. AIDS Res Hum Retro 9, 343-350, 1993. Google Scholar
Yang J., Bogerd H.P.B., Peng S., Wiegand H., Truant R., and Cullen B.R., An ancient family of human endogenous retroviruses encodes a functional homolog of the HIV-1 Rev protein. Proc Natl Acad Sci USA 96, 13404-13408, 1999. Google Scholar
Costas J., Characterisation and intragenomic spread of the human endogenous retrovirus family HERV.W. Mol Biol Evol 19, 526-533, 2002. Google Scholar
Yi J.M., Kim H.M., Lee W.H., and Kim H.S., Molecular cloning and phylogenetic analysis of new human endogenous retrovirus HERV-W family in cancer cells. Curr Microbiol 44, 216-220, 2002. Google Scholar
Pavlicek A., Paces J., Elleder D., and Hejnar J., Processed pseudogenes of human endogenous retroviruses generated by LINEs: their integration, stability, and distribution. Genome Res 12, 391-399, 2002. Google Scholar
Costas J., and Naveira H., Evolutionary history of the human endogenous retrovirus family ERV9. Mol Biol Evol 17, 320-330, 2000. Google Scholar
Taruscio D., Floridia G., Zoraqi G.K., Mantovani A., and Falbo V., Organization and integration sites in the human genome of endogenous retroviral sequences belonging to the HERV.E family. Mamm Gen 13, 216-222, 2002. Google Scholar
Choi J.Y., Kim J.S., Lee J.M., Hyun B.H., and Kim H.S., Isolation and phylogeny of new endogenous retroviral sequences belonging to the HERV.F family. AIDS Res Hum Retro 17, 367-370, 2001. Google Scholar
Kurdyukov S.G., et al. Full-sized HERV.K (HML-2) human endogenous retroviral LTR sequences on human chromosome 21: map locatons and evolutionary history. Gene 273, 51-61, 2001. Google Scholar
Costas J., Evolutionary dynamics of the human endogenous retrovirus family HERV.K inferred from full-length proviral genomes. J Mol Evol 53, 237-243, 2001. Google Scholar
Jurka J., Repbase update: a database and an electronic journal of repetitive elements. Trends Gen 16, 418-420, 2000. Google Scholar
Kidwell M.G., and Lisch D.R., Transposible elements and host genome evolution. TREE 15, 95-99, 2000. Google Scholar
Sverdlov E.D., Retroviruses and primate evolution. Bioessays 22, 161-171, 2000. Google Scholar
Johnson W.E., and Coffin J.M., Constructing primate phylogenies front ancient retrovirus sequences. Proc Natl Acad Sci USA 96, 10254-10260, 1999. Google Scholar
Harvey P.H., May R.M., and Nee S., Phylogenies without fossils. Evolution 48, 523-529, 1994. Google Scholar
Nee S., Holmes E.C., May R.M., and Harvey P.H., Extinction rates can be estimated from molecular phylogenies. Phil Trans R Soc Lond B 344, 72-82, 1994. Google Scholar
Purvis A., Using interspecific phylogenies to test macro-evolutionary hypotheses, in Harvey P.H., Leigh-Brown, Maynard-Smith J., and, Nee S. (eds.), New Uses for New Phylogenies, Oxford University Press, Oxford, 1996. Google Scholar
Van der Kuyl A.C., Dekker J.T., and Goudsmit J., Primate genus Miopithecus: evidence for the existence of species and subspecies of dwarf guenons based on cellular and endogenous viral sequences. Mol Phylogenet Evol 14, 403-413, 2000. Google Scholar
Shimamura M., et al. Molecular evidence from retroposons that whales form a clade within even-toed ungulates. Nature 388, 666-670, 1997. Google Scholar
Khan A., Nucleotide sequence analysis establishes the role of endogenous murine leukemia virus DNA segments in formation of recombinant mink cell focus-forming murine leukemia viruses. J Virol 50, 864-871, 1984. Google Scholar
Stewart M.A., Warnock M., Wheeler A., Wilkie N., Mullins J.I., Onions D.E., and Neil J.C., Nucleotide sequences of feline leukemia viruses subgroup A envelope gene and long terminal repeat and evidence for the recombinational origin of subgroup B viruses. J Virol 58, 825-834, 1986. Google Scholar
Sheets R.L., Pandey R., Jen W.-C., and Roy-Burman P., Recombinant feline leukemia virus genes detected in naturally occurring feline lympho-sarcomas. J Virol 67, 3118-3125, 1993. Google Scholar
Crittenden L.B., Fadly A.M., and Smith E.J., Effect of endogenous leukosis virus genes on response to infection with avian leukosis and reticuloendotheliosis viruses. Avian Dis 26, 279-295, 1982. Google Scholar
Crittenden L.B., Smith E.J., and Fadley A.M., Influence of endogenous viral (ev) gene expression and strain mortality of exogenous avian leukosis virus (ALV) on mortality and ALV infection and shedding in chickens. Avian Dis 28, 1037-1056, 1984. Google Scholar
Gray D.A., Jackson D.P., Percy D.H., and Morris V.L., Activation of _int_-1 and _int_-2 loci in GRf mammary tumors. Virology 154, 271-278, 1986. Google Scholar
Nusse R., The int genes in mammary tumorigenesis and in normal development. Trends Genet 4, 291-295, 1988. Google Scholar
Marchetti A., Robbins J., Campbell G., Buttitta F., Squartini F., Bistocchi M., and Callahan R., Host genetic background effect on the frequency of mouse mammary tumour-induced rearrangements of the _int_-1 and _int_-2 loci in mouse mammary tumours. J Virol 65, 4550-4554, 1991. Google Scholar
Kung H.J., Boerkoel C., and Carter T.H., Retroviral mutagenesis of cellular oncogenes: A review with insights into the mechanisms of insertional activation. Curr Top Microbiol Immunol 171, 1-25, 1991. Google Scholar
Datta S.K., Manny N., Andrzejewski C., Andre-Schwartz J., and Scwartz R.S., Genetic studies of autoimmunity and retrovirus expression in crosses of New Zealand black mice. J Exp Med 147, 872-881, 1978. Google Scholar
Datta S.K., Owen F.L., Womack J.E., and Riblet R.J., Analysis of recombinant inbred lines derived from “autoimmune” (NZB) and “high leukemia” (C58) strains: Independent multigenic systems control B cell hyperactivity, retrovirus expression, and autoimmunity. J Immunol 129, 1539-1544, 1982. Google Scholar
Wu J., Zhou T., He H., and Mountz J.D., Autoimmune disease in mice due to integration of an endogenous retrovirus in an apoptosis gene. Intern Med 40, 80-86, 2001. Google Scholar
Coffin J.M., Retroviridae and their replication, in Fields B.N., and, Knipe D.M. (eds.), Virology, Raven Press, New York, 1990, pp. 1437-1500. Google Scholar
Coffin J.M., Reverse transcriptase and evolution, in Skalka A.M., and, S.P.G. (eds.), Reverse Transcriptase, Cold Spring Harbour Laboratory Press, New York, 1993, pp. 445-479. Google Scholar
Löwer R., The pathogenic potential of endogenous retroviruses: facts and fantasies. TIM 7, 350-356, 1999. Google Scholar
Yolken R.H., Karlsson H., Bayer T.A., Johnston-Wilson N., Yee F., and Fuller Torrey E., Retroviruses, genes and schizophrenia. Clin Neurosci Res 1, 164-169, 2001. Google Scholar
Stoye J.P., The pathogenic potential of endogenous retroviruses; a sceptical view. TIM 7, 430, 1999. Google Scholar
Kazazian H.H., An estimated frequency of endogenous insertional mutations in humans. Nature Genetics 22, 130, 1999. Google Scholar
Brookes S.M., Pandolfino Y.A., Mitchell T.J., Venables P.J.W., Shattles W.G., Clark D.A., Entwistle A., and Maini R.N., The immune response to and expression of cross-reactive retroviral gag sequences in autoimmune disease. Br J Rheumatol 31, 735-742, 1992. Google Scholar
Rasmussen H.B., Lucotte G., and Clausen J., Endogenous retroviruses and multiple sclerosis. J Neurovirol Suppl 6, 80-84, 2000. Google Scholar
Ogasawara H. et al. Quantitative analyses of messenger RNA of human endogenous retrovirus in patients with systemic lupus erythematosus. Mult Scler 1, 82-87, 1995. Google Scholar
Coffin J.M., Superantigens and endogenous retroviruses: A confluence of puzzles. Science 255, 411-413, 1992. Google Scholar
Conrad B., Weissmahr R.N., Böni J., Arcari R., Scüpbach J., and Mach B., A human endogenous retroviral superantigen as a candidate autoimmune gene in Type I diabetes. Cell 90, 303-313, 1997. Google Scholar
Lapatschek M., Dürr S., Löwer R., Magin C., Wagner H., and Miethke T., Functional analysis of the env open reading frame in human endogenous retrovirus IDDMK1,2 encoding superantigen activity. J Virol 74, 6386-6393, 2000. Google Scholar
Karlsson H., Bachmann S., Schröder J., McArthur J., Torrey E.F., and Yolken R.H., Retroviral RNA identified in the cerebospinal fluids and brains of individuals with schizophrenia. Proc Natl Acad Sci USA 98, 4634-4639, 2001. Google Scholar
Hart D.J., Heath R.G., and Sautter F.R.Jr, Antiretroviral antibodies: implications for schizophrenia, schizophrenia spectrum disorders, and bipolar disorder. Biol Psychiatry 45, 704-714, 1999. Google Scholar
Bayer T., Falkai P., and Maier W., Genetic and non-genetic vulnerability factors in schizophrenia. The basis of the 'Two-hit hypothesis'. J Psych Res 33, 543-548, 1999. Google Scholar
Deb-Rinker R., Klempan T.A., Ö'Reilly R.L., Torrey E.F., and Singh S.M., Molecular characteristics of a MSRV-like sequence indentified by RDA from monozygotic twin pairs discordant for schizophrenia. Genomics 61, 133-144, 1999. Google Scholar
Towler E.M. et al. Functional characterization of the protease of human endogenous retrovirus, K10: Can it complement HIV-1 protease?. Biochemistry 37, 17137-17144, 1998. Google Scholar
Padow M., Lai L.L., Fisher R.J., Zhou Y.C., Wu X.Y., Kappes J.C., and Towler E.M., Analysis of human immunodeficiency virus type 1 containing HERV-K protease. Aids Research and Human Retroviruses 16, 1973-1980, 2000. Google Scholar
Leroi A.M., Koufopanou V., and Burt A., Cancer selection. Nat Rev Cancer 3, 226-231, 2003. Google Scholar
Weiss R.A., Griffiths D., Takeuchi Y., Patience C., and Venables P.J., Retroviruses: ancient and modern, Arch Virol Suppl 15., 171-177, 1999. Google Scholar
Blusch J.H., Patience C., and Martin U., Pig endogenous retroviruses and xenotransplantation. Xenotransplantation 9, 242-251, 2002. Google Scholar
Platt J.L., Xenotransplantation—New risks, new gains. Nature 407, 27-30, 2000. Google Scholar
Stoye J.P., and Coffin J.M., The dangers of xenotransplantation. Nat Med 1, 1995.
Patience C., Takeuchi Y., and Weiss R.A., Infection of human cells by an endogenous retroviruses of pigs. Nature Med 3, 282-286, 1997. Google Scholar
van der Laan L.J.W. et al. Infection by porcine endogenous retrovirus after islet xenotransplantation in SCID mice. Nature 407, 90-94, 2000. Google Scholar
Specke V., Rubant S., and Denner J., Productive infection of human primary cells and cell lines with porcine endogenous retroviruses. J Virol 285, 177-180, 2001. Google Scholar
Blusch J.H., Patience C., Takeuchi Y., Templin C., Roos C., Von der Helm K., Steinhoff G., and Martin U., Infection of nonhuman primate cells by pig endogenous retrovirus. J. Virol 74, 7687-7690, 2000. Google Scholar
Herring C., Cunningham D.A., Whittam A.J., Fernandez-Suarez X.M., and Langford G.A., Monitoring xenotransplant recipients for infection by PERV. Clin Biochem 34, 23-27, 2001. Google Scholar
Gao F. et al. Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 397, 436-441, 1999. Google Scholar
Sharp P.M., Bailes E., Chaudhuri R.R., Rodenburg C.M., Santiago M.O., and Hahn B.H., The origins of acquired immune deficiency syndrome viruses: where and when?. Philos Trans R Soc Lond B 356, 867-876, 2001. Google Scholar
Gao F. et al. Human infection by genetically diverse SIVsm-related HIV2 in west Africa. Nature 358, 495-499, 1992. Google Scholar
Page R.D.M., and Holmes E.C.,, Blackwell, Oxford, 1998.
Page R.D.M., University of Chicago Press, Chicago, 2002, pp. 350.
Martin J., Kabat P., and Tristem M., Cospeciation and horizontal transmission rates in the murine leukamia-related retroviruses, in Page R.D.M. (ed.), Tangled Trees, University of Chicago Press, Chicago, 2002, pp. 174-194. Google Scholar
Van der Kuyl A.C., Dekker J.T., and Goudsmit J., Baboon endogenous virus evolution and ecology. Trends Microbiol 4, 455-459, 1996. Google Scholar
Mang R., Maas J., van der Kuyl A.C., and Goudsmit J., Papio cynocephalus endogenous retrovirus among old world monkeys: Evidence for coevolution and ancient cross-species transmissions. J Virol 74, 1578-1586, 2000. Google Scholar
Van der Kuyl A.C., Dekker J.T., and Gousdsmit J., Discovery of a new endogenous type C retrovirus (FcEV) in cats: evidence for RD-114 being an FcEV (Gag/Pol)/baboon endogenous BaEV (Env) recombinant. J Virol 73, 7994-8002, 1999. Google Scholar