title: Characterization of a full-length endogenous beta-retrovirus, EqERV-beta1, in the genome of the horse (Equus caballus).
abstract: Information on endogenous retroviruses fixed in the horse (Equus caballus) genome is scarce. The recent availability of a draft sequence of the horse genome enables the detection of such integrated viruses by similarity search. Using translated nucleotide fragments from gamma-, beta-, and delta-retroviral genera for initial searches, a full-length beta-retrovirus genome was retrieved from a horse chromosome 5 contig. The provirus, tentatively named EqERV-beta1 (for the first equine endogenous beta-retrovirus), was 10434 nucleotide (nt) in length with the usual retroviral genome structure of 5'LTR-gag-pro-pol-env-3'LTR. The LTRs were 1361 nt long, and differed approximately 1% from each other, suggestive of a relatively recent integration. Coding sequences for gag, pro and pol were present in three different reading-frames, as common for beta-retroviruses, and the reading frames were completely open, except that the env gene was interrupted by a single stopcodon. No reading frame was apparent downstream of the env gene, suggesting that EqERV-beta1 does not encode a superantigen like mouse mammary tumor virus (MMTV). A second proviral genome of EqERV-beta1, with no stopcodon in env, is additionally integrated on chromosome 5 downstream of the first virus. Single EqERV-beta1 LTRs were abundantly present on all chromosomes except chromosome 24. Phylogenetically, EqERV-beta1 most closely resembles an unclassified retroviral sequence from cattle (Bos taurus), and the murine beta-retrovirus MMTV.
authors: Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam, Academic Medical Centre of the University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands. a.c.vanderkuyl@amc.uva.nl
authors: Antoinette C
authors: AC
authors: van der Kuyl
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D030121:Betaretrovirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification* / Q000502:physiology; D002417:Cattle; D033481:Chromosomes, Mammalian / Q000235:genetics / Q000821:virology; D020077:Endogenous Retroviruses / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification* / Q000502:physiology; D015751:Genes, pol; D016678:Genome; D006736:Horses / Q000235:genetics / Q000821:virology*; D051379:Mice; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D011533:Proviruses / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D016415:Sequence Alignment; D020079:Terminal Repeat Sequences; D016662:Virus Integration