title: Identification of hypervariable and conserved regions in the surface envelope gene in the bovine lentivirus.
abstract: The surface envelope (SU) gene of nine different isolates of the bovine lentivirus (BIV) were compared for nucleotide and deduced amino acid (aa) sequence diversity. Analyses were done both on isolates derived from the original reference strain, R29, and on field isolates of BIV. Six conserved and six hypervariable regions were identified. Many of the hypervariable regions were located in areas predicted to be on the surface of the SU protein. The SU gene comparison among all isolates showed up to a 50% aa sequence divergence. When a conserved region of the reverse transcriptase gene was compared among eight of the isolates, there was less than 11% aa sequence divergence. When comparing all isolates, the greatest size differences in the SU gene are observed in the 2nd hypervariable region (V2) with up to a 104-aa difference between the largest and smallest variant. R29-106, an infectious molecular clone of the original isolate of BIV, has an 87-bp deletion in V2 as compared to prototype isolate R29-127. All R29-derived isolates sequenced for this study had a SU gene size similar to R29-106. The four field isolates sequenced for this study had SU genes larger than R29-127. R29-derived isolates may not be representative of BIV currently present in United States cattle.
authors.affiliation: National Animal Disease Center, USDA, Agriculture Research Service, Ames, Iowa 50010, USA.
authors.forename: D L
authors.initials: DL
authors.lastname: Suarez
authors.forename: C A
authors.initials: CA
authors.lastname: Whetstone
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002417:Cattle; D017124:Conserved Sequence; D015752:Genes, env / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D017960:Lentiviruses, Bovine / Q000235:genetics*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D014759:Viral Envelope Proteins / Q000737:chemistry / Q000235:genetics*
chemical_list: C096110:SU protein, Bovine immunodeficiency-like virus; D014759:Viral Envelope Proteins