title: A Naturally Occurring rev1-vpu Fusion Gene Does Not Confer a Fitness Advantage to HIV-1.
abstract: BACKGROUND
  Pandemic strains of HIV-1 (group M) encode a total of nine structural (gag, pol, env), regulatory (rev, tat) and accessory (vif, vpr, vpu, nef) genes. However, some subtype A and C viruses exhibit an unusual gene arrangement in which the first exon of rev (rev1) and the vpu gene are placed in the same open reading frame. Although this rev1-vpu gene fusion is present in a considerable fraction of HIV-1 strains, its functional significance is unknown.
  
  
  RESULTS
  Examining infectious molecular clones (IMCs) of HIV-1 that encode the rev1-vpu polymorphism, we show that a fusion protein is expressed in infected cells. Due to the splicing pattern of viral mRNA, however, these same IMCs also express a regular Vpu protein, which is produced at much higher levels. To investigate the function of the fusion gene, we characterized isogenic IMC pairs differing only in their ability to express a Rev1-Vpu protein. Analysis in transfected HEK293T and infected CD4+ T cells showed that all of these viruses were equally active in known Vpu functions, such as down-modulation of CD4 or counteraction of tetherin. Furthermore, the polymorphism did not affect Vpu-mediated inhibition of NF-кB activation or Rev-dependent nuclear export of incompletely spliced viral mRNAs. There was also no evidence for enhanced replication of Rev1-Vpu expressing viruses in primary PBMCs or ex vivo infected human lymphoid tissues. Finally, the frequency of HIV-1 quasispecies members that encoded a rev1-vpu fusion gene did not change in HIV-1 infected individuals over time.
  
  
  CONCLUSIONS
  Expression of a rev1-vpu fusion gene does not affect regular Rev and Vpu functions or alter HIV-1 replication in primary target cells. Since there is no evidence for increased replication fitness of rev1-vpu encoding viruses, this polymorphism likely emerged in the context of other mutations within and/or outside the rev1-vpu intergenic region, and may have a neutral phenotype.
authors.affiliation: Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
authors.forename: Simon M
authors.initials: SM
authors.lastname: Langer
authors.affiliation: Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
authors.forename: Kristina
authors.initials: K
authors.lastname: Hopfensperger
authors.affiliation: Departments of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America.
authors.forename: Shilpa S
authors.initials: SS
authors.lastname: Iyer
authors.affiliation: Departments of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America.
authors.forename: Edward F
authors.initials: EF
authors.lastname: Kreider
authors.affiliation: Departments of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America.
authors.forename: Gerald H
authors.initials: GH
authors.lastname: Learn
authors.affiliation: Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.|Department of Laboratory, Kunming Branch, Taipei City Hospital, 10844, Taipei, Taiwan.
authors.forename: Lan-Hui
authors.initials: LH
authors.lastname: Lee
authors.affiliation: Departments of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States of America.
authors.forename: Beatrice H
authors.initials: BH
authors.lastname: Hahn
authors.affiliation: Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Sauter
mesh_terms: D015967:Gene Expression Regulation, Viral; D050939:Gene Fusion; D057809:HEK293 Cells; D015497:HIV-1 / Q000235:genetics*; D054298:Human Immunodeficiency Virus Proteins / Q000235:genetics*; D006801:Humans; D012367:RNA, Viral / Q000235:genetics; D054334:Viral Regulatory and Accessory Proteins / Q000235:genetics*; D054321:rev Gene Products, Human Immunodeficiency Virus / Q000235:genetics*; D000086082:Viroporin Proteins
chemical_list: D054298:Human Immunodeficiency Virus Proteins; D012367:RNA, Viral; D054334:Viral Regulatory and Accessory Proteins; D054321:rev Gene Products, Human Immunodeficiency Virus; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins