title: Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture.
abstract: BACKGROUND
  Human immunodeficiency virus type 1 (HIV-1) has a biased nucleotide composition different from human genes. This raises the question of how evolution has chosen the nucleotide sequence of HIV-1 that is observed today, or to what extent the actual encoding contributes to virus replication capacity, evolvability and pathogenesis. Here, we applied the previously described synthetic attenuated virus engineering (SAVE) approach to HIV-1.
  
  
  RESULTS
  Using synonymous codon pairs, we rationally recoded and codon pair-optimized and deoptimized different moieties of the HIV-1 gag and pol genes. Deoptimized viruses had significantly lower viral replication capacity in MT-4 and peripheral blood mononuclear cells (PBMCs). Varying degrees of ex vivo attenuation were obtained, depending upon both the specific deoptimized region and the number of deoptimized codons. A protease optimized virus carrying 38 synonymous mutations was not attenuated and displayed a replication capacity similar to that of the wild-type virus in MT-4 cells and PBMCs. Although attenuation is based on several tens of nucleotide changes, deoptimized HIV-1 reverted to wild-type virulence after serial passages in MT-4 cells. Remarkably, no reversion was observed in the optimized virus.
  
  
  CONCLUSIONS
  These data demonstrate that SAVE is a useful strategy to phenotypically affect the replicative properties of HIV-1.
authors.affiliation: Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona 08916, Spain.
authors.forename: Gloria
authors.initials: G
authors.lastname: Martrus
authors.forename: Maria
authors.initials: M
authors.lastname: Nevot
authors.forename: Cristina
authors.initials: C
authors.lastname: Andres
authors.forename: Bonaventura
authors.initials: B
authors.lastname: Clotet
authors.forename: Miguel Angel
authors.initials: MA
authors.lastname: Martinez
mesh_terms: D002478:Cells, Cultured; D003062:Codon; D004252:DNA Mutational Analysis; D015497:HIV-1 / Q000235:genetics / Q000502:physiology*; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D014779:Virus Replication; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics*; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D003062:Codon; D054301:gag Gene Products, Human Immunodeficiency Virus; D054302:pol Gene Products, Human Immunodeficiency Virus