title: Fitness landscape of human immunodeficiency virus type 1 protease quasispecies.
abstract: Here we show, at a high resolution (1%), the human immunodeficiency virus type 1 (HIV-1) protease gene quasispecies landscape from three infected naïve individuals. A huge range of genetic configurations was found (67%, 71%, and 80% of the nucleotide clones from the three individuals, respectively, were different), and these configurations created a dense net that linked different parts of the viral population. Similarly, a vast diversity of different protease activities was also found. Importantly, 65% of the analyzed enzymes had detectable protease activity, and 11% of the minority individual variants showed similar or better fitness than the master (most abundant) enzyme, suggesting that the viral complexity in this genomic region does not exclusively depend on the enzyme's catalytic efficiency. Several high-fitness minority variants had only one substitution compared to the master sequence, supporting the possibility that the rugged HIV-1 protease quasispecies fitness landscape may be formed by a continuous network that can be traversed by single mutational steps without passing through defective or less-adapted proteins.
authors.affiliation: Fundacio irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Barcelona, Spain.
authors.forename: Guerau
authors.initials: G
authors.lastname: Fernàndez
authors.forename: Bonaventura
authors.initials: B
authors.lastname: Clotet
authors.forename: Miguel Angel
authors.initials: MA
authors.lastname: Martínez
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D004279:DNA, Viral / Q000235:genetics; D005814:Genes, Viral; D014644:Genetic Variation; D005838:Genotype; D015658:HIV Infections / Q000821:virology; D016333:HIV Protease / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D015497:HIV-1 / Q000201:enzymology* / Q000235:genetics* / Q000502:physiology; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D017386:Sequence Homology, Amino Acid; D014779:Virus Replication
chemical_list: D004279:DNA, Viral; D016333:HIV Protease