title: Entire genome of a strain of human immunodeficiency virus type 1 with a deletion of nef that was recovered 20 years after primary infection: large pool of proviruses with deletions of env.
abstract: We report the complete sequence analysis of the provirus harbored in a long-term nonprogressor (patient SG1) 20 years after the first infection with a human immunodeficiency virus type 1 strain lacking nef. The sequencing showed large deletions in the nef-nef and nef-U3 regions. Except for vpu, all of the other accessory genes were intact. The gag and pol genes did not show significant alterations. We found large deletions in env, spanning the V1, V2, V3, V4, and V5 regions. We believe that, when down-regulation of the class 1 major histocompatibility complex molecules is inhibited by the lack of nef function, the cells containing Env-defective molecules evade cytotoxic T lymphocyte killing and accumulate progressively.
authors.affiliation: Clinical Microbiology and Virology, University of Rome, Tor Vergata, Rome, Italy.
authors.forename: Graziella
authors.initials: G
authors.lastname: Calugi
authors.forename: Francesco
authors.initials: F
authors.lastname: Montella
authors.forename: Cartesio
authors.initials: C
authors.lastname: Favalli
authors.forename: Arrigo
authors.initials: A
authors.lastname: Benedetto
mesh_terms: D000595:Amino Acid Sequence; D003673:Defective Viruses / Q000235:genetics; D017353:Gene Deletion; D015752:Genes, env / Q000235:genetics*; D015754:Genes, nef / Q000235:genetics*; D016679:Genome, Viral; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000276:immunology / Q000502:physiology; D006801:Humans; D008969:Molecular Sequence Data; D011533:Proviruses / Q000235:genetics*