title: Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy.
abstract: Despite years of plasma HIV-RNA levels <40 copies per milliliter during combination antiretroviral therapy (cART), the majority of HIV-infected patients exhibit persistent seropositivity to HIV-1 and evidence of immune activation. These patients also show persistence of proviruses of HIV-1 in circulating peripheral blood mononuclear cells. Many of these proviruses have been characterized as defective and thus thought to contribute little to HIV-1 pathogenesis. By combining 5'LTR-to-3'LTR single-genome amplification and direct amplicon sequencing, we have identified the presence of "defective" proviruses capable of transcribing novel unspliced HIV-RNA (usHIV-RNA) species in patients at all stages of HIV-1 infection. Although these novel usHIV-RNA transcripts had exon structures that were different from those of the known spliced HIV-RNA variants, they maintained translationally competent ORFs, involving elements of gag, pol, env, rev, and nef to encode a series of novel HIV-1 chimeric proteins. These novel usHIV-RNAs were detected in five of five patients, including four of four patients with prolonged viral suppression of HIV-RNA levels <40 copies per milliliter for more than 6 y. Our findings suggest that the persistent defective proviruses of HIV-1 are not "silent," but rather may contribute to HIV-1 pathogenesis by stimulating host-defense pathways that target foreign nucleic acids and proteins.
authors.affiliation: Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892;
authors.forename: Hiromi
authors.initials: H
authors.lastname: Imamichi
authors.affiliation: Clinical Services Program, Applied and Development Research Directorate, Leidos Biomedical Research, Inc., Frederick, MD 21072;
authors.forename: Robin L
authors.initials: RL
authors.lastname: Dewar
authors.affiliation: Clinical Services Program, Applied and Development Research Directorate, Leidos Biomedical Research, Inc., Frederick, MD 21072;
authors.forename: Joseph W
authors.initials: JW
authors.lastname: Adelsberger
authors.affiliation: Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892;
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Rehm
authors.affiliation: Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104;
authors.forename: Una
authors.initials: U
authors.lastname: O'Doherty
authors.affiliation: Applications and Collaborations, Pacific Biosciences, Menlo Park, CA 94025.
authors.forename: Ellen E
authors.initials: EE
authors.lastname: Paxinos
authors.affiliation: Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; afauci@niaid.nih.gov.
authors.forename: Anthony S
authors.initials: AS
authors.lastname: Fauci
authors.affiliation: Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892;
authors.forename: H Clifford
authors.initials: HC
authors.lastname: Lane
mesh_terms: D044966:Anti-Retroviral Agents / Q000627:therapeutic use*; D004279:DNA, Viral / Q000235:genetics / Q000378:metabolism; D015967:Gene Expression Regulation, Viral; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics / Q000502:physiology; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology; D011533:Proviruses / Q000187:drug effects* / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism*; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D044966:Anti-Retroviral Agents; D004279:DNA, Viral; D012367:RNA, Viral; D014764:Viral Proteins
keywords: HIV-1; activation; latency; provirus