title: Residual human immunodeficiency virus type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4+ T cells.
abstract: Antiretroviral therapy can reduce human immunodeficiency virus type 1 (HIV-1) viremia to below the detection limit of ultrasensitive clinical assays (50 copies of HIV-1 RNA/ml). However, latent HIV-1 persists in resting CD4+ T cells, and low residual levels of free virus are found in the plasma. Limited characterization of this residual viremia has been done because of the low number of virions per sample. Using intensive sampling, we analyzed residual viremia and compared these viruses to latent proviruses in resting CD4+ T cells in peripheral blood. For each patient, we found some viruses in the plasma that were identical to viruses in resting CD4+ T cells by pol gene sequencing. However, in a majority of patients, the most common viruses in the plasma were rarely found in resting CD4+ T cells even when the resting cell compartment was analyzed with assays that detect replication-competent viruses. Despite the large diversity of pol sequences in resting CD4+ T cells, the residual viremia was dominated by a homogeneous population of viruses with identical pol sequences. In the most extensively studied case, a predominant plasma sequence was also found in analysis of the env gene, and linkage by long-distance reverse transcriptase PCR established that these predominant plasma sequences represented a single predominant plasma virus clone. The predominant plasma clones were released for months to years without evident sequence change. Thus, in some patients on antiretroviral therapy, the major mechanism for residual viremia involves prolonged production of a small number of viral clones without evident evolution, possibly by cells other than circulating CD4+ T cells. The sequences have been deposited in GenBank. The accession numbers are DQ 391282 to DQ 391351 (for env) and DQ 391352 to DQ 392955 (for RT).
authors.affiliation: Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Justin R
authors.initials: JR
authors.lastname: Bailey
authors.forename: Ahmad R
authors.initials: AR
authors.lastname: Sedaghat
authors.forename: Tara
authors.initials: T
authors.lastname: Kieffer
authors.forename: Timothy
authors.initials: T
authors.lastname: Brennan
authors.forename: Patricia K
authors.initials: PK
authors.lastname: Lee
authors.forename: Megan
authors.initials: M
authors.lastname: Wind-Rotolo
authors.forename: Christine M
authors.initials: CM
authors.lastname: Haggerty
authors.forename: Ashrit R
authors.initials: AR
authors.lastname: Kamireddi
authors.forename: Yi
authors.initials: Y
authors.lastname: Liu
authors.forename: Jessica
authors.initials: J
authors.lastname: Lee
authors.forename: Deborah
authors.initials: D
authors.lastname: Persaud
authors.forename: Joel E
authors.initials: JE
authors.lastname: Gallant
authors.forename: Joseph
authors.initials: J
authors.lastname: Cofrancesco
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Quinn
authors.forename: Claus O
authors.initials: CO
authors.lastname: Wilke
authors.forename: Stuart C
authors.initials: SC
authors.lastname: Ray
authors.forename: Janet D
authors.initials: JD
authors.lastname: Siliciano
authors.forename: Richard E
authors.initials: RE
authors.lastname: Nettles
authors.forename: Robert F
authors.initials: RF
authors.lastname: Siliciano
mesh_terms: D023241:Antiretroviral Therapy, Highly Active; D001483:Base Sequence; D015496:CD4-Positive T-Lymphocytes / Q000821:virology*; D019143:Evolution, Molecular; D005260:Female; D015686:Gene Products, env / Q000235:genetics*; D015751:Genes, pol / Q000235:genetics*; D015658:HIV Infections / Q000097:blood / Q000188:drug therapy / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000097:blood / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D014766:Viremia / Q000188:drug therapy / Q000235:genetics
chemical_list: D015686:Gene Products, env; D012367:RNA, Viral