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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

Justin R. Bailey,^1, Ahmad R. Sedaghat,^1, Tara Kieffer,^1, Timothy Brennan,¹ Patricia K. Lee,¹ Megan Wind-Rotolo,¹ Christine M. Haggerty,¹ Ashrit R. Kamireddi,¹ Yi Liu,¹ Jessica Lee,¹ Deborah Persaud,² Joel E. Gallant,¹ Joseph Cofrancesco Jr.,¹ Thomas C. Quinn,^1,3 Claus O. Wilke,⁴ Stuart C. Ray,¹ Janet D. Siliciano,¹ Richard E. Nettles,¹ and Robert F. Siliciano^1,5*

Departments of Medicine,¹ Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205,² National Institutes of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892,³ Section of Integrative Biology, University of Texas at Austin, Austin, Texas 78713,⁴ Howard Hughes Medical Institute, Baltimore, Maryland 21205⁵

Received 23 March 2006/ Accepted 19 April 2006

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.

Supplemental material for this article may be found at http://jvi.asm.org/.

These authors contributed equally to this work.

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