Mullins Molecular Retrovirology Lab

  • Department of Microbiology
  • School of Medicine
  • University of Washington
University of Washington/Fred Hutch Center for AIDS Research

Citation Information

Tobin NH, Learn GH, Holte SE, Wang Y, Melvin AJ, McKernan JL, Pawluk DM, Mohan KM, Lewis PF, Mullins JI, Frenkel LM (2005). Evidence that low-level viremias during effective highly active antiretroviral therapy result from two processes: expression of archival virus and replication of virus. Journal of virology, 79(15), 9625-34. (pubmed)


Episodes of low-level viremia (LLV), with plasma human immunodeficiency virus type 1 (HIV-1) RNA levels ranging from 50 to 400 copies ©/ml, occur commonly during highly active antiretroviral therapy (HAART). LLV has been associated with virologic failure of HAART in some studies, while in others LLV did not appear to affect the clinical outcome. To understand the processes leading to LLV, genetic analyses were used to determine whether plasma virions emanated from archived or from newly evolved viral genomes. Episodes of LLV (plasma HIV-1 RNA, 50 to 379 [median, 77] c/ml) were detected in 21/37 (57%) HIV-1-infected children with median plasma HIV-1 RNA levels of <50 c/ml during 79 patient years of HAART. Viral sequences were derived by direct sequencing of PCR products from 21 plasma specimens diluted to end point. In phylogenetic analysis, LLV viral sequences grouped with virus from early in the course of infection in 8/11 subjects. Six specimens had multiple identical viral sequences, suggesting origin from clonally expanded infected cells. LLV plasma virus evolved over time, indicating viral replication, in 3/11 subjects. Two of these had frequent LLV, including the selection of drug-resistant mutants. In summary, plasma virus from episodes of LLV during effective HAART appeared to originate from two distinct processes, (i) clonal outgrowth from long-lived HIV-1-infected cells, presumably following activation and proliferation of these cells, and (ii) ongoing viral replication that included the selection of new drug-resistant mutants. These observations provide a plausible explanation for the divergent clinical outcomes previously associated with LLV.

Supplemental Data

Supplemental Data for Toblin et al.:

1.Model Parameters for Phylogenetic Analysis

gene/region polPR polRT envC2-V5
model class GTR+I+G GTR+I+G TVM+I+G
fA 0.3784 0.45163 0.4538
fC 0.1538 0.15032 0.1657
fG 0.2339 0.17336 0.178
fT 0.2338 0.22468 0.2025
RA↔︎C 5.80316 1.07186 1.8604
RA↔︎G 20.0989 5.31766 4.3451
RA↔︎T 1.17262 0.29502 0.696
RC↔︎G 0.36115 0.53002 0.7504
RC↔︎T 21.9604 7.07181 4.3451
RG↔︎T 1 1 1
p-inv 0.20449 0.26509 0.1358
gamma shape 0.5973 0.76247

2. Divergence Graphs PR: F1 G2 H2 H4 L1 M2 P1 R1 S1 T2 V2

RT: G2 H2 H4 L1 M2 P1 R1 S1 T2 V1

env: F1 G2 H2 H4 L1 M2 P1 R1 S1 V1

3. Alignments PR RT env