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. 2010 Jun;155(6):895-903.
doi: 10.1007/s00705-010-0659-3. Epub 2010 Apr 23.

Characterization of HIV-1 RNA forms in the plasma of patients undergoing successful HAART

Carlos A Lopez  1 , Manuel Vazquez, Martin D Hill, Maria Del C Colon, Tirtsa Porrata-Doria, Ian C D Johnston, Eric Lorenzo
Affiliations

Characterization of HIV-1 RNA forms in the plasma of patients undergoing successful HAART

Carlos A Lopez et al. Arch Virol. 2010 Jun.

Abstract

An assay to characterize plasma human immunodeficiency virus 1 (HIV-1) sequences for patients with low viral loads was developed by combining the selective binding of anti-CD44 MicroBeads with a nested RT-PCR targeting the env C2V4 region. Sequences were obtained from 10 of 20 HIV+ patients who had viral loads below 48 copies/ml. Sequences derived from plasma were compared to those from CD14+ CD16 +monocytes and CD4+ T cells. The plasma sequences were most closely related to those amplified from monocytes, suggesting that during successful antiretroviral therapy, the predominant plasma virus originates from myeloid cells. By characterizing HIV-1 RNA sequences from 8 ml of plasma while avoiding multiple steps, which can lead to contamination and deterioration, this method can help elucidate the viral forms in patients with therapeutically suppressed HIV-1. Understanding the source of residual viremia is crucial in developing approaches for viral eradication.

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Figures

Fig. 1
Fig. 1
Phylogenetic reconstruction for the assay performance assessment. The evolutionary history of the validation sequences was reconstructed in a phylogenetic tree. Neighbor joining was used with the Kimura 2-parameter method in 1,000 bootstrapped replications. The HIV-1 HXB2 sequence (gene location 7002–7400) was used as an outgroup (GenBank accession number K03455). The sample ID is represented by the letter P (patient) and a number. The number after the dash corresponds to the clone number. The scale is at a 2% nucleotide difference
Fig. 2
Fig. 2
Phylogenetic reconstruction of HIV-1 env nucleotide sequences from CD4+ T cells, CD14+ CD16+ monocytes, and plasma isolates of samples P5 and P6. Evolutionary reconstruction of the plasma-derived HIV-1 env sequence was generated using neighbor joining with the Kimura 2-parameter method. Numbers between branch nodes represent bootstrap values (1,000 replicates). a Patient 5, b patient 6. Samples are distributed as follows: closed squares monocytes; open triangles CD4+ T cells; open circles plasma; closed diamonds outgroup (HXB2, GenBank accession number K03455). The number of substitutions per site is indicated by the distance bar shown at the bottom
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