Patient characteristics.

a<p>HAART initiated during acute/early or chronic HIV-1 infection as defined in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003174#s4" target="_blank">Methods</a>.</p>b<p>W, white, non-Hispanic; H, Hispanic; AA, African-American; As, Asian; M, mixed race.</p>c<p>Time after infection before achieving the most proximally documented period of sustained suppression of viremia to <50 copies/ml on HAART. Patients in the acute cohort started therapy within 3 months of infection.</p>d<p>Time of documented continuous suppression of viremia to <50 copies/ml on HAART.</p>e<p>Drug abbreviations: 3TC, lamivudine; ABC, abacavir; ATV/r, atazanavir boosted with ritonavir; d4T, stavudine; ddI, didanosine; DRV/r, darunavir boosted with ritonavir; EFV, efavirnez; ETV, etravirine; FTC, emtricitabine; FPV, fosamprenavir; FPV/r, fosamprenavir boosted with ritonavir; NVP, nevirapine; RAL, raltegravir; TDF, tenofovir disoproxil fumarate.</p

Ratio of infected cell frequencies determined by droplet digital PCR for HIV-1 DNA or by viral outgrowth assay.

<p>Analysis was done on the same sample of purified resting CD4⁺ T cells. * indicates maximum values in cases in which the HIV-1 DNA level was below the limit of detection (2 copies/ml).</p

Characteristics of assays.

a<p>HXB2 coordinates.</p>b<p>Based in standard sample size. Except for residual viremia, LOD is expressed as infectious units or copies per 10⁶ cells. For residual viremia, the LOD is 0.2 copies/ml of plasma.</p>c<p>Dynamic range is reported here as the difference in log units between the highest value measured in these study patients and the limit of detection of the relevant assay.</p>d<p>Based on repeat measurements in the same patient as reported in reference 10 and assuming no decay in the reservoir.</p

HIV-1 persistence assessed by six different assays performed on the indicated cell or tissue obtained from patients starting HAART during acute/early infection (open symbols) or chronic infection (closed symbols).

<p>Geometric mean values are indicated by a horizontal black line. Long red lines indicate the limit of detection (LOD) for the relevant assay with a standard input sample size. Short red lines indicate patient-specific limits of detection in cases where the blood or tissue sample was smaller than normal. Negative assays are indicated by samples plotted below the red LOD lines.</p

Cell types analyzed and viral species detected in assays.

a<p>This form is readily detected in viremic patients but is absent in patients on stable HAART (reference 35).</p>b<p>Infected cells frequencies are normalized based on the fraction of CD4⁺ T cells present in the biopsy sample and assuming that all infected cells are CD4⁺ T cells.</p

Correlation between assays for HIV-1-infected cells in patients on HAART.

<p>(<b>A</b>) Correlation between infected cell frequencies measured in the viral outgrowth assay on purified resting CD4⁺ T cells and the droplet digital PCR assay for HIV-1 DNA in unfractionated PBMC. (<b>B</b>) Correlation between the viral outgrowth assay on purified resting CD4⁺ T cells and the droplet digital PCR assay for HIV-1 DNA in purified resting CD4⁺ T cells. (<b>C</b>) Correlation between the droplet digital PCR assay for HIV-1 DNA and the <i>Alu</i> PCR assay for integrated HIV-1 DNA in PBMC. (<b>D</b>) Correlation between the viral outgrowth assay on purified resting CD4⁺ T cells and the <i>Alu</i> PCR assay for integrated HIV-1 DNA in PBMC. (<b>E</b>) Correlation between the viral outgrowth assay on purified resting CD4⁺ T cells from the blood and the PCR assay for HIV-1 DNA in rectal CD4⁺ T cells. (<b>F</b>) Correlation between the viral outgrowth assay on purified resting CD4⁺ T cells from the blood and the single copy assay for residual viremia. Patients starting HAART during acute/early or chronic infection are indicated by open or closed symbols, respectively. See <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003174#ppat-1003174-g001" target="_blank">Figure 1</a> for patient ID key. The red lines indicate samples that fell below the limit of detection of the relevant assay. These samples were not used in the calculation of the correlation coefficients.</p

Correlation of PCR-based assays with viral outgrowth assay.

a<p>Correlations were analyzed for the entire study population (n = 30) and for subpopulations of study subjects starting HAART during acute/early (n = 10) or chronic (n = 20) HIV-1 infection. Because of limitations in the size of blood or tissue samples, not all assays were performed for all subjects, and the n for each assay is shown in the last column. Correlation coefficients were only computed for n>5.</p>b<p>Correlation coefficient for correlation with the viral outgrowth assay. Except where indicated, the Pearson correlation coefficient is shown.</p>c<p>95% confidence intervals for the correlation coefficient. Strong correlations were considered to be formally excluded when the upper limit of the 95% confidence interval was <0.6.</p>d<p>P values <0.05 are indicated in bold type.</p>e<p>Because of the large number of samples in which 2-LTR circles were below the limit of detection (2 copies/10⁶ cells), a Spearman's rank correlation coefficient was computed using a value of 1 copies/10⁶ cells for the samples in which 2 LTR circles were not detected.</p>f<p>Because of the large number of plasma samples that had HIV-1 RNA levels below the limit of detection (0.2 copies/ml), a Spearman's rank correlation coefficient was computed using a value of 0.1 copies/ml for negative assays.</p