File S1 - Persistence of Viral Reservoirs in Multiple Tissues after Antiretroviral Therapy Suppression in a Macaque RT-SHIV Model

Figure S1 , (A) Host CCR5 and RT-SHIVmne gag DNA were quantified in each tissue obtained from animal 6760. Each bar represents the average of duplicates and error bars represent the standard deviations. The limit of quantification for (B) CCR5 was 10 copies and for (C) gag was 1 copy. Figure S2, (A) RT-SHIVmne gag and 2-LTR circle copies were measured in tissues from animal 6760. Each bar represents the average of duplicates and error bars represent the standard deviations. (B) The limit of quantification of the 2-LTR circle assay was 1 copy. Figure S3, (A) Host CD4 and RT-SHIVmne gag RNA levels were quantified in each tissue obtained from animal 6760. Each bar represents the average of duplicates and error bars represent the standard deviations. The limit of quantification for (B) CD4 was 10 copies and for (C) gag was 1 copy. Figure S4, (A) The ratio of gag copies per 106 CCR5 copies for each tissue of the ART treated RT-SHIV-infected macaques. The average of each qPCR reaction was used for the graph. In addition, the week 1 plasma viral load was included for each animal. Asterisks (*) denote samples that were not collected or in which no significant CCR5 DNA were measured. (B) The amount of gag vDNA detected in each of the lymphoid tissues for each animal was plotted against the week 1 plasma viremia level for all animals (left panel) or excluding GN19 (right panel), giving a Spearman rank-order correlation of 0.6 with a p value of 0.2. (C) The amount of gag vDNA detected in each of the lymphoid tissues for each animal was plotted against the area under the curve (AUC) of plasma viremia between weeks 1-32 postinfection, giving a Spearman rank-order correlation 0.771 with a p value of 0.07. (PDF)