Table 3. Cell types analyzed and viral species detected in assays.

	Cell types analyzed			Replication-competent viral species			Replication-defective viral species
Assay	Resting CD4+ T cells	Activated CD4+ T cells	Monocyte/macrophage	Linear unintegrated HIV-1 DNAa	Integrated HIV-1 DNA	Plasma virus	Linear unintegrated HIV-1 DNAa	Integrated HIV-1 DNA	2-LTR circles	Plasma virus
Viral out-growth assay on resting CD4+ T cells	√			√	√
Droplet digital PCR for HIV-1 DNA in PBMC	√	√	√	√	√		√	√	√
Droplet digital PCR for HIV-1 DNA in resting CD4+ T cells	√			√	√		√	√	√
Alu PCR for integrated HIV-1 DNA in PBMC	√	√	√		√			√
Alu PCR for integrated HIV-1 DNA in resting CD4+ T cells	√				√			√
qPCR for HIV-1 DNA in rectal CD4+ T cells	√	√	√b	√	√		√	√	√
Droplet digital PCR for 2-LTR circles in PBMC	√	√	√						√
Droplet digital PCR for 2-LTR circles in resting CD4+ T cells	√								√
Single copy PCR assay on plasma virus						√				√

^aThis form is readily detected in viremic patients but is absent in patients on stable HAART (reference 35).

^bInfected 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.