Table 3. Longitudinal viral outgrowth results for participants.

Resting memory CD4+ T-cells or total CD4+ T-cells were plated in a limiting dilution format for the qVOA. The number of wells that were positive for p24 production over total wells plated are indicated. Both maximum-likelihood and Bayesian model-based IUPM estimates reported. The Bayesian model-based approach shares information across samples, “smoothing out” apparent rapid changes caused by random sampling from a small frequency of infected cells (e.g., alternation of positive and negative samples from Pt.4)

Patient	Timepoint	Donor replacement	CD4 T-cell plated	Number of cells plated	Viral outgrowth detected	p24 positive wells /total wells	IUPM Estimate
							Maximum- likelihood IUPM estimate	Bayesian model-based IUPM estimate
1	Baseline	-	Total	6·24 x106	No	0/6	0·120	0·099
	Week 12	Complete	Total	10·55 x106	No	0/20	0·066	0·001
	Week 24	Complete	Resting	7·95 x106	No	0/18	0·088	0·001
2	Baseline	-	Resting	20·55 x106	Yes	5/30	0·280	0·242
	Week 12	Incomplete	Resting	5·55 x106	Yes	1/15	0·201	0·112
	Week 24	Incomplete	Resting	5·55 x106	Yes	2/15	0·452	0·155
	Week 36	Incomplete	Resting	12·55 x106	Yes	1/22	0·083	0·108
	Week 52	Incomplete	Resting	9·25 x106	No	0/19	0·075	0·084
	Week 64	Incomplete	Resting	16·05 x106	No	0/26	0·043	0·070
	Week 76	Incomplete	Resting	19·95 x106	Yes	3/30	0·160	0·108
	Week 90	Incomplete	Resting	3·75 x106	No	0/14	0·187	0·089
	Week 103	Incomplete	Resting	23·55 x106	Yes	3/33	0·135	0·107
3	Baseline	-	Resting	22·50 x106	Yes	12/32	0·762	---
4	Baseline	-	Resting	7·55 x106	No	0/17	0·092	0·120
	Week 24	Incomplete	Resting	3·92 x106	Yes	3/14	0·534	0·141
	Week 36	Incomplete	Total	2·55 x106	No	0/12	0·277	0·098
	Week 48	Incomplete	Resting	5·55 x106	Yes	2/15	0·452	0·118
	Week 98	Incomplete	Resting	7·55 x106	No	0/17	0·092	0·074
6	Baseline	-	Resting	12·55 x106	Yes	2/22	0·179	0·146
	Week 12	Complete	Total	9·55 x106	No	0/19	0·073	0·001
	Week 24	Complete	Resting	16·55 x106	No	0/26	0·042	0·001
	Week 36	Complete	Total	7·55 x106	No	0/17	0·092	0·001
	Week 52	Complete	Resting	6·90 x106	No	0/17	0·087	0·001
7	Baseline	-	Resting	21·55 x106	Yes	22/31	2·319	2·199
	Week 12	Complete	Total	11·55 x106	No	0/21	0·060	0·007
	Week 24	Complete	Resting	6·72 x106	No	0/17	0·104	0·007
	Week 36	Complete	Resting	40·55 x106	No	0/50	0·017	0·007
	Week 52	Complete	Resting	30.00 x106	No	0/39	0·023	0·007
	Week 64	Complete	Resting	30·55 x106	Yes	1/40	0·033	0·008
	Week 88	Complete	Total	6·55 x106	No	0/16	0·107	0·007
	Week 100	Complete	Resting	14·55 x106	No	0/24	0·048	0·007
9	Baseline	-	Resting	12·55 x106	Yes	3/22	0·232	0·240
	Week 36	Complete	Total	4·55 x106	No	0/14	0·154	0·002
	Week 52	Complete	Resting	10·55 x106	No	0/22	0·066	0·002
	Week 100	Complete	Resting	12.00 x106	No	0/22	0·070	0·002