Extended Data Table 1 Viral reservoir analysis in blood and gut performed by ddPCR at several timepoints

Months after HSCT	Months into ATI	Material	Cell type	ddPCR assay	# of cells analyzed	HIV copies/ 10⁶ cells	Interpretation
1.5		Formalin-fixed colon biopsy	Mixed bulk	Total proviral HIV DNA	53 436	<18.7*	Undetectable
3		PBMC	CD4+ T cells	CS-IPDA	56 009	<17.8*	Undetectable
5		Formalin-fixed colon biopsy	Mixed bulk	Total proviral HIV DNA	81 138	<12.3*	Undetectable
9		PBMC	CD4+ T cells	CS-IPDA	41 790	<23.9*	Undetectable
27	3	PBMC	CD4+ T cells	CS-IPDA	397 701	<2.5*	Undetectable
48	24	PBMC	CD4+ T cells	Total proviral HIV DNA	2 850 000	1.14 (CI [-0.43, 2.71])	Traces
		PBMC	CD4+ T cells	CS-IPDA	3 040 000	<0.33*	Undetectable
		Ileum biopsy	CD45+ cells	Total proviral HIV DNA	620 000	5.16 (CI [-5.1, 25.8])	Traces
		Sigmoid colon biopsy	CD45+ cells	Total proviral HIV DNA	109 800	<9.11*	Undetectable
		Ileum biopsy	CD45+ cells	IPDA	310 000	<6.22*	Undetectable
		Sigmoid colon biopsy	CD45+ cells	IPDA	54 900	<57.28*	Undetectable

Asterisks indicate undetectable HIV DNA measured by ddPCR that were reported as the assay’s limit of detection related to the number of cells used and interpreted as undetectable (*).’Traces of DNA’ indicates that one to two positive droplets were observed in the ddPCR, but the confidence intervals included zero; therefore these results cannot be considered definitively positive. CS-IPDA, cross-subtype intact proviral DNA assay; PBMC, peripheral blood mononuclear cells.
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