REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse anti-p24	NIH AIDS Reference and Reagent Program	Cat# ARP-6521
Sheep anti-p17 polyclonal serum	NIH AIDS Reference and Reagent Program	Cat# 6123
Sheep anti-Digoxigenin-AP, Fab fragments	Sigma-Aldrich	Cat# 11093274910, RRID:AB_2734716
Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor® 594	Thermo Fisher Scientific	Cat# A-21207, RRID:AB_141637
Donkey anti-Sheep IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor® 488	Thermo Fisher Scientific	Cat# A-11015, RRID:AB_2534082
Donkey anti-Mouse IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor® 647	Thermo Fisher Scientific	Cat# A-31571, RRID: AB_162542
Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed, Alexa Fluor® 647	Thermo Fisher Scientific	Cat# A-31573, RRID:AB_2536183
Donkey anti-Mouse IgG (H + L) Highly Cross-Adsorbed, Alexa Fluor® 594	Thermo Fisher Scientific	Cat# A-21203, RRID:AB_141633
goat anti-mouse IgG (H + L) Polyclonal Antibody (HRP (Horseradish Peroxidase))	Rockland Immunochemicals	Cat# ROCK610-1319, RRID:AB_219659
goat anti-rabbit IgG (H + L) Polyclonal Antibody (HRP (Horseradish Peroxidase))	Rockland Immunochemicals	Cat# ROCK611-1322, RRID:AB_219723
APC-H7 Mouse Anti-Human CD27	BD Biosciences	Cat# 560222 RRID:AB_1645474
BUV737 Mouse Anti-Human CD45RA	BD Biosciences	Cat# 612846 RRID:AB_2738810
APC Mouse Anti-Human CCR7 (CD197)	BD Biosciences	Cat# 566762 RRID:AB_2869854
BV421 Mouse Anti-Human CD4	BD Biosciences	Cat# 566907 RRID:AB_2739448
BB700 Mouse Anti-Human CD279 (PD-1)	BD Biosciences	Cat# 566460 RRID:AB_2744348
BUV395 Mouse Anti-Ki67	BD Biosciences	Cat# 564071
AF647 Mouse Anti-human CD279 (PD-1)	BD Biosciences	Cat# 560838
CD184 BB700 anti-human (CXCR4)	BD Biosciences	Cat# 566553
CD69 Monoclonal Antibody (H1.2F3), PE	Invitrogen	Cat# 12-0691-82 RRID: AB_465732
Ki67	BD Biosciences	Cat# 564071 RRID: AB_2738577
TLR4	BD Biosciences	Cat# 564215 RRID: AB_2738674
BUV395 Mouse Anti-Human IFN-γ	BD Biosciences	Cat# 563563 RRID:AB_2738277
Recombinant Anti-PICALM antibody	Abcam	Cat# ab172962
Recombinant Anti-VAMP2 antibody	Abcam	Cat# ab181869
PACSIN3 Polyclonal Antibody	Thermo Fisher Scientific	Cat# PA5-83690 RRID:AB_2790843
LC3B Antibody	Cell Signaling	Cat# 2775
Anti-LAMP1 antibody	Abcam	Cat# ab25630
Bacterial and virus strains
HIV-1 (NL4-3)	NIH AIDS Reference and Reagent Program	Cat# 114
HIV-1 Nef_CRIMZs	This study
Biological samples
Peripheral blood mononuclear cells – Montreal	Réseau SIDA MI - FRQS	N/A
Peripheral blood mononuclear cells - Manitoba	NetCad (Canadian Blood Service)	N/A
Chemicals, peptides, and recombinant proteins
DMEM	Thermo Fisher Scientific	Cat# 11965-118
RPMI 1640	Invitrogen	Cat# 11875-119
Opti-MEM	Thermo Fisher Scientific	Cat# 31985070
FBS	Wisent	Cat# 080-150
Penicillin-streptomycin	Wisent	Cat# 450-201-EL
JetPrime (PolyPlus)	VWR	Cat# CA89129-924
D-PBS, 1X	Wisent	Cat# 311-425-CL
EDTA-free Protease inhibitor tablets	Roche	Cat# 11873580001
Bradford protein assay	BioRad	Cat# 500-0006
Pierce ECL Plus western blotting Substrate	Thermo Fisher Scientific	Cat# 32132
DIG RNA Labeling Kit	Invitrogen	Cat# 18033-019
DharmaFECT 1 Transfection Reagent	Dharmacon™	Cat# T-2001-02
Puromycin	Invivogen	Cat# ant-pr-1
Poly-L-lysine solution	Sigma-Aldrich	Cat# 25988-63-0
Fixable Viability Stain 510	BD Biosciences	Cat# 564406
Dynabeads™ Human T-Activator CD3/CD28 for T cell Expansion and Activation	Thermo Fisher Scientific	Cat# 11131D
Critical commercial assays
Human Edit-RTM - Membrane Trafficking	Dharmacon™	Cat# GC-005505-01
LIVE/DEAD™ Fixable Near-IR Dead Cell Stain Kit, for 633 or 635 nm excitation	Thermo Fisher Scientific	Cat# L10119
LiveBLAzer™ FRET-B/G Loading Kit with CCF2-AM	Thermo Fisher Scientific	Cat #K1032
Experimental models: Cell lines
HeLa (ATCC® CCL-2)	American Type Culture Collection	N/A
HEK293T/17 (ATCC® CRL-11268)	American Type Culture Collection	N/A
TZM-bl	NIH AIDS Reference and Reagent Program	Cat# 8129
SUP-T1 (ATCC® CRL-1942)	American Type Culture Collection	N/A
MAGI.CCR5	NIH AIDS Reagent Program	Cat# 3522
Recombinant DNA
lentiCRISPRv2	Sanjana et al., 2014117	Addgene Plasmid #52961
pCMV-VSV-G	Stewart et al., 2003118	Addgene Plasmid #8454
psPAX2	Didier Trono Lab (unpublished)	Addgene Plasmid #12260
pNL4-3	NIH AIDS Reference and Reagent Program	Cat# 114
pCMV4-BlaM-Vpr	Cavrois et al., 200266	Addgene Plasmid #21950
Hi.fate	Ratnapriya et al., 2021119
CALM-pmCherryN1	Taylor et al., 201181	Addgene Plasmid #27691
Oligonucleotides
5′-TGC ACG CGT GGA GGG GGC GGT ATG GAT AGC ACT GAG AAC G-3	Forward PCR primer	This work
5′-GCT ACC CGG GTC AGG GCA AGG CGG AGC CGG AGG CG-3′	Reverse PCR primer	This work
Restriction Enzymes
XmaI	NEB	Cat# R0180S
Mlul	NEB	Cat# R0198S
Software and algorithms
Imaris	Bitplane/Andor	https://imaris.oxinst.com/packages
Volocity 6.3	Perkin Elmer	https://www.perkinelmer.com
GraphPad v9 Prism		https://www.graphpad.com/scientific-software/prism
FlowJo	FlowJo	https://www.flowjo.com/solutions/flowjo
BD FACSDiva™ Software	BD Biosciences	https://www.bdbiosciences.com/en-ca/products/software/instrument-software/bd-facsdiva-software
Cytoscape	Cytoscape	https://cytoscape.org/
Search Tool for the Retrieval of Interacting Genes (STRING)	STRING	https://string-db.org/
Other
Leica DM16000B laser confocal microscope	Leica	N/A
WaveFX spinning disk confocal head	Quorum Technologies	N/A
Hamamatsu EM-CCD digital camera Hamamatsu		N/A
LSM800 Confocal Microscope with Airyscan	Zeiss	N/A
DeNovix DS-11 FX Spectrophotometer/Fluorometer	DeNovix	N/A
4-chamber Lab-Tek®II Chambered #1.5 German Coverglass System	VWR	Cat# CA62406-165
12-well plates	DIAMED	Cat# DIATE610-3167
25 × 75 mm × 1 mm thick glass slides	VWR	Cat# 16004-300
18 mm ø No. 1 cover glasses	VWR	Cat# 28143-310
BD LSRFortessa™ Cell Analyzer	BD Biosciences	N/A
ID7000 Spectral Cell Analyzer	Sony Biotechnology	N/A
Anti-Mouse Ig, κ/Negative Control Compensation Particles Set	BD Biosciences	Cat# 552843
UltraComp eBeadsTM Compensation Beads	Thermo Fisher Scientific	Cat# 01-3333-41