REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-CD94 BB790	BD Biosciences	624296 (clone HP-3D9)
Anti-CD3 BB700	BD Biosciences	566575 (clone SK7)
Anti-CD4 BB700	BD Biosciences	566452 (clone RPAT8)
Anti-CD8 BB700	BD Biosciences	566392 (clone SK3)
Anti-CD19 BB700	BD Biosciences	566396 (SJ25C1)
Anti-CD20 BB700	BD Biosciences	745889 (clone 2H7)
Anti-CD203c BB700	BD Biosciences	745913 (clone NP4D6)
Anti-CD34 BB700	BD Biosciences	742246 (clone 563)
Anti-CD123 BB660	BD Biosciences	624295 (clone 7G3)
Anti-CD141 BB630	BD Biosciences	624294 (clone 1A4)
Anti-NKG2A VioBright FITC	Miltenyi	130-113-568 (clone REA110)
Anti-CD57 PE-Cy7	Biolegend	359624 (clone HNK-1)
Anti-CD11c PE-Cy5.5	Invitrogen	MHCD11C18 (clone BU15)
Anti-CD294 PE-dazzle 594	Biolegend	350126 (clone BM16)
Anti-Siglec7 PE	Biolegend	339204 (clone G-434)
Anti-CD127 APC-Fire750	Biolegend	351350 (clone A019D5)
Anti-CD64 Alexa Fluor 700	Biolegend	305040 (clone 10.1)
Anti-CD158e1/e2 APC	Miltenyi	130-104-485 (clone REA168)
Anti-CD117 BV750	BD Biosciences	745414 (clone 104D2)
Anti-NKp30 BV711	BD Biosciences	563383 (clone P30-15)
Anti-CD161 BV650	BD Biosciences	563864 (clone DX12)
Anti-CD15 Biotin	Biolegend	301914 (clone HI98)
Anti-CD33 Biotin	Biolegend	303426 (clone W1453)
Streptavidin BV570	Biolegend	405227
Anti-CD16 BV480	BD Biosciences	566108 (clone 3G18)
Anti-NKG2C BV421	BD Biosciences	748169 (clone 134591)
Anti-CD14 BUV805	BD Biosciences	612902 (clone 35E2)
Anti-CD56 BUV737	BD Biosciences	564447 (clone NCAM16.2)
Anti-HLA-DR BUV661	BD Biosciences	565073 (clone G46-6)
Anti-CD86 BUV563	BD Biosciences	741386 (clone 2331FUN11)
Anti-CD1c BUV395	BD Biosciences	742751 (clone F10/21A3)
Biological samples
PBMC samples from study participants living with HIV-1	Botswana Harvard AIDS Institute Partnership	bhp.org.bw
Chemicals, peptides, and recombinant proteins
Invitrogen dNTP mix (10mM each)	ThermoFisher Scientific	18427088
AMPure XP beads	Beckman Coulter	A63882
LIVE/DEAD™ Fixable Blue Dead Cell Stain Kit	Thermo Fisher	L23105
Paraformaldehyde solution 4% in PBS	Affymetrix	4243418
FcR Blocking Reagent, human	Miltenyi	130-059-901
Critical commercial assays
DNeasy Blood and Tissue Kit	Qiagen	69504
ddPCR Supermix for Probes (No dUTP)	Bio-Rad	1863024
Invitrogen Platinum Taq DNA Polymerase High Fidelity	ThermoFisher Scientific	11304102
Deposited data
GenBank	GenBank	accession numbers MK457765 to MK458272 and MZ766582-MZ766922
CTL epitopes (restricted by autologous HLA class I alleles) that match the clade C and B consensus sequence, respectively and CTL escape variants restricted by selected HLA class I alleles and supertypes.	LANL HIV Immunology Database	https://www.hiv.lanl.gov/content/index
The resistance of proviral species to bnAbs.	Bricault et al. (2019)	Bricault et al. (2019)
Viral tropism.	geno2pheno (g2p)	http://coreceptor.geno2pheno.org/
Diagnostic ratios of APOBEC3G or -3F footprints.	Ebrahimi et al. (2012)	Ebrahimi et al. (2012)
Oligonucleotides
FLIP-Seq oligonucleotides	Millipore Sigma/IDT/Qiagen	N/A
Software and algorithms
Ultracycler v1.0	Seed and Wang, personal communication	https://dnacore.mgh.harvard.edu/new-cgi-bin/site/pages/viral_genome_sequencing_pages/viral_genome_sequencing_data.jsp
Automated in-house proviral intactness bioinformatic pipeline in Python	Lee et al. (2017)	https://github.com/BWH-Lichterfeld-Lab/Intactness-Pipeline
Los Alamos National Laboratory (LANL) HIV Sequence Database Hypermut 2.0	Rose and Korber (2000)	https://www.hiv.lanl.gov/content/sequence/HYPERMUT/background.html
MUSCLE	Edgar (2004)	http://www.drive5.com/muscle/
MEGA X	Kumar et al. (2018)	version 10.2.2
FlowJo	Tree Star, LLC	version 10.5.3
GraphPad	Prism	version 8.0.1
Other
QX200 Droplet Digital PCR System	Bio-Rad	https://www.bio-rad.com/en-us/life-science/digital-pcr/qx200-droplet-digital-pcr-system
C1000 Touch Thermal Cycler with 96-Well Fast Reaction Module	Bio-Rad	1851196
DynaMag-96 Side Skirted Magnet	ThermoFisher Scientific	12027
Illumina MiSeq performed by MGH CCIB DNA Core facility	Illumina/MGH CCIB DNA Core	https://dnacore.mgh.harvard.edu/new-cgi-bin/site/pages/index.jsp
Biorender	https://biorender.com	N/A