Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants

. Author manuscript; available in PMC: 2024 Mar 8.

Published in final edited form as: Cell Host Microbe. 2023 Feb 20;31(3):356–372.e5. doi: 10.1016/j.chom.2023.01.016

Key resources table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
SIVmac₂₅₁ swarm⁵⁷	Dr. Dan Barouch, BIDMC	N/A
Biological samples
SIVmac₂₅₁-infected Rhesus macaque PBMCs	Dr. Dan Barouch, BIDMC	N/A
Chemicals, peptides, and recombinant proteins
Platinum Taq DNA Polymerase High Fidelity	ThermoFisher Scientific	Cat # 11304011
SuperScript III Reverse Transcriptase	ThermoFisher Scientific	Cat # 18-080-044
dNTP Mix (10 mM each)	ThermoFisher Scientific	Cat # 18-427-088
UltraPure 1M Tris-HCl Buffer (pH 8.0)	ThermoFisher Scientific	Cat # 15-568-025
RNaseOUT Recombinant Ribonuclease Inhibitor	ThermoFisher Scientific	Cat # 10777019
Critical commercial assays
QIAamp DNA Mini Kit	Qiagen	Cat # 51304
CD4+ T Cell Isolation Kit, Non-Human Primate	Miltenyi Biotec	Cat # 130-092-144
2X ddPCR Supermix for Probes (no dUTPs)	Bio-Rad	Cat # 186-3024
Deposited data
SIV - plasma RNA sequences	This paper	OQ168641-OQ168979
SIV - non-defective proviral DNA sequences	This paper	OQ168980-OQ170751
SIV - hypermutated (defective) proviral sequences	This paper	OQ170752-OQ170785
Experimental models: Organisms/strains
Rhesus macaque (Macaca mulatta) infected with SIVmac₂₅₁	Indian origin	Animals T523, T530, T537, T544, T545, T623, T624, T625, T627 & T628
Oligonucleotides
Oligonucleotides, standard desalting (Sanger sequencing & ddPCR) - see Methods and Table S8	IDT	N/A
FAM/VIC labeled probes with MGB quencher, HPLC purified (see Table S8)	Applied Biosystems	N/A
Unlabeled competition probes w/MGB quencher, HPLC purified (see Table S8)	Applied Biosystems	N/A
FAM/HEX labeled probes w/MGB-NFQ quencher, HPLC purified (see Table S8)	IDT	N/A
Recombinant DNA
Synthetic double-stranded DNA controls (gBlocks) - see Methods	IDT	N/A
Software and algorithms
QuantaSoft Analysis-Pro	Bio-Rad	http://www.bio-rad.com/en-us/product/qx200-droplet-digital-pcr-system?ID=MPOQQE4VY
Geneious Prime	Dotmatics	https://www.geneious.com/prime/
MEGA v7.0 & v11	MEGA	https://www.megasoftware.net/
Clustal W	EMBL-EBI	http://www.ebi.ac.uk/Tools/msa/clustalw2/
GraphPad Prism	Dotmatics	https://www.graphpad.com/
Monolix 2020R1	Lixoft	https://lixoft.com/
Los Alamos National Labs - Highlighter	Keele et al.⁹¹	https://www.hiv.lanl.gov/content/sequence/HIGHLIGHT/highlighter_top.html
Los Alamos National Labs - Hypermut 2.0	Rose et al.⁹⁹	https://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermut.html