Journal: Cell host & microbe

Article Title: Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants.

doi: 10.1016/j.chom.2023.01.016

Figure Lengend Snippet: Figure 4. Comparison of gag ddPCR and IPDA quantification of SIV DNA (A) Correlation between gag+ SIV DNA copies and intact proviruses quantified using the IPDA. Individual datapoints represent the number of copies detected using either an amplicon in gag (y-axis)65 or the IPDA (x-axis).20 Each point is the geometric mean of 3 replicates. Intact proviruses are corrected for shearing (DSI) and env+2LTR circles. The correlation between the two variables was calculated using Pearson’s coefficient. Data from one animal, T624, were excluded from this analysis due to failure of the gag amplicon resulting from mutations or deletion. (B) Correlation between gag+ SIV DNA copies and intact proviruses, with gag values corrected using the same env+2LTR correction factor applied to the IPDA data, calculated using Pearson’s coefficient. (C) Comparison of the decay of SIV gag copies and intact proviruses for the animals in cohort 18–02. IPDA data are corrected for env+2LTR circles and DNA shearing. Vertical lines represent the standard deviations. See also Figure S4.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains SIVmac251 swarm 56 Dr. Dan Barouch, BIDMC N/A Biological samples N/A SIVmac251-infected Rhesus macaque PBMCs Dr. Dan Barouch, BIDMC N/A Chemicals, peptides, and recombinant proteins Platinum TaqDNA 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 Genbank: OQ168641-OQ168979 SIV – non-defective proviral DNA sequences This paper Genbank: OQ168980-OQ170751 SIV – hypermutated (defective) proviral sequences This paper Genbank: 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 STAR 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 STAR Methods IDT N/A Software and algorithms QuantaSoft Analysis-Pro Bio-Rad http://www.bio-rad.com/en-us/ product/qx200-droplet-digitalpcr-system?ID=MPOQQE4VY Geneious Prime Dotmatics https://www.geneious.com/prime/ MEGA v7.0 & v11 MEGA https://www.megasoftware.net/ (Continued on next page) Cell Host & Microbe 31, 356–372.e1–e5, March 8, 2023 e1

Techniques: Comparison, Amplification