KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and Virus Strains | ||
| SIVmac251 | NIH AIDS Reagent Program | Cat # 253 |
| SHIVSF162P3 | NIH AIDS Reagent Program | Cat # 6526 |
| SIVmac239 SpX | NIH AIDS Reagent Program | Cat # 12249 |
| Biological Samples | ||
| DB SIVmac251-infected RM PBMCs | Dr. Dan Barouch, BIDMC | N/A |
| JL SIVmac239X-infected RM PBMCs | Dr. Jeff Lifson, NCI | N/A |
| JC SIVmac251-infected RM PBMCs | Dr. Janice Clements, JHMI | N/A |
| LP SIVmac239X-infected RM PBMCs | Dr. Louis Picker, OHSU | N/A |
| HIV-2 Patient PBMC samples | Dr. Geoffrey Gottlieb, UW | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Platinum Taq DNA Polymerase High Fidelity | ThermoFisher Scientific | Cat # 11304011 |
| Platinum SuperFi DNA Polymerase | ThermoFisher Scientific | Cat # 12351010 |
| Critical Commercial Assays | ||
| Gentra Puregene Cell Kit | Qiagen | Cat # 158388 |
| QIAamp DNA Mini kit | Qiagen | Cat # 51304 |
| Nextera DNA Library Preparation Kit | Illumina | FC-131–1096 |
| Nextera XT Index Kit v2 Set A | Illumina | FC-131–2001 |
| CD4+ T Cell Isolation Kit, non-human primate | Miltenyi Biotec | 130–092-144 |
| Deposited Data | ||
| SIV, SHIV, HIV-2 sequences | This paper | MK686073 - MK686202 for SHIV, MK686203 - MK686247 for HIV-2, and MK686248 - MK686564 and MK686635 - MK687385 for SIV. |
| Software and Algorithms | ||
| CodonCode Aligner Software | CodonCode | https://www.codoncode.com/aligner/download.htm |
| CLC Genomics Workbench | Qiagen | https://www.qiagenbioinformatics.com/products/clc-genomics-workbench/ |
| QuantaSoft Analysis-Pro | Bio-Rad | http://www.bio-rad.com/en-us/product/qx200-droplet-digital-pcr-system?ID=MPOQQE4VY |
| Clustal W | EMBL-EBI | http://www.ebi.ac.uk/Tools/msa/clustalw2/ |
| MEGA 7.0 | MEGA | https://www.megasoftware.net/ |
| Experimental Models: Organisms/Strains | ||
| Rhesus macaques (Macaca mulatta) infected with SIVmac251 | Indian origin | Animals KIC, Ki6, PZB, DEL5, DEAB, DEKW and DEP0 |
| Rhesus macaques (Macaca mulatta) infected with SIVmac251 | Indian origin | Rh52A |
| Rhesus macaques (Macaca mulatta) infected with SIVmac239X | Indian origin | T028, T154, T158, and T159 |
| Rhesus macaques (Macaca mulatta) infected with SIVmac239 | Indian origin | P27779 and P28129 |
| Rhesus macaques (Macaca mulatta) infected with SHIVSF162P | Indian origin | MH8, PNP, PZN, and MC4 |
| Oligonucleotides | ||
| Please refer to Table S1 | ||