Extended Data Table 1.
Extended information about sample collection, viral loads, cell counts, sequencing results, and compartmentalization tests.
| Site | PID | VisitDate | Days post interruption | Plasma Viral Load | CSF Viral Load | ART | CSF WBC | CD4 | Sequences in figure? | Total BLD TCS (TCS in tree) | Total CSF TCS (TCS in tree) | Total SGA envs | Panmictic Slatkin-Maddison p value | Structured Slatkin-Maddison p value | Fisher’s exact test p value | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| UCSF | 4026 | On ART, viremic | 12/23/1998 | −21 | 19500 | 798 | NFV/d4T/ddi | 3 | 163 | N | ||||||
| 4026 | Interruption | 1/13/1999 | ||||||||||||||
| 4026 | Rebound | 2/8/1999 | 26 | 88800 | 14600 | 4 | 174 | Y | 1520 (200) | 0 | ||||||
| 4026 | Rebound | 3/16/1999 | 62 | 237000 | 143000 | 31 | 98 | Y | 630 (200) | 1248 (200) | 19 CSF | <0.0001 | <0.0001 | <0.0001 | ||
| 6004 | Interruption | 8/2/1999 | 3TC/d4T/IDV | |||||||||||||
| 6004 | On ART, viremic | 8/2/1999 | 0 | 12800 | <20 | 0 | 275 | N | ||||||||
| 6004 | Rebound | 8/20/1999 | 18 | 73600 | 1090 | 4 | 339 | Y | 1293 (200) | 65 (65) | ||||||
| 6004 | Rebound | 9/17/1999 | 46 | 52700 | 23600 | 46 | 192 | Y | 0 | 692 (200) | ||||||
| 6004 | Rebound | 11/1/1999 | 91 | 318000 | 28900 | 12 | 234 | Y | 744 (200) | 1888 (200) | <0.0001 | <0.0001 | 0.0002 | |||
| 6004 | Rebound | 12/10/1999 | 130 | 1815 | 564 | 0 | 247 | N | ||||||||
| 6005 | On ART, viremic | 8/27/1999 | −6 | 62000 | 57 | 3TC/d4T/IDV | 0 | 143 | N | 1896 (0) | 0 | |||||
| 6005 | Interruption | 9/2/1999 | ||||||||||||||
| 6005 | Rebound | 9/13/1999 | 11 | 82900 | 340 | 1 | 170 | N | 0 | 25 (0) | ||||||
| 6005 | Rebound | 10/8/1999 | 36 | 97800 | 818 | 1 | 173 | Y | 0 | 62 (62) | ||||||
| 6005 | Rebound | 11/19/1999 | 78 | 115583 | 8660 | 4 | 124 | Y | 1079 (200) | 1340 (200) | 27 CSF | <0.0001 | <0.0001 | <0.0001 | ||
| 6005 | Rebound | 12/16/1999 | 105 | 103177 | 4360 | 0 | 78 | Y | 2277 (200) | 318 (200) | ||||||
| 6005 | Rebound | 1/6/2000 | 126 | 120000 | 1570 | 0 | 83 | N | 1684 (0) | 79 (0) | ||||||
| 6005 | Rebound | 1/10/2000 | 130 | 28052 | 548 | 1 | 124 | N | ||||||||
| 6006 | Interruption | 9/15/1999 | EFV/NFV/ABC/Adefovir | |||||||||||||
| 6006 | On ART, viremic | 9/16/1999 | 1 | 2790 | 227 | 2 | 196 | N | 76 (0) | 21 (0) | ||||||
| 6006 | Rebound | 10/7/1999 | 22 | 29200 | 2210 | 16 | 112 | Y | 299 (200) | 276 (200) | ||||||
| 6006 | Rebound | 11/19/1999 | 65 | 156735 | 42830 | 46 | 120 | N | 6527 (0) | 1392 (0) | ||||||
| 6006 | Rebound | 12/9/1999 | 85 | 67578 | 63381 | 29 | 99 | Y | 2089 (200) | 821 (200) | <0.0001 | <0.0001 | <0.0001 | |||
| 6006 | Rebound | 1/3/2000 | 110 | 82100 | 54800 | 44 | 69 | Y | 1130 (200) | 348 (200) | ||||||
| 6006 | Rebound | 1/20/2000 | 127 | 123886 | 14747 | 22 | 154 | N | 179 (0) | 13 (0) | ||||||
| 6008 | Interruption | 9/6/2000 | SQV/RTV | |||||||||||||
| 6008 | Rebound | 9/6/2000 | 0 | <20 | 41 | 0 | 834 | N | 0 | |||||||
| 6008 | Rebound | 9/13/2000 | 7 | 929 | 96 | 0 | 793 | N | 4 (0) | 2 (0) | ||||||
| 6008 | Rebound | 10/4/2000 | 28 | 87851 | 18323 | 62 | 798 | Y | 232 (200) | 149 (149) | 14 CSF | <0.0001 | <0.0001 | <0.0001 | ||
| 6008 | Rebound | 10/30/2000 | 54 | 26242 | 3265 | 23 | 738 | Y | 95 (95) | 12 (12) | ||||||
| 6011 | Interruption | 1/9/2001 | EFV/ZDV/3TC | |||||||||||||
| 6011 | Rebound | 1/11/2001 | 2 | 26 | <20 | 2 | 375 | N | ||||||||
| 6011 | Rebound | 1/25/2001 | 16 | 1827 | <20 | 1 | 359 | N | ||||||||
| 6011 | Rebound | 2/15/2001 | 37 | 59052 | 2286 | 4 | 223 | N | 0 | 36 (0) | ||||||
| 6011 | Rebound | 3/8/2001 | 58 | 60609 | 34016 | 33 | 288 | Y | 224 (200) | 690 (2\00) | <0.0001 | <0.0001 | <0.0001 | |||
| 6011 | Rebound | 4/6/2001 | 87 | 34566 | 40156 | 30 | 229 | N | 24 (0) | 399 (0) | ||||||
| 6011 | Rebound | 4/19/2001 | 100 | 30130 | 74650 | 0 | 256 | Y | 344 (200) | 343 (200) | ||||||
| 6011 | Rebound | 6/7/2001 | 149 | 33380 | 16202 | 42 | 208 | Y | 378 (200) | 938 (200) | ||||||
| 6011 | Rebound | 8/24/2001 | 227 | 20887 | 23867 | 46 | 266 | N | 141 (0) | 235 (0) | ||||||
| 6011 | Rebound | 10/23/2001 | 287 | 41600 | 12500 | 31 | 253 | N | 116 (0) | 450 (0) | ||||||
| 6012 | On ART, suppressed | 3/7/2001 | −12 | 37 | <20 | EFV/d4T/3TC | 1 | 464 | N | |||||||
| 6012 | Interruption | 3/19/2001 | ||||||||||||||
| 6012 | Rebound | 4/5/2001 | 17 | 2994 | <20 | 0 | 382 | N | 3 (0) | 0 | ||||||
| 6012 | Rebound | 4/26/2001 | 38 | 59369 | 586 | 2 | 410 | Y | 1818 (200) | 31 (31) | ||||||
| 6012 | Rebound | 5/17/2001 | 59 | 158418 | 2382 | 1 | 325 | Y | 252 (200) | 36 (36) | <0.0001 | 0.454 | 0.27 | |||
| 6012 | Rebound | 6/28/2001 | 101 | 121119 | 1328 | 0 | 225 | Y | 85 (85) | 26 (26) | ||||||
| 6012 | Rebound | 7/20/2001 | 123 | 96583 | 1552 | 2 | 260 | N | 703 (0) | 35 (0) | ||||||
| 6013 | On ART, viremic | 4/9/2001 | −8 | 4843 | <20 | EFV/d4T/3TC | 4 | 618 | N | 23 (0) | 0 | |||||
| 6013 | Interruption | 4/17/2001 | ||||||||||||||
| 6013 | Rebound | 5/3/2001 | 16 | 1558556 | 3193 | 0 | 369 | Y | 224 (200) | 22 (22) | ||||||
| 6013 | Rebound | 5/17/2001 | 30 | 2254433 | 8835 | 18 | 275 | Y | 130 (130) | 117 (117) | <0.0001 | <0.0001 | <0.0001 | |||
| GOT | 5207 | Pre therapy | 9/18/2000 | −371 | 155000 | 110 | N | |||||||||
| 5207 | Pre therapy | 10/5/2000 | −354 | 209000 | 95500 | 147 | Y | 23 (23) | 13 (13) | |||||||
| 5207 | On ART, decay | 12/7/2000 | −291 | 534 | ZDV/3TC+IDV/r | N | ||||||||||
| 5207 | On ART, decay | 2/7/2001 | −229 | 165 | <20 | ZDV/3TC+IDV/r | 1 | 365 | N | |||||||
| 5207 | On ART, suppressed | 5/28/2001 | −119 | <20 | d4T+3TC+IDV/r | 240 | N | |||||||||
| 5207 | On ART, suppressed | 9/24/2001 | 0 | 49 | d4T+3TC+IDV/r | 330 | N | |||||||||
| 5207 | Interruption | 9/24/2001 | ||||||||||||||
| 5207 | Rebound | 10/1/2001 | 7 | 178000 | 230 | N | ||||||||||
| 5207 | Rebound | 11/21/2001 | 58 | 330000 | 55400 | 6 | 244 | Y | 9 (9) | 31 (31) | ||||||
| 5299 | Pre therapy | 5/19/2004 | −933 | 520000 | 181000 | 5 | 240 | Y | 274 (50) | 16 (16) | ||||||
| 5299 | Pre therapy | 8/16/2004 | −844 | 686000 | 120 | N | ||||||||||
| 5299 | Pre therapy | 9/2/2004 | −827 | 443000 | N | |||||||||||
| 5299 | On ART, decay | 9/9/2004 | −820 | 28900 | TDF+3TC+AZV/r | N | ||||||||||
| 5299 | On ART, decay | 9/16/2004 | −813 | 4290 | TDF+3TC+AZV/r | N | ||||||||||
| 5299 | On ART, decay | 9/23/2004 | −806 | 3510 | TDF+3TC+AZV/r | N | ||||||||||
| 5299 | On ART, decay | 10/4/2004 | −795 | 1520 | TDF+3TC+AZV/r | 230 | N | |||||||||
| 5299 | On ART, decay | 11/29/2004 | −739 | 464 | <20 | TDF+3TC+AZV/r | 1 | 390 | N | |||||||
| 5299 | On ART, suppressed | 3/4/2005 | −644 | 150 | TDF+3TC+AZV/r | 220 | N | |||||||||
| 5299 | On ART, suppressed | 3/16/2005 | −632 | <20 | TDF+3TC+AZV/r | N | ||||||||||
| 5299 | On ART, suppressed | 5/31/2005 | −556 | 172 | TDF+3TC+AZV/r | 260 | N | |||||||||
| 5299 | On ART, suppressed | 6/14/2005 | −542 | 23 | TDF+3TC+AZV/r | N | ||||||||||
| 5299 | On ART, suppressed | 8/11/2005 | −484 | 61 | <20 | TDF+3TC+AZV/r | 0 | 330 | N | |||||||
| 5299 | On ART, suppressed | 9/23/2005 | −441 | <20 | TDF+3TC+AZV/r | N | ||||||||||
| 5299 | On ART, suppressed | 1/23/2006 | −319 | 124 | TDF+3TC+AZV/r | 410 | N | |||||||||
| 5299 | On ART, suppressed | 2/2/2006 | −309 | 24 | TDF+3TC+AZV/r | N | ||||||||||
| 5299 | On ART, suppressed | 4/18/2006 | −234 | 86 | TDF+3TC+AZV/r | N | ||||||||||
| 5299 | On ART, suppressed | 5/5/2006 | −217 | <20 | TDF+3TC+AZV/r | N | ||||||||||
| 5299 | On ART, suppressed | 7/24/2006 | −137 | 29 | <20 | TDF+3TC+AZV/r | 1 | 380 | N | |||||||
| 5299 | On ART, suppressed | 12/7/2006 | −1 | 175 | TDF+3TC+AZV/r | 360 | N | |||||||||
| 5299 | Interruption | 12/8/2006 | ||||||||||||||
| 5299 | Rebound | 1/17/2007 | 40 | 316000 | 205000 | 8 | 410 | Y | 768 (50) | 34 (34) | ||||||
| 51126 | Pre therapy | 2/22/2011 | −2173 | 2100000 | 203158 | 3 | 60 | Y | 4948 (50) | 1734 (50) | 21 BL, 14 CSF | |||||
| 51126 | Pre therapy | 3/7/2011 | −2160 | 1500000 | 70 | N | ||||||||||
| 51126 | On ART, decay | 4/4/2011 | −2132 | 6628 | DRV/r+RGV | 320 | N | |||||||||
| 51126 | On ART, decay | 5/9/2011 | −2097 | 4594 | DRV/r+RGV | 280 | N | |||||||||
| 51126 | On ART, viremic | 6/1/2011 | −2074 | 6641 | 48599 | DRV/r+RGV | 3 | 230 | Y | 112 (50) | 51 (50) | |||||
| 51126 | On ART, viremic | 6/20/2011 | −2055 | 12825 | DRV/r+RGV | N | ||||||||||
| 51126 | On ART, viremic | 7/18/2011 | −2027 | 52587 | 60076 | DRV/r+RGV | 4 | 340 | Y | 800 (50) | 174 (50) | 16 BL, 9 CSF | ||||
| 51126 | On ART, decay | 8/22/2011 | −1992 | 7692 | ZDV+3TC+NVP+DRV/r | N | ||||||||||
| 51126 | On ART, decay | 9/28/2011 | −1955 | 3401 | 1645 | ZDV+3TC+NVP+DRV/r | 0 | 140 | N | |||||||
| 51126 | On ART, decay | 10/17/2011 | −1936 | 1006 | ZDV+3TC+NVP+DRV/r | N | ||||||||||
| 51126 | On ART, decay | 11/11/2011 | −1911 | 874 | ZDV+3TC+NVP+DRV/r | 0 | 280 | N | ||||||||
| 51126 | On ART, decay | 12/5/2011 | −1887 | 306 | ZDV+3TC+NVP+DRV/r | N | ||||||||||
| 51126 | On ART, decay | 1/3/2012 | −1858 | 3626 | ZDV+3TC+NVP+DRV/r | 440 | N | |||||||||
| 51126 | On ART, decay | 1/17/2012 | −1844 | 438 | ZDV+3TC+NVP+DRV/r | N | ||||||||||
| 51126 | On ART, decay | 2/2/2012 | −1828 | 319 | ZDV+3TC+NVP+DRV/r | N | ||||||||||
| 51126 | On ART, decay | 2/20/2012 | −1810 | 216 | ZDV+3TC+NVP+DRV/r | N | ||||||||||
| 51126 | On ART, decay | 3/6/2012 | −1795 | 256 | ZDV+3TC+NVP+DRV/r | N | ||||||||||
| 51126 | On ART, decay | 3/20/2012 | −1781 | 189 | ZDV+3TC+NVP+DRV/r | N | ||||||||||
| 51126 | On ART, decay | 4/2/2012 | −1768 | 243 | <20 | ZDV+3TC+NVP+DRV/r | 0 | 400 | N | |||||||
| 51126 | On ART, decay | 5/21/2012 | −1719 | 185 | ZDV+3TC+NVP+DRV/r | 470 | N | |||||||||
| 51126 | On ART, decay | 7/5/2012 | −1674 | 286 | 27 | ZDV+3TC+NVP+DRV/r | 0 | 440 | N | |||||||
| 51126 | On ART, decay | 8/6/2012 | −1642 | 162 | ZDV+3TC+NVP+DRV/r | 460 | N | |||||||||
| 51126 | On ART, decay | 9/26/2012 | −1591 | 270 | ZDV+3TC+NVP+DRV/r | 580 | N | |||||||||
| 51126 | On ART, decay | 11/29/2012 | −1527 | 250 | ZDV+3TC+NVP+DRV/r | N | ||||||||||
| 51126 | On ART, decay | 1/9/2013 | −1486 | 300 | <20 | ZDV+3TC+NVP+DRV/r | 0 | 680 | N | |||||||
| 51126 | On ART, suppressed | 4/29/2013 | −1376 | 106 | ABC+3TC+NVP+DrV/r | 510 | N | |||||||||
| 51126 | On ART, suppressed | 6/11/2013 | −1333 | 87 | ABC+3TC+NVP+DrV/r | N | ||||||||||
| 51126 | On ART, suppressed | 8/30/2013 | −1253 | 95 | ABC+3TC+NVP+DrV/r | N | ||||||||||
| 51126 | On ART, suppressed | 1/28/2014 | −1102 | 33 | <20 | ABC+3TC+DRV/r | 0 | 520 | N | |||||||
| 51126 | On ART, suppressed | 3/28/2014 | −1043 | 81 | ABC+3TC+DRV/r | 640 | N | |||||||||
| 51126 | On ART, suppressed | 4/30/2014 | −1010 | 56 | <20 | ABC+3TC+DRV/r | 0 | 840 | N | |||||||
| 51126 | On ART, suppressed | 8/19/2014 | −899 | <20 | ABC+3TC+DRV/r | N | ||||||||||
| 51126 | On ART, suppressed | 11/17/2014 | −809 | 41 | ABC+3TC+DRV/r | N | ||||||||||
| 51126 | On ART, suppressed | 4/30/2015 | −645 | <20 | <20 | ABC+3TC+DRV/r | 0 | 830 | N | |||||||
| 51126 | On ART, suppressed | 8/7/2015 | −546 | 72 | ABC+3TC+DRV/r | N | ||||||||||
| 51126 | On ART, suppressed | 11/9/2015 | −452 | <20 | ABC+3TC+DRV/r | N | ||||||||||
| 51126 | On ART, suppressed | 6/14/2016 | −234 | 25 | ABC+3TC+DRV/r | 730 | N | |||||||||
| 51126 | On ART, suppressed | 11/3/2016 | −92 | 334 | <20 | ABC+3TC+DRV/r | 0 | 740 | N | |||||||
| 51126 | Interruption | 2/3/2017 | ||||||||||||||
| 51126 | Rebound | 3/16/2017 | 41 | 25000000 | 380 | N | ||||||||||
| 51126 | Rebound | 3/21/2017 | 46 | 4600000 | 1300000 | 20 | 250 | Y | 7675 (50) | 2233 (50) | 11 BL, CSF 20 |