Real-Time PCR: HOS Cell Infection with VSV-G Pseudotyped Virusa
Table S1
Real-Time PCR: HOS Cell Infection With VSV-G Pseudotyped Virusa
Experiment 1Virus / Late/Early / Provirus/Late / TOT/Late
p15 / 22% / (0%)b / 1.0%
NC-SP2 / 43% / 25% / 5.2%
SP2-F16S / 31% / (0%) / 3.0%
NC-N55D / 38% / 7.6% / 3.4%
WT Env(+) / 42% / 25% / 3.9%
Experiment 2
Virus / Late/Early / Provirus/Late / TOT/Late
p15 / 13% / (2.5%) / 0.6%
NC-SP2 / 26% / 83% / 1.6%
SP2-F16S / 18% / (1.3%) / 1.5%
NC-N55D / 16% / 41% / 1.8%
WT Env(+) / 24% / 102% / 2.3%
a- values from Table S2
b- parentheses indicate quantities below quantitative limit of Alu-LTR assay
Table S2
Real-Time PCR: DNA Copies Produced During HOS Cell Infection With VSV-G Pseudotyped Virus Adjusted For Backgrounda
Experiment 1Virus / R-U5 / R-5'UTR / Alu-LTRb / TOT
p15 / 4,816 / 1,054 / (0) / 11
NC-SP2 / 14,846 / 6,313 / 1,587 / 329
SP2-F16S / 2,352 / 721 / (0) / 21
NC-N55D / 30,465 / 11,724 / (891) / 395
WT Env(+) / 9,930 / 4,171 / 1,059 / 165
Experiment 2
Virus / R-U5 / R-5'UTR / Provirus / TOT
p15 / 9,679 / 1,250 / (31) / 7
NC-SP2 / 18,778 / 4,789 / 3,956 / 77
SP2-F16S / 10,328 / 1,825 / (23) / 27
NC-N55D / 25,192 / 3,945 / 1,616 / 71
WT Env(+) / 13,201 / 3,155 / 3,229 / 74
a- values from Table S3
b- parentheses indicate values below quantitation limit of Alu-LTR assay
Table S3
RT-PCR Results From VSVG-Mediated Infections
CCR5-Primer/Probe Set
Virus sample / aa / b / hba / hbNC-N55D / 24,186 / 39,494 / 20,303 / 20,295
NC-SP2 / 18,769 / 32,035 / 24,701 / 37,108
SP2-F16S / 26,615 / 38,442 / 23,320 / 29,880
p15 / 23,483 / 38,633 / 23,728 / 28,406
WT ENV(+) / 20,370 / 26,960 / 26,445 / 28,872
R-U5-Primer/Probe Set
Virus sample / Raw copy numbers / Normalized per cell equivalent / Minus background(heat treated) / Normalized for
Input virusc
a / b / ha / hb / a / b / ha / hb / a / b / a / b / Average / StDev
NC-N55D / 39,590 / 51,304 / 279 / 158 / 30,723 / 26,364 / 258 / 158 / 30,465 / 26,206 / 30,465 / 25,192 / 27,828 / 3,728
NC-SP2 / 1,445,885 / 596,866 / 33 / 4,173 / 1,445,885 / 378,129 / 25 / 2,282 / 1,445,860 / 375,846 / 14,846 / 18,778 / 16,812 / 2,780
SP2-F16S / 21,323 / 52,483 / 0 / 6,646 / 15,037 / 27,708 / 0 / 4,514 / 15,037 / 23,194 / 2,352 / 10,328 / 6,340 / 5,639
p15 / 28,988 / 24,897 / 0 / 56 / 23,168 / 13,079 / 0 / 40 / 23,168 / 13,039 / 4,816 / 9,679 / 7,248 / 3,438
WT ENV(+) / 318,905 / 1,124,072 / 22 / 29 / 293,832 / 846,169 / 15 / 21 / 293,816 / 846,149 / 9,930 / 13,201 / 11,566 / 2,312
R-5`UTR Primer/Probe Set
Virus sample / Raw copy numbers / Normalized per cell equivalent / Minus background(heat treated) / Normalized for
Input virus
a / b / ha / hb / a / b / ha / hb / a / b / a / b / Average / StDev
NC-N55D / 15,204 / 7,986 / 80 / 0 / 11,798 / 4,104 / 74 / 0 / 11,724 / 4,104 / 11,724 / 3,945 / 7,835 / 5,501
NC-SP2 / 614,773 / 151,308 / 4 / 2 / 614,773 / 95,857 / 3 / 1 / 614,770 / 95,856 / 6,313 / 4,789 / 5,551 / 1,077
SP2-F16S / 6,535 / 7,765 / 0 / 0 / 4,609 / 4,099 / 0 / 0 / 4,609 / 4,099 / 721 / 1,825 / 1,273 / 781
p15 / 6,346 / 3,208 / 0 / 1 / 5,072 / 1,685 / 0 / 1 / 5,072 / 1,684 / 1,054 / 1,250 / 1,152 / 138
WT ENV(+) / 133,924 / 268,666 / 0 / 3 / 123,395 / 202,244 / 0 / 2 / 123,395 / 202,242 / 4,171 / 3,155 / 3,663 / 718
TOT Primer/Probe Set
Virus sample / Raw copy numbers / Normalized per cell equivalent / Minus background(heat treated) / Normalized for
Input virus
a / b / ha / hb / a / b / ha / hb / a / b / a / b / Average / StDev
NC-N55D / 509 / 143 / 0 / 0 / 395 / 74 / 0 / 0 / 395 / 74 / 395 / 71 / 233 / 229
NC-SP2 / 32,061 / 2,435 / 0 / 0 / 32,061 / 1,543 / 0 / 0 / 32,061 / 1,543 / 329 / 77 / 203 / 178
SP2-F16S / 194 / 114 / 0 / 0 / 137 / 60 / 0 / 0 / 137 / 60 / 21 / 27 / 24 / 4
p15 / 65 / 19 / 0 / 0 / 52 / 10 / 0 / 0 / 52 / 10 / 11 / 7 / 9 / 2
WT ENV(+) / 5,283 / 6,280 / 0 / 0 / 4,867 / 4,727 / 0 / 0 / 4,867 / 4,727 / 165 / 74 / 119 / 64
Alu-Provirus Primer/Probe Set
Virus sample / Raw copy numbers d / Normalized per cell equivalent / Minus background(heat treated) / Normalized for
Input virus
a / b / ha / hb / a / b / ha / hb / a / b / a / b / Average / StDev
NC-N55D / 1,148 / 3,271 / 0 / 0 / 891 / 1,681 / 0 / 0 / 891 / 1,681 / 891 / 1,616 / 1,253 / 513
NC-SP2 / 154,550 / 125,311 / 0 / (368) / 154,550 / 79,387 / 0 / (201) / 154,550 / 79,186 / 1,587 / 3,956 / 2,772 / 1,675
SP2-F16S / 0 / (104) / 0 / (3) / 0 / (55) / 0 / (2) / 0 / (52) / 0 / (23) / (12) / (17)
p15 / 0 / (84) / 0 / (3) / 0 / (44) / 0 / (2) / 0 / (42) / 0 / (31) / (15) / (22)
WT ENV(+) / 33,997 / 275,004 / 0 / (38) / 31,324 / 207,016 / 0 / (27) / 31,324 / 206,989 / 1,059 / 3,229 / 2,144 / 1,535
a- a,b indicate replicate trials
b- h denotes heat inactivated sample
c- normalized for viral genomes
d- parentheses indicate values below quantitation limit of Alu-LTR assay
Table S4
Real-Time PCR: H9 Cell Infection With Env+ Virusa
Experiment 1Virus / Late/Early / Provirus/Lateb / TOT/Late
p15 / 17% / (1.5%) / 0.60%
NC-SP2 / 30% / 12% / 2.6%
SP2-F16S / 21% / (0.84%) / 1.3%
NC-N55D / 30% / 6.2% / 1.9%
p6-Q2D / 25% / (13%) / 0.47%
WT Env(+) / 27% / (4.0%) / 4.3%
Experiment 2
Virus / Late/Early / Provirus/Late / TOT/Late
p15 / 19% / (0%) / 0.33%
NC-SP2 / 25% / 16% / 2.8%
SP2-F16S / 22% / (0%) / 1.0%
NC-N55D / 25% / 9.4% / 2.8%
p6-Q2D / 24% / (0%) / 0.27%
WT Efv(+) / 29% / (6.4%) / 3.1%
a- values from Table S5
b- parentheses indicate values below quantitation limit of Alu-LTR assay
Table S5
Real-Time PCR: DNA Copies Produced During H9 Cell Infection With Env+ Virus Adjusted For Backgrounda
Experiment 1Virus / R-U5 / R-5`UTR / Alu-LTRb / TOT
p15 / 56,747 / 9,540 / (145) / 58
NC-SP2 / 364,567 / 108,728 / 13,278 / 2,823
SP2-F16S / 29,896 / 6,354 / (53) / 85
NC-N55D / 428,780 / 127,396 / 7,862 / 2,416
p6-Q2D / 26,570 / 6,640 / (865) / 31
WT Env(+) / 58,930 / 16,107 / (651) / 693
Experiment 2
Virus / R-U5 / R-5`UTR / Alu-LTR / TOT
p15 / 45,551 / 8,487 / (0) / 28
NC-SP2 / 263,083 / 65,658 / 10,669 / 1,858
SP2-F16S / 30,869 / 6,699 / (0) / 67
NC-N55D / 587,652 / 147,829 / 13,952 / 4,197
p6-Q2D / 25,097 / 6,008 / (0) / 16
WT Env(+) / 35,074 / 10,309 / (656) / 322
a- values from Table S6
b- parentheses indicate values below quantitation limit of Alu-LTR assay
Table S6
RT-PCR Results From Env-Mediated Infections
CCR5-Primer/Probe Set
Virus sample / aa / b / hba / hbNC-N55D / 188,522 / 222,172 / 246,225 / 214,699
NC-SP2 / 254,772 / 174,290 / 168,037 / 61,819
SP2-F16S / 309,651 / 280,375 / 250,490 / 238,773
p15 / 212,510 / 276,564 / 237,976 / 208,192
p6-Q2D / 243,726 / 262,750 / 229,971 / 222,933
WT ENV(+) / 226,026 / 333,860 / 213,235 / 253,894
R-U5-Primer/Probe Set
Virus sample / Raw copy numbers / Normalized per cell equivalent / Minus background(heat treated) / Normalized for
Input virusc
a / b / ha / hb / a / b / ha / hb / a / b / a / b / Average / StDev
NC-N55D / 352,650 / 568,927 / 2,513 / 2,368 / 431,132 / 590,195 / 2,353 / 2,543 / 428,780 / 587,652 / 21,481 / 29,440 / 25,460 / 5,628
NC-SP2 / 405,219 / 201,017 / 1,466 / 734 / 366,578 / 265,821 / 2,011 / 2,738 / 364,567 / 263,083 / 21,247 / 15,332 / 18,289 / 4,182
SP2-F16S / 40,581 / 37,869 / 336 / 270 / 30,205 / 31,130 / 309 / 261 / 29,896 / 30,869 / 9,377 / 9,682 / 9,530 / 216
p15 / 52,894 / 55,554 / 639 / 674 / 57,366 / 46,297 / 619 / 746 / 56,747 / 45,551 / 10,998 / 8,828 / 9,913 / 1,534
p6-Q2D / 28,407 / 28,860 / 292 / 211 / 26,863 / 25,315 / 293 / 218 / 26,570 / 25,097 / 26,570 / 25,097 / 25,834 / 1,041
WT ENV(+) / 58,146 / 51,029 / 333 / 169 / 59,291 / 35,228 / 360 / 153 / 58,930 / 35,074 / 18,084 / 10,763 / 14,423 / 5,176
R-5`UTR Primer/Probe Set
Virus sample / Raw copy numbers / Normalized per cell equivalent / Minus background(heat treated) / Normalized for
Input virus
a / b / ha / hb / a / b / ha / hb / a / b / a / b / Average / StDev
NC-N55D / 104,648 / 142,958 / 579 / 441 / 127,938 / 148,302 / 542 / 474 / 127,396 / 147,829 / 6,382 / 7,406 / 6,894 / 724
NC-SP2 / 120,307 / 49,658 / 78 / 2 / 108,835 / 65,666 / 107 / 8 / 108,728 / 65,658 / 6,337 / 3,827 / 5,082 / 1,775
SP2-F16S / 8,629 / 8,211 / 75 / 53 / 6,422 / 6,750 / 69 / 51 / 6,354 / 6,699 / 1,993 / 2,101 / 2,047 / 77
p15 / 8,935 / 10,346 / 155 / 122 / 9,691 / 8,622 / 150 / 135 / 9,540 / 8,487 / 1,849 / 1,645 / 1,747 / 144
p6-Q2D / 7,093 / 6,911 / 67 / 52 / 6,707 / 6,062 / 67 / 53 / 6,640 / 6,008 / 6,640 / 6,008 / 6,324 / 447
WT ENV(+) / 15,859 / 14,992 / 60 / 45 / 16,172 / 10,350 / 64 / 41 / 16,107 / 10,309 / 4,943 / 3,163 / 4,053 / 1,258
TOT Primer/Probe Set
Virus sample / Raw copy numbers / Normalized per cell equivalent / Minus background(heat treated) / Normalized for
Input virus
a / b / ha / hb / a / b / ha / hb / a / b / a / b / Average / StDev
NC-N55D / 1,977 / 4,054 / 0 / 8 / 4,206 / 0 / 9 / 2,416 / 4,197 / 121 / 210 / 166 / 63
NC-SP2 / 3,129 / 1,420 / 5 / 5 / 2,831 / 1,877 / 7 / 19 / 2,823 / 1,858 / 165 / 108 / 136 / 40
SP2-F16S / 114 / 81 / 0 / 0 / 85 / 67 / 0 / 0 / 85 / 67 / 27 / 21 / 24 / 4
p15 / 53 / 33 / 0 / 0 / 58 / 28 / 0 / 0 / 58 / 28 / 11 / 5 / 8 / 4
p6-Q2D / 33 / 19 / 0 / 0 / 31 / 16 / 0 / 0 / 31 / 16 / 31 / 16 / 24 / 10
WT ENV(+) / 679 / 466 / 0 / 0 / 693 / 322 / 0 / 0 / 693 / 322 / 213 / 99 / 156 / 80
Alu-Provirus Primer/Probe Set
Virus sample / Raw copy numbers d / Normalized per cell equivalent / Minus background(heat treated) / Normalized for
Input virus
a / b / ha / hb / a / b / ha / hb / a / b / a / b / Average / StDev
NC-N55D / 6,441 / 13,511 / (13) / (60) / 7,874 / 14,016 / 13 / 64 / 7,862 / 13,952 / 394 / 699 / 546 / 216
NC-SP2 / 14,749 / 8,234 / (47) / (59) / 13,343 / 10,888 / 65 / 219 / 13,278 / 10,669 / 774 / 622 / 698 / 108
SP2-F16S / (186) / (28) / (92) / (84) / 139 / 23 / 85 / 81 / 53 / -58 / (17) / (-18) / -1
p15 / (161) / (107) / (30) / (717) / 174 / 89 / 29 / 793 / 145 / -704 / (28) / (-137) / -54
p6-Q2D / (977) / (280) / (58) / (300) / 924 / 246 / 58 / 310 / 865 / -64 / (865) / (-64) / 401
WT ENV(+) / (680) / (965) / (38) / (11) / 693 / 666 / 42 / 10 / 651 / 656 / (200) / (201) / 201 / 1
a- a,b indicate replicate trials
b- h denotes heat inactivated sample
c- normalized for viral genomes
d- parentheses indicate values below quantitation limit of Alu-LTR assay