TABLE 2.
Efficiency of the individual proviral sequencing assay for five subtype B HIV-1-positive individualsa
| Donor ID | No. of NFL-positive MDA reactions | No. (%) of IS-positive MDA reactions | No. (%) of proviruses without IS priming siteb | No. (%) of NFLPAS-positive reactions with mixturesc | Final yield [no. (%)] of single proviral sequencesd | Flanking host length (bp) (mean, range)e |
|---|---|---|---|---|---|---|
| C-02 | 34 | 19 (55.9) | 12 (35.3) | 5 (14.7) | 14 (41.2) | 430, 19–1,090 |
| C-03 | 22 | 16 (72.7) | 1 (4.5) | 2 (9.1) | 14 (63.6) | 318, 18–664 |
| F-07 | 92 | 68 (73.9) | 18 (19.6) | 34 (36.9) | 34 (36.9) | 495, 18–1,363 |
| K-01 | 28 | 20 (71.4) | 3 (10.7) | 5 (17.8) | 15 (53.6) | 510, 22–1,137 |
| R-09 | 33 | 15 (45.5) | 5 (15.2) | 4 (12.2) | 11 (33.3) | 328, 32–923 |
| Median | 33 | 19 (71.4) | 5 (15.2) | 5 (14.7) | 14 (41.2) | 430, 18–1,363 |
a
NFL, near-full-length proviral sequences; MDA, multiple-displacement amplification; IS, integration site; NFLPAS, near-full-length proviral amplification and sequencing.
b
Percentage of NFLPAS sequences containing primer-binding-site deletions for downstream integration site PCR.
c
Number of MDA wells producing NFLPAS and IS amplicons with sequence mixtures.
d
Number of MDA wells producing NFLPAS and IS amplicons without 5′/3′-LTR sequence identity issues.
e
Mean and range of lengths in base pairs of 5′-flanking host sequences upstream of integration sites.