TABLE 3.
Sensitivities of amplification assays for gag-PR, PR, RT, IN, and env from clinical HIV-1 samplesa
| Viral load (RNA copies/ml) | Success rate (% [no. of successes/no. of attempts])
|
|||||
|---|---|---|---|---|---|---|
| Gag-PR (1,998 bp) | PR (559 bp) | RT (2,093 bp) | IN (1,253 bp) | Env (2,519 bp) | Total | |
| 200-1,000 | 100 (1/1) | 100 (3/3) | 100 (3/3) | 90 (9/10) | 100 (11/11) | 96 (27/28) |
| 1,000-5,000 | 89 (8/9) | 90 (12/13) | 90 (7/8) | 89 (17/19) | 100 (5/5) | 91 (49/54) |
| 5,000-10,000 | 100 (6/6) | 100 (9/9) | 100 (5/5) | 89 (8/9) | 100 (1/1) | 97 (29/30) |
| 10,000-100,000 | 100 (15/15) | 100 (21/21) | 100 (26/26) | 100 (27/27) | 100 (2/2) | 100 (91/91) |
| >100,000 | 100 (8/8) | 100 (5/5) | 100 (9/9) | 100 (9/9) | 100 (3/3) | 100 (34/34) |
| Total | 97 (38/39) | 98 (50/51) | 98 (50/51) | 95 (70/74) | 100 (22/22) | 97 (230/237) |
Samples belonged to the genetic forms A (12%), B (17%), C (9%), D, (8%) F (6%), G (8%), H (1%), J (4%), CRF01_AE (8%), CRF02_AG (11%), CRF03_AB (3%), CRF05_DF (1%), CRF12_BF (5%), and CRF13_cpx (5%) or were a unique recombinant form (2%), as determined by the Rega subtyping tool (9; http://www.bioafrica.net/subtypetool/html/). The failed amplifications of the PR and RT regions and one in the IN region were performed on the same sample, belonging to CRF03_AB, and we believe that this can be attributed to poor quality of the extracted RNA (50). Since no more sample was available, we could not reextract the RNA. The other failed amplifications belonged to subtype B (gag-PR), subtype C, CRF01_AE, and CRF02_AG (IN).