Table 1.
Characteristics of HIV-1 sequences and participants in each study.
| Study Feature | RV 217 (ECHO) | CAPRISA 002 |
|---|---|---|
| HIV-1 subtype(s) | CRF01_AE (MSM); A1/D/C and Recombinants (WSM) | C (WSM) |
| Sequencing strategy | Single genome amplification and sequencing | Next generation sequencing (Illumina w/PrimerID) |
| HIV-1 genomic region | Near full length genome (NFLG) | V3 variable loop of the gp120 envelope protein |
| Median bases per HIV-1 sequence (min, IQR, max) | NFLG: 8813 (8624, 8753-8841, 8891); LH:5057 (5027, 5051-5063, 5209); RH:5061 (4898, 5040-5092, 5141) |
498 (495, 498-498, 501) |
| Median HIV-1 sequences per participant after removing recombination and hypermutation (min, IQR, max) | 9.5 (2.6, 8.4-10, 11) NFLG: 10 (2, 8-10, 11) LH: 10 (2, 8-10,10) RH: 10 (3, 8-10, 11) |
352 (26, 142.3-640, 2764) |
| Median HIV-1 sequences removed per participant (min, IQR, max) | 0 (0, 0-1, 8) NFLG: 0 (0, 0-1.3, 8) LH: 0 (0, 0-0, 4) RH: 0 (0, 0-1, 4) |
0 (0, 0-1, 356) |
| Total number of participants | 36 | 21 |
| Number of MSM | 17 | 0 |
| Number of WSM | 19 | 21 |
| N participants with 1-2M sample | 36 | 20 |
| N participants with ~6M sample | 34 | 18 |
| Mean Gold days 1-2M (SD) | 47 (4.3) | 62 (4.9) |
| Mean Gold days ~6M (SD) | 184 (11.3) | 180 (12.1) |
| N Gold isMultiple 1-2M (%) | 10 (28%) | 5 (25%) |
| N Gold isMultiple ~6M (%) | 10 (29%) | 6 (33%) |
| Median bounds width in days 1-2M (min, IQR, max) | 48 (20, 34-76, 308) | 54 (27, 41-70, 108) |
| Median bounds width in days ~6M (min, IQR, max) | 146 (18, 91-195, 369) | 120 (30, 86-170, 183) |
| Mean lPVL 1-2M (SD) | 4.5 (0.8) | 4.9 (0.7) |
| Mean lPVL ~6M (SD) | 4.1 (1.0) | 4.5 (0.8) |
Calculations reflect the evaluated dataset, after removal of sequences with evidence of hypermutation or recombination. NFLG, nearly full length genome; LH, left half genome; RH, right half genome; WSM, women who have sex with men; MSM, men who have sex with men; IQR, interquartile range; lPVL = log10 plasma viral load; SD, standard deviation; Gold = modified center of bounds (COB) timing estimate applied to previously unavailable acute tight diagnostic bounds (prior to the 1-2M sample date) and the agreed-upon gold standard is a multiple indicator, see Methods.