TABLE 1.
Characteristics of the three progression groups and properties of the Nef sequences analyzed
| Progression group | Cohorta (n) | CD4+-cell count (no. per mm3)b | No. of nef genes analyzedc | No. (%) of defective nef genesd | NefProg scoree
|
|
|---|---|---|---|---|---|---|
| Range | Avg | |||||
| NP | C&W (24) | 875/732 (≥8.1/11.2) | 167 (3–10; 7.0) | 9 (5.4) | −4 to +4 | −0.8 |
| Worcester (4) | 1,140 (≥10.8) | 70 (6–14; 17.5) | 7 (10.0) | −4 to −2 | −3.3 | |
| ADARC (10) | 744 (≥13.3) | 90 (6–13; 9.0) | 8 (8.9) | −5 to +0 | −1.8 | |
| SFMHS (3) | 688 (≥8.0) | 27 (8–10; 9.0) | 1 (3.7) | −2 to −3 | −2.3 | |
| Total (41) | 855 (≥9.6) | 354 (3–14; 8.6) | 25 (7.0) | −5 to +4 | −1.4 | |
| SP | C&W (11) | 514/263 (≥8.5/11.1) | 49 (3–7; 4.5) | 4 (8.2) | −3 to +4 | +0.4 |
| Worcester (4) | 305 (≥11.0) | 26 (4–8; 6.5) | 0 (0) | 0 to +5 | +1.8 | |
| SFMHS (3) | 281 (≥7.7) | 32 (9–13; 10.7) | 0 (0) | +1 to +2 | +1.3 | |
| Total (18) | 429 (≥8.7) | 107 (3–13; 5.9) | 4 (3.7) | −3 to +5 | +0.9 | |
| RP | C&W (16) | 119/147 (≥6.3/7.8) | 83 (3–10; 5.1) | 10 (12.0) | −2 to +6 | +2.9 |
| Worcester (4) | 29 (≥7.7) | 29 (5–10; 7.3) | 2 (6.9) | +3 to +7 | +4.8 | |
| SFMHS (3) | 109 (≥7.7) | 29 (9–10; 9.7) | 1 (3.4) | 0 to +1 | +0.7 | |
| Chapel Hill (9) | 80 (NAf) | 30 (2–6; 3.3) | 3 (10) | 0 to +8 | +2.4 | |
| Total (32) | 96 (≥6.8) | 171 (2–10; 5.3) | 16 (9.4) | −2 to +8 | +2.8 | |
Patients analyzed by the Aaron Diamond AIDS Research Center (ADARC) (15), the San Francisco Men’s Health study (SFMHS) (27), and the AIDS Clinical Trials Group at the University of North Carolina Hospitals (Chapel Hill) (38) have been described previously. Average values for each progression group (total) are also given.
Mean values of the absolute CD4+-lymphocyte count at the time point closest to sample preparation for PCR and sequence analysis. Numbers in parentheses give the minimum number of years of documented HIV-1 infection prior to the CD4+-cell count measurement. For the C&W cohort the average number of CD4+ cells determined later in infection (indicated after the slash) is also indicated. Huang et al. (15) have given a range of CD4 values for the 10 LTNPs analyzed. The average value obtained for each patient was used for the calculation.
Only nef alleles obtained from a single time point are listed. Numbers in parentheses give the range and the average number of nef alleles analyzed per patient.
Number and percentage of nef alleles containing premature stop codons, frameshift mutations, and mutations in the initiation codon. nef genes predicting small in-frame deletions or alterations in conserved regions were considered intact.
As described in the text, the NefProg score is the number of Nef amino acid variations more frequently observed in progressors minus the number of properties typically seen in nonprogressors. The Nef sequence variations used for these calculations are shown in Fig. 2.
NA, not analyzed.