TABLE 3.
Nef amino acid variations observed during AIDS progression
| Patient | PBMC sample (mo-yr) | No. of clones | No. (%) of CD4+ cells | No. defec-tivea | PxxP | Amino acid at position:b
|
Properties (RP/NP)c | NefProg score | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 15 | 39 | 51 | 102 | 157 | 163 | 169 | 170 | 182 | ||||||||
| FA | 9-87 | 6 | 537 (29) | 2 | + | T | K | N | Y | N | S | S | T | E | 1/3 | −2 |
| 11-90 | 5 | 266 (14) | 0 | + | T | K4R1 | N4/T1 | Y | N | S | S | T | E | 1/3 | −2 | |
| 5-92 | 5 | 32 (2) | 1 | + | T | K | T3/A1 | Y | N3/T1 | S | S3/N1 | T | E3/Q1 | 2/2 | +0 | |
| 4-94 | 9 | 18 (2) | 0 | + | T | R | T | Y | T | S8/C1 | N | T | Q | 5/1 | +4 | |
| MB | 11-88 | 12 | >1,000 (27) | 3 | +4/−5 | A | K8R1 | N | Y | N | I/T/S | S | L5/Q4 | E7/V/M | 1/2 | −1 |
| 11-91 | 7 | 496 (21) | 0 | + | A | R | N6/S1 | Y | T6/N1 | I/V/S | N | Q | E/M/Q | 6/1 | +5 | |
| 6-93 | 6 | 46 (5) | 1 | + | A | R | N | Y | T | I | N | Q | Q | 6/1 | +5 | |
| 3-94 | 8 | 64 (5) | 1 | + | A | R | N | Y | T | I | N6/S1 | Q | Q | 6/1 | +5 | |
a
Number of clones containing premature stop codons or frameshift mutations (Fig. 6).
b
Amino acid positions refer to the NL4-3 Nef sequence. Amino acids typically observed in RPs are underlined; amino acids that were more often observed in NPs are in boldface. Subscript numbers are the numbers of individual clones for positions at which sequence variations were observed. Only Nef protein sequences predicted from intact nef open reading frames were included in the analysis.
c
Number of properties observed more often in RPs and number of properties typically observed in NPs. Numbers were calculated for the representative consensus sequence.