Table 4.
env clonal analysis of three patient virus populations containing mixed amino acid substitutions that disrupt a PNGS at position 6–8 in V3
| Subject (subtype) |
Viruses a | No. of PNGS at position 6–8 b |
V3 amino acid sequences c | No.of AA changes d |
Coreceptor tropism e |
Infectivity (RLU) f | |
|---|---|---|---|---|---|---|---|
| CXCR4+ cells |
CCR5+ cells |
||||||
| 10(B) | Population | 0/1 | R5 | 54 | 18,687 | ||
| clone (n=8) | 0 |  |
0 | R5 | 74 | 335,296 | |
| clone (n=1) | 0 | 1 | R5 | 100 | 201,829 | ||
| clone (n=1) | 1 | 4 | R5 | 107 | 520,939 | ||
| 11(B) | Population | 0/1 | R5 | 163 | 59,137 | ||
| clone (n=5) | 1 |  |
0 | R5 | 66 | 580,001 | |
| clone (n=1) | 1 | 1 | R5 | 101 | 715,276 | ||
| clone (n=2) | 0 | 4 | R5 | 72 | 34,875 | ||
| clone (n=1) | 0 | 7 | R5 | 74 | 1,563 | ||
| clone (n=1) | 0 | 6 | R5 | 55 | 6,777 | ||
| 12(A) | Population | 0/1 | DM | 20,924 | 216,146 | ||
| clone (n=5) | 1 |  |
0 | R5 | 101 | 950,986 | |
| clone (n=2) | 1 | 0 | Dual-R | 898 | 1,148,595 | ||
| clone (n=1) | 0 | 1 | R5 | 118 | 703,962 | ||
| clone (n=2) | 0 | 12 | Dual-X | 569,619 | 1,785 | ||
Clones with identical V3 sequences and the same coreceptor tropism are grouped together. One R5 clone from subject 11 (indicated in bold) was chosen for site directed mutagenesis.
The absence of the potential N-linked glycosylation site (PNGS) at position 6–8 in V3 are shown in boldface
For V3 amino acid sequences, dots represent amino acids identical to the first sequence. Positions 11, 25 and 6–8 (for PNGS) are underlined.
The number of amino acids that differ from the most prevalent V3 sequence of R5 clones in the same sample is indicated.
Coreceptor tropism was determined by the Trofile assay. Dual clones were further classified as dual-X and dual-R based on efficiently or inefficiently utilized CXCR4, as previously described (Huang et al., 2007).
Infectivity was measured as luciferase activity (relative light units, RLU) in the Trofile assay. RLU <200 on CXCR5+ or CXCR+ cells was considered background luciferase activity in this study. Infectivity of multiple clones with the same V3 sequence is expressed as the average RLU.