TABLE 2.
Amino acid sequence alignment of HIV-1 envelope V3 loopsa
| Patient and isolate | V3 loop sequence by direct PCR sequencing | env clone | V3 loop sequence |
|---|---|---|---|
| SC24 | ∗ ∗ ∗∗ ∗∗∗ ∗ ∗ | ∗ ∗ ∗∗∗∗∗∗ ∗ ∗ | |
| QH0515 | CTRPNNNTRKSIHIGAGKALYTGEIIGDIRQAHC | QH0515#1 | CTRPNNNTRKSIHIEAGKALYTGEIIGDIRQAHC |
| QH0648 | ––––––N–R–––HI–AGK–L––G––––––––––– | QH0648#1 | ––––––N–R–––HIGAGK–L––G––––––––––– |
| QH0797 | ––––––N–R–––HI–PGK–L––G––––––––––– | QH0797#3 | ––––––N–R–––HIGPGK–L––G––––––––––– |
| QH1020 | ––––––N–R–––HI–PGK–L––G––––––––––– | ||
| QH1246 | ––––––N–R–––HI–PGK–L––G––––––––––– | QH1246#3 | ––––––N–R–––HIGPGK–L––G––––––––––– |
| QH1483 | ––––––N–R–––HI–PGK–L––G––––––––––– | QH1483#3 | ––––––N–R–––HIGPGK–L––G––––––––––– |
| QH1503#1 | ––––––N–R–––HIGPGK–L––G––––––––––– | ||
| QH1503#5 | ––––––N–R–––HIGPGK–L––G––––––––––– | ||
| QH1503#12 | ––––––N–R–––HIGPGK–L––G––––––––––– | ||
| QH1520 | ––––––N–R–––RM–IRR–F––R––––––––––– | QH1520#2 | ––––––N–R–––RMGIRR–F––R––––––––––– |
| HI ?GK L G | |||
| QH1549 | ––––––N–R–––RM–IRR–F––R––––––––––– | QH1549#13 | ––––––N–I–––RMGIRR–F––R––––––––––– |
| ? HI ?GK L G | QH1549#1 | ––––––S–I–––RIGIRR–F––R––––––––––– | |
| SC51 | ∗ ∗ ∗∗∗ ∗ | ∗ ∗ ∗∗∗ ∗ ∗ | |
| QH1302 | CTRPNNNTRKSIHLGAGRALYTGEIIGDIRQAHC | QH1302#23A | CTRPNNNTRKSIHLGAGRALYTGEIIGDIRQAHC |
| QH1420 | ––––––N–––S–––––GR–L–––––I–––––––– | QH1420#2 | ––––––N–––S–––––GR–L––G––I–––––––– |
| QH1490 | ––––––N–––S–––––GR–L–––––I–––––––– | QH1490#4A | ––––––N–––S–––––GK–L––G––I–––––––– |
| ? | QH1490#11A | ––––––N–––S–––––GR–L––R––I–––––––– | |
| QH1509 | ––––––N–––S–––––GR–L–––––I–––––––– | QH1509#3 | ––––––N–––S–––––GR–L––G––I–––––––– |
| ? | |||
| QH1521 | ––––––N–––S–––––GK–L–––––I–––––––– | QH1521#28 | ––––––N–––S–––––GK–L––G––I–––––––– |
| H R? F | QH1521#30 | ––––––N–––H–––––RK–F––G––I–––––––– | |
| QH1521#34 | ––––––N–––H–––––GK–F––G––I–––––––– | ||
| QH1536 | ––––––Y–––H–––––RK–F–––––I–––––––– | QH1536#2 | ––––––Y–––H–––––RK–F––G––I–––––––– |
| N L | |||
| QH1558 | ––––––Y–––H–––––RK–F–––––V–––––––– | QH1558#23A | ––––––Y–––H–––––RK–F––G––V–––––––– |
a
Nonsynonymous sequence polymorphisms are indicated by assigning two amino acids or ? (if multiple codons are possible) to the same position. Dashes denote that an amino acid is identical to the residue in the first sequence; asterisks indicate the predicated residues are different.