Table 2. V3 amino acid sequences and co-receptor usage prediction of HIV-1 isolates obtained from the supernatants of PBMCs co-cultures.
Co-receptor usage was determined using various computational methods. V3 loop sequences from PMBCs-derived isolates are presented. Changes in the amino acid sequence as compared to the V3 loop of the Clade B consensus sequence are in red. The PNLG site at position 301 is underlined.
| Clonesa | V3 region | b V3 charge | c11/25 Rule | d Geno2pheno | e PSSM | f Cell tropism |
|---|---|---|---|---|---|---|
| Clade B |
|
5 | R5 | R5 | R5 | - |
|
| ||||||
| Normal | ||||||
| Isolate 1 | ||||||
| 9 |
|
8 | R5 | X4 | R5 | M-tropic |
| 1 |
|
8 | R5 | X4 | R5 | |
|
| ||||||
| Isolate 3 | ||||||
| 6 |
|
7 | X4 / Dg | X4 | X4 | Dual |
| 1 | 7 | X4 / D | X4 | X4 | ||
| 1 | 7 | X4 / D | X4 | X4 | ||
|
| ||||||
| Isolate 7 | ||||||
| 11 |
|
5 | R5 | R5 | R5 | M-tropic |
| 1 | 5 | R5 | R5 | R5 | ||
|
| ||||||
| ANI | ||||||
| Isolate 11 | ||||||
| 3 |
|
6 | R5 | X4 | R5 | M-tropic |
| 6 | 6 | R5 | X4 | R5 | ||
| 1 | 6 | R5 | X4 | R5 | ||
|
| ||||||
| MCMD | ||||||
| Isolate 15 | ||||||
| 3 |
|
6 | R5 | X4 | R5 | T-tropic |
| 2 | 7 | X4 / D | X4 | X4 | ||
| 1 | 7 | X4 / D | X4 | X4 | ||
|
| ||||||
| Isolate 16 | ||||||
| 11 |
|
6 | R5 | X4 | R5 | NDh |
| 1 | 6 | R5 | X4 | R5 | ||
|
| ||||||
| HAD | ||||||
| Isolate 20 | ||||||
| 4 |
|
7 | X4 / D | X4 | X4 | Dual |
| 2 | 5 | R5 | R5 | R5 | ||
| 1 | 5 | R5 | R5 | R5 | ||
|
| ||||||
| Isolate 21 | ||||||
| 5 |
|
8 | X4 / D | X4 | X4 | M-tropic |
| 1 | 8 | X4 / D | X4 | X4 | ||
| 1 | 8 | X4 / D | X4 | |||
| 1 | 9 | X4 / D | X4 | X4 | ||
The number indicates the total number of clones with the same env V3 sequence.
V3 charge was determined by subtracting the total number of negatively charged amino acids (D+E) from the total number of positively charged amino acids (H+K+R). Higher positive charge has been correlated with the likelihood of CXCR4 use.
Sequences with positively charged amino acids at positions 11 and/or 25 within the V3 loop were classified as having an 11/25 genotype (believed as X4 or X4/R5 strain). Positions 11 and 25 are highlighted in grey.
Geno2pheno, env V3 sequence was aligned to the reference strain HXB2 and predicted as to whether the corresponding virus is capable of using CXCR4 as a coreceptor (R5/X4 or X4 variants) or not (R5 variants).
PSSM, Position-specific scoring matrix (PSSMX4R5 and PSSM SINSI)
Cell tropism of viral isolates was previously determined by Toro-Nieves et al. 2007.
D: Dual tropic
ND: not determined because of lack of viral replication in phytohemagglutinin (PHA)-stimulated PBMCs.