Table 2.
Characteristics and results of the competition experiments of selected biological clones
| Clone no. | Ex vivo competition results a | Replication remarks | LTR | Tat | CCR5/CXCR4 use b |
|---|---|---|---|---|---|
| Patient L | |||||
| B1.1 | Against B2.3: lose | B1.1 and B1.2 replicate at similar level ex vivo | 16 and 13 nt insertions | T23N and F32L mutations | CCR5 |
| Against B2.5: lose | |||||
| B1.2 | Against B2.3: lose | n.d. | n.d. | CCR5 | |
| Against B2.5: lose | |||||
| B1.3 | Against B2.3: lose | B1.3 replicates at a lower level than B1.1 and B1.2 ex vivo. | 16 and 13 nt insertions | T23N and F32L mutations | CCR5 |
| Against B2.5: lose | |||||
| B2.3 | Against B1.1: win | Destabilizing mutation in TAR hairpin | CCR5 | ||
| Against B1.2: win | |||||
| Against B1.3: win | B2.3 and B2.5 replicate at similar level ex vivo | ||||
| B2.5 | Against B1.1: win | n.d. | CCR5 | ||
| Against B1.2: win | |||||
| Against B1.3: win | |||||
| Patient P | |||||
| B3.1 | Against B4.1: win | B3.1 replicates at very low levels in vivo | Destabilizing mutation in poly A hairpin | Short variant (86 aa) | CXCR4 |
| Against B4.2: win | |||||
| Against B4.3: lose | |||||
| Against B4.4: lose | |||||
| B4.1 | Against B3.1: lose | CCR5 | |||
| B4.2 | Against B3.1: lose | CCR5 | |||
| B4.3 | Against B3.1: win | B4.3 and B4.4 replicate at similar level ex vivo | CCR5 | ||
| B4.4 | Against B3.1: win | CCR5 | |||
a Primary clones of patient L (B1.1, B1.2 and B1.3) were competed against the superinfecting clones B2.3 and B2.5. For patient P, primary clone B3.1 was competed against all four B4 clones.
b As predicted by the Geno2pheno coreceptor prediction algorithm [70]. Additionally, clone B3.1 grows in MT2 cultures, again suggestive of CXCR4 use.