TABLE 3.
Sensitivity, specificity, and positive and negative predictive values of the bioinformatic tools to predict CXCR4 viruses against the enhanced sensitivity Trofile and original Trofile assaysa
| Bioinformatic tool | % sensitivity (95% CI) |
% specificity (95% CI) |
PPV (95% CI) |
NPV (95% CI) |
||||
|---|---|---|---|---|---|---|---|---|
| ES Trofile | Trofile | ES Trofile | Trofile | ES Trofile | Trofile | ES Trofile | Trofile | |
| Geno2pheno 1% | 20.0 (11.7-22.7) | 20.0 (13.3-20.0) | 98.9 (96.2-99.8) | 100 (95.4-100) | 85.7 (50.2-97.4) | 100 (66.4-100) | 78.9 (76.8-79.7) | 64.6 (61.6-64.6) |
| Geno2pheno 5% | 36.7 (24.7-46.2) | 40.0 (29.6-46.6) | 93.4 (89.4-96.6) | 92.2 (85.0-96.7) | 64.7 (43.5-81.6) | 77.8 (57.6-90.6) | 81.7 (73.8-84.5) | 69.1 (63.8-72.5) |
| Geno2pheno 10% | 56.7 (42.1-69.5) | 57.1 (45.3-66.5) | 83.5 (78.7-87.7) | 84.3 (76.2-90.7) | 53.1 (39.5-65.2) | 71.4 (56.6-83.1) | 85.4 (80.5-89.7) | 74.1 (67.0-79.8) |
| Geno2pheno 20% | 76.7 (61.8-87.5) | 62.9 (50.3-73.8) | 73.6 (68.7-77.2) | 70.6 (61.9-78.1) | 48.9 (39.4-55.8) | 59.5 (47.5-69.8) | 90.5 (84.5-94.9) | 73.5 (64.5-81.3) |
| PSSMX4R5 | 43.3 (31.4-51.0) | 39.4 (29.5-43.7) | 95.6 (91.7-98.1) | 96.0 (89.4-98.9) | 76.5 (55.4-90.0) | 86.7 (64.8-96.2) | 83.7 (80.2-85.9) | 70.6 (65.8-72.7) |
| PSSMsinsi | 40.0 (27.7-49.6) | 39.4 (29.5-43.7) | 93.4 (89.4-96.6) | 96.0 (89.4-98.9) | 66.7 (46.2-82.6) | 86.7 (64.8-96.2) | 82.5 (78.9-85.3) | 70.6 (65.8-72.7) |
| 11/25 rule | 26.7 (15.7-37.5) | 41.2 (31.4-45.5) | 91.2 (87.6-94.8) | 96.0 (89.3-98.9) | 50.0 (29.4-70.3) | 87.5 (66.7-96.4) | 79.0 (75.9-82.1) | 70.6 (65.7-72.7) |
| 11/24/25 rule | 26.7 (15.6-38.0) | 44.1 (34.2-48.3) | 90.1 (86.5-93.8) | 96.0 (89.3-98.9) | 47.1 (27.5-67.1) | 88.2 (68.4-96.6) | 78.8 (75.6-82.1) | 71.6 (66.6-73.8) |
| Net charge rule | 53.3 (38.7-66.8) | 52.9 (40.7-63.4) | 80.2 (75.4-84.7) | 80.0 (71.6-87.1) | 47.1 (34.2-59.0) | 64.3 (49.4-77.0) | 83.9 (78.9-88.6) | 71.4 (64.0-77.8) |
a
PPV, positive predictive value; NPV, negative predictive value.