Table 3. Frequency of SIVmac251 gp120 sequence clusters in macaques at 21 days p.i.
| Cluster* | Cluster (%)† | Percentage of gp120 sequences from plasma at 21 days p.i.‡ | |||||
| D01 | D02 | D03 | D04 | D05 | D06 | ||
| 1 | 41.5 | 33.0 (28.3) | 33.5 (26.5) | 26.5 (17.6) | 28.9 (20) | 52.5 (48.1) | 33 (30.4) |
| 2 | 12.4 | 3.0 (2.2) | 0.6 (0.0) | 0.0 (0.0) | 11.0 (5.0) | 5.6 (0.0) | 7.6 (4.3) |
| 3 | 10.4 | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 17.5 (15) | 0.0 (0.0) | 0.0 (0.0) |
| 4 | 5.2 | 2.2 (2.2) | 1.0 (0.0) | 5.9 (5.9) | 0.0 (0.0) | 7.4 (7.4) | 0.0 (0.0) |
| 5 | 4.2 | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) |
| 6 | 3.1 | 4.3 (4.3) | 2.0 (2.0) | 0.0 (0.0) | 0.0 (0.0) | 7.4 (7.4) | 0.0 (0.0) |
| 7 | 2.6 | 2.2 (0.0) | 1.1 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) |
| 8 | 2.6 | 1.8 (0.0) | 8.9 (6.1) | 2.9 (0.0) | 3.9 (0.0) | 1.2 (0.0) | 12.3 (4.3) |
| 9 | 2.6 | 6.1 (4.3) | 6.1 (6.1) | 5.9 (5.9) | 10.0 (10.0) | 7.4 (7.4) | 8.7 (8.7) |
| 10 | 2.1 | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) |
| 11 | 2.1 | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 10.0 (10.0) | 0.0 (0.0) | 0.0 (0.0) |
| 12 | 2.1 | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 3.7 (3.7) | 0.0 (0.0) |
| 13 | 2.1 | 3.6 (2.2) | 4.4 (2.0) | 0.0 (0.0) | 0.0 (0.0) | 3.7 (3.7) | 0.0 (0.0) |
| 14 | 1.6 | 11.2 (8.7) | 19.4 (16.3) | 11.8 (5.9) | 16.2 (15) | 3.7 (3.7) | 8.0 (0.0) |
| 15 | 1.6 | 3.3 (2.2) | 2.0 (2.0) | 11.8 (5.9) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) |
| 16 | 1.0 | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) |
| 17 | 1.0 | 4.3 (4.3) | 0.5 (0.0) | 5.9 (5.9) | 0.0 (0.0) | 0.0 (0.0) | 0.0 (0.0) |
| UC | 2.1 | 1.1 (0.0) | 0.0 (0.0) | 11.8 (5.9) | 2.5 (0.0) | 0.0 (0.0) | 0.0 (0.0) |
| Total sequences | 193 | 46 | 49 | 17 | 20 | 27 | 23 |
| Classified (%) | 98.2 | 76.1 (58.7) | 79.6 (61) | 82.5 (53) | 100 (75) | 92.6 (81.4) | 69.6 (47.7) |
A cluster is defined by a group of viral swarm sequences sharing ≥99.5 % nucleotide identity. The clusters are numbered and ordered according to the number of viral swarm sequences present in each cluster. Unclustered sequences, (UC) represent those sequences that did not share ≥99.5 % with any other sequence observed in the viral swarm.
Percentage of sequences in the SIVmac251 viral swarm used to infect the macaques represented in a given cluster.
Plasma sequences genetically related to a given cluster differ 0–6 nt from one or more sequences of that cluster. Frequencies outside parentheses are weighted to include sequences ambiguously and unambiguously assigned to a cluster. Frequencies in parentheses are unweighted to include sequences unambiguously assigned to a cluster.