TABLE 2.
Genetic diversity of SIVsmFr sequencesa
| Region sequenced | Intrahost genetic diversity
|
Interhost genetic diversity
|
||||||
|---|---|---|---|---|---|---|---|---|
| Animal | Maximum nucleotide divergence (%) | Animals | Minimum nucleotide divergence (%) | Maximum nucleotide divergence (%) | Clones considered in transmission hypothesis | Nucleotide divergence between clones (%) | Estimated fixation rate of mutations (subst/site/year) | |
| Gag (456 bp) | M66 | 3.39 | M66/F74 | 2.23 | 6.47 | NA | NA | NA |
| F74 | 6.50 | M66/F85 | 2.69 | 8.50 | 74-1/61-5 | 5.77 | 6.01 × 10−3 | |
| F85 | 3.64 | F74/F85 | 2.92 | 9.00 | 60-2/61-5 | 6.26 | 6.52 × 10−3 | |
| TM (538 bp) | M66 | 4.25 | M66/F74 | 2.66 | 5.85 | NA | NA | NA |
| F74 | 4.26 | M66/F85 | 3.45 | 6.09 | 78-1/81-4 | 4.63 | 4.82 × 10−3 | |
| F85 | 2.47 | F74/F85 | 2.08 | 5.05 | 49-1/81-4 | 3.44 | 3.58 × 10−3 | |
a
Intrahost and interhost genetic divergences were evaluated by comparison of the SIVsmFr sequences, which are presented in Fig. 5. The fixation rate of mutations was computed by dividing the observed divergence by 9.6 years. In each case, a hypothesis was made about which animal was the donor of the virus and which was the recipient. The divergence between the clone of the donor that was closest to the sequences of the recipient and the clone of the recipient that was farthest from the sequences of the donor was computed. NA, not applicable (because time since transmission was not known).