Characterization of SIV transmission by intrarectal or intravenous inoculation
| Subject | Initial dose | Cumulative dose before first + vRNA | Time to first + vRNA (wk) | Infection route | Peak viral load | No. of env seq. per animal | No. of identified transmitted variants | Percent max. env diversity | APOBEC-mediated G-to-A mutations | No. of APOBEC-mutated sequences | Intra-host recombination | Starlike phylogenya | Poisson distributionab | Rectal barrierc |
| SIVsmE660-infected animals | ||||||||||||||
| CG7V | 6 × 107 | 1.2 × 108 | 2 | i.r. | 77,871,700 | 96 | 5 | 1.06 | Yes | 2 | Yes | Yes | Yes | |
| CP3C | 6 × 107 | 1.2 × 108 | 2 | i.r. | 1,112,900 | 49 | 3 | 0.84 | Yes | 1 | No | Yes | Yes | |
| CG87 | 6 × 107 | 3.6 × 108 | 6 | i.r. | 479,543 | 56 | 1 | 0.15 | No | – | N/A | Yes | Yes | |
| CG7G | 6 × 106 | 6.0 × 106 | 1 | i.r. | 7,084,600 | 43 | 5 | 1.21 | Yes | 1 | Yes | Yes | Yes | |
| AK9F | 6 × 106 | 3.6 × 107 | 6 | i.r. | 140,795 | 35 | 4 | 1.43 | No | – | No | Yes | Yes | |
| CP37 | 6 × 106 | 4.3 × 108 | 18 | i.v. | 94,394,600 | 62 | >9 | 1.54 | N/Ad | N/Ad | N/Ad | N/Ad | N/Ad | >19,350 |
| CP23e | 6 × 105 | 1.2 × 106 | 2 | i.r. | 74,000,000 | 37 | 1 | 0.33e | Yes | 1 | N/A | Noe | Noe | |
| CR54 | 6 × 105 | 3.7 × 108 | 18 | i.v. | 1,968,800 | 29 | 4 | 1.26 | Yes | 1 | Yes | Yes | Yes | 7,400 |
| SIVmac251-infected animals | ||||||||||||||
| CP1W | 6 × 107 | 6.0 × 107 | 1 | i.r. | 17,797,900 | 137 | 1 | 0.15 | Yes | 5 | N/A | Yes | Yes | |
| CT76 | 6 × 107 | 6.0 × 107 | 1 | i.r. | 18,233,200 | 50 | 4 | 0.66 | Yes | 1 | No | Yes | Yes | |
| PBE | 6 × 107 | 3.0 × 108 | 5 | i.r. | 10,955,200 | 41 | 1 | 0.15 | No | – | N/A | Yes | Yes | |
| CR2A | 6 × 106 | 1.2 × 107 | 2 | i.r. | 4,130,600 | 46 | 1 | 0.07 | No | – | N/A | Yes | Yes | |
| CR53 | 6 × 106 | 3.6 × 107 | 6 | i.r. | 6,341,200 | 30 | 1 | 0.15 | Yes | 1 | N/A | Yes | Yes | |
| AV74 | 6 × 106 | 4.3 × 108 | 18 | i.v. | 18,690,000 | 71 | 1 | 0.18 | Yes | 3 | N/A | Yes | Yes | 2,150 |
| AH4X | 6 × 105 | 2.5 × 108 | 16 | i.r. | 2,611,600 | 23 | 2 | 0.59 | No | – | No | Yes | Yes | |
| CG71 | 6 × 105 | 3.7 × 108 | 18 | i.v. | 8,857,400 | 67 | >8 | 0.73 | Yes | 3 | Yes | Yes | Yes | >14,800 |
| CG5G | 6 × 105 | 3.7 × 108 | 18 | i.v. | 12,938,400 | 71 | 4 | 0.81 | Yes | 2 | Yes | Yes | Yes | 7,400 |
| AV66 | 6 × 105 | 6.7 × 107 | 13 | i.r. | 4,858,300 | 44 | 1 | 0.07 | Yes | 1 | N/A | Yes | Yes | |
| Subject | Initial dose | Cumulative dose before first + vRNA | Time to first + vRNA (wk) | Infection route | Peak viral load | No. of env seq. per animal | No. of identified transmitted variants | Percent max. env diversity | APOBEC-mediated G-to-A mutations | No. of APOBEC-mutated sequences | Intra-host recombination | Starlike phylogenya | Poisson distributionab | Rectal barrierc |
| SIVsmE660-infected animals | ||||||||||||||
| CG7V | 6 × 107 | 1.2 × 108 | 2 | i.r. | 77,871,700 | 96 | 5 | 1.06 | Yes | 2 | Yes | Yes | Yes | |
| CP3C | 6 × 107 | 1.2 × 108 | 2 | i.r. | 1,112,900 | 49 | 3 | 0.84 | Yes | 1 | No | Yes | Yes | |
| CG87 | 6 × 107 | 3.6 × 108 | 6 | i.r. | 479,543 | 56 | 1 | 0.15 | No | – | N/A | Yes | Yes | |
| CG7G | 6 × 106 | 6.0 × 106 | 1 | i.r. | 7,084,600 | 43 | 5 | 1.21 | Yes | 1 | Yes | Yes | Yes | |
| AK9F | 6 × 106 | 3.6 × 107 | 6 | i.r. | 140,795 | 35 | 4 | 1.43 | No | – | No | Yes | Yes | |
| CP37 | 6 × 106 | 4.3 × 108 | 18 | i.v. | 94,394,600 | 62 | >9 | 1.54 | N/Ad | N/Ad | N/Ad | N/Ad | N/Ad | >19,350 |
| CP23e | 6 × 105 | 1.2 × 106 | 2 | i.r. | 74,000,000 | 37 | 1 | 0.33e | Yes | 1 | N/A | Noe | Noe | |
| CR54 | 6 × 105 | 3.7 × 108 | 18 | i.v. | 1,968,800 | 29 | 4 | 1.26 | Yes | 1 | Yes | Yes | Yes | 7,400 |
| SIVmac251-infected animals | ||||||||||||||
| CP1W | 6 × 107 | 6.0 × 107 | 1 | i.r. | 17,797,900 | 137 | 1 | 0.15 | Yes | 5 | N/A | Yes | Yes | |
| CT76 | 6 × 107 | 6.0 × 107 | 1 | i.r. | 18,233,200 | 50 | 4 | 0.66 | Yes | 1 | No | Yes | Yes | |
| PBE | 6 × 107 | 3.0 × 108 | 5 | i.r. | 10,955,200 | 41 | 1 | 0.15 | No | – | N/A | Yes | Yes | |
| CR2A | 6 × 106 | 1.2 × 107 | 2 | i.r. | 4,130,600 | 46 | 1 | 0.07 | No | – | N/A | Yes | Yes | |
| CR53 | 6 × 106 | 3.6 × 107 | 6 | i.r. | 6,341,200 | 30 | 1 | 0.15 | Yes | 1 | N/A | Yes | Yes | |
| AV74 | 6 × 106 | 4.3 × 108 | 18 | i.v. | 18,690,000 | 71 | 1 | 0.18 | Yes | 3 | N/A | Yes | Yes | 2,150 |
| AH4X | 6 × 105 | 2.5 × 108 | 16 | i.r. | 2,611,600 | 23 | 2 | 0.59 | No | – | No | Yes | Yes | |
| CG71 | 6 × 105 | 3.7 × 108 | 18 | i.v. | 8,857,400 | 67 | >8 | 0.73 | Yes | 3 | Yes | Yes | Yes | >14,800 |
| CG5G | 6 × 105 | 3.7 × 108 | 18 | i.v. | 12,938,400 | 71 | 4 | 0.81 | Yes | 2 | Yes | Yes | Yes | 7,400 |
| AV66 | 6 × 105 | 6.7 × 107 | 13 | i.r. | 4,858,300 | 44 | 1 | 0.07 | Yes | 1 | N/A | Yes | Yes | |
If infected with more than one variant, the major lineages were examined for a starlike phylogeny and Poisson distribution of substitutions excluding APOBEC-mediated changes.
APOBEC-mutated sequences excluded.
Rectal barrier was calculated by dividing the cumulative i.r. dose by the i.v. dose multiplied by the number of transmitted viruses.
Not applicable; too many variants to quantify.
Sampled 2 wk after peak viral load.