Table 1.
Sequence-based classification of 2-LTR junctionsa
| Parameter | Value for virus at time after infection (h) |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| WT SIVmac239 |
A87E |
A87D |
|||||||||||||
| 12 | 24 | 24 | 48 | 12 + 24 | 12 | 24 | 12 | 24 | 48 | 12 + 24 | 12 | 24 | 48 | 12 + 24 | |
| Raltegravir (1 μM) treatment | No | No | No | No | Yes | No | No | No | No | No | Yes | No | No | No | Yes |
| Fragment size (bp) | Smear (230–330) | ∼210 | Smear (230–330) | Smear (230–330) | ∼210 | ∼210 | ∼210 | Smear (230–330) | Smear (230–330) | Smear (230–330) | ∼210 | Smear (230–330) | Smear (230–330) | Smear (230–330) | ∼210 |
| No. of sequenced products of class/total no. of sequenced products | |||||||||||||||
| Class I, unprocessed | 12/40 | 7/10 | 17/43 | 9/34 | 6/7 | 8/17 | 3/4 | 1/97 | 0/45 | 3/34 | 7/8 | 5/53 | 0/43 | 4/30 | 21/23 |
| Class II, 3′ processed | 9/40 | 1/10 | 19/43 | 14/34 | 0/7 | 8/17 | 1/4 | 59/97 | 31/45 | 26/34 | 1/8 | 18/53 | 29/43 | 18/30 | 0/23 |
| Class III, 5′ processed | 7/40 | 0/10 | 5/43 | 3/34 | 0/7 | 1/17 | 0/4 | 19/97 | 11/45 | 2/34 | 0/8 | 22/53 | 13/43 | 7/30 | 0/23 |
| Class IV, unknown | 12/40 | 2/10 | 2/43 | 8/34 | 1/7 | 0/17 | 0/4 | 21/97 | 3/45 | 3/34 | 0/8 | 8/53 | 1/43 | 1/30 | 2/23 |
a
The indicated PCR-amplified products from the experiment shown in Fig. 6 were excised from the gel, cloned, and sequenced. The number of sequenced products in each class divided by the total number of sequenced products is shown.