A probability model predicting initiation efficiency of retroviral vectors with two primer-binding sites

Initiation of reverse transcription in retroviruses occurs at a specific point in the viral genome, called the primer-binding site (PBS). The efficiency of reverse transcription initiation is not known. We previously published a paper describing reverse transcription of the retroviral vector S-2PBS containing two PBSs. Reverse transcription of this vector results in a provirus with one of four possible structures, depending, in part, on the PBSs used to initiate reverse transcription. Using Southern blotting analyses of DNA from infected cells, we measured the relative proportions of proviruses with different structures. Although the analysis allowed us to detect multiple initiation events occurring in a single virion, the measurement of frequency of such events was not possible. In this paper, we have built a probability model, which describes the reverse transcription process and predicts the outcomes of different initiation scenarios. By fitting the predicted outcomes to the observed data, we have been able to estimate the initiation efficiency in this system as ∼0.4 initiation per PBS. In addition, we show that even though multiple models of reverse transcription can explain the observed data, all of these models predict approximately the same initiation efficiency. This initiation efficiency is discussed in relation to general replication strategies of retroviruses.