Our aim was to analyze viral recombination in a live host. Consequently, we had to deal with the fact that more than one viral replication cycle occurred during the 21 d that infection lasted in our experiment (we had to wait that long for the disease to develop and to be able to recover sufficient amounts of viral DNA from each infection). Based on the kinetics of gene expression [40] , we postulate that each replication cycle lasts between 2 and 3 d, and that therefore seven to ten cycles occurred between infection and the sampling time. In case this assumption is incorrect, we did calculations assuming five, seven, ten, or 20 replication cycles during these 21 d. As shown, the results were not affected qualitatively, and only slightly quantitatively. It is important to note that we assumed that recombination occurred through a template-switching mechanism, and that therefore, from a recombination point of view, the CaMV genome is linear. The reverse transcription starts and finishes at the position 0 in Figure 1 , which is the point of circularization of the DNA genome. This implies that changes between contiguous markers a-b, b-c, and c-d can be considered as true recombination whereas those between a and d cannot, as they may simply stem from circularization of DNA, during the synthesis of which the polymerase has switched template once anywhere between a-b, b-c, or c-d.