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Bovine viral diarrhea (BVD) virus is the causative agent of fatal mucosal disease (MD) of cattle. Experimental induction of MD can be achieved by superinfection of calves persistently viremic with a noncytopathic (ncp) BVD virus using an antigenically similar cytopathic (cp) BVD virus. Here we describe the characterisation of BVD viruses isolated from three cases of experimentally induced MD. One animal developed clinical symptoms two weeks after superinfection (early onset MD), while the onset of disease in the other two cases occurred with a delay of months (late onset MD). Antigenic characterisation of the viruses was performed using a panel of monoclonal antibodies against the E2 glycoprotein. For genetic analysis, RT-PCR was applied to amplify specific insertions and duplications in the NS2-3 genomic region of the cp BVD viruses. In addition, these amplicons and fragments of the viral E2 genes were sequenced. The results showed that in the case of early onset MD the cp BVD virus isolated after begin of disease was identical to the one used for superinfection. In contrast, the cp BVD viruses isolated from the two animals with late onset MD were obviously the result of genetic recombinations between the persistent ncp and the superinfecting cp BVD viruses. We conclude that early and late onset MD are the consequence of different pathogenic mechanisms.