In theory yes. Although I think we are a little way off creating a whole new disease (although Craig Venter has created his own life from scratch). Much more likely we could cross two different types of pathogens to create a new type.
Ethically however, this is not the sort of thing that scientists do as if by some chance a new disease got out it could possibly destroy humanity as it would be a disease that no one would likely show any immunity to.
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