Fuck trying to re engineer the virus/pathogen, fuck trying to develop medicines and treatments that kill them. Here is what you do - Find a suicide host. Any virus that is depended on fucking up your cells by highjacking could easily be eliminated this way. Picture this: Bob gets AIDS - Bob get injected with millions of CD4-like cells - These cells allow the AIDS virus to enter and then self destruct or have no internal functions the virus can highjack to reproduce - effectively becoming a virus trap.
Someone get developing.